https://microbewiki.kenyon.edu/api.php?action=feedcontributions&user=Sdemetriou&feedformat=atommicrobewiki - User contributions [en]2024-03-28T14:11:29ZUser contributionsMediaWiki 1.39.6https://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=29464Talk:Bioremediation2008-03-22T04:29:59Z<p>Sdemetriou: </p>
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<div>Thank you for your suggestions and corrections. I made the changes which I thought were necessary. Please check out and grade our microbe page created for [[Phanerochaete chrysosporium]]! [[User:Sdemetriou|Sdemetriou]] 04:29, 22 March 2008 (UTC)<br />
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Wow nice page! Two suggestions: 1. a typo "The removal of nitrogen is a two stage stage process than involves nitrification and denitrification" to "The removal of nitrogen is a two stage stage process THAT involves nitrification and denitrification" 2. A sentence about how P putida actually detects/reports presence of TNT would be nice. [[User:Alorloff|Alorloff]] 06:27, 17 March 2008 (UTC)<br />
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corrected typo, thank you [[User:Icclark|Icclark]] 06:28, 21 March 2008 (UTC)<br />
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I like how you included pictures of the different PAH structures. I think it would strengthen the page to show pictures of the other contaminants, and discuss how they are broken down in a bit more detail. Oxic vs. anoxic? byproducts? Great job overall, Heather<br />
<br />
One more thing: the brief description of co-metabolism is a little unclear. <br />
You wrote: "The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5]." <br />
Perhaps you could say something like, "Cometabolism refers to the transformation of a substrate by a microorganism that derives its energy/carbon from a second substrate." Also, in the last sentence I think "by" should be "but." Keep up the good work! [[User:Jmmullane|Jmmullane]] 04:37, 15 March 2008 (UTC)<br />
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Thank you for the comments. I made some changes, hopefully it is more clear now...[[User:Icclark|Icclark]] 00:10, 17 March 2008 (UTC)<br />
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Maybe you guys could consider re-organizing the examples of microorganisms so that they are in the same order as the pollutants that they degrade or even incorporate the microorganisms into the corresponding pollutant section. That might make things flow a little easier.[[User:Jmmullane|Jmmullane]] 04:24, 15 March 2008 (UTC)<br />
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I agree, but not all pollutants have a corresponding microbe, and we like having all the microbes together, so we might stick with the format for now. Thanks [[User:Icclark|Icclark]] 00:34, 17 March 2008 (UTC)<br />
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"Polynuclear aromatic compounds (PAHs)" should be "Polycyclic aromatic hydrocarbons (PAHs)" and under that particular heading, mutagens is misspelled.[[User:Jmmullane|Jmmullane]] 04:19, 15 March 2008 (UTC)<br />
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Thanks Polynuclear changed to polycyclic. [[User:Icclark|Icclark]] 00:10, 17 March 2008 (UTC)<br />
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I love the page! The degradation diagrams that accompany the organic compounds are extremely informative and easy to follow. You did a great job with your citations as well.[[User:Jmmullane|Jmmullane]] 05:57, 14 March 2008 (UTC)<br />
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Verrrrry good, but maybe a bit dense: I agree with Pbwebb. The info is good, but maybe you could put a "lighter" summary in/ just after your intro so someone just mildly interested and knowledgable could get the important stuff without being bogged down in the more technical stuff (I know that would be a lot of work, and won't be at all offended if you ignore this)[[User:Njblackburn|Njblackburn]] 05:09, 14 March 2008 (UTC)<br />
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Thanks, but I don't think reducing the amount of information is worthwhile. [[User:Icclark|Icclark]] 06:28, 21 March 2008 (UTC)<br />
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Italics for the microbes' names! put two apostrophes at the beginning and end of the italicized section like ''this'' [[User:Njblackburn|Njblackburn]] 05:05, 14 March 2008 (UTC)<br />
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yes, italics for the microbes, thanks[[User:Icclark|Icclark]] 06:28, 21 March 2008 (UTC)<br />
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informative yes most def. this is a super complex issue and hot topic in science. work of selling your subject. I felt like I got rushed into the details prematurely. how can your wiki page appeal to a wider audience? what will award your page with more "hits." thats just my 10 cents. cheers [[User:Pbwebb|Pbwebb]] 04:40, 14 March 2008 (UTC) <br />
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Wow, this looks fabulous! I love the images- Great job!<br />
Heather<br />
<br />
Nice job!!I also liked how you presented the illustrations. I read a recent paper that evaluated bioremediation of aquifers contaminated with uranium with the aid of nitrate and nitrate dependent Fe(II)-oxidizing microorganisms. It is in the journal of geomicrobiology by Senko et al., 2005. Check it out..Cheers[[User:Egrgutierrez|Egrgutierrez]] 03:31, 14 March 2008 (UTC)---- <br />
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Also great use of pictures to illustrate aromatic compounds[[User:Njppatel|Njppatel]] 18:44, 13 March 2008 (UTC)<br />
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Great page, i especially liked how you gave a real life example of the exon valdez spill to illustrate the concept of bioremdiation[[User:Njppatel|Njppatel]] 18:43, 13 March 2008 (UTC)<br />
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The Microbe page that our group created is for [[Phanerochaete chrysosporium]] <br />
[[User:Sdemetriou|Sdemetriou]] 01:24, 11 March 2008 (UTC) <br />
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would be good in intro to define in situ vs ex situ remediation. Ex situ then cover the use of bioreactors and other such systems.<br />
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[[User:Kmscow|Kate Scow]] 01:38, 10 March 2008 (UTC)<br />
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looking very good. Make sure you use proper scientific nomenclature for naming organisms: genus starting with caps and species name starting with lower case.<br />
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Also I think it flows better to start with pollutants and put the organisms second. <br />
[[User:Kmscow|Kate Scow]] 01:36, 10 March 2008 (UTC) <br />
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thank you Kate. I made changes per your suggestions. <br />
[[User:Icclark|Icclark]] 06:28, 21 March 2008 (UTC)<br />
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Looking good! Is your source on-line? You can create an external link like [http://ucdavis.edu this]. <br />
- [[User:Irina.chakraborty|Irina C]] 22:49, 10 February 2008 (UTC)<br />
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A lot of information in the page. Good. I would like to merge the metablic pathway to the example pollutant so that everyone can know how the pollutant is degraded.</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29112Bioremediation2008-03-15T08:22:14Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated biphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. Trichloroethylene (TCE) can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in turn, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutagens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polycyclic aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like ''[[Nitrosomonas europaea]]''.The, nitrite is further oxidized by microbes like ''[[Nitrobacter hamburgensis]]''. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, ''[[Phanerochaete chrysosporium]]'', exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of ''[[Deinococcus radiodurans]]'' has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].''[[Phanerochaete chrysosporium]]'', the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
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===Polycyclic aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
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PAHs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
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Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PAH. This has been shown to be an important phenomenon in breaking down larger aromatic chains, but does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
''Pseudomonas putida'' has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize ''P. putida'' as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, ''Nitrosomonas Europea'' has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, ''[Methylibium petroleiphilum]'' has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. ''Methylibium petroleiphilum'' is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of ''M. petroleiphilum'' occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29111Bioremediation2008-03-15T08:21:25Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated biphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. Tricloroethylene (TCE) can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in turn, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutagens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polycyclic aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like ''[[Nitrosomonas europaea]]''.The, nitrite is further oxidized by microbes like ''[[Nitrobacter hamburgensis]]''. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, ''[[Phanerochaete chrysosporium]]'', exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of ''[[Deinococcus radiodurans]]'' has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].''[[Phanerochaete chrysosporium]]'', the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polycyclic aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PAHs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PAH. This has been shown to be an important phenomenon in breaking down larger aromatic chains, but does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
''Pseudomonas putida'' has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize ''P. putida'' as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, ''Nitrosomonas Europea'' has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, ''[Methylibium petroleiphilum]'' has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. ''Methylibium petroleiphilum'' is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of ''M. petroleiphilum'' occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29110Bioremediation2008-03-15T08:19:45Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated biphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. Tricloroethylene (TCE) can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in turn, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutagens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polycyclic aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like ''[[Nitrosomonas europaea]]''.The, nitrite is further oxidized by microbes like ''[[Nitrobacter hamburgensis]]''. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, ''[[Phanerochaete chrysosporium]]'', exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of ''[[Deinococcus radiodurans]]'' has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].''[[Phanerochaete chrysosporium]]'', the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polycyclic aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PAHs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PAH. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
''Pseudomonas putida'' has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize ''P. putida'' as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, ''Nitrosomonas Europea'' has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, ''[Methylibium petroleiphilum]'' has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. ''Methylibium petroleiphilum'' is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of ''M. petroleiphilum'' occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=29109Phanerochaete chrysosporium2008-03-15T08:10:06Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
''Phanerochaete chrysosporium'' is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. ''Phanerochaete chrysosporium'' releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to ''Phanerochaete chrysoporium'' specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, ''Phanerochaete chrysosporium'' is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
''Phanerochaete chrysoporium's'' genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
''P. chrysoporium’s'' importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Phanerochaete chrysosporium'' is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
[[Image:ligninpathway.gif|Right|]]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to ''Phanerochaete chrysosporium'' sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. ''Agrobacterium radiobacter'' was isolated as coexisting with the fungi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
''Phanerochaete chrysosporium'' is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for ''P. chrysosporium''. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
