Dechloromonas aromatica: Difference between revisions
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==Description and significance== | ==Description and significance== | ||
Dechloromonas aromatica have rod shaped cells and are found in aquatic and aquatic sediment habitats. They can oxidize aromatic compounds such as toluene, benzoate, and chlorobenzoate. D. aromatica strain RCB was isolated from Potomic River sediment, Maryland, USA. It is the only organism in pure culture that is capable of oxidizing benzene anaerobically. Optimum growth temperature is 30º C and optimum growth salinity is 0%. (1) | ''Dechloromonas aromatica'' have rod shaped cells and are found in aquatic and aquatic sediment habitats. They can oxidize aromatic compounds such as toluene, benzoate, and chlorobenzoate. ''D. aromatica'' strain RCB was isolated from Potomic River sediment, Maryland, USA. It is the only organism in pure culture that is capable of oxidizing benzene anaerobically. Optimum growth temperature is 30º C and optimum growth salinity is 0%. (1) | ||
It is of significant interest to researchers and | It is of significant interest to researchers and has had its genome sequenced because of its ability to oxidize benzene in absence of oxygen. Benzene is a highly soluble, mobile, toxic, and stable hydrocarbon in ground and surface waters. All of these factors make benzene a pollutant that is very hard to deal with. It is widely used in various manufacturing processes and is also a primary component of petroleum-based fuels and contamination is a significant problem worldwide. Normally benzene is poorly biodegraded in the absence of oxygen, this organism however, has shown to have an unique ability to oxidize benzene anaerobically. For this reason bioremediative strategies using ''D. aromatica'' are of great interest. ''D. aromatica RCB'' is also capable of reducing perchlorate, another environmental hazard that occurs through manufacturing (and naturally) to chloride. They are also the first known organism to chemotax towards perchlorate. This means that they direct their movements towards areas of high perchlorate concentration. (1,2) | ||
[[image: D_Aromatica_RCB_Genome.png|thumb|400px|right|''Entire Genome of Dechloromonas aromatica. Image from University of Alberta]] | [[image: D_Aromatica_RCB_Genome.png|thumb|400px|right|''Entire Genome of Dechloromonas aromatica. Image from University of Alberta]] | ||
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==Genome structure== | ==Genome structure== | ||
Dechloromonas aromatica has a single circular DNA chromosome with a length of 4,501,104 bps and 4,250 genes encoding 4171 predicated proteins and 79 RNAs. The genome has a GC content of approximately 59.2% and 64% of the sequences have been assigned a role in categories.(4) | ''Dechloromonas aromatica'' has a single circular DNA chromosome with a length of 4,501,104 bps and 4,250 genes encoding 4171 predicated proteins and 79 RNAs. The genome has a GC content of approximately 59.2% and 64% of the sequences have been assigned a role in categories.(4) | ||
[[Image:decar.jpg|thumb|400px|right|''Dechloromonas aromatica. Image from the DOE Joint Genome Institute.]] | [[Image:decar.jpg|thumb|400px|right|''Dechloromonas aromatica. Image from the DOE Joint Genome Institute.]] | ||
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==Cell structure and metabolism== | ==Cell structure and metabolism== | ||
Dechloromonas aromatica have rod shaped cells, two membranes, and are gram negative. They are usually either single cells or arranged in chains and are not capable of forming endospore which are dormant, tough, and nonreproductive structures formed by some bacteria. They are capable of forming flagella and thus possess motility.(1) | ''Dechloromonas aromatica'' have rod shaped cells, two membranes, and are gram-negative. They are usually either single cells or arranged in chains and are not capable of forming endospore which are dormant, tough, and nonreproductive structures formed by some bacteria. They are capable of forming flagella and thus possess motility.(1) | ||
As mentioned above Dechloromonas aromatica is capable oxidizing different aromatic compounds. D. aromatica strain RCB is also the only organism in pure culture that is capable of oxidizing benzene in the absence of oxygen. It is recognized as the first organism with the ability to do this, and is the only organism identified capable of this metabolism. The metabolic pathway through which they biodegrade benzene is currently not fully known, studies suggest that it has both a dioxygenase-based aerobic pathway and an as yet fully uncharacterized anaerobic pathway. Research | As mentioned above ''Dechloromonas aromatica'' is capable oxidizing different aromatic compounds. ''D. aromatica'' strain RCB is also the only organism in pure culture that is capable of oxidizing benzene in the absence of oxygen. It is recognized as the first organism with the ability to do this, and is the only organism identified capable of this metabolism. The metabolic pathway through which they biodegrade benzene is currently not fully known, studies suggest that it has both a dioxygenase-based aerobic pathway and an as yet fully uncharacterized anaerobic pathway. Research has shown that it requires a hydroxylation step and a carboxylation step, and produces benzoate and phenol as intermediates.(3) They are also capable of oxidizing Fe(II) and AHDS (a reduced humics compound). | ||
==Ecology== | ==Ecology== | ||
