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Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater.

ABSTRACT: Dehalococcoides mccartyi (Dhc) bacterial strains expressing active reductive dehalogenase (RDase) enzymes play key roles in the transformation and detoxification of chlorinated pollutants, including chlorinated ethenes. Site monitoring regimes traditionally rely on qPCR to assess the presence of Dhc biomarker genes; however, this technique alone cannot directly inform about dechlorination activity. To supplement gene-centric approaches and provide a more reliable proxy for dechlorination activity, we sought to demonstrate a targeted proteomics approach that can characterize Dhc mediated dechlorination in groundwater contaminated with chlorinated ethenes. Targeted peptide selection was conducted in axenic cultures of Dhc strains 195, FL2, and BAV1. These experiments yielded 37 peptides from housekeeping and structural proteins (i.e., GroEL, EF-TU, rpL7/L2 and the S-layer), as well as proteins involved in the reductive dechlorination activity (i.e., FdhA, TceA, and BvcA). The application of targeted proteomics to a defined bacterial consortium and contaminated groundwater samples resulted in the detection of FdhA peptides, which revealed active dechlorination with Dhc strain-level resolution, and the detection of RDases peptides indicating specific reductive dechlorination steps. The results presented here show that targeted proteomics can be applied to groundwater samples and provide protein level information about Dhc dechlorination activity.

SUBMITTER: Solis MIV

PROVIDER: S-EPMC6646388 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater.

Solis Manuel I Villalobos MIV Abraham Paul E PE Chourey Karuna K Swift Cynthia M CM Löffler Frank E FE Hettich Robert L RL

Scientific reports 20190722 1

Dehalococcoides mccartyi (Dhc) bacterial strains expressing active reductive dehalogenase (RDase) enzymes play key roles in the transformation and detoxification of chlorinated pollutants, including chlorinated ethenes. Site monitoring regimes traditionally rely on qPCR to assess the presence of Dhc biomarker genes; however, this technique alone cannot directly inform about dechlorination activity. To supplement gene-centric approaches and provide a more reliable proxy for dechlorination activit ...[more]

PMID: 31332202

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Project description:Dehalococcoides mccartyi strains are corrinoid-auxotrophic Bacteria and axenic cultures that require vitamin B12 (CN-Cbl) to conserve energy via organohalide respiration. Cultures of D. mccartyi strains BAV1, GT and FL2 grown with limiting amounts of 1 µg l(-1) CN-Cbl quickly depleted CN-Cbl, and reductive dechlorination of polychlorinated ethenes was incomplete leading to vinyl chloride (VC) accumulation. In contrast, the same cultures amended with 25 µg l(-1) CN-Cbl exhibited up to 2.3-fold higher dechlorination rates, 2.8-9.1-fold increased growth yields, and completely consumed growth-supporting chlorinated ethenes. To explore whether known cobamide-producing microbes supply Dehalococcoides with the required corrinoid cofactor, co-culture experiments were performed with the methanogen Methanosarcina barkeri strain Fusaro and two acetogens, Sporomusa ovata and Sporomusa sp. strain KB-1, as Dehalococcoides partner populations. During growth with H2/CO2, M. barkeri axenic cultures produced 4.2 ± 0.1 µg l(-1) extracellular cobamide (factor III), whereas the Sporomusa cultures produced phenolyl- and p-cresolyl-cobamides. Neither factor III nor the phenolic cobamides supported Dehalococcoides reductive dechlorination activity suggesting that M. barkeri and the Sporomusa sp. cannot fulfil Dehalococcoides' nutritional requirements. Dehalococcoides dechlorination activity and growth occurred in M. barkeri and Sporomusa sp. co-cultures amended with 10 µM 5',6'-dimethylbenzimidazole (DMB), indicating that a cobalamin is a preferred corrinoid cofactor of strains BAV1, GT and FL2 when grown with chlorinated ethenes as electron acceptors. Even though the methanogen and acetogen populations tested did not produce cobalamin, the addition of DMB enabled guided biosynthesis and generated a cobalamin that supported Dehalococcoides' activity and growth. Guided cobalamin biosynthesis may offer opportunities to sustain and enhance Dehalococcoides activity in contaminated subsurface environments.

Project description:Reductive dehalogenation mediated by organohalide-respiring bacteria plays a critical role in the global cycling of organohalides. Nonetheless, information on the dehalogenation enantioselectivity of organohalide-respiring bacteria remains limited. In this study, we report the enantioselective dechlorination of chiral polychlorinated biphenyls (PCBs) by Dehalococcoides mccartyi CG1. CG1 preferentially removed halogens from the (-)-enantiomers of the three major environmentally relevant chiral PCBs (PCB174, PCB149, and PCB132), and the enantiomer compositions of the dechlorination products depended on their parent organohalides. The in vitro assays with crude cell extracts or concentrated whole cells and the in vivo experiments with living cells showed similar enantioselectivities, in contrast with the distinct enantiomeric enrichment factors (εER) of the substrate chiral PCBs. Additionally, these results suggest that concentrated whole cells might be an alternative to crude cell extracts in in vitro tests of reductive dehalogenation activities. The enantioselective dechlorination of other chiral PCBs that we resolved via gas chromatography further confirmed the preference of CG1 for the (-)-enantiomers.IMPORTANCE A variety of agrochemicals and pharmaceuticals are chiral. Due to the enantioselectivity in biological processes, enantiomers of chiral compounds may have different environmental occurrences, fates, and ecotoxicologies. Many chiral organohalides exist in anaerobic or anoxic soils and sediments, and organohalide-respiring bacteria play a major role in the environmental attenuation and global cycling of these chiral organohalides. Therefore, it is important to investigate the dehalogenation enantioselectivity of organohalide-respiring bacteria. This study reports the discovery of enantioselective dechlorination of chiral PCBs by Dehalococcoides mccartyi CG1, which provides insights into the dehalogenation enantioselectivity of Dehalococcoides and may shed light on future PCB bioremediation efforts to prevent enantioselective biological side effects.

Dataset Information

Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater.

Publications

Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater.

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