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==Introduction==
 
==Introduction==
[[Image:bird in oil spill.jpg|thumb|300px|right|[http://www.oilspillnews.net/oil-spill-clean-up/some-oil-spill-events-from-sunday-june-6-2010-science-news-2/ A bird covered in the Gulf of Mexico oil spill that happened on Jun6, 2010.]]]
 
  
As the demand for crude oil as energy source is fast increasing, accidental and associated [http://en.wikipedia.org/wiki/Oil_spill oil spill]have been more and more frequent during the process of exploration, production, transportation and storage. On land, oil spills are usually localized and the impact is limited in a certain area. However, when oil spills happens in marine system it may result in very serious ecological risks and long-term environmental disturbance (Patin 2004). The primary source of oil input into seas is usually associated with transportation by tankers and pipelines.  
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The use of antibiotics has become common in the livestock production around the world. The growth-promotic effects of antibiotics are undisputed, but the collateral and long-term effect are a cause for a heated debate and banning in the European Union in 2005(OMAFRA, 2005.) Antibiotics increase the efficiency of animal growth by inhibiting the growth of microbes in the gastrointestinal tract which triggers [http://en.wikipedia.org/wiki/Immune_system immune responses] in the host (Gaskins et al., 2002). They have been shown to improve the health of animals raised in close quarters in conventional operations and also reduce microbes on the meat that cause [http://www.foodborneillness.com/ foodborne illnesses] (OMAFRA, 2005). However, there is much concern regarding the development of antibiotic resistance associated with the use of drugs. It is important to study the microbial system within the host organism to carry out further studies related to the controversy.  
  
Once an oil spill happens, the oil will experience a series of physical, chemical and biological change, the effect of which is overall defined as “weathering”. However, this process happens slowly in the natural environment and requires a long time for the contaminated environment to recover. Various remediation methods have been proposed, among which the biological remediation has drawn increasing attention recently. There are two general approaches: to apply fertilizers or surfactants in order to promote the microbial degradation process, and to add naturally occurring adapted microbial hydrocarbon degraders seeding (Mulkinsphillips and Stewart 1974). The rate of biodegradation in a remediation site is highly dependent on the characteristics of spilled oil, the localized physical chemical environment, as well as the indigenous microbe’s communities. In order to better use bioremediation, lots of research are being conducted, focusing on both the biotic and abiotic factors influencing the degradation rate.
 
  
==Physical environment==
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==Host Microbial Community==
Oil spill can happen everywhere, from arctic to tropical marine, from soil to water, and therefore the physical and chemical environment of oil spill can vary significantly from one to other. Many factors have been proved to influence microbial degradation of petroleum, including physical status of oil spill, temperature, oxygen, nutrients, soil type and characteristics, and vegetation etc.
 
  
===Physical status of oil spill===
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All livestock harbor a intestinal microbes in a dense and highly diverse community, which are engaged in complex interactions with one another. Despite the diversity, specific animals have innate microbial communities. For example, in swine, major groups include Bacteroides, Peptostreptococcus, Bifidobacterium, Selenomonas, Clostridium, Butyrivibrio, and Escherichia (Moore et al., 1987). Most of the microbes are found in the large intestine because of slow digesta turnover.  A low number of microbes occupy the small intestine because of low pH and the rapid digesta flow which results in bacterial washout (Gaskins, 2000). [http://en.wikipedia.org/wiki/Gut_flora Gut flora] benefits the host in a variety of ways including digestion of unutilized energy substrates, stimulating cell growth, repressing the growth of harmful microorganisms, training the immune system to respond to pathogens, and defending against some diseases (Guarner et al.,2003). The gut flora and the host form an important mutualistic relationship.
  
Physical status of oil spill is the most important factor determines the environment the petroleum degraders live. The status of oil spill and those environmental factors will have complex interactions and exert mark influence on microbial communities.
 
Generally, there are two kinds of oil spills: Oil spill in water and oil spill in soil. The biggest different between them is the degree of spread. In soil, hydrocarbon is absorbed by plant and soil particles, limiting its spreading. Oil on soil surface will receive relatively ample oxygen which is crucial for biodegradation. Some portion will go deeper into the soil, but still within limited depth. In that situation, when oxygen becomes limiting factor, aeration is needed in order to enhance the bioremediation (Prince 1993).
 
