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Oba K, Suenaga T, Yasuda S, Kuroiwa M, Hori T, Lackner S, Terada A. Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide. Microbes Environ 2024; 39:ME23106. [PMID: 38538312 PMCID: PMC10982107 DOI: 10.1264/jsme2.me23106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria and an exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.
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Affiliation(s)
- Kohei Oba
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2–24–16 Naka-cho, Koganei, Tokyo, 184–8588, Japan
| | - Toshikazu Suenaga
- Department of Chemical Engineering, Hiroshima University, 1–4–1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739–8527, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
| | - Shohei Yasuda
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Megumi Kuroiwa
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2–24–16 Naka-cho, Koganei, Tokyo, 184–8588, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16–1 Onogawa, Tsukuba, Ibaraki, 305–8569, Japan
| | - Susanne Lackner
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
- Department of Civil and Environmental Engineering Science, Institute IWAR, Chair of Water and Environmental Biotechnology Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287, Darmstadt, Germany
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2–24–16 Naka-cho, Koganei, Tokyo, 184–8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
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2
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Hellmold N, Eberwein M, Phan MHT, Kümmel S, Einsle O, Deobald D, Adrian L. Dehalococcoides mccartyi strain CBDB1 takes up protons from the cytoplasm to reductively dehalogenate organohalides indicating a new modus of proton motive force generation. Front Microbiol 2023; 14:1305108. [PMID: 38192294 PMCID: PMC10772276 DOI: 10.3389/fmicb.2023.1305108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Proton translocation across the cytoplasmic membrane is a vital process for all organisms. Dehalococcoides strains are strictly anaerobic organohalide respiring bacteria that lack quinones and cytochromes but express a large membrane-bound protein complex (OHR complex) proposed to generate a proton gradient. However, its functioning is unclear. By using a dehalogenase-based enzyme activity assay with deuterium-labelled water in various experimental designs, we obtained evidence that the halogen atom of the halogenated electron acceptor is substituted with a proton from the cytoplasm. This suggests that the protein complex couples exergonic electron flux through the periplasmic subunits of the OHR complex to the endergonic transport of protons from the cytoplasm across the cytoplasmic membrane against the proton gradient to the halogenated electron acceptor. Using computational tools, we located two proton-conducting half-channels in the AlphaFold2-predicted structure of the OmeB subunit of the OHR complex, converging in a highly conserved arginine residue that could play a proton gatekeeper role. The cytoplasmic proton half-channel in OmeB is connected to a putative proton-conducting path within the reductive dehalogenase subunit. Our results indicate that the reductive dehalogenase and its halogenated substrate serve as both electron and proton acceptors, providing insights into the proton translocation mechanism within the OHR complex and contributing to a better understanding of energy conservation in D. mccartyi strains. Our results reveal a very simple mode of energy conservation in anaerobic bacteria, showing that proton translocation coupled to periplasmic electron flow might have importance also in other microbial processes and biotechnological applications.
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Affiliation(s)
- Nadine Hellmold
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Marie Eberwein
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - My Hanh Thi Phan
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Steffen Kümmel
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Darja Deobald
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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3
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Cimmino L, Duarte AG, Ni D, Ekundayo BE, Pereira IAC, Stahlberg H, Holliger C, Maillard J. Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun 2023; 14:7038. [PMID: 37923808 PMCID: PMC10624902 DOI: 10.1038/s41467-023-42927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA2B2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Babatunde E Ekundayo
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Wiegand S, Sobol M, Schnepp-Pesch LK, Yan G, Iqbal S, Vollmers J, Müller JA, Kaster AK. Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes. Microorganisms 2023; 11:2612. [PMID: 37894270 PMCID: PMC10608941 DOI: 10.3390/microorganisms11102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.
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Affiliation(s)
| | | | | | | | | | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; (S.W.); (M.S.); (L.K.S.-P.); (G.Y.); (S.I.); (J.V.); (J.A.M.)
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5
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Reino C, Ding C, Adrian L. Continuous cultivation of Dehalococcoides mccartyi with brominated tyrosine avoids toxic byproducts and gives tight reactor control. WATER RESEARCH 2023; 229:119396. [PMID: 36463679 DOI: 10.1016/j.watres.2022.119396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Dehalococcoides mccartyi strain CBDB1 is a strictly anaerobic organohalide-respiring bacterium with strong application potential to remediate aquifers and soils contaminated with halogenated aromatics. To date, cultivation of strain CBDB1 has mostly been done in bottles or fed-batch reactors. Challenges with such systems include low biomass yield and difficulties in controlling the growth conditions. Here, we report the cultivation of planktonic D. mccartyi strain CBDB1 in a continuous stirring tank reactor (CSTR) that led to high cell densities (∼8 × 108 cells mL-1) and dominance of strain CBDB1. The reactor culture received acetate, hydrogen, and the brominated amino acid D- or L-3,5-dibromotyrosine as substrates. Both D- and L-3,5-dibromotyrosine were utilized as respiratory electron acceptors and are promising for biomass production due to their decent solubility in water and the formation of a non-toxic debromination product, tyrosine. By monitoring headspace pressure decrease which is indicative of hydrogen consumption, the organohalide respiration rate was followed in real time. Proteomics analyses revealed that the reductive dehalogenase CbdbA238 was highly expressed with both D- and L-3,5-dibromotyrosine, while other reductive dehalogenases including those that were previously suggested to be constitutively expressed, were repressed. Denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA genes indicated that the majority of cells in the community belonged to the Dehalococcoides although the CSTR was operated under non-sterile conditions. Hence, tightly controlled CSTR cultivation of Dehalococcoides opens novel options to improve biomass production for bioaugmentation and for advanced biochemical studies.
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Affiliation(s)
- Clara Reino
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Chang Ding
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
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6
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Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
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Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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7
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Ewald JM, Schnoor JL, Mattes TE. Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants. FEMS Microbiol Ecol 2022; 98:6602352. [PMID: 35665806 DOI: 10.1093/femsec/fiac067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/27/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.