Not only is ''Phanerochaete chrysosporium'' useful because of its biodegradation of harmful chemicals by means of extracellular enzymes, its ability to leave pure white cellulose has been important in the industry of paper. Biopulping would cut out the use of machines to remove brown lignin, which this fungi does naturally, all the while bleaching the cellulose left behind that goes into the mass production of paper. Incorporation of this natural alternative would limit the amount of pollution produced by machines previously designed for this very job, and also decrease the amount of chemicals used for the bleaching of paper. [11] Some limitations to the use of ''P. chrysosporium'' in the biopulping industry include the fact that pulp is a relatively low value product and aerating the fungi may be expensive, many fungi have low growth rates, and large wood chips are resistant to diffusion [12].<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown ''Phanerochaete chrysosporium'' to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br><br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br><br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br> <br />
10. [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycyclic Aromatic Hydrocarbon Degradation by Ligninolytic Fungi." Environmental Health Perspectives 103 (1995). 9 Mar. 2008.]<br><br />
11. [http://www.fpl.fs.fed.us/documnts/pdf1988/blanc88a.pdf Blanchette, Robert A., Todd A. Burns. "Selection of White-Rot Fungi for Biopulping." Department of Plant Pathology, University of Minnesota. Nov. 1987.]<br><br />
12. Kirk, K.T., Richard R. Burgess, and John W. Koning, Jr. "Use of Fungi in Pulping Wood: An Overview of Biopulping Research." Frontier Proceedings of Industrial Mycology symposium, Madison, WI. New York: Routledge, Chapman & Hall, 1992.</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=29108Phanerochaete chrysosporium2008-03-15T08:07:22Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
''Phanerochaete chrysosporium'' is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. ''Phanerochaete chrysosporium'' releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to ''Phanerochaete chrysoporium'' specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, ''Phanerochaete chrysosporium'' is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
''Phanerochaete chrysoporium's'' genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
''P. chrysoporium’s'' importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
''Phanerochaete chrysosporium'' is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
[[Image:ligninpathway.gif|Right|]]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to ''Phanerochaete chrysosporium'' sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. ''Agrobacterium radiobacter'' was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
Not only is Phanerochaete chrysosporium useful because of its biodegradation of harmful chemicals by means of extracellular enzymes, its ability to leave pure white cellulose has been important in the industry of paper. Biopulping would cut out the use of machines to remove brown lignin, which this fungi does naturally, all the while bleaching the cellulose left behind that goes into the mass production of paper. Incorporation of this natural alternative would limit the amount of pollution produced by machines previously designed for this very job, and also decrease the amount of chemicals used for the bleaching of paper. [11] Some limitations to the use of P.chrysosporium in the biopulping industry include the fact that pulp is a relatively low value product and aerating the fungi may be expensive, many fungi have low growth rates, and large wood chips are resistant to diffusion [12].<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br><br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br><br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br> <br />
10. [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycyclic Aromatic Hydrocarbon Degradation by Ligninolytic Fungi." Environmental Health Perspectives 103 (1995). 9 Mar. 2008.]<br><br />
11. [http://www.fpl.fs.fed.us/documnts/pdf1988/blanc88a.pdf Blanchette, Robert A., Todd A. Burns. "Selection of White-Rot Fungi for Biopulping." Department of Plant Pathology, University of Minnesota. Nov. 1987.]<br><br />
12. Kirk, K.T., Richard R. Burgess, and John W. Koning, Jr. "Use of Fungi in Pulping Wood: An Overview of Biopulping Research." Frontier Proceedings of Industrial Mycology symposium, Madison, WI. New York: Routledge, Chapman & Hall, 1992.</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29107Bioremediation2008-03-15T08:05:03Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like ''[[Nitrosomonas europaea]]''.The, nitrite is further oxidized by microbes like ''[[Nitrobacter hamburgensis]]''. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, ''[[Phanerochaete chrysosporium]]'', exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of ''[[Deinococcus radiodurans]]'' has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].''[[Phanerochaete chrysosporium]]'', the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
''Pseudomonas putida'' has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize ''P. putida'' as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, ''Nitrosomonas Europea'' has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, ''[Methylibium petroleiphilum]'' has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. ''Methylibium petroleiphilum'' is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of ''M. petroleiphilum'' occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29106Bioremediation2008-03-15T08:03:07Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like ''[[Nitrosomonas europaea]]''.The, nitrite is further oxidized by microbes like ''[[Nitrobacter hamburgensis]]''. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, ''Phanerochaete chrysosporium'', exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of ''[[Deinococcus radiodurans]]'' has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].[[Phanerochaete chrysosporium]], the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
''Pseudomonas putida'' has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize ''P. putida'' as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, ''Nitrosomonas Europea'' has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, ''[Methylibium petroleiphilum]'' has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. ''Methylibium petroleiphilum'' is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of ''M. petroleiphilum'' occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29105Bioremediation2008-03-15T07:59:39Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like[[Nitrosomonas europaea]].The, nitrite is further oxidized by microbes like [[Nitrobacter hamburgensis]]. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like[[Paracoccus denitrificans]][2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, Phanerochaete chrysosporium, exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
Methylibium petroleiphilum(formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].[[Phanerochaete chrysosporium]], the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, Nitrosomonas Europea has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, [Methylibium petroleiphilum] has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. Methylibium petroleiphilum is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of M. petroleiphilum occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=29104Bioremediation2008-03-15T07:58:59Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
New techniques are beginning to be implemented in bioremediation. Green technology involves making products which degrade easier and are environmentally safe. The study of interactions and relationships between the organism, the substrate, and the environment are ias the organic increasing with the green technology movement.<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [['Pseudomonas putida']] ===<br />
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Dechloromonas]]=== <br />
A soil bacteria genus which are capable of degrading perchlorate and aromatic compounds. <br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like[[Nitrosomonas europaea]].The, nitrite is further oxidized by microbes like [[Nitrobacter hamburgensis]]. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like[[Paracoccus denitrificans]][2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, Phanerochaete chrysosporium, exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
Methylibium petroleiphilum(formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls (PCBs)===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen in the metabolic pathways diagram. Energy is obtained through the oxidation of the large hydrocarbons [15].[[Phanerochaete chrysosporium]], the white rot fungus described earlier, is thought to have the ability to degrade PCB by non-selective means.<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, Nitrosomonas Europea has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, [Methylibium petroleiphilum] has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. Methylibium petroleiphilum is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of M. petroleiphilum occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PAHs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
15. [http://www.springerlink.com/content/pwy3yh3u1xcrtmcg/ Zylstra, GJ and E Kim. " Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1." Journal of Industrial Microbiology and Biotechnology, 19 (1997): 408-414.]<br />
<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=28929Talk:Bioremediation2008-03-14T07:25:32Z<p>Sdemetriou: </p>
<hr />
<div>I love the page! The degradation diagrams that accompany the organic compounds are extremely informative and easy to follow. You did a great job with your citations as well.[[User:Jmmullane|Jmmullane]] 05:57, 14 March 2008 (UTC)<br />
----<br />
<br />
<br />
Verrrrry good, but maybe a bit dense: I agree with Pbwebb. The info is good, but maybe you could put a "lighter" summary in/ just after your intro so someone just mildly interested and knowledgable could get the important stuff without being bogged down in the more technical stuff (I know that would be a lot of work, and won't be at all offended if you ignore this)[[User:Njblackburn|Njblackburn]] 05:09, 14 March 2008 (UTC)<br />
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Italics for the microbes' names! put two apostrophes at the beginning and end of the italicized section like ''this'' [[User:Njblackburn|Njblackburn]] 05:05, 14 March 2008 (UTC)<br />
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informative yes most def. this is a super complex issue and hot topic in science. work of selling your subject. I felt like I got rushed into the details prematurely. how can your wiki page appeal to a wider audience? what will award your page with more "hits." thats just my 10 cents. cheers [[User:Pbwebb|Pbwebb]] 04:40, 14 March 2008 (UTC) <br />
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Wow, this looks fabulous! I love the images- Great job!<br />
Heather<br />
<br />
Nice job!!I also liked how you presented the illustrations. I read a recent paper that evaluated bioremediation of aquifers contaminated with uranium with the aid of nitrate and nitrate dependent Fe(II)-oxidizing microorganisms. It is in the journal of geomicrobiology by Senko et al., 2005. Check it out..Cheers[[User:Egrgutierrez|Egrgutierrez]] 03:31, 14 March 2008 (UTC)---- <br />
<br />
<br />
Also great use of pictures to illustrate aromatic compounds[[User:Njppatel|Njppatel]] 18:44, 13 March 2008 (UTC)<br />
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Great page, i especially liked how you gave a real life example of the exon valdez spill to illustrate the concept of bioremdiation[[User:Njppatel|Njppatel]] 18:43, 13 March 2008 (UTC)<br />
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The Microbe page that our group created is for [[Phanerochaete chrysosporium]] <br />
[[User:Sdemetriou|Sdemetriou]] 01:24, 11 March 2008 (UTC) <br />
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would be good in intro to define in situ vs ex situ remediation. Ex situ then cover the use of bioreactors and other such systems.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:38, 10 March 2008 (UTC)<br />
<br />
looking very good. Make sure you use proper scientific nomenclature for naming organisms: genus starting with caps and species name starting with lower case.<br />
<br />
Also I think it flows better to start with pollutants and put the organisms second. <br />
[[User:Kmscow|Kate Scow]] 01:36, 10 March 2008 (UTC) <br />
<br />
<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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Looking good! Is your source on-line? You can create an external link like [http://ucdavis.edu this]. <br />
- [[User:Irina.chakraborty|Irina C]] 22:49, 10 February 2008 (UTC)</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Flooded_Soils&diff=28927Talk:Flooded Soils2008-03-14T07:17:29Z<p>Sdemetriou: </p>
<hr />