In the present, the role of Dechloromonas aromatica in the environment is yet unknown. However, it can have a significant contribution on the environment due to their unique ability to biodegrade benzene, perchlorate, and other similar compounds mentioned above. Many of these compounds are the result of common industrial processes used around the world. These compounds are harsh pollutants that create seriously problems for the environment, humans, and other organisms and are a result of human presence and technology. | In the present, the role of ''Dechloromonas aromatica'' in the environment is yet unknown. However, it can have a significant contribution on the environment due to their unique ability to biodegrade benzene, perchlorate, and other similar compounds mentioned above. Many of these compounds are the result of common industrial processes used around the world. These compounds are harsh pollutants that create seriously problems for the environment, humans, and other organisms and are a result of human presence and technology. | ||
For example, eating for drinking foods contaminated with benzene can lead to vomiting, stomach ache, and death in humans. It has also been shown to lead to anemia, lowered immune response, decreased size of ovaries in women, and has been classified by the US Department of Health and Human Services as a carcinogen. Other animals have been shown to have low birth weights, delayed bone formation, and bone morrow damage when pregnant animals were exposed to benzene in studies. In the US alone there are over 100,000 sites of benzene soil or groundwater contamination. Environmental contamination levels are worse in rapidly industrializing nations such as China where in 2005, the entire water supply to Harbin, a city with a population of almost 9 million was cut off due to benzene contamination from an explosion at a China National Petroleum Corporation factory.(5) | For example, eating for drinking foods contaminated with benzene can lead to vomiting, stomach ache, and death in humans. It has also been shown to lead to anemia, lowered immune response, decreased size of ovaries in women, and has been classified by the US Department of Health and Human Services as a carcinogen. Other animals have been shown to have low birth weights, delayed bone formation, and bone morrow damage when pregnant animals were exposed to benzene in studies. In the US alone there are over 100,000 sites of benzene soil or groundwater contamination. Environmental contamination levels are worse in rapidly industrializing nations such as China where in 2005, the entire water supply to Harbin, a city with a population of almost 9 million was cut off due to benzene contamination from an explosion at a China National Petroleum Corporation factory.(5) | ||
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==Application to Biotechnology== | ==Application to Biotechnology== | ||
Dechloromonas aromatica is being studied for their ability to biodegrade benzene, perchloate and other compounds which as mentioned above can lead to a wide range of health problems for humans and other organisms. Their unique ability to do so in the absence of oxygen can make them extremely useful if they are deployed to areas where there is contaminated soil or groundwater in bioremediation projects. Researchers have discovered that it | ''Dechloromonas aromatica'' is being studied for their ability to biodegrade benzene, perchloate and other compounds which as mentioned above can lead to a wide range of health problems for humans and other organisms. Their unique ability to do so in the absence of oxygen can make them extremely useful if they are deployed to areas where there is contaminated soil or groundwater in bioremediation projects. Researchers have discovered that it produces a diooxygense for the aerobic oxidation of benzene, but the anerobic pathway is still unclear.(1,2) In research, soil containing radioactive labeled benzene was inoculated with ''Dechloromonas aromatica'' and the benzene was quickly oxidized to CO2.(1)Also see current research section. | ||
==Current Research== | ==Current Research== | ||
1. This is when Dechloromonas aromatica was first isolated and shown to have the ability of metabolize benzene and perchlorate. The researchers isolated two unrelated strains, RCB and JJ, from two very diverse environments and they both had the ability to oxidize benzene to carbon dioxide in the absence of oxygen using nitrate as the election acceptor. In an experiment, the number of cells in culture was shown to increase with the disappearance of benzene. The researchers believed that this was the first known organism to be able to do this and can be utilized for bioremediation of benzene contaminated sites. | 1. This is when ''Dechloromonas aromatica'' was first isolated and shown to have the ability of metabolize benzene and perchlorate. The researchers isolated two unrelated strains, RCB and JJ, from two very diverse environments and they both had the ability to oxidize benzene to carbon dioxide in the absence of oxygen using nitrate as the election acceptor. In an experiment, the number of cells in culture was shown to increase with the disappearance of benzene. The researchers believed that this was the first known organism to be able to do this and can be utilized for bioremediation of benzene contaminated sites. | ||
Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. John D. Coates, Romy Chakraborty, Joseph G. Lack, Susan M. O'Connor, Kimberly A. Cole, Kelly S. Bender & Laurie A. Achenbach | Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. John D. Coates, Romy Chakraborty, Joseph G. Lack, Susan M. O'Connor, Kimberly A. Cole, Kelly S. Bender & Laurie A. Achenbach | ||
2. These researchers wanted to further investigate the benzene oxidizing ability of Dechloromonas aromatica strain RCB. They discovered that in addition to nitrate, these organisms can also use perchlorate or chlorate as electron acceptors in the aerobic or anaerobic oxidation of benzene. Their research also revealed that Dechloromonas aromatica strain RCB can also | 2. These researchers wanted to further investigate the benzene oxidizing ability of ''Dechloromonas aromatica'' strain RCB. They discovered that in addition to nitrate, these organisms can also use perchlorate or chlorate as electron acceptors in the aerobic or anaerobic oxidation of benzene. Their research also revealed that ''Dechloromonas aromatica'' strain RCB can also use toluene, ethylbenzene, and xylene as electron donors when nitrate is used as an electron acceptor. On top of that, ''Dechloromonas aromatica'' strain RCB can degrade benzene and toluene simultaneously. | ||
Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and Xylene Compounds by Dechloromonas Strain RCB. Romy Chakraborty, Susan M. O'Connor, Emily Chan, and John D. Coates | Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and Xylene Compounds by Dechloromonas Strain RCB. Romy Chakraborty, Susan M. O'Connor, Emily Chan, and John D. Coates | ||
3. In | 3. In this research paper, the researchers basically summarized why benzene biodegradation is important and why several methods previously studied were not effective or efficient. More importantly they have gained some knowledge on the pathway ''Dechloromonas aromatica'' strain RCB uses to oxidize benzene to CO2. They discovered that the pathway requires an initial hydroxylation reaction, subsequent carboxylation reaction, and loss of hydroxyl group to form benzoate as an intermediate. | ||
Hydroxylation and Carboxylation—Two Crucial Steps of Anaerobic Benzene Degradation by Dechloromonas Strain RCB. Romy Chakraborty and John D. Coates | Hydroxylation and Carboxylation—Two Crucial Steps of Anaerobic Benzene Degradation by Dechloromonas Strain RCB. Romy Chakraborty and John D. Coates | ||
Revision as of 13:11, 14 July 2007
Classification
Higher order taxa
Bacteria;Proteobacteria;Betaproteobacteria;Rhodocyclales;Rhodocyclaceae;Dechloromonas
Genus
Dechloromonas aromatica
|
NCBI: Taxonomy |
Description and significance
Dechloromonas aromatica have rod shaped cells and are found in aquatic and aquatic sediment habitats. They can oxidize aromatic compounds such as toluene, benzoate, and chlorobenzoate. D. aromatica strain RCB was isolated from Potomic River sediment, Maryland, USA. It is the only organism in pure culture that is capable of oxidizing benzene anaerobically. Optimum growth temperature is 30º C and optimum growth salinity is 0%. (1)
It is of significant interest to researchers and has had its genome sequenced because of its ability to oxidize benzene in absence of oxygen. Benzene is a highly soluble, mobile, toxic, and stable hydrocarbon in ground and surface waters. All of these factors make benzene a pollutant that is very hard to deal with. It is widely used in various manufacturing processes and is also a primary component of petroleum-based fuels and contamination is a significant problem worldwide. Normally benzene is poorly biodegraded in the absence of oxygen, this organism however, has shown to have an unique ability to oxidize benzene anaerobically. For this reason bioremediative strategies using D. aromatica are of great interest. D. aromatica RCB is also capable of reducing perchlorate, another environmental hazard that occurs through manufacturing (and naturally) to chloride. They are also the first known organism to chemotax towards perchlorate. This means that they direct their movements towards areas of high perchlorate concentration. (1,2)
Genome structure
Dechloromonas aromatica has a single circular DNA chromosome with a length of 4,501,104 bps and 4,250 genes encoding 4171 predicated proteins and 79 RNAs. The genome has a GC content of approximately 59.2% and 64% of the sequences have been assigned a role in categories.(4)
Cell structure and metabolism
Dechloromonas aromatica have rod shaped cells, two membranes, and are gram-negative. They are usually either single cells or arranged in chains and are not capable of forming endospore which are dormant, tough, and nonreproductive structures formed by some bacteria. They are capable of forming flagella and thus possess motility.(1)
As mentioned above Dechloromonas aromatica is capable oxidizing different aromatic compounds. D. aromatica strain RCB is also the only organism in pure culture that is capable of oxidizing benzene in the absence of oxygen. It is recognized as the first organism with the ability to do this, and is the only organism identified capable of this metabolism. The metabolic pathway through which they biodegrade benzene is currently not fully known, studies suggest that it has both a dioxygenase-based aerobic pathway and an as yet fully uncharacterized anaerobic pathway. Research has shown that it requires a hydroxylation step and a carboxylation step, and produces benzoate and phenol as intermediates.(3) They are also capable of oxidizing Fe(II) and AHDS (a reduced humics compound).