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Affiliation(s)
- Jessica M Ewald
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Jerald L Schnoor
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
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8
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Chen WY, Wu JH. Microbiome composition resulting from different substrates influences trichloroethene dechlorination performance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 303:114145. [PMID: 34844052 DOI: 10.1016/j.jenvman.2021.114145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/05/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen-releasing substrates can stimulate the reductive dechlorination of trichloroethene (TCE) mediated by organohalide-respiring bacteria (OHRB) at contaminated sites. However, how the substrate affects microbiome assembly and the accompanying influences on the growth of OHRB and reductive TCE dechlorination remains unclear. We evaluated the effects of microbial community structures and potential functions on the reductive dechlorination of TCE in three anaerobic reactors with acetate, soybean oil, or molasses as the substrate and no cobalamin or amino acid supplementation. The molasses-fed reactor exhibited superior performance and dechlorination of TCE loadings to ethene, and the oil-fed reactor exhibited a high growth rate of the key OHRB, Dehalococcoides. This finding suggests an effect of the substrate on reductive dechlorination and the growth of Dehalococcoides. The three reactors developed distinct microbial community structures and the predicted metagenomes were distinguished on the basis of vitamin and amino acid metabolisms as well as fermentation pathways. In addition to the diversified hydrogen-producing pathways, the molasses-induced microbiome exhibited high potential to synthesize the cobalamin, which may account for its high Dehalococcoides activity and thus effective dechlorination performance. The substrate dependence of microbiomes may provide insight into strategies of exogenous amino acid supplementation to benefit Dehalococcoides growth. This study adds novel insight into the interplay of hydrogen-releasing substrates and OHRB. The results may contribute to the development of tailored and cost-effective management for the reductive dechlorination of chlorinated solvents in bioremediation.
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Affiliation(s)
- Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, Taiwan; Center of Microbiome Science and Technology, National Cheng Kung University, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Taiwan.
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9
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Matturro B, Zeppilli M, Lai A, Majone M, Rossetti S. Metagenomic Analysis Reveals Microbial Interactions at the Biocathode of a Bioelectrochemical System Capable of Simultaneous Trichloroethylene and Cr(VI) Reduction. Front Microbiol 2021; 12:747670. [PMID: 34659183 PMCID: PMC8516407 DOI: 10.3389/fmicb.2021.747670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
Bioelectrochemical systems (BES) are attractive and versatile options for the bioremediation of organic or inorganic pollutants, including trichloroethylene (TCE) and Cr(VI), often found as co-contaminants in the environment. The elucidation of the microbial players' role in the bioelectroremediation processes for treating multicontaminated groundwater is still a research need that attracts scientific interest. In this study, 16S rRNA gene amplicon sequencing and whole shotgun metagenomics revealed the leading microbial players and the primary metabolic interactions occurring in the biofilm growing at the biocathode where TCE reductive dechlorination (RD), hydrogenotrophic methanogenesis, and Cr(VI) reduction occurred. The presence of Cr(VI) did not negatively affect the TCE degradation, as evidenced by the RD rates estimated during the reactor operation with TCE (111±2 μeq/Ld) and TCE/Cr(VI) (146±2 μeq/Ld). Accordingly, Dehalococcoides mccartyi, the primary biomarker of the RD process, was found on the biocathode treating both TCE (7.82E+04±2.9E+04 16S rRNA gene copies g-1 graphite) and TCE/Cr(VI) (3.2E+07±2.37E+0716S rRNA gene copies g-1 graphite) contamination. The metagenomic analysis revealed a selected microbial consortium on the TCE/Cr(VI) biocathode. D. mccartyi was the sole dechlorinating microbe with H2 uptake as the only electron supply mechanism, suggesting that electroactivity is not a property of this microorganism. Methanobrevibacter arboriphilus and Methanobacterium formicicum also colonized the biocathode as H2 consumers for the CH4 production and cofactor suppliers for D. mccartyi cobalamin biosynthesis. Interestingly, M. formicicum also harbors gene complexes involved in the Cr(VI) reduction through extracellular and intracellular mechanisms.
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Affiliation(s)
| | - Marco Zeppilli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Agnese Lai
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Mauro Majone
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
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Li Y, Zhao HP, Zhu L. Iron Sulfide Enhanced the Dechlorination of Trichloroethene by Dehalococcoides mccartyi Strain 195. Front Microbiol 2021; 12:665281. [PMID: 34140942 PMCID: PMC8203822 DOI: 10.3389/fmicb.2021.665281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022] Open
Abstract
Iron sulfide (FeS) nanoparticles have great potential in environmental remediation. Using the representative species Dehalococcoides mccartyi strain 195 (Dhc 195), the effect of FeS on trichloroethene (TCE) dechlorination was studied with hydrogen and acetate as the electron donor and carbon source, respectively. With the addition of 0.2 mM Fe2+ and S2–, the dechlorination rate of TCE was enhanced from 25.46 ± 1.15 to 37.84 ± 1.89 μmol⋅L–1⋅day–1 by the in situ formed FeS nanoparticles, as revealed through X-ray diffraction. Comparing the tceA gene copy numbers between with FeS and without FeS, real-time polymerase chain reaction (PCR) indicated that the abundance of the tceA gene increased from (2.83 ± 0.13) × 107 to (4.27 ± 0.21) × 108 copies/ml on day 12. The transcriptional activity of key genes involved in the electron transport chain was upregulated after the addition of FeS, including those responsible for the iron–sulfur cluster assembly protein gene (DET1632) and transmembrane transport of iron (DET1503, DET0685), cobalamin (DET0685, DET1139), and molybdenum (DET1161) genes. Meanwhile, the reverse transcription of tceA was increased approximately five times on the 12th day. These upregulations together suggested that the electron transport of D. mccartyi strain 195 was enhanced by FeS for apparent TCE dechlorination. Overall, the present study provided an eco-friendly and effective method to achieve high remediation efficiency for organohalide-polluted groundwater and soil.
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Affiliation(s)
- Yaru Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou, China
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11
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Kruse S, Türkowsky D, Birkigt J, Matturro B, Franke S, Jehmlich N, von Bergen M, Westermann M, Rossetti S, Nijenhuis I, Adrian L, Diekert G, Goris T. Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene. THE ISME JOURNAL 2021; 15:1794-1809. [PMID: 33479489 PMCID: PMC8163811 DOI: 10.1038/s41396-020-00887-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Microbial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In co-cultures, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase-mandatory for D. mccartyi-was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B12 produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.
