Global gene expression of <i>Dehalococcoides</i> within a robust dynamic TCE‐dechlorinating community under conditions of periodic substrate supply

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dCorrinoids are essential cofactors of reductive dehalogenases in Dehalococcoides mccartyi, an important bacterium in bioremediation, yet sequenced D. mccartyi strains do not possess the complete pathway for de novo corrinoid biosynthesis. Pelosinus sp. and Desulfovibrio sp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growing D. mccartyi strain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)-and lactateamended medium in cocultures with Desulfovibrio vulgaris Hildenborough (DvH) or Pelosinus fermentans R7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.C hlorinated solvents such as tetra-and trichloroethene (PCE/ TCE) have been among the most common subsurface contaminants in the United States for decades (1, 2). In situ bioremediation is an effective, economical, and environmentally friendly technology for treating chlorinated solvents (2, 3). Dehalococcoides mccartyi is the only known bacterium capable of carrying out respiratory reductive dechlorination of chloroethenes to nontoxic ethene and plays a key role in the bioremediation of contaminated groundwater (4, 5).As cofactors of reductive dehalogenases (RDases), the enzymes responsible for reductive dechlorination, corrinoids (e.g., cobalamin) are essential nutrients for supporting D. mccartyi growth and dechlorination. Genomic analyses of sequenced D. mccartyi strains reveal a lack of complete corrinoid biosynthesis pathways, rendering D. mccartyi incapable of synthesizing corrinoids de novo (6, 7). Exogenous cobalamin (a specific corrinoid also known as vitamin B 12 ) is generally added to grow D. mccartyi in isolation (8). Cobalamin, 5-methylbenzimidazolylcobamide ([5-MeBza]Cba), and 5-methoxyb...

Section: Discussionsupporting

confidence: 90%

Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia

Men

Seth

et al. 2014

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“…All procedures were performed with minimal modifications to the protocols in section 3 of the GeneChip expression analysis technical manual (Affymetrix, Santa Clara, CA). The microarray data analysis methods were described previously (15,31).…”

Section: Methodsmentioning

confidence: 99%

Efficient Metabolic Exchange and Electron Transfer within a Syntrophic Trichloroethene-Degrading Coculture of Dehalococcoides mccartyi 195 and Syntrophomonas wolfei

Mao

Stenuit

Polasko

et al. 2015

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bDehalococcoides mccartyi 195 (strain 195) and Syntrophomonas wolfei were grown in a sustainable syntrophic coculture using butyrate as an electron donor and carbon source and trichloroethene (TCE) as an electron acceptor. The maximum dechlorination rate (9.9 ؎ 0.1 mol day ؊1 ) and cell yield [(1.1 ؎ 0.3) ؋ 10 8 cells mol ؊1 Cl ؊ ] of strain 195 maintained in coculture were, respectively, 2.6 and 1.6 times higher than those measured in the pure culture. The strain 195 cell concentration was about 16 times higher than that of S. wolfei in the coculture. Aqueous H 2 concentrations ranged from 24 to 180 nM during dechlorination and increased to 350 ؎ 20 nM when TCE was depleted, resulting in cessation of butyrate fermentation by S. wolfei with a theoretical Gibbs free energy of ؊13.7 ؎ 0.2 kJ mol ؊1 . Carbon monoxide in the coculture was around 0.06 mol per bottle, which was lower than that observed for strain 195 in isolation. The minimum H 2 threshold value for TCE dechlorination by strain 195 in the coculture was 0.6 ؎ 0.1 nM. Cell aggregates during syntrophic growth were observed by scanning electron microscopy. The interspecies distances to achieve H 2 fluxes required to support the measured dechlorination rates were predicted using Fick's law and demonstrated the need for aggregation. Filamentous appendages and extracellular polymeric substance (EPS)-like structures were present in the intercellular spaces. The transcriptome of strain 195 during exponential growth in the coculture indicated increased ATP-binding cassette transporter activities compared to the pure culture, while the membrane-bound energy metabolism related genes were expressed at stable levels. Groundwater contamination by trichloroethene (TCE), a potential human carcinogen, poses a serious threat to human health and can lead to the generation of vinyl chloride (VC), which is a known human carcinogen (1). Strains of Dehalococcoides mccartyi are the only known bacteria that can completely degrade TCE to the benign end product ethene. Biostimulation of indigenous Dehalococcoides spp. and bioaugmentation using Dehalococcoides-containing cultures are recognized as the most reliable in situ bioremediation technologies resulting in the complete dechlorination of TCE to ethene (2). However, the mechanisms that regulate the activity of D. mccartyi within natural ecosystems and shape its functional robustness in disturbed environments are poorly understood due to multiscale microbial community complexity and heterogeneity of biogeochemical processes involved in the sequential degradation (3, 4). D. mccartyi exhibits specific restrictive metabolic requirements for a variety of exogenous compounds, such as hydrogen, acetate, corrinoids, biotin, and thiamine, which can be supplied by other microbial genera through a complex metabolic network (1,(5)(6)(7)(8). Therefore, the growth of D. mccartyi is more robust within functionally diverse microbial communities that are deterministically assembled than in pure cultures (5,8,9). Previous studies have shown t...

“…Previous community studies focused primarily on the physiological and transcriptional responses of D. mccartyi to different growth conditions (27)(28)(29)(30)(31), with limited knowledge of the corresponding responses of the coexisting supportive microorganisms, particularly at the transcriptional level. Total RNA sequencing (metatranscriptomics) can complement total DNA sequencing (metagenomics) by providing information about active community members and the taxonomic or functional dynamics over a time course or across different environmental conditions (32).…”

Section: Importancementioning

confidence: 99%

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

Men

Bælum

et al. 2017

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The aim of this study is to obtain a systems-level understanding of the interactions between and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid biosynthesis pathway was also assigned to the bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. The key chloroethene-dechlorinating bacterium is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of species in the communities compared to other coexisting community members in producing and providing corrinoids for species under cobalamin-limited conditions.