<div>I'd love to see a "Current Research" section that highlights some of the recent findings. Also, a "Monitoring" section would be great in order to show different ways in the laboratory or in the environment that one can monitor a flooded soil environment. For example, in lab we compared flooded soil over a duration of time, but we could achieve the same results by observing the changes that occur with depth in the Winogradsky columns. Kate Scow had a great visual in her powerpoint slides that compared the two methods, which may be a nice addition to your page. Other than that, this page is incredibly well-done! [[User:Sdemetriou|Sdemetriou]] 07:17, 14 March 2008 (UTC)<br />
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<br />
A few minor things- the "Recover from flooded soils" section is missing text and the spacing between sections is huge in some spots.<br />
You say, "When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes." ---> Is this true that aerobic respiration is prevalent in flooded soils, or is it predominantly anaerobic respiration that rebounds the pH? I can see some aerobic processes happening at the surface, but is significant O2 diffusion occurring? <br />
<br />
[[User:Icclark|Icclark]] 06:47, 14 March 2008 (UTC)<br />
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Did I miss your current research section? Other than that, I absolutely love all the visuals! They really break up the monotony of the text. Your page really reinforces the concepts of the class and the lab. Kudos to you! [[User:Jmmullane|Jmmullane]] 06:16, 14 March 2008 (UTC)<br />
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IMO, get rid of the overwatered pot plant, probably not a good look for the page:-( but I like the ambition.[[User:Pbwebb|Pbwebb]] 05:21, 14 March 2008 (UTC)<br />
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In your Processes section, you say "Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox..." To me it would make more sense if you changed the "or" to an "and", as in: Through this variation of soil condition, various gases are emitted into the atmosphere and environmental factors, such as redox...)[[User:Njblackburn|Njblackburn]] 05:01, 14 March 2008 (UTC)<br />
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I like the page! I would like to see a link to the carbon cycle page where you mention greenhouse gases in the intro, though (I did the carbon cycle page, so of course I would)[[User:Njblackburn|Njblackburn]] 04:55, 14 March 2008 (UTC)<br />
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Very nice job people. As others have said, looks good, especially with the pictures (visuals always help people understand better in my opinion). There are only a few things that I want to suggest. In terms of linking to other sites, I'm not sure if any of you know or maybe someone else in the class does, but is there any way to link to regular wikipedia directly without having to use the URL? I was thinking it would be nice to put links to things like pH, soil aggregates, and other such things for people to click on if they don't know much about them. I was also thinking that maybe there is some way to link within your own page so that when you say "see electron tower theory" you can click that to go to that section. I looked a bit on the help and also just within other pages but I didn't see anything. In terms of content I didn't read everything thoroughly, but i felt a bit confused by the "electron tower" section. I understood it because I have learned it in this class, but I was thinking in terms of someone first being introduced to it the content might not be broken down in a logical way. Also, when you were discussing pH changes in flooded soils I remember Kate saying something like "pH rises after initial drop due to carbonate production that buffers." That might be something to include. Anyways, take it or leave it, that's my thoughts. Great work.[[User:Kjmuzikar|Kjmuzikar]] 00:18, 14 March 2008 (UTC)<br />
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Very awesome site. The pictures are a bit small, however. And perhaps I didn't catch it, but did you ever mention the color change that occurs with flooded soils? Soils kept in anaerobic conditions get this cool gleyed color; a blue tint to them. Anyways, just a thought. Great job though! Lots of interesting information! [[User:Lapeacock|Leslie Peacock]] 11:54, 13 March 2008 (UTC)<br />
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As mentioned before it looks great but i dont know if this is required but you could add a section regarding current research[[User:Njppatel|Njppatel]] 18:40, 13 March 2008 (UTC)<br />
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Wow you site looks great, i like how you included pictures to help solidify concepts.[[User:Njppatel|Njppatel]] 18:40, 13 March 2008 (UTC)<br />
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Great job group! This site looks fantastic! The fermentation stuff is great, and thanks for adding links for the microbes, Heather <br />
<br />
Overall its a very good job, I did have one comment on the section processes, the sentience : ‘Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed’.. needs some editing to make it clear what your trying to say.[[User:Calgilbert|Calgilbert]] 15:37, 12 March 2008 (UTC)<br />
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way to go group, way to pull through at the last minute. Good job everybody especially sung ho. -david [[User:Dtla|Dtla]] 07:50, 10 March 2008 (UTC)````<br />
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I would remove section 2.3.2. Move that material (renamed microbial activity) as part of the intro to microorganisms involved. I would rename that section something like key microbial processes and organisms involved.<br />
<br />
[[User:Kmscow|Kate Scow]] 02:09, 10 March 2008 (UTC)<br />
<br />
I fixed it <br />
[[User:Jokang|Sungho]] 05:27, 10 March 2008 (UTC)<br />
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wow this is looking nice!<br />
Methaneous organisms needs to be changes to methanogens. You also need to add the fermenting organisms as a category. <br />
Also include some of the broader changes with flooding: gleying, and what happens when oxygen becomes available again.<br />
[[User:Kmscow|Kate Scow]] 02:04, 10 March 2008 (UTC)<br />
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are the plants linked to microbes now?-david [[User:Dtla|Dtla]] 01:07, 10 March 2008 (UTC)<br />
<br />
It's better, bur organize the information (one main idea per paragraph). [[User:Irina.chakraborty|Irina C]] 01:12, 10 March 2008 (UTC)<br />
<br />
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im doing effects on life, plants, microorganisms? -david ````[[User:Dtla|Dtla]] 00:10, 10 March 2008 (UTC)<br />
<br />
<br />
The section called "Effects on life" seems out of place. Also, if you want to talk about effects on plants, you need to link it to microbes (i.e. what do microbes to in flooded soils that would effect plants). As it is now, there is no connection to plants. Make sure you site your sources and do not just copy and paste text as you did with at least some of the phrases in your section. You have to paraphrase AND cite the source of the information. Your section on microorganisms is ok but seems try to make it more clear and make sure it doesn't contain info that is covered elsewhere on the page (compare to "electron tower" section) [[User:Irina.chakraborty|Irina C]] 00:29, 10 March 2008 (UTC)<br />
ok-david<br />
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<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
<br />
It looks good. You guys need more detail in some sections. Have you decided among yourselves how to split up the work? [[User:Irina.chakraborty|Irina C]] 06:42, 9 March 2008 (UTC)<br />
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I erased your "edits and dates" section. We don't need this since we can see who did what and when in the history tab.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 23:37, 6 March 2008 (UTC)<br />
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<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
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<br />
I would suggest slightly different organization.<br />
<br />
Maybe under flooded soils could be....<br />
#Overall definition and description of phenomenon of flooded soils. You can put a figure here. You can also say that this type of phenomenon can also be observed in other types of situations.....aggregates and pollutant plumes in groundwater<br />
#Chemical changes : Make sure you focus this on redox. organize these by changes in dominant electron acceptors being used and make the connection to electron tower. ALso include fate of products generated during electron acceptor untilization. e.g. methane migrates up. Sulfides.....<br />
#Changes in microbial community composition<br />
#Changes when the flooded soil is unflooded and oxygen comes in<br />
<br />
Maybe something else??<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
<br />
----<br />
* You don't need to have a list of topics because that is automatically created for you at the top of the page.<br />
* Please put back the text that says "crated by the students of Kate Scow" at the bottom of the template page<br />
* You don't need to sign your names at the end. We can see who did what by looking at the history of the page. Also, Laleh's name is mentioned but it doesn't look like she's logged in. Please make sure you log in and make edits through your own account, since otherwise we can't tell who did what.<br />
[[User:Irina.chakraborty|Irina C]] 19:05, 8 February 2008 (UTC)</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Flooded_Soils&diff=28926Talk:Flooded Soils2008-03-14T07:17:00Z<p>Sdemetriou: </p>
<hr />
<div>I'd love to see a "Current Research" section that highlights some of the recent findings is missing. Also, a "Monitoring" section would be great in order to show different ways in the laboratory or in the environment that one can monitor a flooded soil environment. For example, in lab we compared flooded soil over a duration of time, but we could achieve the same results by observing the changes that occur with depth in the Winogradsky columns. Kate Scow had a great visual in her powerpoint slides that compared the two methods, which may be a nice addition to your page. Other than that, this page is incredibly well-done! [[User:Sdemetriou|Sdemetriou]] 07:17, 14 March 2008 (UTC)<br />
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<br />
<br />
A few minor things- the "Recover from flooded soils" section is missing text and the spacing between sections is huge in some spots.<br />
You say, "When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes." ---> Is this true that aerobic respiration is prevalent in flooded soils, or is it predominantly anaerobic respiration that rebounds the pH? I can see some aerobic processes happening at the surface, but is significant O2 diffusion occurring? <br />
<br />
[[User:Icclark|Icclark]] 06:47, 14 March 2008 (UTC)<br />
----<br />
Did I miss your current research section? Other than that, I absolutely love all the visuals! They really break up the monotony of the text. Your page really reinforces the concepts of the class and the lab. Kudos to you! [[User:Jmmullane|Jmmullane]] 06:16, 14 March 2008 (UTC)<br />
----<br />
IMO, get rid of the overwatered pot plant, probably not a good look for the page:-( but I like the ambition.[[User:Pbwebb|Pbwebb]] 05:21, 14 March 2008 (UTC)<br />
----<br />
In your Processes section, you say "Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox..." To me it would make more sense if you changed the "or" to an "and", as in: Through this variation of soil condition, various gases are emitted into the atmosphere and environmental factors, such as redox...)[[User:Njblackburn|Njblackburn]] 05:01, 14 March 2008 (UTC)<br />
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I like the page! I would like to see a link to the carbon cycle page where you mention greenhouse gases in the intro, though (I did the carbon cycle page, so of course I would)[[User:Njblackburn|Njblackburn]] 04:55, 14 March 2008 (UTC)<br />
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<br />
<br />
Very nice job people. As others have said, looks good, especially with the pictures (visuals always help people understand better in my opinion). There are only a few things that I want to suggest. In terms of linking to other sites, I'm not sure if any of you know or maybe someone else in the class does, but is there any way to link to regular wikipedia directly without having to use the URL? I was thinking it would be nice to put links to things like pH, soil aggregates, and other such things for people to click on if they don't know much about them. I was also thinking that maybe there is some way to link within your own page so that when you say "see electron tower theory" you can click that to go to that section. I looked a bit on the help and also just within other pages but I didn't see anything. In terms of content I didn't read everything thoroughly, but i felt a bit confused by the "electron tower" section. I understood it because I have learned it in this class, but I was thinking in terms of someone first being introduced to it the content might not be broken down in a logical way. Also, when you were discussing pH changes in flooded soils I remember Kate saying something like "pH rises after initial drop due to carbonate production that buffers." That might be something to include. Anyways, take it or leave it, that's my thoughts. Great work.[[User:Kjmuzikar|Kjmuzikar]] 00:18, 14 March 2008 (UTC)<br />
----<br />
<br />
