Dehalococcoides ethenogenes: Difference between revisions

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===Species===
===Species===


''Dehalococcoides ethenogenes''
''Dehalococcoides ethenogenes'' (strain 195)
 
[[Image:Dehalococcoides_ethenogenes.jpg|right|thumbnail|www.mdsg.umd.edu]]


==Description and significance==
==Description and significance==
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.
Include a picture or two (with sources) if you can find them.


Dehalococcoides ethenogenes has many cellular features. This bacteria is Gram-positive, which generally means it has a very thick cell wall and a single membrane layer. From a three-dimensional prospective, it appears to have an irregular, spherical shape. The species moves spontaneously and independently. It is most suitable in moderate temperature environment around 25 and 40°C with an optimal temperature of 35°C. In the bacteria, there does not exist the following electron acceptors: oxygen, nitrate or sulfate (formally known as anaerobic). It can live in multiple habitats because it has a living temperature similar to soil, the human body, animals, etc. Thankfully, it is not pathogenic, which means it doesn't spread diseases or illnesses its host.
''Dehalococcoides ethenogenes'' is Gram-positive, which generally means it has a very thick cell wall and a single membrane layer. From a three-dimensional perspective, it appears to have an irregular, spherical shape known as coccoid. Motility is spontaneous and independent. ''D. ehtenogenes'' is mesophilic and neutrophilic, liking neutral pH environments from 25 to 40°C, with an optimal temperature of 35°C. It is anaerobic and cannot use inorganic electron acceptors.  


This specific strand of genome was sequenced, and it was discovered to help decontaminate toxic chemicals in many industries. Specifically, this species reduces chlorinated hydrocarbons in contaminated environments. Chlorinated hydrocarbons are significantly toxic to humans. Also, it can cause irreparable damage in groundwater areas when the chemical is not handled properly.  
This specific strand of genome was sequenced, and it was discovered to help decontaminate toxic chemicals from many industries. Specifically, this species reduces chlorinated hydrocarbons in contaminated environments to harmless daughter compounds (ethene) . Chlorinated hydrocarbons are significantly toxic to humans and contaminate groundwater where the chemical is not handled properly.


It is the only known bacterium which completely dechlorinates tetrachloroethene (PCE) to ethylene.
==Genome structure==


This organism can be isolated from environments polluted with chemicals such as PCE and trichloroethane (TCE).
''Dehalococcoides ethenogenes'' has 1,469,720 or 1.5 Mbp nucleotide base pairs in its genome. Only one gene encoding reductive dehalogenase has been isolated and characterized. Strain 195 is the only known bacterium, to date, which completely dechlorinates tetrachloroethene (PCE) and trichloroethene (TCE), to ethene. Strains show >98% nucleotide and >85% amino acid similarity; however, different strains utilize different ranges of haloorganic compounds as electron acceptors.


[[Image:DE2.jpg|right|thumbnail|wwwscielo.isciii.es]]
==Cell structure and metabolism==


==Genome structure==
''D. ethenogenes'' mediates reductive dechlorination reaction via hydrogenolysis or dichloroelimination. In hydrogenolysis, chlorine is replaced by hydrogen, with a net input of one proton and two electrons. In dechloroelimination, chlorine substituents are replaced via the formation of a double bond between the two associated carbon atoms. The dechloroelimination reaction has a net input of two electrons. The biological process mostly undergoes hydrogenolysis.  
Describe the size and content of the genome. How many chromosomes?  Circular or linear?  Other interesting features?  What is known about its sequence?
Does it have any plasmids?  Are they important to the organism's lifestyle?


Dehalococcoides ethenogenes has many features in its genome. The total nucleotide base pairs in this genome is around 1,469,720 or 1.5 Mb. It has one chromosome referring to strain 195. The species has a circular shape, although not perfectly circular (irregular coccus).
Importantly, ''D. ethenogenes'' conserves energy when hydrogen serves as electron donor, halogenated compounds are electron acceptors, and the enzyme reductive dehalogenase catalyzes the reaction. Each intermediate reaction, from PCE to TCE to cis-DCE to VC is energy-yielding for ''D. ethenogenes''; however, the VC to ethene intermediate is cometabolic and does not provide the beneift of energy to the microbe. While the process from VC to ethene is not beneficial to the microbe, it is critical to remediating the contaminated environment.


==Cell structure and metabolism==
The redox potentials for each intermediate reaction range from 260 to 570 mV. ''D. ethenogenes'' can dehalorespirate using chloroethenes, chlorophenols, and polychlorinated biphenyls/dioxins as terminal electron acceptors.
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.