[[Image: oil release and subsequent fate.jpg|400px|thumb|left|[http://www.asascience.com/news/newsletter/index.shtml  oil release and subsequent fate that results in different physical status of oil spill]]]
 
  
In marine environment, there can be a lot of forms of oil; each has its own typical environment. Most of the oil normally spreads, forming a thin slick on the top of water body. A large portion of the oil also forms emulsions or dissolves in the water. Some heavy portions will settle into to the bottom. Oxygen can be relatively easily obtained in the slick oil spill, but the nutrients are sometimes limited. The dissolved oil or oil emulsion droplets usually have chance to obtain both oxygen and nutrient when they travel through water column. The environment in the sediments is low in oxygen although the nutrient may not be limited. The difference in these environmental factors can create a big difference in the petroleum degradation process. For example, it was found that the petroleum hydrocarbons would persist for longer periods  in reduced sediments than would it do in aerated surface oil layers (Hamnrick et al. 1980). In addition, the toxic concentration, which is mostly caused by aromatic hydrocarbons, will vary within several orders of magnitude among different microbes. The toxicity has been proven to be crucial factor for biodegradation of petroleum hydrocarbon.
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==Immunological Interactions==
  
===Temperature===
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The non-pathogenic microbes benefit their host by stimulating the development of immune responses. The host organism develops defensive responses such as the constant mucus production and high cell turnover of the GI tract (Gaskins et al., 2002). The immune responses result in bacterial washout, controlling the growth rate of the enteric bacteria (Gaskins et al., 2002). The washout leads to the prevention of  the pathogen growth, defending against diseases.  Also, indigenous bacteria are proposed to prevent the colonization of nonindigenous bacteria via competition for nutrients and mucosal attachment sites, or alteration of the growth environment by producing antimicrobial compounds and modified bile acids (Rolfe, 1997). Studies with germfree animals show that the absence of indigenous bacteria leads to an underdeveloped immune system and less effective response to pathogens (Gaskins, 2000). Thus, the normal intestinal microbes provide the host with important defense by outcompeting pathogenic bacteria and preventing enteric diseases (Nisbet, 1998). 
The influence of temperature on biodegradation are interactive with other factors, such as the quality of the hydrocarbon mixtures and the composition of the microbial community. First, the temperature affects the physical status of petroleum. Higher temperature will result in higher viscosity, the volatilization of toxic alkanes is reduced, and their water solubility increased, delaying the rate of biodegradations. The second effect is on microbial activity. Higher temperature usually resulted in better activity of enzymes and therefore increased rate of metabolism. Actually, biodegradation activity has been found in almost all environments with extreme temperatures. Biodegradation can occur at very low temperature, e.g. 5 ºC even in arctic zone (Mulkinsphillips and Stewart 1974), and tropical area(Teralmoto et al. 2009). In addition, temperature will affect other environmental parameters that might be crucial to petroleum biodegrading microbes, for example, the availability of liquid water. Atlas (1978) found that the petroleum hydrocarbons from Prudhoe Bay crude oil in Arctic marine’s ice ecosystems were degraded extremely slowly mainly because of the lack of liquid water rather than the temperature itself.
 
  
===Nutrients===
 
Microorganisms require nitrogen and phosphorus for decomposition of hydrocarbons and incorporation into biomass, therefore the availability of these nutrients are important for bioremediation. Still, the nutrient availability depends heavily on the physical status of oil spill, whether it is in soil or marine, whether it is in dissolved forms or slick. However, in most studies, there seems to be insufficient nutrients to carry out best degradation performance. Many researchers have reported that the amendment of nutrient can significantly improve the degradation of petroleum pollutants both in water and soil (Xu and Obbard 2004, Liang et al. 2011; Tyagi et al.  2011)
 
  
===Oxygen===
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==Immunity vs. Growth efficiency==
The major degradation pathways for petroleum hydrocarbons involves oxygenates and molecular oxygen, indicating the (Boufadel et al. 2010) importance of oxygen for oil degradation microbes. There are anaerobes capable of degradation, but the rate is significantly lower. For instance, within anoxic basins or sediments, the hypolimnion of stratified lakes, and benthic sediments, oxygen may severely limit biodegradation. Oxygen consumption by oil-degrading bacteria is high, even in some environment such as the water surface where oxygen is readily available right after the oil spill happens, oxygen may rapidly become limiting factor due to slow oxygen diffusion rates and its limited solubility in water. Since most of the degradation is aerobic processes, maintenance of aerobic conditions is important in the bioremediation (Atlas 1991)
 
  
===Salinity and pressure===
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[[Image:Pig growth.jpeg|thumb|300px|right|[http://foodsafety.news21.com/wp-content/uploads/2011/08/antibiotics_graphic_piggrowth.jpg A pig's growing cycle from birth to slaughter]]]
The influence of several other environmental factors on hydrocarbon biodegradation has been studied. Typically these factors are associated with the localized environment features such as saline lakes or deep seas where high hydrostatic pressure exists. Studies have shown that generally the biodegradation rate decreases as  salinity increases. The deep benthic zone in marine ecosystems has been found to be one of those with least microbial activity, partly due to the higher pressure that limits the microbial activity (Shin and Pardue 2001).
 
