Primers That Target Functional Genes of Organohalide-Respiring Bacteria

Lu, Yue; Atashgahi, Siavash; Hug, Laura; Smidt, Hauke

doi:10.1007/8623_2015_75

Cited by 11 publications

(9 citation statements)

References 69 publications

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“…This may indicate similar regulation systems of the rdh genes in the Desulfoluna strains studied here. The conserved motifs from known RDases (RR, C1−C5, FeS1, and FeS2) [56,57] are also conserved among all the RdhAs of the Desulfoluna strains, except for RdhA1 of MSL71 T , which lacks the RR motif (Fig. S7).…”

Section: Comparison Of the Rdh Gene Region Of The Desulfoluna Strainsmentioning

confidence: 94%

Organohalide-respiring Desulfoluna species isolated from marine environments

Peng

Goris

et al. 2020

The ISME Journal

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The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1 T and D. butyratoxydans MSL71 T , of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.

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Section: Comparison Of the Rdh Gene Region Of The Desulfoluna Strainsmentioning

confidence: 94%

Organohalide-respiring Desulfoluna species isolated from marine environments

Peng

Goris

et al. 2020

The ISME Journal

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“…Interestingly, the TAT motif was also absent from the Smkt1 cluster of rdhA genes obtained from (Kawai et al, 2014). If similar rdhA genes lacking a TAT signal are present in environments investigated in the framework of former PCR-based surveys of subseafloor sediments (Futagami et al, 2009;, they have obviously been overlooked since the key RRF2 primer applied in these studies targets the conserved TAT motif region (Krajmalnik-Brown et al, 2004;Lu et al, 2015).…”

Section: Ohr In Marine Environmentsmentioning

confidence: 99%

Organohalide respiration in pristine environments: implications for the natural halogen cycle

Atashgahi

Häggblom

Smidt

2017

Environmental Microbiology

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Summary Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration. Originally discovered in a quest for biodegradation of anthropogenic organohalogens, these organohalide‐respiring bacteria (OHRB) were soon found to reside in pristine environments, such as the deep subseafloor and Arctic tundra soil with limited/no connections to anthropogenic activities. As such, accumulating evidence suggests an important role of OHRB in local natural halogen cycles, presumably taking advantage of natural organohalogens. In this minireview, we integrate current knowledge regarding the natural origin and occurrence of industrially important organohalogens and the evolution and spread of OHRB, and describe potential implications for natural halogen and carbon cycles.

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“…Among these are the enzymes catalyzing the conversion of PCE to cDCE (coded by the pceA gene) and TCE to VC (coded by the tceA gene), as well as the RDases catalyzing the conversion of cDCE to ethene (coded by the bvcA and vcrA genes) ( Magnuson et al, 1998 , 2000 ; Krajmalnik-Brown et al, 2004 ; Müller et al, 2004 ; Fung et al, 2007 ; Tang et al, 2016 ). Quantitative PCR methods that target these specific genes have been developed and are being increasingly used as prognostic and diagnostic tools in the field to overcome the limitations of the 16S rRNA gene ( Rahm et al, 2006b ; Ritalahti et al, 2006 , 2010 ; Lee et al, 2012 ; Lu et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi (D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments

Pérez‐de‐Mora

Lacourt

McMaster³

et al. 2018

Front. Microbiol.

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Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.

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Primers That Target Functional Genes of Organohalide-Respiring Bacteria

Cited by 11 publications

References 69 publications

Organohalide-respiring Desulfoluna species isolated from marine environments

Organohalide-respiring Desulfoluna species isolated from marine environments

Organohalide respiration in pristine environments: implications for the natural halogen cycle

Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi (D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments

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