Cellular features: Gram Positive; Shape: Irregular coccus; Environment: Non-Methanogenic, Non-Acetogenic, Mesophilic, Anaerobic, Multiple Habitat
==Ecology==


There are at least 15 organisms from different metabolic groups such as acetogens and methanogens that are able to metabolize PCE. Some of these organisms remove their halogen atoms to conserve energy. Also, they utilize PCE as the only source of energy while others dehalogenate tetrachloroethene. This culture is able to grow with hydrogen as the electron donor, indicating that hydrogen and PCE serves as an electron donor or acceptor for energy conservation and growth.
Bioremediation strategies may be critically enhanced if the dehalorespiration process and mechanisms can be thoroughly understood and induced in contaminated groundwater environments. The anaerobic process may prove more effective in removing halogens atoms than aerobic reductive dehalogenation.


==Ecology==
Growing pure cultures of strain 195 is difficult, as ''D. ethenogenes'' prefer life in consortia with other microbes. It is challenging to maintain the microbe as an axenic culture. Growth is slow and consequently, biomass yields are small. Amplifying samples using real-time PCR methods has been essential to research efforts.
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.


Dehalococcoides ethenogenes most common use is for cleaning toxic messes by PCE. PCE is a suspected human carcinogen. Short-term exposure causes dizziness, headaches, and problems with balance, while long-term exposure has been linked to cancers of the esophagus, bladder, and blood. Therefore, D. ethenogenes breakdown the PCE to minimize its symptoms.
When using bioaugmentation to dose contaminated groundwater with ''D. ethenogenes'', biostimulation with carbon sources should be applied carefully to ensure that carbon concentrations favor growth of strain 195. High carbon concentrations may favor growth of competing strains that cannot reduce PCE completely to ethene.


==Pathology==
==Pathology==
How does this organism cause disease?  Human, animal, plant hosts?  Virulence factors, as well as patient symptoms.


This organism can use hydrogen to render PCE, a toxic chemical used by the dry cleaning industry, completely harmless as ethene and chlorine.
This organism does not produce disease or illness to its host.


==Application to Biotechnology==
==Application to Biotechnology==
Does this organism produce any useful compounds or enzymes?  What are they and how are they used?


Dehalococcoides ethenogenes is only known bacteria that can breakdown PCE, a dangerous and toxic carcinogen in chemical working environments. This organism converts PCE and Hydrogen to Chlorine and Ethene, which render the toxin completely harmless.
''Dehalococcoides ethenogenes'' is only known bacteria that can fully degrade PCE to ethene. The bacteria "come in stainless steel vessels that contain roughly 2000 billion ''Dehalococcoides'' bacteria ready for injection into groundwater" (495). This system of removing contamination from groundwater was named "pump-and-treat". Field studies at industrial sites have documented the full transformation of PCE to ethene in groundwater bioaugmented with strain 195. Data shows high initial concentrations of PCE followed by degradation and time offset spikes and declines of each intermediate compound, until the final data documents high ethene concentration and low presence of all other states.


==Current Research==
==Current Research==


Enter summaries of the most recent research here--at least three required
Presence of a single 16S rRNA cannot prove the purity of a culture, as prior believed. Microbes with similar genes may have different dehalogenation characteristics. Study of reductive dehalogenase genes will prove more useful in expanding knowledge of processes and mechanisms than research of less specific ribosomal DNA. Documented use of varied halogenated compounds as electron acceptors attests to the evolution of dehalorespiring microbes. The basic process is likely ancient. However, as anthropogenically introduced compounds pose increasing challenges, dehalorespirating microbes adapt to answer the call.


1) The solvents tetrachloroethene (PCE) and trichloroethene(TCE) are among the most pollutants at contaminated groundwater sites. Under aerobic conditions, PCE is considered can't be reduced, while TCE can be broken down to mainly nontoxic products by certain nonspecific oxygenases. Under anaerobic conditions, PCE and TCE have been reductively dechlorinated to less-chlorinated ethenes.
Balance between concentration and production of hydrogen allow for most efficient reductive dehalogenation to take place. The functions and relationships of reductive dehalogenase encoding genes need to be further defined. In order to gain understanding of the synergistic and competitive interactions of ''D. ethenogenes'', more research is needed to investigate the bioremediation potential of dehalogenating consortia in situ.