Very awesome site. The pictures are a bit small, however. And perhaps I didn't catch it, but did you ever mention the color change that occurs with flooded soils? Soils kept in anaerobic conditions get this cool gleyed color; a blue tint to them. Anyways, just a thought. Great job though! Lots of interesting information! [[User:Lapeacock|Leslie Peacock]] 11:54, 13 March 2008 (UTC)<br />
----<br />
<br />
As mentioned before it looks great but i dont know if this is required but you could add a section regarding current research[[User:Njppatel|Njppatel]] 18:40, 13 March 2008 (UTC)<br />
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Wow you site looks great, i like how you included pictures to help solidify concepts.[[User:Njppatel|Njppatel]] 18:40, 13 March 2008 (UTC)<br />
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Great job group! This site looks fantastic! The fermentation stuff is great, and thanks for adding links for the microbes, Heather <br />
<br />
Overall its a very good job, I did have one comment on the section processes, the sentience : ‘Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed’.. needs some editing to make it clear what your trying to say.[[User:Calgilbert|Calgilbert]] 15:37, 12 March 2008 (UTC)<br />
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<br />
<br />
way to go group, way to pull through at the last minute. Good job everybody especially sung ho. -david [[User:Dtla|Dtla]] 07:50, 10 March 2008 (UTC)````<br />
----<br />
<br />
I would remove section 2.3.2. Move that material (renamed microbial activity) as part of the intro to microorganisms involved. I would rename that section something like key microbial processes and organisms involved.<br />
<br />
[[User:Kmscow|Kate Scow]] 02:09, 10 March 2008 (UTC)<br />
<br />
I fixed it <br />
[[User:Jokang|Sungho]] 05:27, 10 March 2008 (UTC)<br />
----<br />
<br />
wow this is looking nice!<br />
Methaneous organisms needs to be changes to methanogens. You also need to add the fermenting organisms as a category. <br />
Also include some of the broader changes with flooding: gleying, and what happens when oxygen becomes available again.<br />
[[User:Kmscow|Kate Scow]] 02:04, 10 March 2008 (UTC)<br />
----<br />
<br />
---- <br />
are the plants linked to microbes now?-david [[User:Dtla|Dtla]] 01:07, 10 March 2008 (UTC)<br />
<br />
It's better, bur organize the information (one main idea per paragraph). [[User:Irina.chakraborty|Irina C]] 01:12, 10 March 2008 (UTC)<br />
<br />
----<br />
im doing effects on life, plants, microorganisms? -david ````[[User:Dtla|Dtla]] 00:10, 10 March 2008 (UTC)<br />
<br />
<br />
The section called "Effects on life" seems out of place. Also, if you want to talk about effects on plants, you need to link it to microbes (i.e. what do microbes to in flooded soils that would effect plants). As it is now, there is no connection to plants. Make sure you site your sources and do not just copy and paste text as you did with at least some of the phrases in your section. You have to paraphrase AND cite the source of the information. Your section on microorganisms is ok but seems try to make it more clear and make sure it doesn't contain info that is covered elsewhere on the page (compare to "electron tower" section) [[User:Irina.chakraborty|Irina C]] 00:29, 10 March 2008 (UTC)<br />
ok-david<br />
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<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
<br />
It looks good. You guys need more detail in some sections. Have you decided among yourselves how to split up the work? [[User:Irina.chakraborty|Irina C]] 06:42, 9 March 2008 (UTC)<br />
----<br />
I erased your "edits and dates" section. We don't need this since we can see who did what and when in the history tab.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 23:37, 6 March 2008 (UTC)<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
----<br />
<br />
I would suggest slightly different organization.<br />
<br />
Maybe under flooded soils could be....<br />
#Overall definition and description of phenomenon of flooded soils. You can put a figure here. You can also say that this type of phenomenon can also be observed in other types of situations.....aggregates and pollutant plumes in groundwater<br />
#Chemical changes : Make sure you focus this on redox. organize these by changes in dominant electron acceptors being used and make the connection to electron tower. ALso include fate of products generated during electron acceptor untilization. e.g. methane migrates up. Sulfides.....<br />
#Changes in microbial community composition<br />
#Changes when the flooded soil is unflooded and oxygen comes in<br />
<br />
Maybe something else??<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
<br />
----<br />
* You don't need to have a list of topics because that is automatically created for you at the top of the page.<br />
* Please put back the text that says "crated by the students of Kate Scow" at the bottom of the template page<br />
* You don't need to sign your names at the end. We can see who did what by looking at the history of the page. Also, Laleh's name is mentioned but it doesn't look like she's logged in. Please make sure you log in and make edits through your own account, since otherwise we can't tell who did what.<br />
[[User:Irina.chakraborty|Irina C]] 19:05, 8 February 2008 (UTC)</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Rhizosphere_Interactions&diff=28922Talk:Rhizosphere Interactions2008-03-14T07:01:12Z<p>Sdemetriou: </p>
<hr />
<div>I would suggest reading through the sections again to catch misspelled words. For example, ‘rhizosphere’ is frequently spelled incorrectly throughout your page. In addition, many of the sentences on the page begin without the first letter capitalized. Scanning through the page to catch simple grammatical errors may strength it significantly! [[User:Sdemetriou|Sdemetriou]] 07:01, 14 March 2008 (UTC)<br />
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In the pH section under "Physical Environment" some of the words at the beginning of the sentences need to be capitalized. Where did you include the current research information? [[User:Jmmullane|Jmmullane]] 06:32, 14 March 2008 (UTC)<br />
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Pictures would be a nice addition. [[User:Jmmullane|Jmmullane]] 06:28, 14 March 2008 (UTC)<br />
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You and I may know that CFU means colony forming unit, but it is nice to always include the full title before using an abbreviation. <br />
<br />
You have a Bacteria section where you talk about soil bacteria in general. It might be more informative to talk about rhizosphere bacteria in this section, as people visiting your page are looking for information on the rhizosphere. <br />
[[User:Icclark|Icclark]] 06:19, 14 March 2008 (UTC)<br />
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Hey i saw this paper by ''Cartmill et al.'' they did an interesting study titled: Abuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water. I dunno if this helps you but it seems like it could fit in under the plant/microbe intereaction area. pretty interesting stuff [[User:Pbwebb|Pbwebb]] 05:00, 14 March 2008 (UTC)<br />
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You should capitalize and italicize all microbe names. Italicize with two apostrophes at either end of a word, like ''this''.[[User:Njblackburn|Njblackburn]] 04:44, 14 March 2008 (UTC)<br />
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Grammar note: "The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere." should be "the plant roots with which the rhizosphere is associated can affect (NOT EFFECT!) the physical environment of the rhizoshpere" [[User:Njblackburn|Njblackburn]] 04:41, 14 March 2008 (UTC)<br />
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Nice amount of detail. Some interesting tidbits. I too would be interested to see some more pictures. Only technical issue is some sentences not being capitalized. Other than that, very thorough. [[User:Kamackey]]<br />
<br />
Good job!! You guys mention some information about soil texture, but I could be relevant to introduce more information related with soil aggregate formation and how fungi contribute to this process[[User:Egrgutierrez|Egrgutierrez]] 03:24, 14 March 2008 (UTC)----<br />
<br />
Great job root people! This seems like a tough topic to tackle with so much going on, but I think this page looks great. A couple comments: I remember from class Kate was saying that the rhizosphere zone (or distance from the root) will vary depending on what soil feature you’re looking at, and that the root shaking is more of an operationally defined approach for laboratory methods. This might be worth mentioning in the intro…just a thought….—Also, for the microbial community section, you may want to elaborate a little bit more on the bacteria and fungi sections? Maybe even just some pictures to beef up those sections a bit. Great job overall! -Heather <br />
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MAybe you guys could include some pretty pictures of the different kinds of organisms, fungi u talked about. -David La [[User:Dtla|Dtla]] 02:48, 14 March 2008 (UTC)````<br />
<br />
Also you page may benefit from the addition of a picture to show what mychorrizae look like[[User:Njppatel|Njppatel]] 18:31, 13 March 2008 (UTC)<br />
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Information looks good, however i heard that mychorrizae can increase the disease resistance of some plant species, if true you may want to incorporate that into the page. I would add more information regarding the mutualistic relationship between plants and the fungi.[[User:Njppatel|Njppatel]] 18:30, 13 March 2008 (UTC)<br />
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I saw some errors on the words, such as rizoplane, risosphere.And you miss some references in Reference section. For example, (Martin, 2008),(Rodreguez, 2008)<br />
[[User:Tantayotai|Tantayotai]] 00:58, 13 March 2008 (UTC) <br />
<br />
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Overall you all did a good job, my one comment is, if you could add more to the section on the <br />
Microbial communities I beleive it would strenthen the page[[User:Calgilbert|Calgilbert]] 15:43, 12 March 2008 (UTC)<br />
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Sorry, my bad. I didn't see your comment. I hope you didn't do too much preparation. <br />
[[User:Alorloff|Alorloff]] 07:48, 10 March 2008 (UTC)<br />
<br />
&#126;&#126;&#126;&#126;<br />
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<br />
<br />
Looking good. It would be good to include the N fixers under symbiotic organisms. You may not need so much detail under the root exudates: all that could be included under just one major heading.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:42, 10 March 2008 (UTC)<br />
<br />
The Rhizoplane, Rhizosphere, and Physical Environment Sections I was planning on doing have been completed by Amber. Therefore, I have changed my topics to Plant Exudates, Microbial Communities, and Mycorrhizal Fungi. Please let me know if you intend to take these topics so I do not do anymore unnecessary work. Thanks. [[User:Metotman|Metotman]] 22:28, 9 March 2008 (UTC)<br />
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<br />
<br />
I edited the outline to better match the recommendations of Prof. Scow (see below). I will be responsible for the following topics: Introduction, Rhizoplane, Physical Environment (under Rhizosphere), Fungi (under Microbial Communities), and Mycorrhizal Fungi (under Symbiotic Relationships). I will assume the rest of you are OK with this unless I hear otherwise from you. [[User:Metotman|Metotman]] 20:17, 8 March 2008 (UTC)<br />
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<br />
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[http://www.physorg.com/news123945390.html Interesting article on mycorrhizae] that you could look into for your current research sections (you would need to find the original paper if you want to use this) [[User:Irina.chakraborty|Irina C]] 22:41, 6 March 2008 (UTC)<br />
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<br />
And of course include the inoculants as its own subheading.<br />
[[User:Kmscow|Kate Scow]]<br />
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<br />
I would suggest a modification to your outline something along these lines......<br />
# The soil environment associated with plants (?)<br />
## rhizoplane<br />
## rhizosphere (this would be bulk of your effort; under rhizosphere heading you could have..)<br />
### physical environment<br />
### plant exudates<br />
### microbial communities<br />
## other ? not really necessary<br />
# Biotic interactions in the rhizosphere<br />
## General impacts on plants of rhizosphere microorganisms<br />
## General impacts on rhizosphere microorganisms of plant<br />
## Symbiotic relationships<br />
### mycorrhizal fungi<br />
### etc.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
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<br />
Other members of my group- I just chose three topics because I lost the list or never wrote it down. I'm not trying to set this in stone, I can reserach whatever, just let me know) 14:52, 9 February 2008 [[user:Metotman]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28737Talk:Nitrogen Cycle2008-03-13T07:29:25Z<p>Sdemetriou: </p>
<hr />
<div>Great job! Under the Nitrogen Fixation section, I would suggest expanding on the Key Microorganisms by name dropping a few microbes that have exhibited the ability to fix nitrogen. I would suggest mentioning: [[Rhizobium]], [[Bradyrhizobium]] and [[Azotobacter]]. [[User:Sdemetriou|Sdemetriou]] 07:28, 13 March 2008 (UTC)<br />