  
==Microbial communities==
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However, those innate immune responses are offered at the expense of the growth efficiency (Gaskins et al., 2002). Building the defense against the microbial community in the GI tract requires disproportionate amounts of energy and resources. For example, in swine, although the GI tissues only represent 5% of the total body weight, they receive 15 to 35% of the whole body oxygen consumption and protein turnover because of high metabolic rate (Gaskins, 2000). Germfree organisms do not have to develop such immune responses, and instead, they can make effective use of their energy by investing it in weight growth.
  
===Microbial community composition===
 
A very diverse group and microbes have been showed to have the ability to degrade petroleum hydrocarbons (Atlas 1981, 180-209), among which bacteria and fungi appear to be the prevalent hydrocarbon degraders in oil contaminated ecosystems.
 
  
====Bacteria and archaea====
 
[[Image: alkane bacteria.jpg|300px|thumb|right|[http://www.scientificamerican.com/slideshow.cfm?id=gulf-oil-eating-microbes-slide-show  <i>Alcanivorax borkumensis</i>] is a rod-shaped bacteria that uses oil hydrocarbons as its exclusive source of carbon and energy. ]]
 
  
Many bacterial strains have been reported to have the ability to degrade recalcitrant compounds in petroleum.  More than 20 genera of hydrocarbon degrading bacteria has been isolated including Alpha-, Beta- and <i>[http://en.wikipedia.org/wiki/Gammaproteobacteria Gammaproteobacteria]</i>; [http://en.wikipedia.org/wiki/Gram-positive Gram positives]; <i>Flexibacter–Cytophaga–Bacteroides</i> (Teralmoto et al. 2009). On the other hand, fast development of molecular microbiological tool has enabled the identification of many un-culturable microbes and therefore extended the list of microbial species with petroleum hydrocarbon degrading abilities. Species of <i>[http://microbewiki.kenyon.edu/index.php/Pseudomonas Pseudomonas]</i>, <i>[http://microbewiki.kenyon.edu/index.php/Mycobacterium Mycobacterium]</i>, <i>[http://en.wikipedia.org/wiki/Haemophilus Haemophilus]</i>, <i>[http://microbewiki.kenyon.edu/index.php/Rhodococcus Rhodococcus]</i>, <i>[http://en.wikipedia.org/wiki/Paenibacillus Paenibacillus]</i> and <i>[http://en.wikipedia.org/wiki/Ralstonia Ralstonia]</i>, are some of the most extensively studied bacteria for their bioremediation capability.
 
  
Archaea have been detected in several oil-containing environments, such as petroleum reservoirs, underground crude oil storage cavities, and hydrocarbon-polluted aquifers. Archaea have also been found in oil contaminated environment degrading petroleum hydrocarbons.  Lots of Archaea  species are found in oil reservoirs, such as [http://en.wikipedia.org/wiki/Thermococcus_celer <i>Thermococcus celer</i>], [http://en.wikipedia.org/wiki/Pyrococcus <i>Pyrococcus lithotrophicus</i>], [http://en.wikipedia.org/wiki/Archaeoglobus <i>Archaeoglobus fulgidus</i>] (Ollivier et al. 2000;de Brito et al. 2004).
 
  
As the molecular biology are developing, scientists and engineers are probing more and more into the mechanisms and genetic traits of these oil-eaters, and are expecting to better utilize them to clean up oil spill faster and more efficient. Pseudomonas species is one of the most common species that have been isolated from oil spill bacteria. The genetic information for hydrocarbon degradation has been found to occur on plasmids (Vila et al. 2010) and this genetic trait shows potential to be transferred to other microbes to make some potential “supermicrobes”. Another interesting bacterium, [http://microbewiki.kenyon.edu/index.php/Alcanivorax <i>Alcanivorax borkumensis</i>], as shown in the Figure on the right, is the first carbonnoclastic bacterium that has been sequenced (Santos et al. 2006) in order to get valuable insights into its unusual metabolic capability in oil hydrocarbon degradation.Although barely detectable in unpolluted water body, it blooms right after an oil spill. It was found in oil spills from Alaska (Exxon Valdez) to the Mediterranean waters near Spain (Prestige). It has specific ability to both break down the alkanes that make up part of the oil, and spread a biosurfactant that helps make oil more bioavailable to other microbes. These unique combination of these features provides this microbe with a competitive edge in oil-polluted environment and therefore it was of special interest of many scientists.
 