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Affiliation(s)
- Stefan Kruse
- grid.9613.d0000 0001 1939 2794Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Dominique Türkowsky
- grid.7492.80000 0004 0492 3830Department Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Jan Birkigt
- grid.7492.80000 0004 0492 3830Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Bruna Matturro
- grid.435629.f0000 0004 1755 3971Water Research Institute, IRSA-CNR, Monterotondo, Rome, Italy
| | - Steffi Franke
- grid.7492.80000 0004 0492 3830Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany ,Present Address: Eurofins Institute Dr. Appelt Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- grid.7492.80000 0004 0492 3830Department Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Martin von Bergen
- grid.7492.80000 0004 0492 3830Department Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Martin Westermann
- grid.275559.90000 0000 8517 6224Center for Electron Microscopy of the University Hospital Jena, Jena, Germany
| | - Simona Rossetti
- grid.435629.f0000 0004 1755 3971Water Research Institute, IRSA-CNR, Monterotondo, Rome, Italy
| | - Ivonne Nijenhuis
- grid.7492.80000 0004 0492 3830Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lorenz Adrian
- grid.6734.60000 0001 2292 8254Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany ,grid.7492.80000 0004 0492 3830Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Gabriele Diekert
- grid.9613.d0000 0001 1939 2794Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Tobias Goris
- grid.9613.d0000 0001 1939 2794Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany ,grid.418213.d0000 0004 0390 0098Present Address: German Institute of Human Nutrition, Department Molecular Toxicology, Research Group Intestinal Microbiology, Potsdam-Rehbrücke, Nuthetal, Germany
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12
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Trueba-Santiso A, Wasmund K, Soder-Walz JM, Marco-Urrea E, Adrian L. Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M. J Proteome Res 2020; 20:613-623. [PMID: 32975419 PMCID: PMC7786376 DOI: 10.1021/acs.jproteome.0c00569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Bacteria
of the genus Dehalogenimonas respire
with vicinally halogenated alkanes via dihaloelimination.
We aimed to describe involved proteins and their supermolecular organization.
Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained
31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for
membrane-anchoring proteins. Shotgun proteomics of cells grown with
1,2-dichloropropane as an electron acceptor identified 1152 proteins
representing more than 60% of the total proteome. Ten RdhA proteins
were detected, including a DcpA ortholog, which was the strongest
expressed RdhA. Blue native gel electrophoresis
(BNE) demonstrating maximum activity was localized in a protein complex
of 146–242 kDa. Protein mass spectrometry revealed the presence
of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake
hydrogenase subunits (HupL and HupS), an iron–sulfur protein
(HupX), and subunits of a redox protein with a molybdopterin-binding
motif (OmeA and OmeB) in the complex. BNE after protein solubilization
with different detergent concentrations revealed no evidence for an
interaction between the putative respiratory electron input module
(HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated
with the organohalide respiration complex. Based on genomic and proteomic
analysis, we propose quinone-independent respiration in Dehalogenimonas.
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Affiliation(s)
- Alba Trueba-Santiso
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra 08193, Spain
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1010, Austria
| | - Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra 08193, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra 08193, Spain
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin 10623, Germany
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13
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Deobald D, Hanna R, Shahryari S, Layer G, Adrian L. Identification and characterization of a bacterial core methionine synthase. Sci Rep 2020; 10:2100. [PMID: 32034217 PMCID: PMC7005905 DOI: 10.1038/s41598-020-58873-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/20/2020] [Indexed: 11/18/2022] Open
Abstract
Methionine synthases are essential enzymes for amino acid and methyl group metabolism in all domains of life. Here, we describe a putatively anciently derived type of methionine synthase yet unknown in bacteria, here referred to as core-MetE. The enzyme appears to represent a minimal MetE form and transfers methyl groups from methylcobalamin instead of methyl-tetrahydrofolate to homocysteine. Accordingly, it does not possess the tetrahydrofolate binding domain described for canonical bacterial MetE proteins. In Dehalococcoides mccartyi strain CBDB1, an obligate anaerobic, mesophilic, slowly growing organohalide-respiring bacterium, it is encoded by the locus cbdbA481. In line with the observation to not accept methyl groups from methyl-tetrahydrofolate, all known genomes of bacteria of the class Dehalococcoidia lack metF encoding for methylene-tetrahydrofolate reductase synthesizing methyl-tetrahydrofolate, but all contain a core-metE gene. We heterologously expressed core-MetECBDB in E. coli and purified the 38 kDa protein. Core-MetECBDB exhibited Michaelis-Menten kinetics with respect to methylcob(III)alamin (KM ≈ 240 µM) and L-homocysteine (KM ≈ 50 µM). Only methylcob(III)alamin was found to be active as methyl donor with a kcat ≈ 60 s-1. Core-MetECBDB did not functionally complement metE-deficient E. coli strain DH5α (ΔmetE::kan) suggesting that core-MetECBDB and the canonical MetE enzyme from E. coli have different enzymatic specificities also in vivo. Core-MetE appears to be similar to a MetE-ancestor evolved before LUCA (last universal common ancestor) using methylated cobalamins as methyl donor whereas the canonical MetE consists of a tandem repeat and might have evolved by duplication of the core-MetE and diversification of the N-terminal part to a tetrahydrofolate-binding domain.
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Affiliation(s)
- Darja Deobald
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany
| | - Rafael Hanna
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Freiburg University, Institute of Pharmaceutical Sciences, Stefan-Meier-Straße 19, 79104, Freiburg im Breisgau, Germany
| | - Shahab Shahryari
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany
| | - Gunhild Layer
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Freiburg University, Institute of Pharmaceutical Sciences, Stefan-Meier-Straße 19, 79104, Freiburg im Breisgau, Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany.
- Technische Universität Berlin, Chair of Geobiotechnology, Ackerstraße 76, 13355, Berlin, Germany.
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14
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Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater. Sci Rep 2019; 9:10604. [PMID: 31332202 PMCID: PMC6646388 DOI: 10.1038/s41598-019-46901-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022] Open
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.
