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Umezawa K, Kojima H, Kato Y, Fukui M. Dissulfurispira thermophila gen. nov., sp. nov., a thermophilic chemolithoautotroph growing by sulfur disproportionation, and proposal of novel taxa in the phylum Nitrospirota to reclassify the genus Thermodesulfovibrio. Syst Appl Microbiol 2021; 44:126184. [PMID: 33676265 DOI: 10.1016/j.syapm.2021.126184] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 01/23/2023]
Abstract
Recently, presence of sulfur-disproportionating bacterial species belonging to the phylum Nitrospirota was indicated by an enrichment culture-based study. In the present study, a strain representing that species was isolated and characterized. The strain, strain T55JT, was isolated from a microbial mat of a hot spring. The cells were motile, and rods or spiral forms with width of 0.32-0.49 μm. The strain grew autotrophically, only by disproportionation of thiosulfate or elemental sulfur. Growth was observed at a temperature range of 25-60°C, with optimum growth at 53-57°C. The pH range for growth was 5.5-9.0, with optimum pH of 7.0-8.0. The complete genome of strain T55JT is composed of a circular chromosome (2,370,875 bp), with G+C content of 38.7%. Thermodesulfovibrio hydrogeniphilus Hdr5T showed the highest sequence similarity of the 16S rRNA gene to strain T55JT, but it was only 88.2%. On the basis of the phylogenetic and physiologic properties, strain T55JT (= DSM 110365T=NBRC 114245T) is proposed as type strain of a novel species in a new genus, Dissulfurispira thermophila gen. nov., sp. nov. To assign the new genus to family and higher taxa, its taxonomic position was assessed by genome-based phylogeny. As a result, it was shown that the novel genus and Thermodesulfovibrio belong to different families. It was also shown that Thermodesulfovibrio should be reclassified at levels from class to family and creation of some novel taxa is required. Based on these results, Thermodesulfovibrionia class. nov., Thermodesulfovibrionales ord. nov., Thermodesulfovibrionaceae fam. nov., and Dissulfurispiraceae fam. nov. are proposed.
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Affiliation(s)
- Kazuhiro Umezawa
- The Institute of Low Temperature Science, Hokkaido University. Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan.
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University. Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan.
| | - Yukako Kato
- The Institute of Low Temperature Science, Hokkaido University. Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University. Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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52
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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53
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Singh A, Schnürer A, Westerholm M. Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level. Environ Microbiol 2021; 23:1620-1637. [PMID: 33400377 DOI: 10.1111/1462-2920.15388] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/15/2020] [Accepted: 01/02/2021] [Indexed: 01/04/2023]
Abstract
Inefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high-ammonia anaerobic digesters, but propionate-degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia-tolerant syntrophic propionate-oxidising bacteria using propionate enrichment at high ammonia levels (0.7-0.8 g NH3 L-1 ) in continuously-fed reactors. We reconstructed 30 high-quality metagenome-assembled genomes (MAGs) from the propionate-fed reactors, which revealed two novel species from the families Peptococcaceae and Desulfobulbaceae as syntrophic propionate-oxidising candidates. Both MAGs possess genomic potential for the propionate oxidation and electron transfer required for syntrophic energy conservation and, similar to ammonia-tolerant acetate degrading syntrophs, both MAGs contain genes predicted to link to ammonia and pH tolerance. Based on relative abundance, a Peptococcaceae sp. appeared to be the main propionate degrader and has been given the provisional name "Candidatus Syntrophopropionicum ammoniitolerans". This bacterium was also found in high-ammonia biogas digesters, using quantitative PCR. Acetate was degraded by syntrophic acetate-oxidising bacteria and the hydrogenotrophic methanogenic community consisted of Methanoculleus bourgensis and a yet to be characterised Methanoculleus sp. This work provides knowledge of cooperating syntrophic species in high-ammonia systems and reveals that ammonia-tolerant syntrophic propionate-degrading populations share common features, but diverge genomically and taxonomically from known species.
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
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54
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Appel L, Willistein M, Dahl C, Ermler U, Boll M. Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148379. [PMID: 33460586 DOI: 10.1016/j.bbabio.2021.148379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
In methanogenic archaea, the archetypical complex of heterodisulfide reductase (HdrABC) and hydrogenase (MvhAGD) couples the endergonic reduction of CO2 by H2 to the exergonic reduction of the CoB-S-S-CoM heterodisulfide by H2 via flavin-based electron bifurcation. Presently known enzymes containing HdrA(BC)-like components play key roles in methanogenesis, acetogenesis, respiratory sulfate reduction, lithotrophic reduced sulfur compound oxidation, aromatic compound degradation, fermentations, and probably many further processes. This functional diversity is achieved by a modular architecture of HdrA(BC) enzymes, where a big variety of electron input/output modules may be connected either directly or via adaptor modules to the HdrA(BC) components. Many, but not all HdrA(BC) complexes are proposed to catalyse a flavin-based electron bifurcation/confurcation. Despite the availability of HdrA(BC) crystal structures, fundamental questions of electron transfer and energy coupling processes remain. Here, we address the common properties and functional diversity of HdrA(BC) core modules integrated into electron-transfer machineries of outstanding complexity.
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Affiliation(s)
- Lena Appel
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany
| | - Max Willistein
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Matthias Boll
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany.
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55
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Abstract
A balanced gut microbiota contributes to health, but the mechanisms maintaining homeostasis remain elusive. Microbiota assembly during infancy is governed by competition between species and by environmental factors, termed habitat filters, that determine the range of successful traits within the microbial community. These habitat filters include the diet, host-derived resources, and microbiota-derived metabolites, such as short-chain fatty acids. Once the microbiota has matured, competition and habitat filtering prevent engraftment of new microbes, thereby providing protection against opportunistic infections. Competition with endogenous Enterobacterales, habitat filtering by short-chain fatty acids, and a host-derived habitat filter, epithelial hypoxia, also contribute to colonization resistance against Salmonella serovars. However, at a high challenge dose, these frank pathogens can overcome colonization resistance by using their virulence factors to trigger intestinal inflammation. In turn, inflammation increases the luminal availability of host-derived resources, such as oxygen, nitrate, tetrathionate, and lactate, thereby creating a state of abnormal habitat filtering that enables the pathogen to overcome growth inhibition by short-chain fatty acids. Thus, studying the process of ecosystem invasion by Salmonella serovars clarifies that colonization resistance can become weakened by disrupting host-mediated habitat filtering. This insight is relevant for understanding how inflammation triggers dysbiosis linked to noncommunicable diseases, conditions in which endogenous Enterobacterales expand in the fecal microbiota using some of the same growth-limiting resources required by Salmonella serovars for ecosystem invasion. In essence, ecosystem invasion by Salmonella serovars suggests that homeostasis and dysbiosis simply represent states where competition and habitat filtering are normal or abnormal, respectively.