  
====Fungi====
 
Fungi, including yeast and filamentous fungi have also been found to have the ability to degrade petroleum carbon. Species reported include <i>[http://en.wikipedia.org/wiki/Candida_(fungus) Candida]</i>,  <i>[http://en.wikipedia.org/wiki/Rhodotorula Rhodotorula]</i>, <i>[http://microbewiki.kenyon.edu/index.php/Saccharomyces Saccharomyces]</i>, <i>Sporobolomyces</i>, and <i>[http://en.wikipedia.org/wiki/Trichosporon Trichosporon] </i>etc. (Liu et al. 2009; Atlas 1981).
 
  
====Algae and cyanobacteria====
 
[[Image: red algae_1.jpg|200px|thumb|left|[http://web.biosci.utexas.edu/utex/algaeDetail.aspx?algaeID=2696 <i>Porphyridium</i> sp., red algae species ]]]
 
[[Image: green alga.jpg|200px|thumb|left|[http://web.biosci.utexas.edu/utex/algaeDetail.aspx?algaeID=4630 <i>Chlorella </i> sp., one of the most abundant freshwater green algae species]]]
 
Interestingly, the ability to oxidize petroleum hydrocarbons is widely distributed, not only among bacteria and fungi, but also among the cyanobacteria and algae. Cerniglia et al. found that the ability to oxidize aromatic hydrocarbons is widely distributed among algae and cyanobacteria. They tested the capability of naphthalene degradation among nine cyanobacteria, five green algae, one red alga, one brown alga, and two diatoms. Results showed that [http://en.wikipedia.org/wiki/Oscillatoria <i>Oscillatoria</i> spp.], <i>Microcoleus</i> sp., [http://en.wikipedia.org/wiki/Anabaena <i>Anabaena</i> spp.],<i> Agmenellum</i> sp., <i>Cylindretheca sp.</i>,<i>Coccochloris</i> sp., [http://en.wikipedia.org/wiki/Ulva <i>Ulva</i> sp.], [http://en.wikipedia.org/wiki/Nostoc <i>Nostoc </i>sp.], <i>Aphanocapsa sp.</i>, [http://en.wikipedia.org/wiki/Chlorella <i>Chlorella</i> spp.], [http://en.wikipedia.org/wiki/Dunaliella <i>Dunaliella</i> sp.], [http://en.wikipedia.org/wiki/Chlamydomonas <i>Chlamydomonas</i> sp.], <i>Amphora</i> sp., <i>Porphyridium sp.</i>, and <i>Petalonia</i> are all capable of oxidizing naphthalene(Gibson et al. 1980). Except various low molecular weight organics, algae also showed ability to degrade high molecular weight PAHs, such as benzo[a]pyrene(Naidu and Juhasz 2000). Beside single compounds, some researchers also investigated the algae/cyanobacteria capability of degrading the whole matrix of oil. For example, Gamila and Ibrahim (Ibrahim and Gamila 2004) valuate the potential role of freshwater isolated algae strains in biodegradation of crude oil (Egyptian light crude oil, specific gravity 0.85) though an algal bioassay. They found that the diatom strain, [http://en.wikipedia.org/wiki/Nitzschia <i>Nitzschia] linearis</i>, and green alga [http://en.wikipedia.org/wiki/Scenedesmus <i>Scenedesmus] obliquus</i> treated with 0.1% crude oil showed almost similar capability for degradation of the petroleum hydrocarbons. Interestingly, they also observed the effect of the crude oil on the morphological characters of these two algae. The most pronounced feature is that the algal cells in both strains were aggregated in clusters containing oil drops between their cells, forming an abnormal shape comparing with control culture.
 