<br />
----<br />
I suggested putting 2.4 as a subheading under 2.3 though now I see it is about both mineralization and immobilization. I still think it is a little odd to have it called out as its own heading after these 2 processes. Perhaps you could include it within mineralization section and not as heading. Or you could combine mineral/immob and have C/N as first subsection. It is up to you folks, though.<br />
<br />
[[User:Kmscow|Kate Scow]] 15:18, 11 March 2008 (UTC)<br />
----<br />
It is really an issue assocdo you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
----<br />
<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
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* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
<br />
For the greenhouse gas and environmental section you mention the note of mass destruction of earth due to greenhouse gases. What is this mass destruction which would occur if the greenhouses get out of control. Is it just heating of the globe or is it much more than this. Other than that looks great.[[User:Njppatel|Njppatel]] 03:24, 12 March 2008 (UTC)<br />
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<br />
Hmm for the section on chemistry i would suggest adding a short definition of what nitrogenase is[[User:Njppatel|Njppatel]] 03:20, 12 March 2008 (UTC)<br />
----<br />
----<br />
Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28736Talk:Nitrogen Cycle2008-03-13T07:29:00Z<p>Sdemetriou: </p>
<hr />
<div>Great job! Under the Nitrogen Fixation section, I would suggest expanding on the Key Microorganisms by name dropping a few microbes that have exhibited the ability to fix nitrogen. I would suggest mentioning: [[Rhizobium]] and [[Azotobacter]]. [[User:Sdemetriou|Sdemetriou]] 07:28, 13 March 2008 (UTC)<br />
<br />
----<br />
I suggested putting 2.4 as a subheading under 2.3 though now I see it is about both mineralization and immobilization. I still think it is a little odd to have it called out as its own heading after these 2 processes. Perhaps you could include it within mineralization section and not as heading. Or you could combine mineral/immob and have C/N as first subsection. It is up to you folks, though.<br />
<br />
[[User:Kmscow|Kate Scow]] 15:18, 11 March 2008 (UTC)<br />
----<br />
It is really an issue assocdo you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
----<br />
<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
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<br />
For the greenhouse gas and environmental section you mention the note of mass destruction of earth due to greenhouse gases. What is this mass destruction which would occur if the greenhouses get out of control. Is it just heating of the globe or is it much more than this. Other than that looks great.[[User:Njppatel|Njppatel]] 03:24, 12 March 2008 (UTC)<br />
----<br />
<br />
Hmm for the section on chemistry i would suggest adding a short definition of what nitrogenase is[[User:Njppatel|Njppatel]] 03:20, 12 March 2008 (UTC)<br />
----<br />
----<br />
Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28735Talk:Nitrogen Cycle2008-03-13T07:28:29Z<p>Sdemetriou: </p>
<hr />
<div>Great job! Under the Nitrogen Fixation section, I would suggest expanding on the Key Microorganisms present by name dropping a few microbes that have exhibited the ability to fix nitrogen. I would suggest mentioning: [[Rhizobium]] and [[Azotobacter]]. [[User:Sdemetriou|Sdemetriou]] 07:28, 13 March 2008 (UTC)<br />
<br />
----<br />
I suggested putting 2.4 as a subheading under 2.3 though now I see it is about both mineralization and immobilization. I still think it is a little odd to have it called out as its own heading after these 2 processes. Perhaps you could include it within mineralization section and not as heading. Or you could combine mineral/immob and have C/N as first subsection. It is up to you folks, though.<br />
<br />
[[User:Kmscow|Kate Scow]] 15:18, 11 March 2008 (UTC)<br />
----<br />
It is really an issue assocdo you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
----<br />
<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
<br />
For the greenhouse gas and environmental section you mention the note of mass destruction of earth due to greenhouse gases. What is this mass destruction which would occur if the greenhouses get out of control. Is it just heating of the globe or is it much more than this. Other than that looks great.[[User:Njppatel|Njppatel]] 03:24, 12 March 2008 (UTC)<br />
----<br />
<br />
Hmm for the section on chemistry i would suggest adding a short definition of what nitrogenase is[[User:Njppatel|Njppatel]] 03:20, 12 March 2008 (UTC)<br />
----<br />
----<br />
Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=28536Talk:Bioremediation2008-03-11T01:24:08Z<p>Sdemetriou: </p>
<hr />
<div>The Microbe page that our group created is for [[phanerochaete chrysosporium]] [[User:Sdemetriou|Sdemetriou]] 01:24, 11 March 2008 (UTC) <br />
----<br />
<br />
would be good in intro to define in situ vs ex situ remediation. Ex situ then cover the use of bioreactors and other such systems.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:38, 10 March 2008 (UTC)<br />
<br />
looking very good. Make sure you use proper scientific nomenclature for naming organisms: genus starting with caps and species name starting with lower case.<br />
<br />
Also I think it flows better to start with pollutants and put the organisms second. <br />
[[User:Kmscow|Kate Scow]] 01:36, 10 March 2008 (UTC) <br />
<br />
<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
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----<br />
<br />
Looking good! Is your source on-line? You can create an external link like [http://ucdavis.edu this]. <br />
- [[User:Irina.chakraborty|Irina C]] 22:49, 10 February 2008 (UTC)</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=28535Talk:Bioremediation2008-03-11T01:23:49Z<p>Sdemetriou: </p>
<hr />
<div>The Microbe page that our group created is for [[phanerochaete chrysosporium]] [[User:Sdemetriou|Sdemetriou]] 01:23, 11 March 2008 (UTC) <br />
----<br />
<br />
would be good in intro to define in situ vs ex situ remediation. Ex situ then cover the use of bioreactors and other such systems.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:38, 10 March 2008 (UTC)<br />
<br />
looking very good. Make sure you use proper scientific nomenclature for naming organisms: genus starting with caps and species name starting with lower case.<br />
<br />
Also I think it flows better to start with pollutants and put the organisms second. <br />
[[User:Kmscow|Kate Scow]] 01:36, 10 March 2008 (UTC) <br />
<br />
<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
<br />
Looking good! Is your source on-line? You can create an external link like [http://ucdavis.edu this]. <br />
- [[User:Irina.chakraborty|Irina C]] 22:49, 10 February 2008 (UTC)</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=28332Bioremediation2008-03-10T02:32:04Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like[[Nitrosomonas europaea]].The, nitrite is further oxidized by microbes like [[Nitrobacter hamburgensis]]. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like[[Paracoccus denitrificans]][2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, Phanerochaete chrysosporium, exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
Methylibium petroleiphilum(formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls PCBs===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen the the metabolic pathways diagram. Energy is obtained through the oxidation of these large hydrocarbons [12].<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, Nitrosomonas Europea has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, [Methylibium petroleiphilum] has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. Methylibium petroleiphilum is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of M. petroleiphilum occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=28331Bioremediation2008-03-10T02:30:20Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like[[Nitrosomonas europaea]].The, nitrite is further oxidized by microbes like [[Nitrobacter hamburgensis]]. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like[[Paracoccus denitrificans]][2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, Phanerochaete chrysosporium, exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
Methylibium petroleiphilum(formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls PCBs===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen the the metabolic pathways diagram. Energy is obtained through the oxidation of these large hydrocarbons [12].<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, Nitrosomonas Europea has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, [Methylibium petroleiphilum] has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. Methylibium petroleiphilum is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of M. petroleiphilum occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28329Phanerochaete chrysosporium2008-03-10T02:28:29Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
[[Image:ligninpathway.gif|Right|]]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br><br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br><br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br> <br />
10. [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycyclic Aromatic Hydrocarbon Degradation by Ligninolytic Fungi." Environmental Health Perspectives 103 (1995). 9 Mar. 2008.]<br><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28328Phanerochaete chrysosporium2008-03-10T02:27:07Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
[[Image:ligninpathway.gif|Right|]]<br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br><br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br><br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br> <br />
10. [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycyclic Aromatic Hydrocarbon Degradation by Ligninolytic Fungi." Environmental Health Perspectives 103 (1995). 9 Mar. 2008.]<br><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28327Phanerochaete chrysosporium2008-03-10T02:26:16Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
[[Image:ligninpathway.gif|Right|]]<br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br />
<br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br />
<br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br />
10. [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycyclic Aromatic Hydrocarbon Degradation by Ligninolytic Fungi." Environmental Health Perspectives 103 (1995). 9 Mar. 2008.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:Ligninpathway.gif&diff=28326File:Ligninpathway.gif2008-03-10T02:24:54Z<p>Sdemetriou: A portion of lignin showing the arylglycerol-ß-aryl ether structure and principal sites of side chain cleavage by fungal activity [1]
1) [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycy</p>
<hr />
<div> A portion of lignin showing the arylglycerol-ß-aryl ether structure and principal sites of side chain cleavage by fungal activity [1]<br />
<br />
1) [http://www.ehponline.org/realfiles/members/1995/Suppl-5/hammell-full.html Hammel, Kenneth E. "Mechanisms for Polycyclic Aromatic Hydrocarbon Degradation by Ligninolytic Fungi." Environmental Health Perspectives 103 (1995). 9 Mar. 2008.]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28324Phanerochaete chrysosporium2008-03-10T02:20:19Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
[[Image:ligninpathway.gif|Right|]]<br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br />
<br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br />
<br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28319Phanerochaete chrysosporium2008-03-10T02:16:24Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br />
<br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br />
<br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28318Phanerochaete chrysosporium2008-03-10T02:12:57Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Degradation of lignin and polutants is made possible by the production of extracellular enzymes. Components such as lignin peroxidase and manganese peroxidase take part in the remediation of various pesticides, polyaromatic hydrocarbons, PCBs, TNT, carbon tetrachloride and various poisons. [8]<br />
<br />
[[Image:Lignin structure.svg|thumb|200px| A possible lignin structure]]<br />
<br />
===Metabolism of Lignin===<br />
Reseach in the degradation of lignin has resulted in numerous substituted benzene ring products. An important catalyst in these reactions are phenol-oxidizing enzymes. [9]<br />
<br />
The process of lignin breakdown is carried out by means of cleavage reactions. These extracellular enzymes release free-radicals to initiate spontaneious break down to phenyl propane units in the Secondary metablism or stationary phase. [8]<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br />
<br />
8. Scow, Kate. "Lecture 6: Carbon Cycle." Winter, 2008.<br />
<br />