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15
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Chen Y, Wang L, Dai F, Tao M, Li X, Tan Z. Biostimulants application for bacterial metabolic activity promotion and sodium dodecyl sulfate degradation under copper stress. CHEMOSPHERE 2019; 226:736-743. [PMID: 30965244 DOI: 10.1016/j.chemosphere.2019.03.180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 02/13/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
In this study, the metabolic activity (adenosine triphosphate, ATP; electron transfer system, ETS; and dehydrogenase activity, DHA) response of a sodium dodecyl sulfate (SDS) degrading bacterium Pseudomonas sp. SDS-N2 to copper stress conditions were investigated. Results showed that the ATP content, ETS activity, and DHA activity of strain SDS-N2 were significantly correlated with substrate removal efficiency and bacterial growth under copper stress conditions. Based on the metabolic response patterns of strain SDS-N2, biostimulants citric acid, proline as well as FeSO4 were used to promote the metabolic activity of strain SDS-N2 at 0.8 mg L-1 copper stress condition. Plackett-Burman design and analysis proved that citric acid and FeSO4 were significant factors for enhanced SDS removal; and the optimum biostimulation conditions (FeSO4 72 mg L-1 and citric acid 100 mg L-1) for SDS removal were obtained by using steepest ascent experiment and central composite design. Under the optimum biostimulation conditions, ATP, ETS, DHA activity as well as bacterial growth were 14.1, 45.5, 0.5 and 2.3-fold higher than that of the control (without FeSO4 and citric acid addition) after 12.5 h biodegradation, and the substrate removal efficiency was increase by 37.6%.
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Affiliation(s)
- Yangwu Chen
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China; University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Le Wang
- BYD (Shangluo) Co., Ltd, 726000, Shangluo, PR China
| | - Fazhi Dai
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China
| | - Mei Tao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China
| | - Xudong Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China
| | - Zhouliang Tan
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, PR China.
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16
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Heavner GLW, Mansfeldt CB, Wilkins MJ, Nicora CD, Debs GE, Edwards EA, Richardson RE. Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site. Front Microbiol 2019; 10:1433. [PMID: 31316484 PMCID: PMC6610324 DOI: 10.3389/fmicb.2019.01433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022] Open
Abstract
RNA-based biomarkers have been successfully detected at field sites undergoing in situ bioremediation, but the detection of expressed enzymes is a more direct way to prove activity for a particular biocatalytic process of interest since they provide evidence of potential in situ activity rather than simply confirming presence and abundance of genes in a given population by measurement of DNA copies using qPCR. Here we successfully applied shotgun proteomics to field samples from a trichloroethene (TCE)-contaminated industrial site in southern Ontario, Canada that had been bio-augmented with the commercially available KB-1TM microbial culture. The KB-1TM culture contains multiple strains of Dehalococcoides mccartyi (D. mccartyi) as well as an organohalide respiring Geobacter species. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to the KB-1TM-bioaugemented enhanced in situ bioremediation system, and two control wells that showed evidence of low levels of native organohalide respiring bacteria (OHRB), Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of D. mccartyi, chemotaxis proteins, and ATPases. The most highly expressed RDase in the bioaugmentation culture (VcrA) was the most highly detected enzyme overall in the bioaugmented groundwater samples. In one background groundwater well, we found high expression of the Geobacter pceA RDase. The DNA and RNA biomarkers detected using qPCR-based assays were a set of orthologs of Dehalococcoides reductive dehalogenases (VcrA, TceA, BvcA, dehalogenase “DET1545”), and the Ni-Fe uptake hydrogenase, HupL. Within a sample, RNA levels for key enzymes correlated with relative protein abundance. These results indicate that laboratory observations of TCE-bioremediation biomarker protein expression are recapitulated in field environmental systems and that both RNA and protein biomarker monitoring hold promise for activity monitoring of in situ populations of OHRB.
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Affiliation(s)
- Gretchen L W Heavner
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Cresten B Mansfeldt
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Michael J Wilkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Garrett E Debs
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
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17
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Abstract
Hydrogenases are metal-containing biocatalysts that reversibly convert protons and electrons to hydrogen gas. This reaction can contribute in different ways to the generation of the proton motive force (PMF) of a cell. One means of PMF generation involves reduction of protons on the inside of the cytoplasmic membrane, releasing H2 gas, which being without charge is freely diffusible across the cytoplasmic membrane, where it can be re-oxidized to release protons. A second route of PMF generation couples transfer of electrons derived from H2 oxidation to quinone reduction and concomitant proton uptake at the membrane-bound heme cofactor. This redox-loop mechanism, as originally formulated by Mitchell, requires a second, catalytically distinct, enzyme complex to re-oxidize quinol and release the protons outside the cell. A third way of generating PMF is also by electron transfer to quinones but on the outside of the membrane while directly drawing protons through the entire membrane. The cofactor-less membrane subunits involved are proposed to operate by a conformational mechanism (redox-linked proton pump). Finally, PMF can be generated through an electron bifurcation mechanism, whereby an exergonic reaction is tightly coupled with an endergonic reaction. In all cases the protons can be channelled back inside through a F1F0-ATPase to convert the 'energy' stored in the PMF into the universal cellular energy currency, ATP. New and exciting discoveries employing these mechanisms have recently been made on the bioenergetics of hydrogenases, which will be discussed here and placed in the context of their contribution to energy conservation.
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Affiliation(s)
- Constanze Pinske
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany
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18
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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19
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Budhraja R, Ding C, Walter P, Wagner S, Reemtsma T, Gary Sawers R, Adrian L. The impact of species, respiration type, growth phase and genetic inventory on absolute metal content of intact bacterial cells. Metallomics 2019; 11:925-935. [DOI: 10.1039/c9mt00009g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Absolute metal ion content was determined from whole cells of different microbial species and changes were related to growth conditions and change of encoded genes.