  
===Microbial community dynamics===
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==Efficacy and Mechanism of Antibiotics==
Both laboratory and field studies have shown that hydrocarbon contamination shifts the overall microbial community structure (Cerniglia et al.1980). Once the site is contaminated, the microbial community composition will be greatly changed both in quantity and composition. Populations of hydrocarbon-degraders normally constitute less than 1% of the total microbial communities, but when oil pollutants are present these hydrocarbon-degrading populations increase, Certain hydrocarbon-degrading taxa become dominant in oil-impacted environments because of natural selection resulting from the pressure of oil contaminants typically to 10% of the community, or even 100%(Tyagi et al. 2011).
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[[Image:Efficacy.jpeg|thumb|300px|right|Figure 1. Efficacy of antibiotics as Growth promoters for pigs at different growth stages.
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The pigs in the starting phase is between 7-25kg, the growing phase is between 17-49kg, and growing finishing phase is between 24-89kg. It summarizes the data from Table 18.3 (Cromwell, 2000), acquired from 1194 experiments performed in the US from 1950 to 1985.]]
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Numerous researches have shown that antibiotics increase the rate and efficiency of growth in animals. Figure 1 shows that antibiotics are effective in pigs of all growth stages, but they are the most effective when the pigs are young and weanling.  The growth rate of pigs in starting phase (7-25kg) improved by an average of 16.4% and reduced the amount of feed required by 6.9%. However, the experiments are controlled and performed at clean and disease-free research facilities. Thus, the antibiotics are predicted to be more beneficial when used at the farm, where it is less clean, and thus, easier to catch diseases. (Cromwell, 2000). The exact mechanisms by which antibiotics favor growth are not known; however, researches propose that they possibly promote growth by depressing  the growth of microbes that are toxic or steal nutrients from the host, leading to the increased nutrition utilization and reduced energy investment in maintaining immune responses in the GI tract (Gaskins et al., 2002).  
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==Debate regarding Resistance==
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Since antibiotics have been introduced as growth promoters, there have been concerns about [http://www.who.int/mediacentre/factsheets/fs194/en/ antimicrobial resistance]. Frequent use of antibiotics leads to increasing resistance in enteric bacteria that can infect people or transfer their resistance to other pathogenic bacteria (OMAFRA, 2005). When infected by multi-drug resistant bacteria, treatment options are limited, recovery is slow, and treatment is more costly (WHO, 2012). The concerns especially involve resistance against [http://en.wikipedia.org/wiki/Penicillin penicillin] and [http://en.wikipedia.org/wiki/Tetracycline tetracycline] because they are used in human medicine as well (Cromwell, 2000). Antibiotic resistance is controlled by decreasing the use of unnecessary antibiotics. For example, the use of antibiotics in the livestock and poultry industries is completely banned in the European Union (EU) (OMAFRA, 2005). 
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[[Image:Anti route.gif|thumb|300px|left|[http://momentscount.com/wp-content/uploads/2012/04/antibiotics-for-agriculture.gif Route of Antibiotic from Farm Animals to Humans.]]]
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However, there has been no concrete evidence that shows that use of antibiotics in animal food production poses a threat to human health, and studies are still under way to find the direct linkage (OMAFRA, 2005). The process involving the transfer of antibiotic resistance plasmid between animal and human bacteria is not well known yet (Cromwell, 2002). Also, there is a study which shows that the amount of antibiotic resistance transfer from resistant E.coli to E.coli in the GI tract is small, and animal strains are poor at colonizing the human intestinal tract (Smith, 1969).  The question whether the use of antibiotics in animals presents a potential threat to human health will continue to be controversial.
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==Microbial processes==
 
  
===Aerobic processes===
 
Oil is a complex mixture of various components, with different affinity with microbes. The biodegradability of the oil components generally decreases in the following order: n-alkanes, branched-chain alkanes, branched alkenes, low molecular-weight n-alkyl aromatics, monoaromatics, cyclic alkanes, polycyclic aromatic hydrocarbons (PAHs) and asphaltenes (Atlas 1981). No matter what form the component is, these compounds are eventually converted to carbon dioxide and water by microorganisms if in aerobic degradation process, the most common biodegradation.
 
The initial steps in the aerobic biodegradation by bacteria and fungi involve the oxidation of the substrate by oxygenases for which molecular oxygen is required. Aerobic conditions are, therefore, necessary for microbial oxidation of hydrocarbons in various environments. The availability of  oxygen in soils,  sediments, and  aquifers  is  often limiting  and  dependent  on  the  type  of  soil, whether the soil is aerated, weather the water is well mixed etc.
 
  
===Anaerobic processes===
 
Anaerobic degradation exists, however, the rate of which is very low and the ecological significance appears to be minor. Anaerobic respiration of oil hydrocarbons can be found in the sediments or anoxic zones, where Mn<sup>+2</sup>, Fe<sup>+2</sup> can be the terminal electron acceptor (Atlas 1991; Essaid 1995).
 