9. [http://www.springerlink.com/content/x3377k4n7117g34l/ Toshiaki Umezawa1, Fumiaki Nakatsubo1, and Takayoshi Higuchi1. "Lignin degradation byPhanerochaete chrysosporium: Metabolism of a phenolic phenylcoumaran substructure model compound." Archives of Microbiology, 131(2): March 1982.] <br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=28314Bioremediation2008-03-10T01:58:48Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like[[Nitrosomonas europaea]].The, nitrite is further oxidized by microbes like [[Nitrobacter hamburgensis]]. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like[[Paracoccus denitrificans]][2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, Phanerochaete chrysosporium, exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
Methylibium petroleiphilum(formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls PCBs===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen the the metabolic pathways diagram. Energy is obtained through the oxidation of these large hydrocarbons [12].<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, Nitrosomonas Europea has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, [Methylibium petroleiphilum] has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. Methylibium petroleiphilum is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of M. petroleiphilum occurs at the soil subsurface with pH of 6.5 and 30°C. The upper temperature limit of this bacterium is 37°C. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=28313Bioremediation2008-03-10T01:56:31Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy for cleaning polluted soil and water due to its safety and convenience. Bioremediation allows scientists to concentrate clean-up efforts at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
A widely used approach to bioremediation involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." Biostimulation can be achieved through changes in pH, moisture, and aeration. One of the most common approaches to bioremediation involves in-situ addition of nutrients and oxygen. The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously. Bioreactors can also be employed for remediation. In such cases, soil and groundwater from the contaminated site are transported to the reactor, where conditions favorable for biological reactions are enhanced [5].<br />
<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
=== [[Pseudomonas putida]] ===<br />
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===[[Nitrosomonas europaea]], [[Nitrobacter hamburgensis]], and [[Paracoccus denitrificans]]===<br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage stage process than involves nitrification and denitrification (see [[Nitrogen cycle including GHG]]). During nitrification, ammonium is oxidized to nitrite by organisms like[[Nitrosomonas europaea]].The, nitrite is further oxidized by microbes like [[Nitrobacter hamburgensis]]. <br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like[[Paracoccus denitrificans]][2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
=== [[Phanerochaete chrysosporium]]===<br />
The lignin-degrading white rot fungus, Phanerochaete chrysosporium, exhibits strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
=== [[Deinococcus radiodurans]] ===<br />
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
===[[Methylibium petroleiphilum]]===<br />
Methylibium petroleiphilum(formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Pollutants that are being studied for bioremediation potential are listed below. The remediation of some of these pollutants will be discussed in greater depth in the following sections. <br />
<br />
===Petroleum byproducts===<br />
BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are harder to degrade than BTEX [3].<br />
<br />
===Methyl tert-butyl ether===<br />
MTBE is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
===Polychlorinated bhiphenols===<br />
PCBs are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
===Chlorinated solvents===<br />
Chlorinated solvents are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
===Polynuclear aromatic compounds===<br />
PAHs are found in high concentrations at industrial sites especially sites that use or process petroleum products. The are considered carcinogens and mutanogens, and are very recalcitrant, pervading for many years in the natural environment. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
== Bioremediation Applications ==<br />
<br />
=== Exxon Valdez Oil Spill in Prince William Sound ===<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]]<br />
Bioremediation was employed to treat the 1989 Exxon Valdez oil spill in Prince William Sound, Alaska. Hydrocarbon degrading microbes exist in marine systems because natural sources of hydrocarbon exists as a result of geological seeps and other sources. During the Exxon cleanup effort, the activity of these organisms was enhanced through the addition of nitrogen and phosphorus to oil laden beaches [9]. This is an example of bio-stimulation.<br />
<br />
== Metabolic Pathways ==<br />
Microorganisms use a wide range of metabolic pathways to harvest energy from their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor (ex. perchlorate degradation). This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. The degradation pathways for a few of the pollutants listed above are explored.<br />
<br />
=== Polychlorinated Biphenyls PCBs===<br />
<br />
Metabolism of polychlorinated biphenyls is generally through to proceed through the addition of two oxygens to the aromatic ring, followed by ring cleavage as seen the the metabolic pathways diagram. Energy is obtained through the oxidation of these large hydrocarbons [12].<br />
<br />
[[Image:PCB_degradation.jpg|PCB_degradation.jpg]]<br />
<br />
===Polynuclear aromatic compounds (PAHs)===<br />
Examples of PAHs are seen below:<br />
<br />
[[Image:PAH.jpg|Right|Example PAHs[5]|Border]]<br />
<br />
PHAs in contaminated soils can be treated with bioremediation. The oxidation of PAH involves oxygenases (monooxygenases and dioxygenases). Fungi complete the process by adding an oxygen to the substrate PAH to form arene oxides and then enzymatically adding water to form trans-dihydrodiols and phenols. Bacteria mainly use dioxygenases, adding two oxygens to the substrate and the further oxidizing it to dihydrodiols and dihydroxy products. Ring oxidation is the rate limiting step in the reaction, and subsequent reactions occur fairly quickly, yielding the typical metabolic intermediate Catechol found in Lignin degradation as well as Gentisic and Protocatechuic Acids (see diagram below) [5].<br />
<br />
[[Image:PAH_degradation.jpg|Right|]]<br />
<br />
Intermediate metabolites degrade further through ortho and meta ring cleavage to produce succinic, fumaric, pyruvic, and acetic acids and acetyl-CoA, which are shunted into major metabolic and anabolic pathways [11]. The byproducts of these reactions are carbon dioxide and water. The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5].<br />
<br />
==Monitoring==<br />
<br />
To monitor the bioremedation potential of a soil one can probe for the existence of specific degradation pathways in the soil community or monitor for specific enzymes involved in the process. There are two common ways to test for functional genes involved in the degradation of a compound. First, specific DNA hybridization probes can be used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment[3]. <br />
<br />
The actual change in pollutant concentration or degradation byproducts can also be monitored to determine the amount of pollutant removal. To determine if the degradation of a desired compound is the result of abiotic or biotic activity, controlled laboratory experiments are used. The concentration of a pollutant in a non-sterile microcosm containing soil from the environment of interest is compared to a sterile control. The sterile control shows the non-biological contribution to the disappearance of the pollutant due to, for example, adsorption to clay particles or precipitation. The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment, but also includes other abiotic mechanisms. The microbial contribution to pollutant disappearance is the difference between removal in the biologically active bottle and removal in the sterile control. This helps to quantify whether the disappearance of the pollutant is the result of biological or non-biological mechanisms. [3]<br />
<br />
==Current Research==<br />
===Pseduomonas putida===<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
===Nitrosomonas Europaea===<br />
One possible treatment for the purification of water has been the use of Trihalomethanes or THM's. Recent studies have linked these four chemicals, tricholormethane or chloroform, bromomethane, dibromomethane and dichlorobromomethane have been linked to colon cancer. [12] Because of its nitrogen oxidizing properties, Nitrosomonas Europea has been studied under ammonia rich conditions and THM rich conditions, recognized as limiting reactants in the conversion of ammonia. [13]<br />
<br />
===Methylibium petroleiphilum===<br />
A motile, gram-negative facultative anaerobic bacterium, [Methylibium petroleiphilum] has been isolated because its ability to completely mineralize methyl tert-butyl ether (MTBE), a gasoline additive. Methylibium petroleiphilum is capable of consuming a diverse range of gasoline derivatives as its sole carbon source, including: methanol, ethanol, toluene, benzene, ethylbenzene, and dihydroxybenzenes. Optimal growth of M. petroleiphilum occurs at the soil subsurface with pH of 6.5 and 30uC. The upper temperature limit of this bacterium is 37uC. [14]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
10. Pritchard, PH. 1991. "Bioremediation as a technology: experiences with the Exxon Valdez oil spill." Journal of Hazardous Materials 28:115-130. <br />
<br />
11. Scow, Kate. "Lectures in Soil Microbiology." UC Davis, Winter 2008. <br />
<br />
12. [http://www.water-research.net/trihalomethanes.htm Oram, Brian. "Disinfection By-Products Trihalomethanes." Wilkes University, 2003]<br />
<br />
13. [http://aem.asm.org/cgi/reprint/71/12/7980.pdf?ck=nck Weahmen, David G., Lynn E. Katz, Gerald E. Speitel, Jr. "Comotabolism of Trihalomethanes by Nitrosomonas Europaea." Applied and Environmental Microbiology, 12: vol. 71 (7980-7986)]<br />
<br />
14. [http://ijs.sgmjournals.org/cgi/reprint/56/5/983 Nakatsu, Cindy H., Krassimira Hristova, Satoshi Hanada, Xian-Ying Meng, Jessica R. Hanson, Kate M. Scow, and Yoichi Kamagata. "Methylibium Petroleiphilum Gen. Nov., Sp. Nov.,." International Journal of Systematic and Evolutionary Microbiology 56 (2006): 983-989. 9 Mar. 2008.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=28057Bioremediation2008-03-09T11:06:20Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy to clean-ups due to its safety and convenience. The process relies on the microorganisms that are natural to the soil, and also allows scientists to solve the problem right at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
New applications of bioremediation continue to be developed to degrade hazardous chemicals, although there are similarities between approaches. A widely used approach involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Some priority pollutants and their origins are found below:<br />
<br />
1) Petroleum byproducts: BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are hard to degrade than BTEX [3].<br />
<br />
2) MTBE - Methyl tert-butyl ether is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
3) PCB - Polychlorinated bhiphenols are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
4) Chlorinated solvents (example TCE and PCE) are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Applications of Bioremediation==<br />
<br />
<br />
<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]] <br />
<br />
Polynuclear aromatic compounds (PHAs)in contaminated soils can be treated with bioremediation [5]<br />
<br />
Exxon Valdez Oil Spill in Prince William Sound [9]<br />
<br />
===Monitoring===<br />
<br />
To monitor bioremedation presence in soil, one can search for special activity that microorganisms can preform in the environment. There are two common ways to test for functional genes involved for the desired degradation of a compound. First, specific DNA hybridization probes are used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment. [3]<br />
<br />
To determine if the degradation of a desired compound is the result of abiotic or biotic activity, one can performed a controlled laboratory experiment with the presence of the pollutant in a sterile control and a non-sterile microcosm of the environment of interest. The sterile control shows the non-biological contribution to the degradation or disappearance of the pollutant (e.g. adsorption to clay particles). The non-sterile microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment. From the results of the experiment shows whether the disappearance of the pollutant was the result of microbial biodegradation or non-biological mechanism. [3]<br />
<br />
===Degradation Pathways===<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
[[Pseudomonas putida]] is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
Industrial bioremediation is used to clean up wastewater. Most treatment systems rely on microbial activity to remove unwanted compounds from the wastewater, for example fixed nitrogen compounds (i.e. ammonia). The reduction of ammonia to dinitrogen gas involves two different microbes. First, [[Nitrosomonas europaea]] reduces ammonia to nitrite. Then, [[Paracoccus denitrificans]] reduces nitrite to dinitrogen gas. Therefore, the nitrogen pollution in the wastewater is eliminated as the gas escapes to the atmosphere. Denitrification is the process of consuming fixed forms of nitrogen as the electron acceptor in anaerobic conditions and reducing it to dinitrogen gas [2].<br />