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56
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Williamson AJ, Engelbrektson AL, Liu Y, Huang LL, Kumar A, Menon AR, Thieme J, Carlson HK, Coates JD. Tungstate Control of Microbial Sulfidogenesis and Souring of the Engineered Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:16119-16127. [PMID: 33253556 DOI: 10.1021/acs.est.0c04682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sulfide accumulation in oil reservoir fluids (souring) from the activity of sulfate-reducing microorganisms (SRM) is of grave concern because of the associated health and facility failure risks. Here, we present an assessment of tungstate as a selective and potent inhibitor of SRM. Dose-response inhibitor experiments were conducted with a number of SRM isolates and enrichments at 30-80 °C and an increase in the effectiveness of tungstate treatment at higher temperatures was observed. To explore mixed inhibitor treatment modes, we tested synergy or antagonism between several inhibitors with tungstate, and found synergism between WO42- and NO2-, while additive effects were observed with ClO4- and NO3-. We also evaluated SRM inhibition by tungstate in advective upflow oil-sand-packed columns. Although 2 mM tungstate was initially sufficient to inhibit sulfidogenesis, subsequent temporal CaWO4 precipitation resulted in loss of the bioavailable inhibitor from solution and a concurrent increase in effluent sulfide. Mixing 4 mM sodium carbonate with the 2 mM tungstate was enough to promote tungstate solubility to reach inhibitory concentrations, without precipitation, and completely inhibit SRM activity. Overall, we demonstrate the effectiveness of tungstate as a potent SRM inhibitor, particularly at higher temperatures, and propose a novel carbonate-tungstate formulation for application to soured oil reservoirs.
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Affiliation(s)
- Adam J Williamson
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Anna L Engelbrektson
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Yi Liu
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Leah L Huang
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Aarti Kumar
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Aruna R Menon
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Juergen Thieme
- NSLS-II Brookhaven National Laboratory, Brookhaven, New York 11973, United States
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John D Coates
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
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57
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Peterson BD, McDaniel EA, Schmidt AG, Lepak RF, Janssen SE, Tran PQ, Marick RA, Ogorek JM, DeWild JF, Krabbenhoft DP, McMahon KD. Mercury Methylation Genes Identified across Diverse Anaerobic Microbial Guilds in a Eutrophic Sulfate-Enriched Lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15840-15851. [PMID: 33228362 PMCID: PMC9741811 DOI: 10.1021/acs.est.0c05435] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mercury (Hg) methylation is a microbially mediated process that converts inorganic Hg into bioaccumulative, neurotoxic methylmercury (MeHg). The metabolic activity of methylating organisms is highly dependent on biogeochemical conditions, which subsequently influences MeHg production. However, our understanding of the ecophysiology of methylators in natural ecosystems is still limited. Here, we identified potential locations of MeHg production in the anoxic, sulfidic hypolimnion of a freshwater lake. At these sites, we used shotgun metagenomics to characterize microorganisms with the Hg-methylation gene hgcA. Putative methylators were dominated by hgcA sequences divergent from those in well-studied, confirmed methylators. Using genome-resolved metagenomics, we identified organisms with hgcA (hgcA+) within the Bacteroidetes and the recently described Kiritimatiellaeota phyla. We identified hgcA+ genomes derived from sulfate-reducing bacteria, but these accounted for only 22% of hgcA+ genome coverage. The most abundant hgcA+ genomes were from fermenters, accounting for over half of the hgcA gene coverage. Many of these organisms also mediate hydrolysis of polysaccharides, likely from cyanobacterial blooms. This work highlights the distribution of the Hg-methylation genes across microbial metabolic guilds and indicate that primary degradation of polysaccharides and fermentation may play an important but unrecognized role in MeHg production in the anoxic hypolimnion of freshwater lakes.
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Affiliation(s)
- Benjamin D. Peterson
- Environmental Science & Technology Program, University of Wisconsin - Madison, 660 N. Park Street, Madison, WI 53706, USA
- Corresponding author:
| | - Elizabeth A. McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Anna G. Schmidt
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Ryan F. Lepak
- Environmental Science & Technology Program, University of Wisconsin - Madison, 660 N. Park Street, Madison, WI 53706, USA
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
- U.S. Environmental Protection Agency Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Sarah E. Janssen
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
- Department of Integrative Biology, University of Wisconsin - Madison, 250 N. Mills St.Madison, WI 53706, USA
| | - Robert A. Marick
- Department of Biochemistry, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Jacob M. Ogorek
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - John F. DeWild
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - David P. Krabbenhoft
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
- Department of Civil and Environmental Engineering, University of Wisconsin – Madison, 1415 Engineering Drive, Madison WI 53706, USA
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58
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Zinke LA, Evans PN, Santos-Medellín C, Schroeder AL, Parks DH, Varner RK, Rich VI, Tyson GW, Emerson JB. Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environ Microbiol 2020; 23:340-357. [PMID: 33185945 DOI: 10.1111/1462-2920.15316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.