  
=== Nitrogen fixation===
 
As previously described, nutrients are important for oil-degrading microbes to survive and therefore fertilization with nitrogen can stimulate the bioremediation of oil contaminated sites. However, in natural environment, there is another process which can bring extra nitrogen to the microbes-[http://en.wikipedia.org/wiki/Nitrogen_fixation nitrogen fixation]. Prantera et al. found that two bacterial strains, which belongs to the genera of [http://en.wikipedia.org/wiki/Agrobacterium <i>Agrobacterium</i>] and [http://en.wikipedia.org/wiki/Alcaligenes <i>Alcaligenes </i>] respectively exhibited ability to degrade gasoline aromatic compounds and fix nitrogen at the same time (Drozdowicz et al. 2002). Chen et al. (1993) examined six species of free-living nitrogen fixing bacteria, [http://en.wikipedia.org/wiki/Azomonas_agilis <i>Azomonas agilis</i>],  [http://en.wikipedia.org/wiki/Azotobacter <i>Azotobacter] chroococcum</i>, [http://en.wikipedia.org/wiki/Azotobacter_vinelandii <i>Azotobacter vinelandii</i>], and <i>Beijerinckia mobilis</i> for their ability to grow and fix N<sub>2</sub> using aromatic compounds as sole carbon and energy source and the result showed that all six species grew and expressed nitrogenase activity on oil components such as benzoate.
 
Except nitrogen fixation by [http://en.wikipedia.org/wiki/Heterotrophic heterotrophic] growth, [http://en.wikipedia.org/wiki/Autotrophic autotrophic] growth is also an important process for nitrogen fixation in oil contaminated sites. Phototrophic N<sub>2</sub>-fixing bacteria such as [http://microbewiki.kenyon.edu/index.php/Pseudomonas <i>Pseudomonas] stutzeri</i>, [http://microbewiki.kenyon.edu/index.php/Azospirillum_brasilense <i>Azospirillum brasilense</i>], <i>Aquaspirillum</i> sp.(Eckford 2002) have been identified and isolated from oil contaminated soils, snow, sea ice in Antarctic. Musat et al. (2006) even found that phototrophic cyanobacteria are the main contributors of fixed nitrogen to oil-contaminated and pristine sediments if nitrogen is a limiting factor and if light is available. As a consequence, the oil-degrading heterotrophic community may receive a significant part of combine nitrogen from cyanobacteria.
 
  
==Current Research==
 
1. <b>A study of the microbial community composition and functional genes in oil contaminated soil </b>
 
  
In order to compare microbial functional diversity in different oil contaminated soils, and to find the relationship between the contamination and environmental factors, Liang et al. analyses soil samples from 5 different oil filed and used GeoChip to evaluate the microbial functional genes. Results showed that the samples were clustered by geographic locations and the contaminant degradations genes presented similar patterns under oil contaminant stress. Canonical analysis results also indicated that the local environmental variables significantly affect the microbial functional patterns (Liang et al. 2011).
 
  
2. <b>A case study of the environmental condition after Exxon Valdez oil spill</b>
 
  
In order to evaluate the long-term environmental effect of Exxon Valdez oil spill in 1989, a series of measurements of the background concentration of nutrients, dissolved oxygen (DO), and salinity were obtained from a contaminated beach. Results showed that both nutrients and DO are limiting factors for biodegradation. Also, the lowest nitrate and DO values were found in the oiled pits, implying that the microbial oil degradation was probably under anoxic conditions associated with denitrification (Boufadel et al. 2010).
 
  
3. <b>The application of bioautmentation</b>
 
  
The feasibility of a bioaugmentation strategy based on use of microbial formula tailored with selected native strains to remediate diesel contaminated site was assessed. The biodegradation process of diesel oil was assessed by monitoring the DO composition, CO<sub>2</sub> evolution rate, microbial load and composition of the community by T-RFLP, physiological profile in Biolog® ECOplates and ecotoxicity. The mixture of microbes that combines 10 bacterial strains selected for resistance to heavy metals was found to efficiently facilated and speed up the bioremediation of diesel hydrocarbons and heavey metals (Alisi et al. 2009)
 
  
==References==
 
  
1. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V78-4VJJW79-4&_user=571676&_coverDate=04%2F01%2F2009&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C000029040&_version=1&_urlVersion=0&_userid=571676&md5=7d3632285cd519d32d58e293caa43ba2&searchtype=a Alisi C, Musella R, Tasso F, Ubaldi C, Manzo S, Cremisini C, Sprocati AR (2009) Bioremediation of diesel oil in a co-contaminated soil by bioaugmentation with a microbial formula tailored with native strains selected for heavy metals resistance. Sci Total Environ 407:3024-3032 ]
 
  
2. [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=pmc&term=0146-0749%5Bjour%5D%20AND%201981%5Bdp%5D%20AND%2045%5Bvolume%5D%20AND%201%5Bissue%5D%20AND%20180%5Bpage%5D Atlas R (1981) Microbial-degradation of petroleum-hydrocarbons-an environmental perspective. Microbiol Rev 45:180-209]
 
