An isolated Desulforhopalus-dominated consortium for organohalide respiration
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PROVIDER: PRJEB61380 | ENA |
REPOSITORIES: ENA
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Project description:Organohalide respiration in a pristine hypersaline lake
| PRJEB14107 | ENA
Project description:Sulfurospirillum multivorans is one of the few bacteria, which can anaerobically respire organohalides such as tetrachloroethene. The regulation of this organohalide respiration is in most parts unknown. Sulfurospirillum multivorans was shown to downregulate the expression of organohalide respiration-specific genes slowly when no substrate is present, over the time of approximately 100 generations. To unravel the molecular details of this peculiar regulation and the involved factors, we sequenced the primary transcriptome of the organism.
2020-10-23 | GSE139083 | GEO
Project description:Organohalide respiration is an environmentally relevant type of anaerobic respiration. We show that Sulfurospirillum halorespirans undergoes the same type of downregulation of the organohalide respiratory genes as had been overserved before in S. multivorans when cultivated without chlorinated ethenes for a long period of time. We compared the proteomes and acetylomes of S. halorespirans cells cultivated in the presence of PCE with those of cells long- and short-term cultivated with nitrate as sole electron acceptor.
2018-04-05 | PXD008953 | Pride
Project description:The organohalide-respiring Sulfurospirillum multivorans uses chlorinated ethenes as electron acceptors for growth under anoxic conditions. However, little is known about the interaction of these substrates with proteins. Here, we apply thermal proteome profiling (TPP) to analyze enzyme-trichloroethene interactions. TPP is commonly used to investigate protein-ligand binding through protein melting curve shifts. Several modifications in the protocol, e.g. performing the incubation under anaerobic conditions and increasing the temperature range up to 97°C, improved the detection range and allowed the investigation of oxygen-sensitive proteins. Enzymatic reductive dehalogenation was prevented by omitting the electron donor during incubations. This enabled detecting the interaction of the tetrachloroethene reductive dehalogenase PceA with trichloroethene and confirms the enzyme’s specificity for this substrate. Another 19 proteins showed significant melting curve shifts with trichloroethene, pointing to other proteins directly or indirectly interacting with trichloroethene. Interestingly, a putative response regulator reacted similarly towards trichloroethene, which is potentially in line with its proposed role in regulating trichloroethene respiration. The TPP approach is here proven to facilitate the identification of substrate-enzyme interactions of strictly anaerobic reductive dehalogenases and probably their regulators. This strategy can be used to identify yet unknown substrate specificities and potential signal-sensing proteins in other difficult to study bacteria.
2018-06-06 | PXD009308 | Pride
Project description:The strictly anaerobic bacterium Dehalococcoides mccartyi is obligatory dependent on organohalide respiration for energy conservation and growth. Due to its capability to reductively dehalogenate a multitude of toxic halogenated electron acceptors, it plays an important role in the attenuation of these compounds at respective contaminated sites. Here, D. mccartyi strain CBDB1, specialized on the dehalogenation of chloroaromatic compounds, was grown in a two-liquid phase system with 1,2,3-trichlorobenzene as electron acceptor, acetate plus CO2 as carbon source and hydrogen as electron donor. The proteome and Nε-lysine acetylome were analyzed in the lag, exponential and stationary phases. The high and almost invariable abundance of the membrane-localized organohalide respiration complex consisting of the reductive dehalogenases CbrA and CbdbA80, the uptake hydrogenase HupLS and the organohalide respiration molybdoenzyme OmeAB was shown throughout growth and also after a prolonged stationary phase. Quantification of transcripts of reductive dehalogenase genes revealed their major synthesis starting in the lag phase, which might be a prerequisite for balanced growth in the exponential phase. The analyses of the coverage of functional pathways as well as indicator analysis revealed the growth-phase specificity of the proteome, with regulatory proteins identified as important indicators for the stationary phase. The number of acetylated proteins increased from the lag to the stationary phase. We detected pronounced acetylation of key proteins of the acetate metabolism, i.e. the synthesis of acetyl-CoA and its processing via gluconeogenesis and the incomplete Wood-Ljungdahl pathway, as well as of proteins central for the biosynthesis of amino acids, co-factors and terpenoids. In addition, the partial acetylation of the reductive dehalogenases as well as of TatA, a component of the twin-arginine translocation machinery, suggests that acetylation might be directly involved in the maintenance of the organohalide respiration capacity of D. mccartyi over periods without access to halogenated electron acceptors.
2021-02-15 | PXD018912 | Pride
Project description:<p>A variety of anthropogenic organohalide contaminants generated from industry are released into the environment, and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by whole-metagenome sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavobạcteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes (MAGs) were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 MAGs were identified, suggesting that the potential for hydrolytic organohalide dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.</p>
2022-11-21 | MTBLS3916 | MetaboLights
Project description:We compared the global transcriptomic analysis of Desulfoluna spongiiphila strain AA1, an organohalide-respiring Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with 2,6-dibromophenol.
2020-01-10 | GSE141466 | GEO
Project description:Managing tradeoffs through gene regulation is believed to be critical for the success of a generalist in a fluctuating resource environment. To investigate this hypothesis in depth, we imposed a fluctuating environment that required a representative community of the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Counterintuitively, the community rapidly collapsed and went extinct because extensive gene regulation during shifts drove precipitous decline in intracellular abundance of essential transcripts and proteins. We demonstrate that extensive gene regulation can be catastrophic for a generalist when resources fluctuate rapidly, and that the extinction phenomenon can be prevented by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment. Two strains were profiled at early and mid-log phase of growth during Sulfate Respiration and Syntrophy, and after transition between them. 2 biological replicates, 24 samples
2015-09-17 | E-GEOD-73105 | biostudies-arrayexpress
Project description:Genome sequence of organohalide-respiring Desulfoluna spongiiphila DBB and Desulfoluna butyratoxydans MSL71T
| PRJEB31368 | ENA
Project description:Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
| S-EPMC9303371 | biostudies-literature