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Affiliation(s)
- Laura A Zinke
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | | | - Alena L Schroeder
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Donovan H Parks
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ruth K Varner
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA.,Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, Qld, 4102, Australia
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA
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59
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Campbell MA, Grice K, Visscher PT, Morris T, Wong HL, White RA, Burns BP, Coolen MJL. Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. Front Microbiol 2020; 11:560336. [PMID: 33312167 PMCID: PMC7702295 DOI: 10.3389/fmicb.2020.560336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/09/2020] [Indexed: 11/25/2022] Open
Abstract
Microbial mat communities possess extensive taxonomic and functional diversity, which drive high metabolic rates and rapid cycling of major elements. Modern microbial mats occurring in hypersaline environments are considered as analogs to extinct geobiological formations dating back to ∼ 3.5 Gyr ago. Despite efforts to understand the diversity and metabolic potential of hypersaline microbial mats in Shark Bay, Western Australia, there has yet to be molecular analyses at the transcriptional level in these microbial communities. In this study, we generated metatranscriptomes for the first time from actively growing mats comparing the type of mat, as well as the influence of diel and seasonal cycles. We observed that the overall gene transcription is strongly influenced by microbial community structure and seasonality. The most transcribed genes were associated with tackling the low nutrient conditions by the uptake of fatty acids, phosphorus, iron, and nickel from the environment as well as with protective mechanisms against elevated salinity conditions and to prevent build-up of ammonium produced by nitrate reducing microorganisms. A range of pathways involved in carbon, nitrogen, and sulfur cycles were identified in mat metatranscriptomes, with anoxygenic photosynthesis and chemoautotrophy using the Arnon–Buchanan cycle inferred as major pathways involved in the carbon cycle. Furthermore, enrichment of active anaerobic pathways (e.g., sulfate reduction, methanogenesis, Wood–Ljungdahl) in smooth mats corroborates previous metagenomic studies and further advocates the potential of these communities as modern analogs of ancient microbialites.
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Affiliation(s)
- Matthew A Campbell
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Pieter T Visscher
- Departments of Marine Sciences and Geoscience, University of Connecticut, Storrs, CT, United States.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Therese Morris
- Applied Geology, Curtin University, Perth, WA, Australia
| | - Hon Lun Wong
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,Plant Pathology, Washington State University, Pullman, WA, United States.,RAW Molecular Systems (RMS) LLC, Spokane, WA, United States
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Marco J L Coolen
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
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60
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Zhang X, Zhang D, Huang Y, Wu S, Lu P. The anodic potential shaped a cryptic sulfur cycling with forming thiosulfate in a microbial fuel cell treating hydraulic fracturing flowback water. WATER RESEARCH 2020; 185:116270. [PMID: 32784035 DOI: 10.1016/j.watres.2020.116270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 07/22/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The flowback water (FW) from shale gas exploitation can be effectively treated by bioelectrochemical technology, but sulfide overproduction remains to be addressed. Herein, sulfate-reducing bacteria (SRB) meditated microbial fuel cells (MFCs) with anodic potential control were used. COD removal gradually increased to 67.4 ± 5.1% in electrode-potential-control (EPC) MFCs and 78.9 ± 2.4% in the MFC with open circuit (OC-MFC). However, in EPC MFCs sulfate removal stabilized at much lower levels (no more than 19.9 ± 1.9%) along with much lower sulfide concentrations, but in OC-MFC it increased and finally stabilized at 59.9 ± 0.1%. Partial sulfur reuse in EPC MFCs was indicated by the current production. Notably, thiosulfate was specially detected under low potentials and effectively oxidized in EPC MFCs, especially under -0.1 V vs. SHE, which probably related to the sulfur reuse. Metagenomics analysis showed that the anode with -0.1 and -0.2 V likely shunted electrons from cytochromes that used for reducing DsrC-S0 trisulfide and thus contributed to producing thiosulfate and decreasing sulfide production. Meanwhile, the anode with -0.1 V specially accumulated sulfur-oxidizing system (Sox) genes regarding thiosulfate and sulfite oxidation to sulfate, which concurred to the effective thiosulfate oxidation and also indicated the possible direct sulfite oxidation to sulfate during the sulfur cycling. But the anode of -0.2 V highly accumulated genes for thiosulfate and sulfite reduction. Both anodes also distinctly accumulated genes regarding thiosulfate oxidation to tetrathionate and sulfide oxidation to sulfur or polysulfide. Further, sulfur-oxidizing bacteria were specially enriched in EPC MFCs and likely contributed to thiosulfate and sulfite oxidation. Thus, we suggested that the higher electrode potential (e.g. -0.1 V) can shape a cryptic sulfur cycling, in which sulfate was first reduced to sulfite, and then reoxidized to sulfate by forming thiosulfate as an important intermediate or by direct sulfite oxidation. The results provide new sights on the bioelectrochemical treatment of wastewater containing complex organics and sulfate.
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Affiliation(s)
- Xiaoting Zhang
- Department of Environmental Science, Chongqing University, Chongqing 400044, China
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, Chongqing University, Chongqing 400044, China.
| | - Yongkui Huang
- Department of Environmental Science, Chongqing University, Chongqing 400044, China
| | - Shanshan Wu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Department of Environmental Science, Chongqing University, Chongqing 400044, China
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61
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Pandey CB, Kumar U, Kaviraj M, Minick KJ, Mishra AK, Singh JS. DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139710. [PMID: 32544704 DOI: 10.1016/j.scitotenv.2020.139710] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO3- occurs in two steps; in the first step, NO3- is reduced to NO2-; and in the second, unlike denitrification, NO2- is reduced to NH4+ without intermediates. There are two sets of NO3-/NO2- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N2O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N2O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO2-/NO3- ratio, and concentrations of ferrous iron (Fe2+) and sulfide (S2-). Under low-redox conditions, a high C/NO3- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO3- are equal, the NO2-/NO3- ratio modulates partitioning of NO3-, and a high NO2-/NO3- ratio favours DNRA. A high S2-/NO3- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO3- to NH4+, it is essential for protecting NO3- from leaching and gaseous (N2O) losses and enriches soils with readily available NH4+-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO3- pollution, enhance soil health and improve environmental quality.
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Affiliation(s)
- C B Pandey
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India.
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India.