<br />
The lignin-degrading white rot fungus, [[Phanerochaete chrysosporium]], exhibit strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
The radiation-resistant [[Deinococcus radiodurans]] is an extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
[[Methylibium petroleiphilum]] (formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
==Current Research==<br />
<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28056Phanerochaete chrysosporium2008-03-09T10:58:00Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br><br />
6. [http://www.ncbi.nlm.nih.gov/pubmed/15122302?dopt=Abstract Martinez D et al., "Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.", Nat Biotechnol, 2004 Jun;22(6):695-700]<br><br />
7. [http://www.biomedcentral.com/1471-2164/6/92 Doddapaneni, Harshavardhan, Ranajit Chakraborty, and Jagjit Yadav. "Genome-Wide Structural and Evolutionary Analysis of the P450 Monooxygenase Genes (P450ome) in the White Rot Fungus Phanerochaete Chrysosporium : Evidence for Gene Duplications and Extensive Gene Clustering." BMC Genomics 6 (2005). 9 Mar. 2008.]<br />
<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28055Phanerochaete chrysosporium2008-03-09T10:56:23Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is the model white rot fungus because of its specialized ability to degrade the abundant aromatic polymer lignin, while leaving the white cellulose nearly untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced. [6]<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysoporium’s genome consists of approximately 29.6-million base pairs arranged in ten linear chromosomes [6]. Genomic analysis provides structural, comparative, and functional information about the organisms. <br />
<br />
P. chrysoporium’s importance in the field of biotechnology lead to the analysis P450 monooxygenase genes to provide information about the complex protein interactions and distinct components involved in the production of the polyaromatic degrading extracellular enzyme. In the P450 genes, microexons were detected to suggest the mechanisms of alternative splicing during transcription, which may explain this organism’s evolution of diverse metabolic activity. [7]<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
<br />
[[Image:whiterot.jpg|right|Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]]]<br />
<br />
Phanerochaete chrysosporium is a saprophytic fungus capable of organic breakdown of the woody part of dead plants. Therefore, plants that are in the process of dieing or dead serve as an optimal substrate for P. chrysosporium. Symptoms may include white patches of cellulose due to the disappearance of lignin from the plant structure. <br />
<br />
This fungus is not a known pathogen of humans or animals.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:Whiterot.jpg&diff=28054File:Whiterot.jpg2008-03-09T10:55:55Z<p>Sdemetriou: </p>
<hr />
<div>Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DN JGI.]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:Whiterot.jpg&diff=28053File:Whiterot.jpg2008-03-09T10:54:35Z<p>Sdemetriou: Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&</p>
<hr />
<div>Degradation of a dead tree by ''Phanerochaete chrysosporium''; Mag. .5x. Photograph courtesy of [http://images.google.com/imgres?imgurl=http://www.jgi.doe.gov/sequencing/why/whiterot.jpg&imgrefurl=http://www.jgi.doe.gov/sequencing/why/whiterot.html&h=143&w=227&sz=17&hl=en&start=39&sig2=iaAc9DoSYFHBsUhnP31wkQ&tbnid=38oyQ1EMtswLSM:&tbnh=68&tbnw=108&ei=RL_TR53mM56wgQOU-tXODg&prev=/images%3Fq%3Dwhite%2Brot%26start%3D20%26ndsp%3D20%26hl%3Den%26lr%3D%26sa%3DNJoi.]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=28015Bioremediation2008-03-09T01:23:04Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy to clean-ups due to its safety and convenience. The process relies on the microorganisms that are natural to the soil, and also allows scientists to solve the problem right at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
New applications of bioremediation continue to be developed to degrade hazardous chemicals, although there are similarities between approaches. A widely used approach involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Some priority pollutants and their origins are found below:<br />
<br />
1) Petroleum byproducts: BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are hard to degrade than BTEX [3].<br />
<br />
2) MTBE - Methyl tert-butyl ether is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
3) PCB - Polychlorinated bhiphenols are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
4) Chlorinated solvents (example TCE and PCE) are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Applications of Bioremediation==<br />
<br />
<br />
<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]] <br />
<br />
Polynuclear aromatic compounds (PHAs)in contaminated soils can be treated with bioremediation [5]<br />
<br />
Exxon Valdez Oil Spill in Prince William Sound [9]<br />
<br />
===Monitoring===<br />
<br />
To monitor bioremedation presence in soil, one can search for special activity that microorganisms can preform in the environment. There are two common ways to test for functional genes involved for the desired degradation of a compound. First, specific DNA hybridization probes are used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment [3]. <br />
<br />
To determine if the degradation of a desired compound is the result of abiotic or biotic activity, one can performed a controlled laboratory experiment with the presence of the pollutant in a sterile control and a microcosm of the environment of interest. The sterile control shows the non-biological contribution to the degradation or disappearance of the pollutant (e.g. adsorption to clay particles). The microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment. From the results of the experiment shows whether the disappearance of the pollutant was the result of microbial biodegradation or non-biological mechanism [3]. <br />
<br />
===Degradation Pathways===<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
[[Pseudomonas putida]] is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
Industrial bioremediation is used to clean up wastewater. Most treatment systems rely on microbial activity to remove unwanted compounds from the wastewater, for example fixed nitrogen compounds (i.e. ammonia). The reduction of ammonia to dinitrogen gas involves two different microbes. First, [[Nitrosomonas europaea]] reduces ammonia to nitrite. Then, [[Paracoccus denitrificans]] reduces nitrite to dinitrogen gas. Therefore, the nitrogen pollution in the wastewater is eliminated as the gas escapes to the atmosphere. Denitrification is the process of consuming fixed forms of nitrogen as the electron acceptor in anaerobic conditions and reducing it to dinitrogen gas [2].<br />
<br />
The lignin-degrading white rot fungus, [[Phanerochaete chrysosporium]], exhibit strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
The radiation-resistant [[Deinococcus radiodurans]] is an extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
[[Methylibium petroleiphilum]] (formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
==Current Research==<br />
<br />
Pseudomonas putida has been found to be useful in the detection of certain chemicals, such as land mines. On the grand scale, a linkage between the bacteria's ability to degrade TNT and the explosive compound found in land mines has inspired research to utilize P. putida as a way of detecting land mines from soil content. [http://www.epa.gov/oppt/biotech/pubs//submissions/4-5dec.htm TSCA Experimental Release Application Approved for Pseudomonas putida Strains]<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28014Phanerochaete chrysosporium2008-03-09T01:20:16Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is called a white rot fungus for its specialized ability to degrade lignin, while leaving the white cellulose untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced.<br />
<br />
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.<br />
Include a picture or two (with sources) if you can find them.<br />
<br />
==Genome structure==<br />
<br />
The genome consists of 30-million base pairs<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
Does it have any plasmids? Are they important to the organism's lifestyle?<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.html Tom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28013Phanerochaete chrysosporium2008-03-09T01:19:52Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is called a white rot fungus for its specialized ability to degrade lignin, while leaving the white cellulose untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced.<br />
<br />
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.<br />
Include a picture or two (with sources) if you can find them.<br />
<br />
==Genome structure==<br />
<br />
The genome consists of 30-million base pairs<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
Does it have any plasmids? Are they important to the organism's lifestyle?<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [http://botit.botany.wisc.edu/toms_fungi/feb2007.htmlTom Volk's Fungus of the Month for February 2007]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28012Phanerochaete chrysosporium2008-03-09T01:19:12Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is called a white rot fungus for its specialized ability to degrade lignin, while leaving the white cellulose untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the [[bioremediation]] of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced.<br />
<br />
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.<br />
Include a picture or two (with sources) if you can find them.<br />
<br />
==Genome structure==<br />
<br />
The genome consists of 30-million base pairs<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
Does it have any plasmids? Are they important to the organism's lifestyle?<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [Tom Volk's Fungus of the Month for February 2007 http://botit.botany.wisc.edu/toms_fungi/feb2007.html]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=28011Phanerochaete chrysosporium2008-03-09T01:18:13Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is called a white rot fungus for its specialized ability to degrade lignin, while leaving the white cellulose untouched. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Due to Phanerochaete chrysoporium specialized degradation abilities, extensive research is seeking ways to understand the mechanism in order to enhance the bioremediation of a diverse range of pollutants. Therefore, Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequenced.<br />
<br />
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.<br />
Include a picture or two (with sources) if you can find them.<br />
<br />
==Genome structure==<br />
<br />
The genome consists of 30-million base pairs<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
Does it have any plasmids? Are they important to the organism's lifestyle?<br />
<br />
==Cell structure and metabolism==<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Due to Phanerochaete chrysosporium sustainability at moderate to higher temperatures, specifically 40 degrees celcius, this white-rot fungus can be found in forests ranging from North America, to areas of Europe and in Iran. [4] A main role it assumes is that of degradation of the complex lignin from various trees and plants. This process reduces lignin into less complex molecules, maintaining the cycle of the decomposer of plants. <br />
<br />
Recent studies have revealed an association of a certain bacteria found in conjunction with this strain of fungi. Agrobacterium radiobacter was isolated as coexisting with the fugi, and very difficult to separate. [5] Discovery of how bacteria and fungi affect each other physiologically is yet to be conclusive, but further research could give further evidence of mutualism, and its affect on bioremdiation.<br />
<br />
==Pathology==<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Finding a way to degrade everyday plastics has been a concern for sometime now. Research has shown Phanerochaete chrysosporium to be a degrader of phenolic resins found in such plastics within particle board and Formica, the constitutent of many counters and table tops. Research ensues as other types of fungi are found to be inclined to degrade complex components of plastic. [Tom Volk's Fungus of the Month for February 2007 http://botit.botany.wisc.edu/toms_fungi/feb2007.html]<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br><br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br><br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br><br />
4. Burdsall, H. (1985) Mycologia Memoir 10, 61-63<br><br />
5. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1388895 F. Seigle-Murandi, P. Guiraud, J. Croize, E. Falsen, and K. L. Eriksson, "Bacteria Are Omnipresent on Phanerochaete chrysosporium Burdsall." "Applied and Environmental Microbiology Journal." 1996 July; 62(7): p.2477–2481.]<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:OilSheenFromValdezSpill.jpg&diff=27934File:OilSheenFromValdezSpill.jpg2008-03-08T09:45:06Z<p>Sdemetriou: </p>
<hr />
<div>During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [http://response.restoration.noaa.gov/photos/exxon/05.html]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=27921Phanerochaete chrysosporium2008-03-08T05:25:09Z<p>Sdemetriou: </p>
<hr />