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Affiliation(s)
- Rohit Budhraja
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
- Chair of Geobiotechnology
| | - Chang Ding
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
| | - Philipp Walter
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
| | - Stephan Wagner
- Helmholtz Centre for Environmental Research – UFZ
- Department of Analytical Chemistry
- Leipzig
- Germany
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research – UFZ
- Department of Analytical Chemistry
- Leipzig
- Germany
| | - R. Gary Sawers
- Institute of Biology/Microbiology
- Martin-Luther Universität
- Halle
- Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
- Chair of Geobiotechnology
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20
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Dragomirova N, Rothe P, Schwoch S, Hartwig S, Pinske C, Sawers RG. Insights Into the Redox Sensitivity of Chloroflexi Hup-Hydrogenase Derived From Studies in Escherichia coli: Merits and Pitfalls of Heterologous [NiFe]-Hydrogenase Synthesis. Front Microbiol 2018; 9:2837. [PMID: 30519233 PMCID: PMC6258894 DOI: 10.3389/fmicb.2018.02837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/05/2018] [Indexed: 11/13/2022] Open
Abstract
The highly oxygen-sensitive hydrogen uptake (Hup) hydrogenase from Dehalococcoides mccartyi forms part of a protein-based respiratory chain coupling hydrogen oxidation with organohalide reduction on the outside of the cell. The HupXSL proteins were previously shown to be synthesized and enzymatically active in Escherichia coli. Here we examined the growth conditions that deliver active Hup enzyme that couples H2 oxidation to benzyl viologen (BV) reduction, and identified host factors important for this process. In a genetic background lacking the three main hydrogenases of E. coli we could show that additional deletion of genes necessary for selenocysteine biosynthesis resulted in inactive Hup enzyme, suggesting requirement of a formate dehydrogenase for Hup activity. Hup activity proved to be dependent on the presence of formate dehydrogenase (Fdh-H), which is typically associated with the H2-evolving formate hydrogenlyase (FHL) complex in the cytoplasm. Further analyses revealed that heterologous Hup activity could be recovered if the genes encoding the ferredoxin-like electron-transfer protein HupX, as well as the related HycB small subunit of Fdh-H were also deleted. These findings indicated that the catalytic HupL and electron-transferring HupS subunits were sufficient for enzyme activity with BV. The presence of the HupX or HycB proteins in the absence of Fdh-H therefore appears to cause inactivation of the HupSL enzyme. This is possibly because HupX or HycB aided transfer of electrons to the quinone pool or other oxidoreductase complexes, thus maintaining the HupSL heterodimer in a continuously oxidized state causing its inactivation. This proposal was supported by the observation that growth under either aerobic or anaerobic respiratory conditions did not yield an active HupSL. These studies thus provide a system to understand the redox sensitivity of this heterologously synthesized hydrogenase.
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Affiliation(s)
- Nadya Dragomirova
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Patricia Rothe
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Stefan Schwoch
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Stefanie Hartwig
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Constanze Pinske
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle, Germany
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Wang S, Qiu L, Liu X, Xu G, Siegert M, Lu Q, Juneau P, Yu L, Liang D, He Z, Qiu R. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol Adv 2018; 36:1194-1206. [DOI: 10.1016/j.biotechadv.2018.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/08/2023]
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Schubert T, Adrian L, Sawers RG, Diekert G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol Ecol 2018; 94:4923014. [DOI: 10.1093/femsec/fiy035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
- Department of Geobiotechnology, Technische Universität Berlin, Ackerstraße 74, D-13355 Berlin, Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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Zhang S, Adrian L, Schüürmann G. Interaction Mode and Regioselectivity in Vitamin B 12-Dependent Dehalogenation of Aryl Halides by Dehalococcoides mccartyi Strain CBDB1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1834-1843. [PMID: 29283566 DOI: 10.1021/acs.est.7b04278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The bacterium Dehalococcoides, strain CBDB1, transforms aromatic halides through reductive dehalogenation. So far, however, the structures of its vitamin B12-containing dehalogenases are unknown, hampering clarification of the catalytic mechanism and substrate specificity as basis for targeted remediation strategies. This study employs a quantum chemical donor-acceptor approach for the Co(I)-substrate electron transfer. Computational characterization of the substrate electron affinity at carbon-halogen bonds enables discriminating aromatic halides ready for dehalogenation by strain CBDB1 (active substrates) from nondehalogenated (inactive) counterparts with 92% accuracy, covering 86 of 93 bromobenzenes, chlorobenzenes, chlorophenols, chloroanilines, polychlorinated biphenyls, and dibenzo-p-dioxins. Moreover, experimental regioselectivity is predicted with 78% accuracy by a site-specific parameter encoding the overlap potential between the Co(I) HOMO (highest occupied molecular orbital) and the lowest-energy unoccupied sigma-symmetry substrate MO (σ*), and the observed dehalogenation pathways are rationalized with a success rate of 81%. Molecular orbital analysis reveals that the most reactive unoccupied sigma-symmetry orbital of carbon-attached halogen X (σC-X*) mediates its reductive cleavage. The discussion includes predictions for untested substrates, thus providing opportunities for targeted experimental investigations. Overall, the presently introduced orbital interaction model supports the view that with bacterial strain CBDB1, an inner-sphere electron transfer from the supernucleophile B12 Co(I) to the halogen substituent of the aromatic halide is likely to represent the rate-determining step of the reductive dehalogenation.