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - K J Minick
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - A K Mishra
- International Rice Research Institute, New Delhi 110012, India
| | - J S Singh
- Ecosystem Analysis Lab, Centre of Advanced Study in Botany, Banaras Hindu University (BHU), Varanasi 221005, India
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Shima S, Huang G, Wagner T, Ermler U. Structural Basis of Hydrogenotrophic Methanogenesis. Annu Rev Microbiol 2020; 74:713-733. [DOI: 10.1146/annurev-micro-011720-122807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2and H2to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1species to the C1carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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Umezawa K, Kojima H, Kato Y, Fukui M. Disproportionation of inorganic sulfur compounds by a novel autotrophic bacterium belonging to Nitrospirota. Syst Appl Microbiol 2020; 43:126110. [DOI: 10.1016/j.syapm.2020.126110] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/21/2022]
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Ernst C, Kayastha K, Koch T, Venceslau SS, Pereira IAC, Demmer U, Ermler U, Dahl C. Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans. FEBS J 2020; 288:1664-1678. [PMID: 32750208 DOI: 10.1111/febs.15505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/03/2020] [Accepted: 07/31/2020] [Indexed: 02/01/2023]
Abstract
Many bacteria and archaea employ a novel pathway of sulfur oxidation involving an enzyme complex that is related to the heterodisulfide reductase (Hdr or HdrABC) of methanogens. As a first step in the biochemical characterization of Hdr-like proteins from sulfur oxidizers (sHdr), we structurally analyzed the recombinant sHdrA protein from the Alphaproteobacterium Hyphomicrobium denitrificans at 1.4 Å resolution. The sHdrA core structure is similar to that of methanogenic HdrA (mHdrA) which binds the electron-bifurcating flavin adenine dinucleotide (FAD), the heart of the HdrABC-[NiFe]-hydrogenase catalyzed reaction. Each sHdrA homodimer carries two FADs and two [4Fe-4S] clusters being linked by electron conductivity. Redox titrations monitored by electron paramagnetic resonance and visible spectroscopy revealed a redox potential between -203 and -188 mV for the [4Fe-4S] center. The potentials for the FADH•/FADH- and FAD/FADH• pairs reside between -174 and -156 mV and between -81 and -19 mV, respectively. The resulting stable semiquinone FADH• species already detectable in the visible and electron paramagnetic resonance spectra of the as-isolated state of sHdrA is incompatible with basic principles of flavin-based electron bifurcation such that the sHdr complex does not apply this new mode of energy coupling. The inverted one-electron FAD redox potentials of sHdr and mHdr are clearly reflected in the different FAD-polypeptide interactions. According to this finding and the assumption that the sHdr complex forms an asymmetric HdrAA'B1C1B2C2 hexamer, we tentatively propose a mechanism that links protein-bound sulfane oxidation to sulfite on HdrB1 with NAD+ reduction via lipoamide disulfide reduction on HdrB2. The FAD of HdrA thereby serves as an electron storage unit. DATABASE: Structural data are available in PDB database under the accession number 6TJR.
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Affiliation(s)
- Corvin Ernst
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Tobias Koch
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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Fernandez L, Peura S, Eiler A, Linz AM, McMahon KD, Bertilsson S. Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake. Front Microbiol 2020; 11:1500. [PMID: 32714313 PMCID: PMC7341956 DOI: 10.3389/fmicb.2020.01500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/09/2020] [Indexed: 12/28/2022] Open
Abstract
Aquatic N-fixation is generally associated with the growth and mass development of Cyanobacteria in nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data and nif gene clusters analysis. Groups with diazotrophic operons were functionally divergent and included Cholorobi, Geobacter, Desulfobacterales, Methylococcales, and Acidobacteria. In addition to nifH (a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within the Chlorobi population, the nitrogenase (nifH) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence of rnf genes (related to the expression of H+/Na+-translocating ferredoxin: NAD+ oxidoreductase) in Methylococcales and Desulfobacterales suggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes.
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Affiliation(s)
- Leyden Fernandez
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alexander Eiler
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | - Alexandra M. Linz
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin–Madison, Madison, WI, United States
| | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, WI, United States
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY. Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica. PLoS One 2020; 15:e0231053. [PMID: 32282803 PMCID: PMC7153904 DOI: 10.1371/journal.pone.0231053] [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: 08/30/2019] [Accepted: 03/15/2020] [Indexed: 11/19/2022] Open
Abstract
Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.
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Affiliation(s)
- Megan L. Dillon
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States of America
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Hamilton, Waikato, New Zealand
| | - Anne D. Jungblut
- Life Sciences Department, Natural History Museum, London, England, United Kingdom
| | - Tyler J. Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Peter T. Doran
- Geology and Geophysics Department, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States of America
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" Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata. Appl Environ Microbiol 2020; 86:AEM.02549-19. [PMID: 32060020 PMCID: PMC7117923 DOI: 10.1128/aem.02549-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/26/2020] [Indexed: 02/03/2023] Open
Abstract
The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host. The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name “Candidatus Desulfobulbus rimicarensis” is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps. IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.
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Hidalgo KJ, Teramoto EH, Soriano AU, Valoni E, Baessa MP, Richnow HH, Vogt C, Chang HK, Oliveira VM. Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135152. [PMID: 31812384 DOI: 10.1016/j.scitotenv.2019.135152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (13C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.
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Affiliation(s)
- K J Hidalgo
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, Campinas, SP. ZIP 13083-862, Brazil.
| | - E H Teramoto
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - A U Soriano
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - E Valoni
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - M P Baessa
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - H H Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - C Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - H K Chang
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - V M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Paulínia, Brazil, Av. Alexandre Cazellato, 999, ZIP 13148-218, Brazil
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Fatehi-Pouladi S, Anderson BC, Wootton B, Wallace SJ, Bissegger S, Rozema L, Weber KP. Influence of Plant Species on Microbial Activity and Denitrifier Population Development in Vegetated Denitrifying Wood-Chip Bioreactors. PLANTS (BASEL, SWITZERLAND) 2020; 9:E289. [PMID: 32110935 PMCID: PMC7154878 DOI: 10.3390/plants9030289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 11/20/2022]
Abstract
The microbial characteristics of four vegetated and one unplanted wood-chip bioreactors treating greenhouse effluent were investigated in a continuous experiment operated for over 2.5 years. The bioreactors were designed to reduce nitrate concentrations via naturally induced microbial denitrification. The vegetation type and reactor depth were both found to be significant factors in defining the mixed microbial activity. However, a consistent correlation between the abundance of the denitrifying communities and reactor depth could not be found across all reactors. The media samples from the unit planted with Typha angustifolia displayed higher microbial activities compared with the other reactors. This plant's root-associated bacteria also demonstrated the greatest copies of the denitrifying genes nirK and nosZ. The most abundant denitrifier communities and those encoding the nosZ gene were found in the unplanted reactor, followed by the T. angustifolia unit. The T. angustifolia reactor demonstrated greater microbial activity and denitrification capacity at the depth of 20 cm, while the greatest denitrification capacity in the unplanted reactor was found at the depth of 60 cm. These findings indicated the importance of the T. angustifolia rhizosphere to support microbial community establishment and growth in the vicinity of the plant's roots, although those populations may eventually develop in an unplanted environment.