2) The anaerobic bacterium Dehalococcoides ethenogenes is the only known organism that can completely dechlorinate tetrachloroethene or trichloroethene (TCE) to ethene. One of two enzymes responsible for this pathway, TCE reductive dehalogenase (TCE-RDase) catalyzes the dechlorination of TCE to ethene. This info about the substrates of TCE-RDase may be used to predict the reactivity and the products of other environmental or industrial significance. Some of the compounds that were examined are pollutants.
==References==
Edited:
Aulenta, F. et al. Enhanced anaerobic bioremediation of chlorinated solvents: environmental factors influencing microbial activity and their relevance under field conditions. 2006. J Chem Technol Biotechnol. 81: 1463-1474.


3) Today, in the United States, the bacteria have been used to clean up chlorinated solvents in ten states at 17 sites including Kelly Air Force Base in Texas and Caldwell Trucking Superfund Site in New Jersey. For SiREM, business has been good; 13 of the sites were done in the past 18 months.
Cupples, A. Real-time PCR quantification of ''Dehalococcoides'' populations: Methods and applications. 2008. Journal of Microbiological Methods. 72: 1-11.


==References==
Hiraishi, A. Biodiversity of dehalorespiring bacteria with special emphasis on polychlorinated biphenyl/dioxin dechlorinators. 2008. Microbes Environ. 23: 1-12.
[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.]


[Real reference] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15637277&dopt=Abstract Seshadri R et al., "Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.", Science, 2005 Jan 7;307(5706):105-8]
Original:
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15637277&dopt=Abstract Seshadri R et al., "Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.", Science, 2005 Jan 7;307(5706):105-8]


[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11823182 Hendrickson, E.R. et al. Molecular analysis of Dehalococcoides 16S Ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Applied and Environmental Microbiology 68, 485-495 (February 2002).]
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11823182 Hendrickson, E.R. et al. Molecular analysis of Dehalococcoides 16S Ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Applied and Environmental Microbiology 68, 485-495 (February 2002).]
Line 76: Line 69:
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9171062 Maymo-Gatell, X. et al. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276, 1568-1571 (June 6, 1997).]
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9171062 Maymo-Gatell, X. et al. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276, 1568-1571 (June 6, 1997).]


Edited by Tim Hou of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
Duhamel et al. 2002, Water Research, Vol 36, p 4193
 
Maymo-Gatell, X., 1997, Science, Vol 276
 
B. Sun et al., 2002, Science, Vol 298 p. 1023
 
Edited by Angelique Tacia and Tracy Svanda of [mailto:lennon@msu.edu Jay Lennon] April 2008
Original by Tim Hou of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano

Latest revision as of 15:45, 1 July 2011

This is a curated page. Report corrections to Microbewiki.

A Microbial Biorealm page on the genus Dehalococcoides ethenogenes

Classification

Higher order taxa

Domain: Bacteria; Phylum: Chloroflexi; Class: Dehalococcoidetes; Order: Dehalococcoides

Species

Dehalococcoides ethenogenes (strain 195)

Description and significance

Dehalococcoides ethenogenes is Gram-positive, which generally means it has a very thick cell wall and a single membrane layer. From a three-dimensional perspective, it appears to have an irregular, spherical shape known as coccoid. Motility is spontaneous and independent. D. ehtenogenes is mesophilic and neutrophilic, liking neutral pH environments from 25 to 40°C, with an optimal temperature of 35°C. It is anaerobic and cannot use inorganic electron acceptors.

This specific strand of genome was sequenced, and it was discovered to help decontaminate toxic chemicals from many industries. Specifically, this species reduces chlorinated hydrocarbons in contaminated environments to harmless daughter compounds (ethene) . Chlorinated hydrocarbons are significantly toxic to humans and contaminate groundwater where the chemical is not handled properly.

Genome structure

Dehalococcoides ethenogenes has 1,469,720 or 1.5 Mbp nucleotide base pairs in its genome. Only one gene encoding reductive dehalogenase has been isolated and characterized. Strain 195 is the only known bacterium, to date, which completely dechlorinates tetrachloroethene (PCE) and trichloroethene (TCE), to ethene. Strains show >98% nucleotide and >85% amino acid similarity; however, different strains utilize different ranges of haloorganic compounds as electron acceptors.

Cell structure and metabolism

D. ethenogenes mediates reductive dechlorination reaction via hydrogenolysis or dichloroelimination. In hydrogenolysis, chlorine is replaced by hydrogen, with a net input of one proton and two electrons. In dechloroelimination, chlorine substituents are replaced via the formation of a double bond between the two associated carbon atoms. The dechloroelimination reaction has a net input of two electrons. The biological process mostly undergoes hydrogenolysis.