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Affiliation(s)
- Shangwei Zhang
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Technical University Bergakademie Freiberg , Institute for Organic Chemistry, Leipziger Straße 29, 09596 Freiberg, German y
| | - Lorenz Adrian
- UFZ Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Technische Universität Berlin , Chair of Geobiotechnology, Ackerstraße 76, 13355 Berlin, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Technical University Bergakademie Freiberg , Institute for Organic Chemistry, Leipziger Straße 29, 09596 Freiberg, German y
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Atashgahi S, Häggblom MM, Smidt H. Organohalide respiration in pristine environments: implications for the natural halogen cycle. Environ Microbiol 2017; 20:934-948. [PMID: 29215190 DOI: 10.1111/1462-2920.14016] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 11/29/2022]
Abstract
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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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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David C, Schmid A, Adrian L, Wilde A, Bühler K. Production of 1,2-propanediol in photoautotrophic Synechocystis is linked to glycogen turn-over. Biotechnol Bioeng 2017; 115:300-311. [PMID: 29143978 DOI: 10.1002/bit.26468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/03/2017] [Accepted: 10/05/2017] [Indexed: 11/10/2022]
Abstract
We utilized a photoautotrophic organism to synthesize 1,2-propanediol from carbon dioxide and water fueled by light. A synthetic pathway comprising mgsA (methylglyoxal synthase), yqhD (aldehyde reductase), and adh (alcohol dehydrogenase) was inserted into Synechocystis sp. PCC6803 to convert dihydroxyacetone phosphate to methylglyoxal, which is subsequently reduced to acetol and then to 1,2-propanediol. 1,2-propanediol could be successfully produced by Synechocystis, at an approximate rate of 55 μmol h-1 gCDW-1 . Surprisingly, maximal productivity was observed in the stationary phase. The production of 1,2-propanediol was clearly coupled to the turn-over of intracellular glycogen. Upon depletion of the glycogen pool, product formation stopped. Reducing the carbon flux to glycogen significantly decreased final product titers. Optimization of cultivation conditions allowed final product titers of almost 1 g L-1 (12 mM), which belongs to the highest values published so far for photoautotrophic production of this compound.
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Affiliation(s)
- Christian David
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Isotope-Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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Affiliation(s)
- Maeva Fincker
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
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Mortan SH, Martín-González L, Vicent T, Caminal G, Nijenhuis I, Adrian L, Marco-Urrea E. Detoxification of 1,1,2-trichloroethane to ethene in a bioreactor co-culture of Dehalogenimonas and Dehalococcoides mccartyi strains. JOURNAL OF HAZARDOUS MATERIALS 2017; 331:218-225. [PMID: 28273571 DOI: 10.1016/j.jhazmat.2017.02.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/30/2017] [Accepted: 02/23/2017] [Indexed: 06/06/2023]
Abstract
1,1,2-Trichloroethane (1,1,2-TCA) is a non-flammable organic solvent and common environmental contaminant in groundwater. Organohalide-respiring bacteria are key microorganisms to remediate 1,1,2-TCA because they can gain metabolic energy during its dechlorination under anaerobic conditions. However, all current isolates produce hazardous end products such as vinyl chloride, monochloroethane or 1,2-dichloroethane that accumulate in the medium. Here, we constructed a syntrophic co-culture of Dehalogenimonas and Dehalococcoides mccartyi strains to achieve complete detoxification of 1,1,2-TCA to ethene. In this co-culture, Dehalogenimonas transformed 1,1,2-TCA via dihaloelimination to vinyl chloride, whereas Dehalococcoides reduced vinyl chloride via hydrogenolysis to ethene. Molasses, pyruvate, and lactate supported full dechlorination of 1,1,2-TCA in serum bottle co-cultures. Scale up of the cultivation to a 5-L bioreactor operating for 76d in fed-batch mode was successful with pyruvate as substrate. This synthetic combination of bacteria with known complementary metabolic capabilities demonstrates the potential environmental relevance of microbial cooperation to detoxify 1,1,2-TCA.
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Affiliation(s)
- Siti Hatijah Mortan
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Lucía Martín-González
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Gloria Caminal
- Institut de Química Avançada de Catalunya (IQAC) CSIC, Barcelona, Spain
| | - Ivonne Nijenhuis
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain.
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Zhang S, Wondrousch D, Cooper M, Zinder SH, Schüürmann G, Adrian L. Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3714-3724. [PMID: 28233989 DOI: 10.1021/acs.est.6b05730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dehalococcoides mccartyi strain CBDB1 and Dehalobacter strain 14DCB1 are organohalide-respiring microbes of the phyla Chloroflexi and Firmicutes, respectively. Here, we report the transformation of chloroanilines by these two bacterial strains via dissimilar dehalogenation pathways and discuss the underlying mechanism with quantum chemically calculated net atomic charges of the substrate Cl, H, and C atoms. Strain CBDB1 preferentially removed Cl doubly flanked by two Cl or by one Cl and NH2, whereas strain 14DCB1 preferentially dechlorinated Cl that has an ortho H. For the CBDB1-mediated dechlorination, comparative analysis with Hirshfeld charges shows that the least-negative Cl discriminates active from nonactive substrates in 14 out of 15 cases and may represent the preferred site of primary attack through cob(I)alamin. For the latter trend, three of seven active substrates provide strong evidence, with partial support from three of the remaining four substrates. Regarding strain 14DCB1, the most positive carbon-attached H atom discriminates active from nonactive chloroanilines in again 14 out of 15 cases. Here, regioselectivity is governed for 10 of the 11 active substrates by the most positive H attached to the highest-charge (most positive or least negative) aromatic C carrying the Cl to be removed. These findings suggest the aromatic ring H as primary site of attack through the supernucleophile Co(I), converting an initial H bond to a full electron transfer as start of the reductive dehalogenation. For both mechanisms, one- and two-electron transfer to Cl (strain CBDB1) or H (strain 14DCB1) are compatible with the presently available data. Computational chemistry research into reaction intermediates and pathways may further aid in understanding the bacterial reductive dehalogenation at the molecular level.
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Affiliation(s)
- Shangwei Zhang
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | - Dominik Wondrousch
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | | | - Stephen H Zinder
- Department of Microbiology, Cornell University , Ithaca, New York 14853, United States
| | - Gerrit Schüürmann
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | - Lorenz Adrian
- Fachgebiet Applied Biochemistry, Technische Universität Berlin , Gustav-Meyer-Allee 25, 13355 Berlin, Germany
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Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions. Appl Environ Microbiol 2017; 83:AEM.03508-16. [PMID: 28188205 DOI: 10.1128/aem.03508-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/04/2017] [Indexed: 12/21/2022] Open
Abstract
The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides 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 Veillonellaceae 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 de novo biosynthesis pathway was also assigned to the Veillonellaceae 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 Dehalococcoides 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.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides 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 Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.