Ecology
In the present, the role of Dechloromonas aromatica in the environment is yet unknown. However, it can have a significant contribution on the environment due to their unique ability to biodegrade benzene, perchlorate, and other similar compounds mentioned above. Many of these compounds are the result of common industrial processes used around the world. These compounds are harsh pollutants that create seriously problems for the environment, humans, and other organisms and are a result of human presence and technology.
For example, eating for drinking foods contaminated with benzene can lead to vomiting, stomach ache, and death in humans. It has also been shown to lead to anemia, lowered immune response, decreased size of ovaries in women, and has been classified by the US Department of Health and Human Services as a carcinogen. Other animals have been shown to have low birth weights, delayed bone formation, and bone morrow damage when pregnant animals were exposed to benzene in studies. In the US alone there are over 100,000 sites of benzene soil or groundwater contamination. Environmental contamination levels are worse in rapidly industrializing nations such as China where in 2005, the entire water supply to Harbin, a city with a population of almost 9 million was cut off due to benzene contamination from an explosion at a China National Petroleum Corporation factory.(5)
Pathology
There is no known virulence.
Application to Biotechnology
Dechloromonas aromatica is being studied for their ability to biodegrade benzene, perchloate and other compounds which as mentioned above can lead to a wide range of health problems for humans and other organisms. Their unique ability to do so in the absence of oxygen can make them extremely useful if they are deployed to areas where there is contaminated soil or groundwater in bioremediation projects. Researchers have discovered that it produces a diooxygense for the aerobic oxidation of benzene, but the anerobic pathway is still unclear.(1,2) In research, soil containing radioactive labeled benzene was inoculated with Dechloromonas aromatica and the benzene was quickly oxidized to CO2.(1)Also see current research section.
Current Research
1. This is when Dechloromonas aromatica was first isolated and shown to have the ability of metabolize benzene and perchlorate. The researchers isolated two unrelated strains, RCB and JJ, from two very diverse environments and they both had the ability to oxidize benzene to carbon dioxide in the absence of oxygen using nitrate as the election acceptor. In an experiment, the number of cells in culture was shown to increase with the disappearance of benzene. The researchers believed that this was the first known organism to be able to do this and can be utilized for bioremediation of benzene contaminated sites.
Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. John D. Coates, Romy Chakraborty, Joseph G. Lack, Susan M. O'Connor, Kimberly A. Cole, Kelly S. Bender & Laurie A. Achenbach
2. These researchers wanted to further investigate the benzene oxidizing ability of Dechloromonas aromatica strain RCB. They discovered that in addition to nitrate, these organisms can also use perchlorate or chlorate as electron acceptors in the aerobic or anaerobic oxidation of benzene. Their research also revealed that Dechloromonas aromatica strain RCB can also use toluene, ethylbenzene, and xylene as electron donors when nitrate is used as an electron acceptor. On top of that, Dechloromonas aromatica strain RCB can degrade benzene and toluene simultaneously.
Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and Xylene Compounds by Dechloromonas Strain RCB. Romy Chakraborty, Susan M. O'Connor, Emily Chan, and John D. Coates
3. In this research paper, the researchers basically summarized why benzene biodegradation is important and why several methods previously studied were not effective or efficient. More importantly they have gained some knowledge on the pathway Dechloromonas aromatica strain RCB uses to oxidize benzene to CO2. They discovered that the pathway requires an initial hydroxylation reaction, subsequent carboxylation reaction, and loss of hydroxyl group to form benzoate as an intermediate.
Hydroxylation and Carboxylation—Two Crucial Steps of Anaerobic Benzene Degradation by Dechloromonas Strain RCB. Romy Chakraborty and John D. Coates
References
1. Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. John D. Coates, Romy Chakraborty, Joseph G. Lack, Susan M. O'Connor, Kimberly A. Cole, Kelly S. Bender & Laurie A. Achenbach
2. Anaerobic Degradation of Benzene, Toluene, Ethylbenzene, and Xylene Compounds by Dechloromonas Strain RCB. Romy Chakraborty, Susan M. O'Connor, Emily Chan, and John D. Coates
3. Hydroxylation and Carboxylation—Two Crucial Steps of Anaerobic Benzene Degradation by Dechloromonas Strain RCB. Romy Chakraborty and John D. Coates
4. Dechloromonas aromatica RCB genome project at DOE Joint Genome Institute. Retrieved April 20, 2007, from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=9635
5. Benzne. (2007, May 31). In Wikipedia, The Free Encyclopedia. Retrieved June 1, 2007, from http://en.wikipedia.org/wiki/Benzene
Edited by Akira Noda, student of Rachel Larsen and Kit Pogliano