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Affiliation(s)
| | - Bruce C. Anderson
- Department of Civil Engineering, Queen’s University, 58 University Ave., Kingston, ON K7L 3N6, Canada
| | - Brent Wootton
- Centre for Advancement of Water and Wastewater Technologies, Fleming College, 200 Albert Street South, Lindsay, ON K9V 5E6, Canada
| | - Sarah J. Wallace
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Station Forces, Kingston, ON K7K 7B4, Canada
| | - Sonja Bissegger
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Station Forces, Kingston, ON K7K 7B4, Canada
| | - Lloyd Rozema
- Aqua Treatment Technologies, 4250 Fly Road, Campden, ON L0R 1G0, Canada
| | - Kela P. Weber
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Station Forces, Kingston, ON K7K 7B4, Canada
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Liu J, Adrian L, Häggblom MM. Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor. Appl Environ Microbiol 2020; 86:e02146-19. [PMID: 31836581 PMCID: PMC7028966 DOI: 10.1128/aem.02146-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/10/2019] [Indexed: 01/31/2023] Open
Abstract
Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites.IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Fachgebiet Geobiotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
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Active sulfur cycling in the terrestrial deep subsurface. ISME JOURNAL 2020; 14:1260-1272. [PMID: 32047278 DOI: 10.1038/s41396-020-0602-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/09/2022]
Abstract
The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.
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From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst. ISME JOURNAL 2020; 14:1125-1140. [PMID: 31996786 DOI: 10.1038/s41396-020-0595-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 11/08/2022]
Abstract
Coupling microbial electrosynthesis to renewable energy sources can provide a promising future technology for carbon dioxide conversion. However, this technology suffers from a limited number of suitable biocatalysts, resulting in a narrow product range. Here, we present the characterization of the first thermoacidophilic electroautotrophic community using chronoamperometric, metagenomic, and 13C-labeling analyses. The cathodic biofilm showed current consumption of up to -80 µA cm-2 over a period of 90 days (-350 mV vs. SHE). Metagenomic analyses identified members of the genera Moorella, Desulfofundulus, Thermodesulfitimonas, Sulfolobus, and Acidianus as potential primary producers of the biofilm, potentially thriving via an interspecies sulfur cycle. Hydrogenases seem to be key for cathodic electron uptake. An isolation campaign led to a pure culture of a Knallgas bacterium from this community. Growth of this organism on cathodes led to increasing reductive currents over time. Transcriptomic analyses revealed a distinct gene expression profile of cells grown at a cathode. Moreover, pressurizable flow cells combined with optical coherence tomography allowed an in situ observation of cathodic biofilm growth. Autotrophic growth was confirmed via isotope analysis. As a natural polyhydroxybutyrate (PHB) producer, this novel species, Kyrpidia spormannii, coupled the production of PHB to CO2 fixation on cathode surfaces.
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Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities. Appl Environ Microbiol 2019; 86:AEM.01993-19. [PMID: 31653790 PMCID: PMC6912079 DOI: 10.1128/aem.01993-19] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment. Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen. IMPORTANCE Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment.
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Effect of Quorum Sensing on the Ability of Desulfovibrio vulgaris To Form Biofilms and To Biocorrode Carbon Steel in Saline Conditions. Appl Environ Microbiol 2019; 86:AEM.01664-19. [PMID: 31628147 DOI: 10.1128/aem.01664-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/13/2019] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are key contributors to microbe-induced corrosion (MIC), which can lead to serious economic and environmental impact. The presence of a biofilm significantly increases the MIC rate. Inhibition of the quorum-sensing (QS) system is a promising alternative approach to prevent biofilm formation in various industrial settings, especially considering the significant ecological impact of conventional chemical-based mitigation strategies. In this study, the effect of the QS stimulation and inhibition on Desulfovibrio vulgaris is described in terms of anaerobic respiration, cell activity, biofilm formation, and biocorrosion of carbon steel. All these traits were repressed when bacteria were in contact with QS inhibitors but enhanced upon exposure to QS signal molecules compared to the control. The difference in the treatments was confirmed by transcriptomic analysis performed at different time points after treatment application. Genes related to lactate and pyruvate metabolism, sulfate reduction, electron transfer, and biofilm formation were downregulated upon QS inhibition. In contrast, QS stimulation led to an upregulation of the above-mentioned genes compared to the control. In summary, these results reveal the impact of QS on the activity of D. vulgaris, paving the way toward the prevention of corrosive SRB biofilm formation via QS inhibition.IMPORTANCE Sulfate-reducing bacteria (SRB) are considered key contributors to biocorrosion, particularly in saline environments. Biocorrosion imposes tremendous economic costs, and common approaches to mitigate this problem involve the use of toxic and hazardous chemicals (e.g., chlorine), which raise health and environmental safety concerns. Quorum-sensing inhibitors (QSIs) can be used as an alternative approach to inhibit biofilm formation and biocorrosion. However, this approach would only be effective if SRB rely on QS for the pathways associated with biocorrosion. These pathways would include biofilm formation, electron transfer, and metabolism. This study demonstrates the role of QS in Desulfovibrio vulgaris on the above-mentioned pathways through both phenotypic measurements and transcriptomic approach. The results of this study suggest that QSIs can be used to mitigate SRB-induced corrosion problems in ecologically sensitive areas.
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Colman DR, Lindsay MR, Amenabar MJ, Boyd ES. The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems. ASTROBIOLOGY 2019; 19:1505-1522. [PMID: 31592688 DOI: 10.1089/ast.2018.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.
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Affiliation(s)
- Daniel R Colman
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| | - Melody R Lindsay
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| | | | - Eric S Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
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76
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Schoelmerich MC, Müller V. Energy-converting hydrogenases: the link between H 2 metabolism and energy conservation. Cell Mol Life Sci 2019; 77:1461-1481. [PMID: 31630229 DOI: 10.1007/s00018-019-03329-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/17/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Abstract
The reversible interconversion of molecular hydrogen and protons is one of the most ancient microbial metabolic reactions and catalyzed by hydrogenases. A widespread yet largely enigmatic group comprises multisubunit [NiFe] hydrogenases, that directly couple H2 metabolism to the electrochemical ion gradient across the membranes of bacteria and of archaea. These complexes are collectively referred to as energy-converting hydrogenases (Ech), as they reversibly transform redox energy into physicochemical energy. Redox energy is typically provided by a low potential electron donor such as reduced ferredoxin to fuel H2 evolution and the establishment of a transmembrane electrochemical ion gradient ([Formula: see text]). The [Formula: see text] is then utilized by an ATP synthase for energy conservation by generating ATP. This review describes the modular structure/function of Ech complexes, focuses on insights into the energy-converting mechanisms, describes the evolutionary context and delves into the implications of relying on an Ech complex as respiratory enzyme for microbial metabolism.
