The little bacteria that can – diversity, genomics and ecophysiology of ‘<i>Dehalococcoides</i>’ spp. in contaminated environments

Taş, Neslihan; Eekert, M.H.A. van; Vos, Willem M. de; Smidt, Hauke

doi:10.1111/j.1751-7915.2009.00147.x

Cited by 105 publications

(50 citation statements)

References 115 publications

(227 reference statements)

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“…These microbes are important because they can use priority pollutants such as trichloroethene (TCE), dichloroethene (DCE), and vinyl chloride (VC) as electron acceptors for energy metabolism [4]. Dehalococcoides bacteria hold a prominent role among the organohalide respirers isolated to date, as these are the only ones having the proven ability to detoxify chloroethenes to the innocuous end product, ethene [1,5].…”

Section: Introductionmentioning

confidence: 99%

Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes

et al. 2012

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BackgroundBuffering to achieve pH control is crucial for successful trichloroethene (TCE) anaerobic bioremediation. Bicarbonate (HCO3−) is the natural buffer in groundwater and the buffer of choice in the laboratory and at contaminated sites undergoing biological treatment with organohalide respiring microorganisms. However, HCO3− also serves as the electron acceptor for hydrogenotrophic methanogens and hydrogenotrophic homoacetogens, two microbial groups competing with organohalide respirers for hydrogen (H2). We studied the effect of HCO3− as a buffering agent and the effect of HCO3−-consuming reactions in a range of concentrations (2.5-30 mM) with an initial pH of 7.5 in H2-fed TCE reductively dechlorinating communities containing Dehalococcoides, hydrogenotrophic methanogens, and hydrogenotrophic homoacetogens.ResultsRate differences in TCE dechlorination were observed as a result of added varying HCO3− concentrations due to H2-fed electrons channeled towards methanogenesis and homoacetogenesis and pH increases (up to 8.7) from biological HCO3− consumption. Significantly faster dechlorination rates were noted at all HCO3− concentrations tested when the pH buffering was improved by providing 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) as an additional buffer. Electron balances and quantitative PCR revealed that methanogenesis was the main electron sink when the initial HCO3− concentrations were 2.5 and 5 mM, while homoacetogenesis was the dominant process and sink when 10 and 30 mM HCO3− were provided initially.ConclusionsOur study reveals that HCO3− is an important variable for bioremediation of chloroethenes as it has a prominent role as an electron acceptor for methanogenesis and homoacetogenesis. It also illustrates the changes in rates and extent of reductive dechlorination resulting from the combined effect of electron donor competition stimulated by HCO3− and the changes in pH exerted by methanogens and homoacetogens.

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Section: Introductionmentioning

confidence: 99%

Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes

et al. 2012

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“…mccartyi has been found in many different environments, including groundwater, subsurface soil, and river and marine sediments (21,50). In these environments, D. mccartyi coexists with microbes that perform a variety of corrinoid-dependent metabolic functions such as the fermentation of short-chain organic compounds, acetogenesis, and methanogenesis (4,12,35,41).…”

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confidence: 99%

Versatility in Corrinoid Salvaging and Remodeling Pathways Supports Corrinoid-Dependent Metabolism in Dehalococcoides mccartyi

Seth

Men

et al. 2012

Appl Environ Microbiol

111

158

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dCorrinoids are cobalt-containing molecules that function as enzyme cofactors in a wide variety of organisms but are produced solely by a subset of prokaryotes. Specific corrinoids are identified by the structure of their axial ligands. The lower axial ligand of a corrinoid can be a benzimidazole, purine, or phenolic compound. Though it is known that many organisms obtain corrinoids from the environment, the variety of corrinoids that can serve as cofactors for any one organism is largely unstudied. Here, we examine the range of corrinoids that function as cofactors for corrinoid-dependent metabolism in Dehalococcoides mccartyi strain 195. Dehalococcoides bacteria play an important role in the bioremediation of chlorinated solvents in the environment because of their unique ability to convert the common groundwater contaminants perchloroethene and trichloroethene to the innocuous end product ethene. All isolated D. mccartyi strains require exogenous corrinoids such as vitamin B 12 for growth. However, like many other corrinoid-dependent bacteria, none of the well-characterized D. mccartyi strains has been shown to be capable of synthesizing corrinoids de novo. In this study, we investigate the ability of D. mccartyi strain 195 to use specific corrinoids, as well as its ability to modify imported corrinoids to a functional form. We show that strain 195 can use only specific corrinoids containing benzimidazole lower ligands but is capable of remodeling other corrinoids by lower ligand replacement when provided a functional benzimidazole base. This study of corrinoid utilization and modification by D. mccartyi provides insight into the array of strategies that microorganisms employ in acquiring essential nutrients from the environment.

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“…exhibit a wide range of substrate specificities on halogenated compounds (12,24,37,52). The reductive dehalogenases are the enzyme family capable of catalyzing the removal of chlorine ions from a substrate (23,47).…”

mentioning

confidence: 99%

Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp

Hug

Salehi

Nuin

et al. 2011

Appl Environ Microbiol

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Dehalococcoides spp. are an industrially relevant group of Chloroflexi bacteria capable of reductively dechlorinating contaminants in groundwater environments. Existing Dehalococcoides genomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishing Dehalococcoides strains. Here we describe an oligonucleotide microarray probe set designed based on clustered Dehalococcoides genes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This "pangenome" probe set provides coverage of core Dehalococcoides genes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknown Dehalococcoides strains. The pangenome probe set was compared to probe sets designed independently for each of the five Dehalococcoides strains. The pangenome probe set demonstrated better predictability and higher detection of Dehalococcoides genes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. An in silico analysis of the expected probe hybridization against the recently released Dehalococcoides strain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization of Dehalococcoides from contaminated sites. It has the potential to become a common platform for Dehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined.The genus Dehalococcoides contains obligate anaerobes capable of reductively dechlorinating a variety of common groundwater contaminants (1,12,18,31). The utility of Dehalococcoides in bioremediation of chlorinated-solvent-contaminated sites has lead to the development of Dehalococcoidescontaining cultures utilized as industrial tools (12, 29), methods for identifying and tracking Dehalococcoides growth and dechlorination (26,45,54), and methods for identifying the novel metabolism associated with the dechlorination reaction (2,27,30,40). The Dehalococcoides appear to be globally distributed; they have been isolated from sites in North America (e.g., strains DET195 [37], MB [7], and FL2 [19]) and Europe (e.g., strain CBDB1 [3]) and identified at many contaminated sites and more remote environments (1,15,22). Genome sequences currently exist for five strains of Dehalococcoides, strain DET195 (48), strain CBDB1 (31), strain BAV1 (38), strain VS (38), and strain GT (http://genome.jgi -psf.org/deh_g/deh_g.home.html). Several more genome sequences are in progress from mixed-culture metagenomes, including from the KB-1 enrichment consortium, ...

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The little bacteria that can – diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

Cited by 105 publications

References 115 publications

Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes

Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes

Versatility in Corrinoid Salvaging and Remodeling Pathways Supports Corrinoid-Dependent Metabolism in Dehalococcoides mccartyi

Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp

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