  
3. [http://openurl.library.uiuc.edu/sfxlcl3?sid=Refworks%3AUniversity%20of%20Illinois&charset=utf-8&__char_set=utf8&genre=article&aulast=Atlas&auinit=R.&title=Journal%20of%20the%20Fisheries%20research%20board%20of%20Canada&date=1978&volume=35&pages=585-590&issue=5&issn=0008-2686&atitle=Prudhoe%20crude-oil%20in%20Arctic%20Marine%20ice%2C%20water%2C%20and%20sediment%20ecosystems-degradation%20and%20interactions%20with%20microbial%20and%20benthic%20communities&spage=585&au=Atlas%2CR.&au=Horowitz%2CA.&au=Busdosh%2CM.& Atlas R, Horowitz A, Busdosh M (1978) Prudhoe crude-oil in Arctic Marine ice, water, and sediment ecosystems-degradation and interactions with microbial and benthic communities. Journal of the Fisheries research board of Canada 35:585-590]
 
  
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Edited by Yan Zhou, a student of Angela Kent at the University of Illinois at Urbana-Champaign.
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by SungEun Cho, a student of Dr.W.Mohn at the University of British Columbia

Latest revision as of 19:55, 12 December 2012

This student page has not been curated.

Introduction

The use of antibiotics has become common in the livestock production around the world. The growth-promotic effects of antibiotics are undisputed, but the collateral and long-term effect are a cause for a heated debate and banning in the European Union in 2005(OMAFRA, 2005.) Antibiotics increase the efficiency of animal growth by inhibiting the growth of microbes in the gastrointestinal tract which triggers immune responses in the host (Gaskins et al., 2002). They have been shown to improve the health of animals raised in close quarters in conventional operations and also reduce microbes on the meat that cause foodborne illnesses (OMAFRA, 2005). However, there is much concern regarding the development of antibiotic resistance associated with the use of drugs. It is important to study the microbial system within the host organism to carry out further studies related to the controversy.


Host Microbial Community

All livestock harbor a intestinal microbes in a dense and highly diverse community, which are engaged in complex interactions with one another. Despite the diversity, specific animals have innate microbial communities. For example, in swine, major groups include Bacteroides, Peptostreptococcus, Bifidobacterium, Selenomonas, Clostridium, Butyrivibrio, and Escherichia (Moore et al., 1987). Most of the microbes are found in the large intestine because of slow digesta turnover.  A low number of microbes occupy the small intestine because of low pH and the rapid digesta flow which results in bacterial washout (Gaskins, 2000). Gut flora benefits the host in a variety of ways including digestion of unutilized energy substrates, stimulating cell growth, repressing the growth of harmful microorganisms, training the immune system to respond to pathogens, and defending against some diseases (Guarner et al.,2003). The gut flora and the host form an important mutualistic relationship.


Immunological Interactions

The non-pathogenic microbes benefit their host by stimulating the development of immune responses. The host organism develops defensive responses such as the constant mucus production and high cell turnover of the GI tract (Gaskins et al., 2002). The immune responses result in bacterial washout, controlling the growth rate of the enteric bacteria (Gaskins et al., 2002). The washout leads to the prevention of  the pathogen growth, defending against diseases.  Also, indigenous bacteria are proposed to prevent the colonization of nonindigenous bacteria via competition for nutrients and mucosal attachment sites, or alteration of the growth environment by producing antimicrobial compounds and modified bile acids (Rolfe, 1997). Studies with germfree animals show that the absence of indigenous bacteria leads to an underdeveloped immune system and less effective response to pathogens (Gaskins, 2000). Thus, the normal intestinal microbes provide the host with important defense by outcompeting pathogenic bacteria and preventing enteric diseases (Nisbet, 1998). 


Immunity vs. Growth efficiency

However, those innate immune responses are offered at the expense of the growth efficiency (Gaskins et al., 2002). Building the defense against the microbial community in the GI tract requires disproportionate amounts of energy and resources. For example, in swine, although the GI tissues only represent 5% of the total body weight, they receive 15 to 35% of the whole body oxygen consumption and protein turnover because of high metabolic rate (Gaskins, 2000). Germfree organisms do not have to develop such immune responses, and instead, they can make effective use of their energy by investing it in weight growth.





Efficacy and Mechanism of Antibiotics

Figure 1. Efficacy of antibiotics as Growth promoters for pigs at different growth stages. The pigs in the starting phase is between 7-25kg, the growing phase is between 17-49kg, and growing finishing phase is between 24-89kg. It summarizes the data from Table 18.3 (Cromwell, 2000), acquired from 1194 experiments performed in the US from 1950 to 1985.