Importantly, D. ethenogenes conserves energy when hydrogen serves as electron donor, halogenated compounds are electron acceptors, and the enzyme reductive dehalogenase catalyzes the reaction. Each intermediate reaction, from PCE to TCE to cis-DCE to VC is energy-yielding for D. ethenogenes; however, the VC to ethene intermediate is cometabolic and does not provide the beneift of energy to the microbe. While the process from VC to ethene is not beneficial to the microbe, it is critical to remediating the contaminated environment.

The redox potentials for each intermediate reaction range from 260 to 570 mV. D. ethenogenes can dehalorespirate using chloroethenes, chlorophenols, and polychlorinated biphenyls/dioxins as terminal electron acceptors.

Ecology

Bioremediation strategies may be critically enhanced if the dehalorespiration process and mechanisms can be thoroughly understood and induced in contaminated groundwater environments. The anaerobic process may prove more effective in removing halogens atoms than aerobic reductive dehalogenation.

Growing pure cultures of strain 195 is difficult, as D. ethenogenes prefer life in consortia with other microbes. It is challenging to maintain the microbe as an axenic culture. Growth is slow and consequently, biomass yields are small. Amplifying samples using real-time PCR methods has been essential to research efforts.

When using bioaugmentation to dose contaminated groundwater with D. ethenogenes, biostimulation with carbon sources should be applied carefully to ensure that carbon concentrations favor growth of strain 195. High carbon concentrations may favor growth of competing strains that cannot reduce PCE completely to ethene.

Pathology

This organism does not produce disease or illness to its host.

Application to Biotechnology

Dehalococcoides ethenogenes is only known bacteria that can fully degrade PCE to ethene. The bacteria "come in stainless steel vessels that contain roughly 2000 billion Dehalococcoides bacteria ready for injection into groundwater" (495). This system of removing contamination from groundwater was named "pump-and-treat". Field studies at industrial sites have documented the full transformation of PCE to ethene in groundwater bioaugmented with strain 195. Data shows high initial concentrations of PCE followed by degradation and time offset spikes and declines of each intermediate compound, until the final data documents high ethene concentration and low presence of all other states.

Current Research

Presence of a single 16S rRNA cannot prove the purity of a culture, as prior believed. Microbes with similar genes may have different dehalogenation characteristics. Study of reductive dehalogenase genes will prove more useful in expanding knowledge of processes and mechanisms than research of less specific ribosomal DNA. Documented use of varied halogenated compounds as electron acceptors attests to the evolution of dehalorespiring microbes. The basic process is likely ancient. However, as anthropogenically introduced compounds pose increasing challenges, dehalorespirating microbes adapt to answer the call.

Balance between concentration and production of hydrogen allow for most efficient reductive dehalogenation to take place. The functions and relationships of reductive dehalogenase encoding genes need to be further defined. In order to gain understanding of the synergistic and competitive interactions of D. ethenogenes, more research is needed to investigate the bioremediation potential of dehalogenating consortia in situ.

References

Edited: Aulenta, F. et al. Enhanced anaerobic bioremediation of chlorinated solvents: environmental factors influencing microbial activity and their relevance under field conditions. 2006. J Chem Technol Biotechnol. 81: 1463-1474.

Cupples, A. Real-time PCR quantification of Dehalococcoides populations: Methods and applications. 2008. Journal of Microbiological Methods. 72: 1-11.

Hiraishi, A. Biodiversity of dehalorespiring bacteria with special emphasis on polychlorinated biphenyl/dioxin dechlorinators. 2008. Microbes Environ. 23: 1-12.

Original: Seshadri R et al., "Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.", Science, 2005 Jan 7;307(5706):105-8

Hendrickson, E.R. et al. Molecular analysis of Dehalococcoides 16S Ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Applied and Environmental Microbiology 68, 485-495 (February 2002).

Major, D. W. et al. Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environmental Science and Technology 36, 5106-5116 (November 2002).

Maymo-Gatell, X. et al. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276, 1568-1571 (June 6, 1997).

Duhamel et al. 2002, Water Research, Vol 36, p 4193

Maymo-Gatell, X., 1997, Science, Vol 276

B. Sun et al., 2002, Science, Vol 298 p. 1023

Edited by Angelique Tacia and Tracy Svanda of Jay Lennon April 2008 Original by Tim Hou of Rachel Larsen and Kit Pogliano