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Affiliation(s)
- Marie Charlotte Schoelmerich
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.,Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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77
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Slobodkin AI, Slobodkina GB. Diversity of Sulfur-Disproportionating Microorganisms. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050138] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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78
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Barton LL, Granat AS, Lee S, Xu H, Ritz NL, Hider R, Lin HC. Bismuth(III) interactions with Desulfovibrio desulfuricans: inhibition of cell energetics and nanocrystal formation of Bi2S3 and Bi0. Biometals 2019; 32:803-811. [DOI: 10.1007/s10534-019-00213-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/29/2019] [Indexed: 02/04/2023]
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79
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Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei AŞ, Ghai R, Sorokin DY, Muyzer G. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biol 2019; 17:69. [PMID: 31438955 PMCID: PMC6704655 DOI: 10.1186/s12915-019-0688-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. RESULTS Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. CONCLUSIONS The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.
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Affiliation(s)
- Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Cherel Balkema
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Rutger van Hall
- Department of Ecosystem & Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Biotechnology, Environmental Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands.
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Abstract
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.
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81
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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82
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Liang J, Huang H, Wang S. Distribution, Evolution, Catalytic Mechanism, and Physiological Functions of the Flavin-Based Electron-Bifurcating NADH-Dependent Reduced Ferredoxin: NADP + Oxidoreductase. Front Microbiol 2019; 10:373. [PMID: 30881354 PMCID: PMC6405883 DOI: 10.3389/fmicb.2019.00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) is an electron-bifurcating enzyme first discovered in the strict anaerobes Clostridium kluyveri and Moorella thermoacetica. In vivo, Nfn catalyzes the endergonic reduction of NADP+ with NADH coupled to the exergonic reduction of NADP+ with reduced ferredoxin. Most Nfn homologs consist of two subunits, although in certain species Nfn homologs are fused. In contrast to other electron-bifurcating enzymes, Nfn possess a simpler structure. Therefore, Nfn becomes a perfect model to determine the mechanism of flavin-based electron bifurcation, which is a novel energy coupling mode distributed among anaerobic bacteria and archaea. The crystal structures of Nfn from Thermotoga maritima and Pyrococcus furiosus are known, and studies have shown that the FAD molecule of the NfnB (b-FAD) is the site of electron bifurcation, and other cofactors, including a [2Fe2S] cluster, two [4Fe4S] clusters, and the FAD molecule on the NfnA subunit, contribute to electron transfer. Further, the short-lived anionic flavin semiquinone (ASQ) state of b-FAD is essential for electron bifurcation. Nfn homologs are widely distributed among microbes, including bacteria, archaea, and probably eukaryotes, most of which are anaerobes despite that certain species are facultative microbes and even aerobes. Moreover, potential evidence shows that lateral gene transfer may occur in the evolution of this enzyme. Nfn homologs present four different structural patterns, including the well-characterized NfnAB and three different kinds of fused Nfn homologs whose detailed properties have not been characterized. These findings indicate that gene fusion/fission and gene rearrangement may contribute to the evolution of this enzyme. Under physiological conditions, Nfn catalyzes the reduction of NADP+ with NADH and reduced ferredoxin, which is then used in certain NADPH-dependent reactions. Deletion of nfn in several microbes causes low growth and redox unbalance and may influence the distribution of fermentation products. It’s also noteworthy that different Nfn homologs perform different functions according to its circumstance. Physiological functions of Nfn indicate that it can be a potential tool in the metabolic engineering of industrial microorganisms, which can regulate the redox potential in vivo.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Haiyan Huang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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83
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Bukhtiyarova PA, Antsiferov DV, Brasseur G, Avakyan MR, Frank YA, Ikkert OP, Pimenov NV, Tuovinen OH, Karnachuk OV. Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins. Anaerobe 2019; 56:66-77. [PMID: 30776428 DOI: 10.1016/j.anaerobe.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/27/2019] [Accepted: 02/14/2019] [Indexed: 01/19/2023]
Abstract
Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with 35SO42- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H2S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu2+(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.
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Affiliation(s)
- Polina A Bukhtiyarova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, Mediterranean Institute of Microbiology, Marseille, France
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia.
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84
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Kraiselburd I, Brüls T, Heilmann G, Kaschani F, Kaiser M, Meckenstock RU. Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation. Environ Microbiol 2019; 21:1267-1286. [PMID: 30680888 PMCID: PMC6849830 DOI: 10.1111/1462-2920.14527] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As oxygen is rapidly depleted in water‐saturated PAH‐contaminated sites, anaerobic microorganisms are crucial for their consumption. Here, we report the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of Deltaproteobacteria and genome‐resolved metagenomics led to the reconstruction of its genome along with a handful of genomes from lower abundance bacteria. Proteogenomic analyses confirmed metabolic capabilities for dissimilatory sulfate reduction and indicated the presence of the Embden‐Meyerhof‐Parnas pathway, a complete tricarboxylic acid cycle as well as a complete Wood‐Ljungdahl pathway. Genes encoding enzymes putatively involved in the degradation of phenanthrene were identified. This includes two gene clusters encoding a multisubunit carboxylase complex likely involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses, and provide the first insights into the metabolic pathway responsible for the anaerobic degradation of three‐ringed PAHs.
