Dehalococcoides ethenogenes: Difference between revisions

From MicrobeWiki, the student-edited microbiology resource
No edit summary
 
(19 intermediate revisions by 3 users not shown)
Line 1: Line 1:
{{Curated}}
{{Biorealm Genus}}
{{Biorealm Genus}}


Line 13: Line 14:
==Description and significance==
==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 prospective, it appears to have an irregular, spherical shape.  The species has a circular shape, although not perfectly circular (irregular coccus). 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. ''D. ethenogenes'' is anaerobic and cannot use oxygen, nitrate, or sulfate as electron acceptors.  
''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 coccoidMotility 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 can cause irreparable damage in groundwater areas where 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.
 
This organism can be isolated from environments polluted with chemicals such as perchloroethene (PCE) and trichloroethene (TCE).


==Genome structure==
==Genome structure==


''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.  It is the only known bacterium which completely dechlorinates tetrachloroethene (PCE) and trichloroethene, to ethylene. This is important because PCE and trichlorothene are common chemical groundwater pollutants featured in many commercial industry cleaners.
''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.


Apparently, ''Dehalococcoides ethenogenes'' has plasmids called pUA969, pUA970, pUA971. These plasmids work to bind ''D. ethenogenes'' LexA gene to ''Bacillus subtilis''. This is significant because it makes the first Gram-negative bacterium sharing LexA binding site like that of ''B. subtilis''.
==Cell structure and metabolism==


==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. 


PCE can be metabolize for energy by at least 15 different organisms such as acetogens and methanogens. Acetogens can use PCE to produce energy and carbon. The most common energy and carbon produced are carbon dioxide and hydrogen, respectively. Methanogens also produce energy and carbon of the same kind. Where they differ is some carbon dioxide will react with hydrogen to produce methane, which creates a gradient that generates ATP. Basically, these organisms benefit from PCE,  from which ''Dehalococcoides ethenogenes'' stems. Some organisms in this category produce energy from tetrachloroethene. These organisms are able to react with hydrogen (carbon source) as the electron donor, indicating that hydrogen and PCE serve as electron donors or acceptors for energy growth. The exchange of electrons are responsible for the generation of energy through PCE.
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==
==Ecology==


''Dehalococcoides ethenogenes'' most common use is for cleaning toxic messes by PCE. PCE is a suspected human carcinogen. Basically without this bacterium, PCE cancer spread to humans and animals. The symptoms of short-term exposure to PCE cause dizziness, headaches, and problems with balance, while long-term exposure of PCE has been linked to cancers of the esophagus, bladder, and blood. Therefore, ''D. ethenogenes'' is used to manipulate PCE and to minimize its symptoms. Not only does ''D. ethenogenes'' stop the spread of cancer to humans, but protect the groundwater that are PCE exposed.
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==
==Pathology==


This organism can be known as pathogen-free. It does not produce disease or illness to its host.
This organism does not produce disease or illness to its host.


==Application to Biotechnology==
==Application to Biotechnology==


''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. 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". Basically, they would inject the bacteria into groundwater to convert PCE into ethylene. Research indicates that the level of ethylene rises; therefore, the injection was an success.
''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==


1) The solvents tetrachloroethene (PCE) and trichloroethene (TCE) are among the most pollutants at contaminated groundwater sites. Under aerobic conditions, PCE is considered difficult to reduce, while TCE can be broken down to non-toxic products. This poses a problem because PCE is a harmful chemical to the environment, but cannot be controlled when oxygen is present. Therefore, there are flaws that ''D. ethenogenes'' cannot fix completely. However under anaerobic conditions, PCE and TCE have been able to reduce to ethylene, which deems them less harmless.  
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.


2) Bioremediation Consulting Inc. (BCI), of Watertown, Massachusetts identified at least 4 natural microbes containing ''Dehalococcoides ethenogenes'' that are known as TCA-tolerant ''D. ethenogenes''. Also, found growing there was ''Dehalobacter''. TCA is converted to chloroethane by ''Dehalobacter''. There is also dechlorination TCE and DCE to ethene and TCA dechlorinated to chloroethane. This research indicated the difference between using natural microbes or bacteria like ''Dehalobacter'' to treat the contaminated areas.
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.


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.
Original:
 
==References==
 
[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&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]


Line 68: Line 75:
B. Sun et al., 2002, Science, Vol 298 p. 1023
B. Sun et al., 2002, Science, Vol 298 p. 1023


Edited by Tim Hou of [mailto:ralarsen@ucsd.edu Rachel Larsen] and Kit Pogliano
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