Numerous researches have shown that antibiotics increase the rate and efficiency of growth in animals. Figure 1 shows that antibiotics are effective in pigs of all growth stages, but they are the most effective when the pigs are young and weanling.  The growth rate of pigs in starting phase (7-25kg) improved by an average of 16.4% and reduced the amount of feed required by 6.9%. However, the experiments are controlled and performed at clean and disease-free research facilities. Thus, the antibiotics are predicted to be more beneficial when used at the farm, where it is less clean, and thus, easier to catch diseases. (Cromwell, 2000). The exact mechanisms by which antibiotics favor growth are not known; however, researches propose that they possibly promote growth by depressing  the growth of microbes that are toxic or steal nutrients from the host, leading to the increased nutrition utilization and reduced energy investment in maintaining immune responses in the GI tract (Gaskins et al., 2002).     








Debate regarding Resistance

Since antibiotics have been introduced as growth promoters, there have been concerns about antimicrobial resistance. Frequent use of antibiotics leads to increasing resistance in enteric bacteria that can infect people or transfer their resistance to other pathogenic bacteria (OMAFRA, 2005). When infected by multi-drug resistant bacteria, treatment options are limited, recovery is slow, and treatment is more costly (WHO, 2012). The concerns especially involve resistance against penicillin and tetracycline because they are used in human medicine as well (Cromwell, 2000). Antibiotic resistance is controlled by decreasing the use of unnecessary antibiotics. For example, the use of antibiotics in the livestock and poultry industries is completely banned in the European Union (EU) (OMAFRA, 2005). 


However, there has been no concrete evidence that shows that use of antibiotics in animal food production poses a threat to human health, and studies are still under way to find the direct linkage (OMAFRA, 2005). The process involving the transfer of antibiotic resistance plasmid between animal and human bacteria is not well known yet (Cromwell, 2002). Also, there is a study which shows that the amount of antibiotic resistance transfer from resistant E.coli to E.coli in the GI tract is small, and animal strains are poor at colonizing the human intestinal tract (Smith, 1969).  The question whether the use of antibiotics in animals presents a potential threat to human health will continue to be controversial.













References

1. Cromwell, G. “Why and how antibiotics are used in swine production.” Animal Biotechnology, 2002, DOI: 10.1081/ABIO-120005767

2. Cromwell, G. “Antimicrobial and Promicrobial Agents.” In Swine Nutrition, Second Edition, 2000, CRC Press, USA.

3. Gaskins, H., Collier, C., and Anderson, D. “Antibiotics as growth promotants: Mode of action.” Animal Biotechnology, 2002,DOI: 10.1081/ABIO-120005768

4. Gaskins, H. “Intestinal Bacteria and their influence on Swine Growth.” In Swine Nutrition, Second Edition, 2000, CRC Press, USA. PMID:9861967

5. Guarner, F., and Malagelada, JR. 2003."Gut flora in health and disease." Lancet, 361(9356): 512–9.DOI:10.1016/S0140-6736(03)12489-0. PMID:12583961.

6. Moore, W., Moore, L., Cato, E., Wilkins T., and Kornegay E. “Effect of High-Fiber and High-Oil Diets on the Fecal Flora of Swine.” Applied and Environmental Microbiology, 1987, 53(7):1638-1644

7. Nisbet, J. 1998. Use of competitive exclusion in food animals. Journal of the American Veterinary Medical Association. 213(12):1774-6

8. Ontario Ministry of Agriculture, Food, and Rurual Affairs. Antibioitc Use for Growth Improvement- Controversy and Resolution [online. [Last reviewed in June 2005].

9. Rolfe, R. 1997. “Colonization resistance.” In Gastrointestinal Microbiology, Vol. 2, Mackie, R., White, B., and Isaacson, R. , Eds., Chapman & Hall, New York.

10. Smith, H. “Transfer of antibioitc resistance from animal and human strains of E. Coil to resistant E.Coli in the alimentary tract of man.” The Lancet, 1969, DOI: 10.1016/S0140-6736(69)92164-3

11. Stokstad, E., Jukes, J., Pierce, A., Page, Jr., and Franklin, A. 1949. “The multiple nature of the animal protein factor.” Journal of Biological Chemistry, 130:648

12. World Health Organization. Antimicrobial resistance. [online[Last reviewed in March 2012]]



by SungEun Cho, a student of Dr.W.Mohn at the University of British Columbia