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Affiliation(s)
- Ivana Kraiselburd
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope, Evry, France.,CNRS-UMR8030, Université Paris-Saclay, Evry, France
| | - Geronimo Heilmann
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Rainer U Meckenstock
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
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85
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Sivakumar K, Scarascia G, Zaouri N, Wang T, Kaksonen AH, Hong PY. Salinity-Mediated Increment in Sulfate Reduction, Biofilm Formation, and Quorum Sensing: A Potential Connection Between Quorum Sensing and Sulfate Reduction? Front Microbiol 2019; 10:188. [PMID: 30787924 PMCID: PMC6373464 DOI: 10.3389/fmicb.2019.00188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/23/2019] [Indexed: 11/30/2022] Open
Abstract
Biocorrosion in marine environment is often associated with biofilms of sulfate reducing bacteria (SRB). However, not much information is available on the mechanism underlying exacerbated rates of SRB-mediated biocorrosion under saline conditions. Using Desulfovibrio (D.) vulgaris and Desulfobacterium (Db.) corrodens as model SRBs, the enhancement effects of salinity on sulfate reduction, N-acyl homoserine lactone (AHL) production and biofilm formation by SRBs were demonstrated. Under saline conditions, D. vulgaris and Db. corrodens exhibited significantly higher specific sulfate reduction and specific AHL production rates as well as elevated rates of biofilm formation compared to freshwater medium. Salinity-induced enhancement traits were also confirmed at transcript level through reverse transcription quantitative polymerase chain reaction (RT-qPCR) approach, which showed salinity-influenced increase in the expression of genes associated with carbon metabolism, sulfate reduction, biofilm formation and histidine kinase signal transduction. In addition, by deploying quorum sensing (QS) inhibitors, a potential connection between sulfate reduction and AHL production under saline conditions was demonstrated, which is most significant during early stages of sulfate metabolism. The findings collectively revealed the interconnection between QS, sulfate reduction and biofilm formation among SRBs, and implied the potential of deploying quorum quenching approaches to control SRB-based biocorrosion in saline conditions.
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Affiliation(s)
- Krishnakumar Sivakumar
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Giantommaso Scarascia
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anna H Kaksonen
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Floreat, WA, Australia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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86
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Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE. A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environ Microbiol 2019; 21:784-799. [PMID: 30536693 DOI: 10.1111/1462-2920.14500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 11/30/2022]
Abstract
Bacterial genes for molybdenum-containing and tungsten-containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA-binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate-specific transporting systems as well as molybdo/tungsto-enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten-containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten-specific ABC-type transporter tupABC genes under tungsten-replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.
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Affiliation(s)
- L Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - M E Garber
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA
| | - G M Zane
- Biochemistry and Molecular Microbiology & Immunology Department, University of Missouri, Columbia, MO, 65211, USA
| | - M N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - I Dubchak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J D Wall
- Biochemistry and Molecular Microbiology & Immunology Department, University of Missouri, Columbia, MO, 65211, USA
| | - P S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Energy, Knowledge Base, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - A Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - A E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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87
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Significance of MccR, MccC, MccD, MccL and 8-methylmenaquinone in sulfite respiration of Wolinella succinogenes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:12-21. [DOI: 10.1016/j.bbabio.2018.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/26/2018] [Accepted: 10/13/2018] [Indexed: 11/17/2022]
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88
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Duarte AG, Catarino T, White GF, Lousa D, Neukirchen S, Soares CM, Sousa FL, Clarke TA, Pereira IAC. An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation. Nat Commun 2018; 9:5448. [PMID: 30575735 PMCID: PMC6303296 DOI: 10.1038/s41467-018-07839-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023] Open
Abstract
The bioenergetics of anaerobic metabolism frequently relies on redox loops performed by membrane complexes with substrate- and quinone-binding sites on opposite sides of the membrane. However, in sulfate respiration (a key process in the biogeochemical sulfur cycle), the substrate- and quinone-binding sites of the QrcABCD complex are periplasmic, and their role in energy conservation has not been elucidated. Here we show that the QrcABCD complex of Desulfovibrio vulgaris is electrogenic, as protons and electrons required for quinone reduction are extracted from opposite sides of the membrane, with a H+/e− ratio of 1. Although the complex does not act as a H+-pump, QrcD may include a conserved proton channel leading from the N-side to the P-side menaquinone pocket. Our work provides evidence of how energy is conserved during dissimilatory sulfate reduction, and suggests mechanisms behind the functions of related bacterial respiratory complexes in other bioenergetic contexts. The bacterial complex QrcABCD plays a key role in the bioenergetics of sulfate respiration. Here, Duarte et al. show that this complex is electrogenic, with protons and electrons required for quinone reduction being extracted from opposite sides of the membrane.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.,Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Gaye F White
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Sinje Neukirchen
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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89
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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90
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Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, Scheller S, Tavormina PL, Hettich RL, Mukhopadhyay B, Orphan VJ. Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. Front Microbiol 2018; 9:2917. [PMID: 30559729 PMCID: PMC6286981 DOI: 10.3389/fmicb.2018.02917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/13/2018] [Indexed: 01/17/2023] Open
Abstract
Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.
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Affiliation(s)
- Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States.,Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA, United States
| | - Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Silvan Scheller
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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91
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The physiology and biotechnology of dark fermentative biohydrogen production. Biotechnol Adv 2018; 36:2165-2186. [DOI: 10.1016/j.biotechadv.2018.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 02/02/2023]
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92
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Zacarias S, Vélez M, Pita M, De Lacey AL, Matias PM, Pereira IAC. Characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough. Methods Enzymol 2018; 613:169-201. [PMID: 30509465 DOI: 10.1016/bs.mie.2018.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The [NiFeSe] hydrogenases are a subgroup of the well-characterized family of [NiFe] hydrogenases, in which a selenocysteine is a ligand to the nickel atom in the binuclear NiFe active site instead of cysteine. These enzymes display very interesting catalytic properties for biological hydrogen production and bioelectrochemical applications: high H2 production activity, bias for H2 evolution, low H2 inhibition, and some degree of O2 tolerance. Here we describe the methodologies employed to study the [NiFeSe] hydrogenase isolated from the sulfate-reducing bacteria D. vulgaris Hildenborough and the creation of a homologous expression system for production of variant forms of the enzyme.