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Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns. Appl Microbiol Biotechnol 2017; 101:4799-4813. [PMID: 28213734 DOI: 10.1007/s00253-017-8180-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/03/2017] [Indexed: 10/20/2022]
Abstract
The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems. Bioaugmentation of one column of each treatment with Bachman Road enrichment culture did not change Dhc populations nor the eventual degree of TCE dehalogenation. Pyrosequencing revealed high diversity among Dhc strains. There were 13 OTUs that were represented by more than 1000 sequences each. Cornell group-related populations dominated in complete TCE dehalogenating columns, while Pinellas group related Dhc dominated in all other treatments. General microbial communities varied with biostimulation, and three distinct microbial communities were established: one each for whey, oils, and control treatments. Bacterial genera, including Dehalobacter, Desulfitobacterium, Sulfurospirillum, Desulfuromonas, and Geobacter, all capable of partial TCE dehalogenation, were abundant in the limited and partial TCE dehalogenating systems. Dhc strain diversity was wider than previously reported and their composition within the community varied significantly depending on the nature of the carbon source applied and/or changes in the Dhc associated partners that fostered different biogeochemical conditions across the columns.
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Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J.M. Stams A, Springael D, Dejonghe W, Smidt H. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol 2016; 19:968-981. [DOI: 10.1111/1462-2920.13531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Yue Lu
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Ying Zheng
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | | | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health; Ingolstädter Landstrasse 1 Neuherberg D-85764 Germany
| | - Alfons J.M. Stams
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
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Kublik A, Deobald D, Hartwig S, Schiffmann CL, Andrades A, von Bergen M, Sawers RG, Adrian L. Identification of a multi-protein reductive dehalogenase complex inDehalococcoides mccartyistrain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement. Environ Microbiol 2016; 18:3044-56. [DOI: 10.1111/1462-2920.13200] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/03/2015] [Accepted: 12/23/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Anja Kublik
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Darja Deobald
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Stefanie Hartwig
- Institute of Microbiology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle Germany
| | - Christian L. Schiffmann
- Department of Proteomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Adarelys Andrades
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Proteomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
- Department of Metabolomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
- Centre for Microbial Communities; University of Aalborg; Fredrik Bajers Vej 7H 9220 Aalborg East Denmark
| | - R. Gary Sawers
- Institute of Microbiology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
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Choi KY. Non-enzymatic PLP-dependent oxidative deamination of amino acids induces higher alcohol synthesis. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0434-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Rodionova IA, Li X, Plymale AE, Motamedchaboki K, Konopka AE, Romine MF, Fredrickson JK, Osterman AL, Rodionov DA. Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:204-10. [PMID: 25345570 DOI: 10.1111/1758-2229.12227] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/23/2014] [Indexed: 05/15/2023]
Abstract
Bacteria from the Chloroflexi phylum are dominant members of phototrophic microbial mat communities in terrestrial thermal environments. Vitamins of B group are key intermediates (precursors) in the biosynthesis of indispensable enzyme cofactors driving numerous metabolic processes in all forms of life. A genomics-based reconstruction and comparative analysis of respective biosynthetic and salvage pathways and riboswitch regulons in over 20 representative Chloroflexi genomes revealed a widespread auxotrophy for some of the vitamins. The most prominent predicted phenotypic signature, auxotrophy for vitamins B1 and B7 was experimentally confirmed for the best studied model organism Chloroflexus aurantiacus. These observations along with identified candidate genes for the respective uptake transporters pointed to B vitamin cross-feeding as an important aspect of syntrophic metabolism in microbial communities. Inferred specificities of homologous substrate-binding components of ABC transporters for vitamins B1 (ThiY) and B2 (RibY) were verified by thermofluorescent shift approach. A functional activity of the thiamine-specific transporter ThiXYZ from C. aurantiacus was experimentally verified by genetic complementation in E. coli. Expanding the integrative approach, which was applied here for a comprehensive analysis of B-vitamin metabolism in Chloroflexi would allow reconstruction of metabolic interdependencies in microbial communities.
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Affiliation(s)
- Irina A Rodionova
- Sanford-Burnham Medical Research Institute, La Jolla, CA, 92037, USA
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Mao X, Stenuit B, Polasko A, Alvarez-Cohen L. Efficient metabolic exchange and electron transfer within a syntrophic trichloroethene-degrading coculture of Dehalococcoides mccartyi 195 and Syntrophomonas wolfei. Appl Environ Microbiol 2015; 81:2015-24. [PMID: 25576615 PMCID: PMC4345365 DOI: 10.1128/aem.03464-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/02/2015] [Indexed: 01/07/2023] Open
Abstract
Dehalococcoides 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 μmol day(-1)) and cell yield [(1.1 ± 0.3) × 10(8) cells μmol(-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 H2 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 μmol per bottle, which was lower than that observed for strain 195 in isolation. The minimum H2 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 H2 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.
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Affiliation(s)
- Xinwei Mao
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Benoit Stenuit
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Alexandra Polasko
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Rupakula A, Lu Y, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J. Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23. Front Microbiol 2015; 5:751. [PMID: 25610435 PMCID: PMC4285132 DOI: 10.3389/fmicb.2014.00751] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/10/2014] [Indexed: 12/03/2022] Open
Abstract
De novo corrinoid biosynthesis represents one of the most complicated metabolic pathways in nature. Organohalide-respiring bacteria (OHRB) have developed different strategies to deal with their need of corrinoid, as it is an essential cofactor of reductive dehalogenases, the key enzymes in OHR metabolism. In contrast to Dehalococcoides mccartyi, the genome of Dehalobacter restrictus strain PER-K23 contains a complete set of corrinoid biosynthetic genes, of which cbiH appears to be truncated and therefore non-functional, possibly explaining the corrinoid auxotrophy of this obligate OHRB. Comparative genomics within Dehalobacter spp. revealed that one (operon-2) of the five distinct corrinoid biosynthesis associated operons present in the genome of D. restrictus appeared to be present only in that particular strain, which encodes multiple members of corrinoid transporters and salvaging enzymes. Operon-2 was highly up-regulated upon corrinoid starvation both at the transcriptional (346-fold) and proteomic level (46-fold on average), in line with the presence of an upstream cobalamin riboswitch. Together, these data highlight the importance of this operon in corrinoid homeostasis in D. restrictus and the augmented salvaging strategy this bacterium adopted to cope with the need for this essential cofactor.