<div>{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is called a white rot fungus for its specialized ability to degrade lignin, while leaving the white cellulose available for degradation by other organisms. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
<br />
<br />
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.<br />
Include a picture or two (with sources) if you can find them.<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequence. The genome consists of 30-million base pairs<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
Does it have any plasmids? Are they important to the organism's lifestyle?<br />
<br />
==Cell structure and metabolism==<br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
==Application to Biotechnology==<br />
<br />
[[Bioremediation]]<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Enter summaries of the most recent research here--at least three required<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br />
<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Phanerochaete_chrysosporium&diff=27920Phanerochaete chrysosporium2008-03-08T05:17:43Z<p>Sdemetriou: </p>
<hr />
<div><br />
{{Biorealm Genus}}<br />
<br />
==Classification==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
===Higher order taxa===<br />
<br />
Eukaryota; Fungi/Metazoa group; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetes incertae sedis; Corticiales; Corticiaceae; Phanerochaete<br />
<br />
===Species===<br />
<br />
{|<br />
| height="10" bgcolor="#FFDF95" |<br />
'''NCBI: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock Taxonomy]'''<br />
|}<br />
<br />
''Phanerochaete chrysosporium''<br />
<br />
<br />
==Description and significance==<br />
<br />
Phanerochaete chrysosporium is called a white rot fungus for its specialized ability to degrade lignin, while leaving the white cellulose available for degradation by other organisms. Phanerochaete chrysosporium releases extracellular enzymes to break-up the complex three-dimensional structure of lignin into components that can be utilized by its metabolism. The extracellular enzymes are non-specific oxidizing agents (hydrogen peroxide, hydroxyl radicals) used to cleave the lignin bonds. [3]<br />
<br />
Phanerochaete chrysosporium is a crust fungi, which forms flat fused reproductive fruiting bodies instead of the mushroom structure. This fungi exhibit an interesting pattern of septate hyphae, giving a stronger line of defense in times of distress. The hyphae network has some branching, with diameters ranging from 3-9 µm. At the ends of the hyphae rests chlamydospores, thick-walled spores varying from 50-60 µm. The conidiophore gives rise to round asexual blastoconidia, which are 6-9 µm in diameter. [1,2] <br />
<br />
<br />
<br />
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated.<br />
Include a picture or two (with sources) if you can find them.<br />
<br />
==Genome structure==<br />
<br />
Phanerochaete chrysosporium is the first member of the Basidiomycetes to have its complete genome sequence. The genome consists of 30-million base pairs<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
Does it have any plasmids? Are they important to the organism's lifestyle?<br />
<br />
==Cell structure and metabolism==<br />
<br />
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.<br />
<br />
==Ecology==<br />
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.<br />
<br />
==Pathology==<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
<br />
==Application to Biotechnology==<br />
<br />
Bioremediation<br />
<br />
Does this organism produce any useful compounds or enzymes? What are they and how are they used?<br />
<br />
==Current Research==<br />
<br />
Enter summaries of the most recent research here--at least three required<br />
<br />
==References==<br />
<br />
1. Burdsall, H. (1985) Mycologia Memoir 10, 61-63.<br />
2. Nakasone, K. (1990) Mycologia Memoir 15, 224-225.<br />
3. Burdsall, H. (1974) Mycotaxon 1, 124.<br />
<br />
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:040504062021.jpg&diff=27919File:040504062021.jpg2008-03-08T05:15:59Z<p>Sdemetriou: </p>
<hr />
<div>Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:040504062021.jpg&diff=27918File:040504062021.jpg2008-03-08T05:15:45Z<p>Sdemetriou: </p>
<hr />
<div>[[Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:040504062021.jpg&diff=27917File:040504062021.jpg2008-03-08T05:15:23Z<p>Sdemetriou: </p>
<hr />
<div>[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:OilSheenFromValdezSpill.jpg&diff=27916File:OilSheenFromValdezSpill.jpg2008-03-08T05:13:36Z<p>Sdemetriou: </p>
<hr />
<div>During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [http://response.restoration.noaa.gov/photos/exxon/05.html] <br />
<br />
{{PD-USGov-NOAA}}]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:OilSheenFromValdezSpill.jpg&diff=27915File:OilSheenFromValdezSpill.jpg2008-03-08T05:13:20Z<p>Sdemetriou: </p>
<hr />
<div>[[During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [http://response.restoration.noaa.gov/photos/exxon/05.html] <br />
<br />
{{PD-USGov-NOAA}}]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=File:OilSheenFromValdezSpill.jpg&diff=27914File:OilSheenFromValdezSpill.jpg2008-03-08T05:12:07Z<p>Sdemetriou: </p>
<hr />
<div>[http://response.restoration.noaa.gov/photos/exxon/05.html] <br />
<br />
{{PD-USGov-NOAA}}]]</div>Sdemetriouhttps://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=27913Bioremediation2008-03-08T05:10:58Z<p>Sdemetriou: </p>
<hr />
<div>==Introduction==<br />
<br />
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental, and especially human risks.<br />
It has become an accepted remedy to clean-ups due to its safety and convenience. The process relies on the microorganisms that are natural to the soil, and also allows scientists to solve the problem right at the site of contamination. [1] Bioremediation processes typically involve many different microbes acting in parallel or sequence to complete the degradation process. The ability of microbes to degrade a vast array of pollutants makes bioremediation a widely applicable technology that can applied in different soil conditions [3]. <br />
<br />
New applications of bioremediation continue to be developed to degrade hazardous chemicals, although there are similarities between approaches. A widely used approach involves stimulating a group of organisms in order to shift the microbial ecology toward the desired process. This is termed "Biostimulation." The other widely used approach is termed "Bioaugmentation" where organisms selected for high degradation abilities are used to inoculate the contaminated site [3].<br />
<br />
==Example Pollutants==<br />
<br />
Pollutants found in soils present a variety of different human health risks including direct toxicity, as well as bioaccumulation in plant and animal tissue eventually consumed by humans. Some priority pollutants and their origins are found below:<br />
<br />
1) Petroleum byproducts: BTEX - benzene, toluene, ethylbenzene, and xylene - are byproducts of petroleum products. The biodegradability of these compounds is relatively well known and remediation can be achieved by creating favorable conditions for BTEX degrader's growth. PAH - Polycyclic aromatic compounds remain on the soil surface and are hard to degrade than BTEX [3].<br />
<br />
2) MTBE - Methyl tert-butyl ether is a gasoline additive introduced to replace lead. MTBE raises the oxygen content of fuel, allowing for more complete combustion and less emissions. MTBE, however, is highly soluble, does not adsorb well in soil and can therefore move quickly through soil and into groundwater [4]. <br />
<br />
3) PCB - Polychlorinated bhiphenols are used in industrial applications, are very recalcitrant, and many are known carcinogens. <br />
<br />
4) Chlorinated solvents (example TCE and PCE) are used extensively as cleaning agents. Plumes have been found to contaminate groundwater below dry cleaners in many places, including Davis, Ca. Many chlorinated solvents are carcinogenic. TCE can be degraded to vinyl chloride under anaerobic conditions. Vinyl chloride, in tern, needs different conditions to transform, and this should be seriously considered due to its high toxicity [3]. <br />
<br />
Other contaminants include residuals from flares (perchlorate) and explosives (TNT, RDX); metals (chromium, lead); plutonium and uranium; polynuclear aromatic compounds; potassium and nitrogen. Much of the high levels of these contaminants found in nature is a result of human activity [3]<br />
<br />
==Applications of Bioremediation==<br />
<br />
<br />
<br />
[[Image:OilSheenFromValdezSpill.jpg|right|During the first few days of the Exxon Valdez Oil Spill in Prince William Sound, which used bioremediation to facilitate the degradation of the pollutant. [[NOAA]] photo and text.]] <br />
<br />
Polynuclear aromatic compounds (PHAs)in contaminated soils can be treated with bioremediation [5]<br />
<br />
Exxon Valdez Oil Spill in Prince William Sound [9]<br />
<br />
===Monitoring===<br />
<br />
To monitor bioremedation presence in soil, one can search for special activity that microorganisms can preform in the environment. There are two common ways to test for functional genes involved for the desired degradation of a compound. First, specific DNA hybridization probes are used to indicate potential for the organisms to degrade the desired compound. Second, specific RNA hybridization probes are used to indicate the expression of the functional genes in the environment [3]. <br />
<br />
To determine if the degradation of a desired compound is the result of abiotic or biotic activity, one can performed a controlled laboratory experiment with the presence of the pollutant in a sterile control and a microcosm of the environment of interest. The sterile control shows the non-biological contribution to the degradation or disappearance of the pollutant (e.g. adsorption to clay particles). The microcosm simulates the microbial contribution to the degradation of the pollutant in the natural environment. From the results of the experiment shows whether the disappearance of the pollutant was the result of microbial biodegradation or non-biological mechanism [3]. <br />
<br />
===Degradation Pathways===<br />
==Example Microorganisms==<br />
<br />
[[Image:040504062021.jpg|right|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x. Photograph courtesy of UC Reagents.]]<br />
<br />
[[Pseudomonas putida]] is a gram-negative soil bacterium that is involved in the bioremediation of toulene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
Industrial bioremediation is used to clean up wastewater. Most treatment systems rely on microbial activity to remove unwanted compounds from the wastewater, for example fixed nitrogen compounds (i.e. ammonia). The reduction of ammonia to dinitrogen gas involves two different microbes. First, [[Nitrosomonas europaea]] reduces ammonia to nitrite. Then, [[Paracoccus denitrificans]] reduces nitrite to dinitrogen gas. Therefore, the nitrogen pollution in the wastewater is eliminated as the gas escapes to the atmosphere. Denitrification is the process of consuming fixed forms of nitrogen as the electron acceptor in anaerobic conditions and reducing it to dinitrogen gas [2].<br />
<br />
The lignin-degrading white rot fungus, [[Phanerochaete chrysosporium]], exhibit strong potential for bioremediation of: pesticides, polyaromatic hydrocarbons, PCBs, dioxins, dyes, TNT and other nitro explosives, cyanides, azide, carbon tetrachloride, and pentachlorophenol. White rot fungi degrade lignin with nonselective extracellular peroxidases, which can also facilitate the degradation of other compounds containing similar structure to lignin within the proximity of the enzymes released [6]. <br />
<br />
The radiation-resistant [[Deinococcus radiodurans]] is an extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered stain of [[Deinococcus radiodurans]] has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7]. <br />
<br />
[[Methylibium petroleiphilum]] (formally known as PM1) is a bacterium is capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
==References==<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdfUnited States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. [http://www.epa.gov/mtbe/gas.htmUnited States Environmental Protection Agency, "MTBE," 2007]<br />
<br />
5. Wilson, S. C., and Kevin C. Jones (1993). "Bioremediation of Soil Contaminated with Polynuclear Aromatic Hydrocarbons (PHAs): A review." Environmental Pollution. 81: 229-49.<br />
<br />
6. [http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1995/11/i04/f-pdf/f_bp00034a002.pdf?sessid=6006l3Paszczynsk, Andrzej, and Ronald L. Crawford. "Potential for Bioremediation of Xenobiotic Compounds by The White-Rot Fungus Phanerochaete chrysosporium." Biotechnol. Prog. 11 (1995): 368-379. 2 Mar. 2008 ]<br />
<br />
7. [http://www.usuhs.mil/pat/deinococcus/FrontPage_DR_Web_work/Pages/Lab_info/Daly_papers/Brim_2000.pdf/Brim, Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008]<br />
<br />
8. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=91645Hanson, Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008 ]<br />
<br />
9. [http://www.springerlink.com/content/h73q62860661p022/Pritchard, P H., J G. Mueller, J C. Rogers, F V. Kremer, and J A. Glaser. "Oil Spill Bioremediation: Experiences, Lessons and Results From the Exxon Valdez Oil Spill in Alaska." Biodegradation 3 (1992): 315-335. 2 Mar. 2008 ]<br />
<br />
<br />
Edited by student of [mailto:kmscow@ucdavis.edu Kate Scow]</div>Sdemetriou