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Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | - Marcos Pita
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | | | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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93
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Florentino AP, Pereira IAC, Boeren S, van den Born M, Stams AJM, Sánchez-Andrea I. Insight into the sulfur metabolism of Desulfurella amilsii by differential proteomics. Environ Microbiol 2018; 21:209-225. [PMID: 30307104 PMCID: PMC6378623 DOI: 10.1111/1462-2920.14442] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 08/28/2018] [Accepted: 10/05/2018] [Indexed: 11/30/2022]
Abstract
Many questions regarding proteins involved in microbial sulfur metabolism remain unsolved. For sulfur respiration at low pH, the terminal electron acceptor is still unclear. Desulfurella amilsii is a sulfur-reducing bacterium that respires elemental sulfur (S0 ) or thiosulfate, and grows by S0 disproportionation. Due to its versatility, comparative studies on D. amilsii may shed light on microbial sulfur metabolism. Requirement of physical contact between cells and S0 was analyzed. Sulfide production decreased by around 50% when S0 was trapped in dialysis membranes, suggesting that contact between cells and S0 is beneficial, but not strictly needed. Proteome analysis was performed under the aforementioned conditions. A Mo-oxidoreductase suggested from genome analysis to act as sulfur reductase was not detected in any growth condition. Thiosulfate and sulfite reductases showed increased abundance in thiosulfate-reducing cultures, while rhodanese-like sulfurtransferases were highly abundant in all conditions. DsrE and DsrL were abundantly detected during thiosulfate reduction, suggesting a modified mechanism of sulfite reduction. Proteogenomics suggest a different disproportionation pathway from what has been reported. This work points to an important role of rhodaneses in sulfur processes and these proteins should be considered in searches for sulfur metabolism in broader fields like meta-omics.
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Affiliation(s)
- Anna P Florentino
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Inês A C Pereira
- Instituto de Tecnologia Quimica e Biologica António Xavier, Universidade Nova de Lisboa, Av. da Republica-EAN, 2780-157, Oeiras, Portugal
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Michael van den Born
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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94
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Lee JZ, Everroad RC, Karaoz U, Detweiler AM, Pett-Ridge J, Weber PK, Prufert-Bebout L, Bebout BM. Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PLoS One 2018; 13:e0202792. [PMID: 30204767 PMCID: PMC6133358 DOI: 10.1371/journal.pone.0202792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.
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Affiliation(s)
- Jackson Z. Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
- * E-mail:
| | - R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Angela M. Detweiler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Leslie Prufert-Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Brad M. Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
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95
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Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, Hettich RL, Balmer L, Frutschi M, Sommer G, Bernier-Latmani R. Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. Front Microbiol 2018; 9:2129. [PMID: 30245678 PMCID: PMC6137086 DOI: 10.3389/fmicb.2018.02129] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO2 came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface.
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Affiliation(s)
- Emma Bell
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Johannes Alneberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Louise Balmer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Manon Frutschi
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Guillaume Sommer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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96
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Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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97
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Li X, Lan SM, Zhu ZP, Zhang C, Zeng GM, Liu YG, Cao WC, Song B, Yang H, Wang SF, Wu SH. The bioenergetics mechanisms and applications of sulfate-reducing bacteria in remediation of pollutants in drainage: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 158:162-170. [PMID: 29684746 DOI: 10.1016/j.ecoenv.2018.04.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/30/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
Sulfate-reducing bacteria (SRB), a group of anaerobic prokaryotes, can use sulfur species as a terminal electron acceptor for the oxidation of organic compounds. They not only have significant ecological functions, but also play an important role in bioremediation of contaminated sites. Although numerous studies on metabolism and applications of SRB have been conducted, they still remain incompletely understood and even controversial. Fully understanding the metabolism of SRB paves the way for allowing the microorganisms to provide more beneficial services in bioremediation. Here we review progress in bioenergetics mechanisms and application of SRB including: (1) electron acceptors and donors for SRB; (2) pathway for sulfate reduction; (3) electron transfer in sulfate reduction; (4) application of SRB for economical and concomitant treatment of heavy metal, organic contaminants and sulfates. Moreover, current knowledge gaps and further research needs are identified.
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Affiliation(s)
- Xin Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Shi-Ming Lan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhong-Ping Zhu
- School of Minerals processing and Bioengineering, Central South University, No. 932 South Lushan road, Changsha, Hunan 410083, PR China
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guang-Ming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yun-Guo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wei-Cheng Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Hong Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Sheng-Fan Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Shao-Hua Wu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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98
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Müller V, Chowdhury NP, Basen M. Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism. Annu Rev Microbiol 2018; 72:331-353. [PMID: 29924687 DOI: 10.1146/annurev-micro-090816-093440] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A decade ago, a novel mechanism to drive thermodynamically unfavorable redox reactions was discovered that is used in prokaryotes to drive endergonic electron transfer reactions by a direct coupling to an exergonic redox reaction in one soluble enzyme complex. This process is referred to as flavin-based electron bifurcation, or FBEB. An important function of FBEB is that it allows the generation of reduced low-potential ferredoxin (Fdred) from comparably high-potential electron donors such as NADH or molecular hydrogen (H2). Fdred is then the electron donor for anaerobic respiratory chains leading to the synthesis of ATP. In many metabolic scenarios, Fd is reduced by metabolic oxidoreductases and Fdred then drives endergonic metabolic reactions such as H2 production by the reverse, electron confurcation. FBEB is energetically more economical than ATP hydrolysis or reverse electron transport as a driving force for endergonic redox reactions; thus, it does "save" cellular ATP. It is essential for autotrophic growth at the origin of life and also allows for heterotrophic growth on certain low-energy substrates.
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Affiliation(s)
- Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Mirko Basen
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
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99
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Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. THE ISME JOURNAL 2018; 12:1715-1728. [PMID: 29467397 PMCID: PMC6018805 DOI: 10.1038/s41396-018-0078-0] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 11/16/2022]
Abstract
A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, Berkeley, CA, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Sean P Jungbluth
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adi Lavy
- Department of Earth and Planetary Science, Berkeley, CA, USA
| | - Lesley A Warren
- Department of Civil Engineering, University of Toronto, Toronto, ON, Canada
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Brian C Thomas
- Department of Earth and Planetary Science, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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100
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Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A. Peatland Acidobacteria with a dissimilatory sulfur metabolism. THE ISME JOURNAL 2018; 12:1729-1742. [PMID: 29476143 PMCID: PMC6018796 DOI: 10.1038/s41396-018-0077-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
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Affiliation(s)
- Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | | | - Martin Huemer
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ulrich Stingl
- Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, UF/IFAS, University of Florida, Davie, FL, USA
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cecilia Wentrup
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Leibniz Institute DSMZ, Braunschweig, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
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