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Affiliation(s)
- Aamani Rupakula
- Laboratory for Environmental Biotechnology, ENAC-IIE-LBE, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Yue Lu
- Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University Wageningen, Netherlands
| | - Thomas Kruse
- Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University Wageningen, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Agrotechnology and Food Sciences, Wageningen University Wageningen, Netherlands
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, ENAC-IIE-LBE, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Hauke Smidt
- Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University Wageningen, Netherlands
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, ENAC-IIE-LBE, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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Röling WFM. Maths on microbes: adding microbial ecophysiology to metagenomics. Microb Biotechnol 2014; 8:21-2. [PMID: 25488506 PMCID: PMC4321363 DOI: 10.1111/1751-7915.12233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Wilfred F M Röling
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
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Shan H, Wang H, Yu R, Jacob P, Freedman DL. Biodegradation of high concentrations of halomethanes by a fermentative enrichment culture. AMB Express 2014; 4:48. [PMID: 25401061 PMCID: PMC4230812 DOI: 10.1186/s13568-014-0048-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/14/2014] [Indexed: 11/20/2022] Open
Abstract
A fermentative enrichment culture (designated DHM-1) that grows on corn syrup was evaluated for its ability to cometabolically biodegrade high concentrations of chloroform (CF), carbon tetrachloride (CT), and trichlorofluoromethane (CFC-11). When provided with corn syrup and vitamin B12 (0.03 mol B12 per mol CF), DHM-1 grew and biodegraded up to 2,000 mg/L of CF in 180 days, with only minor transient accumulation of dichloromethane and chloromethane. CT (15 mg/L) and CFC-11 (25 mg/L) were also biodegraded without significant accumulation of halomethane daughter products. The rate of CF biodegradation followed a Michaelis-Menten-like pattern with respect to the B12 concentration; one-half the maximum rate (66 mg CF/L/d) occurred at 0.005 mol B12 per mol CF. DHM-1 was able to biodegrade 500 mg/L of CF at an inoculum level as low as 10−8 mg protein/L. The highest rate of CF biodegradation occurred at pH 7.7; activity decreased substantially below pH 6.0. DHM-1 biodegraded mixtures of CT, CFC-11, and CF, although CFC-11 inhibited CF biodegradation. Evidence for compete defluorination of CFC-11 was obtained based on a fluoride mass balance. Overall, the results suggest that DHM-1 may be effective for bioaugmentation in source zones contaminated with thousands of milligrams per liter of CF and tens of milligrams per liter of CT and CFC-11.
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Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit. Appl Environ Microbiol 2014; 80:6062-72. [PMID: 25063656 DOI: 10.1128/aem.02130-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6±0.6 μM Cl-/h)- and fast (22.9±9.6 μM Cl-/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n=53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112).
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Men Y, Seth EC, Yi S, Crofts TS, Allen RH, Taga ME, Alvarez-Cohen L. Identification of specific corrinoids reveals corrinoid modification in dechlorinating microbial communities. Environ Microbiol 2014; 17:4873-84. [PMID: 24803319 DOI: 10.1111/1462-2920.12500] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 04/16/2014] [Accepted: 04/30/2014] [Indexed: 11/27/2022]
Abstract
Cobalamin and other corrinoids are essential cofactors for many organisms. The majority of microbes with corrinoid-dependent enzymes do not produce corrinoids de novo, and instead must acquire corrinoids produced by other organisms in their environment. However, the profile of corrinoids produced in corrinoid-dependent microbial communities, as well as the exchange and modification of corrinoids among community members have not been well studied. In this study, we applied a newly developed liquid chromatography tandem mass spectrometry-based corrinoid detection method to examine relationships among corrinoids, their lower ligand bases and specific microbial groups in microbial communities containing Dehalococcoides mccartyi that has an obligate requirement for benzimidazole-containing corrinoids for trichloroethene respiration. We found that p-cresolylcobamide ([p-Cre]Cba) and cobalamin were the most abundant corrinoids in the communities. It suggests that members of the family Veillonellaceae are associated with the production of [p-Cre]Cba. The decrease of supernatant-associated [p-Cre]Cba and the increase of biomass-associated cobalamin were correlated with the growth of D. mccartyi by dechlorination. This supports the hypothesis that D. mccartyi is capable of fulfilling its corrinoid requirements in a community through corrinoid remodelling, in this case, by importing extracellular [p-Cre]Cba and 5,6-dimethylbenzimidazole (DMB) (the lower ligand of cobalamin), to produce cobalamin as a cofactor for dechlorination. This study also highlights the role of DMB, the lower ligand produced in all of the studied communities, in corrinoid remodelling. These findings provide novel insights on roles played by different phylogenetic groups in corrinoid production and corrinoid exchange within microbial communities. This study may also have implications for optimizing chlorinated solvent bioremediation.
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Affiliation(s)
- Yujie Men
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720, USA
| | - Erica C Seth
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Shan Yi
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720, USA
| | - Terence S Crofts
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Robert H Allen
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor. J Proteomics 2014; 98:59-64. [DOI: 10.1016/j.jprot.2013.12.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/25/2013] [Accepted: 12/16/2013] [Indexed: 11/22/2022]
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Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl Environ Microbiol 2014; 80:2133-41. [PMID: 24463969 DOI: 10.1128/aem.03477-13] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Corrinoids 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 lactate-amended 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.
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Leys D, Adrian L, Smidt H. Organohalide respiration: microbes breathing chlorinated molecules. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120316. [PMID: 23479746 DOI: 10.1098/rstb.2012.0316] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacterial respiration has taken advantage of almost every redox couple present in the environment. The reduction of organohalide compounds to release the reduced halide ion drives energy production in organohalide respiring bacteria. This process is centred around the reductive dehalogenases, an iron-sulfur and corrinoid containing family of enzymes. These enzymes, transcriptional regulators and the bacteria themselves have potential to contribute to future bioremediation solutions that address the pollution of the environment by halogenated organic compounds.
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Affiliation(s)
- David Leys
- Manchester Institute of Biotechnology, University of Manchester, MIB 131 Princess Street, Manchester, UK.
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