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Qiu YY, Zou J, Xia J, Li H, Zhen Y, Yang Y, Guo J, Zhang L, Qiu R, Jiang F. Adaptability of sulfur-disproportionating bacteria for mine water remediation under the pressures of heavy metal ions and high sulfate content. WATER RESEARCH 2024; 249:120898. [PMID: 38086206 DOI: 10.1016/j.watres.2023.120898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 01/03/2024]
Abstract
Biological sulfide production processes mediated by sulfate/sulfur reduction have gained attention for metal removal from industrial wastewater (e.g., mine water (MW) and metallurgical wastewater) via forming insoluble metal sulfides. However, these processes often necessitate the addition of external organic compounds as electron donors, which poses a constraint on the broad application of this technology. A recent proof of concept study reported that microbial sulfur disproportionation (SD) produced sulfide with no demand for organics, which could achieve more cost-benefit MW treatment against the above-mentioned processes. However, the resistance of SD bioprocess to different metals and high sulfate content in MW remains mysterious, which may substantially affect the practical applicability of such process. In this study, the sulfur-disproportionating bacteria (SDB)-dominated consortium was enriched from a previously established SD-driven bioreactor, in which Dissulfurimicrobium sp. with a relative abundance of 39.9 % was the predominated SDB. When exposed to the real pretreated acidic MW after the pretreatment process of pH amelioration, the sulfur-disproportionating activity remained active, and metals were effectively removed from the MW. Metal tolerance assays further demonstrated that the consortium had a good tolerance to different metal ions (i.e., Pb2+, Cu2+, Ni2+, Mn2+, Zn2+), especially for Mn2+ with a concentration of approximately 20 mg/L. It suggested the robustness of Dissulfurimicrobium sp. likely due to the presence of genes encoding for the enzymes associated with metal(loid) resistance/uptake. Additionally, although high sulfate content resulted in a slight inhibition on the sulfur-disproportionating activity, the consortium still achieved sulfide production rates of 27.3 mg S/g VSS-d on average under an environmentally relevant sulfate level (i.e., 1100 mg S/L), which is comparable to those reported in sulfate reduction. Taken together, these findings imply that SDB could ensure sustainable MW treatment in a more cost-effective and organic-free way.
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Affiliation(s)
- Yan-Ying Qiu
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jiahui Zou
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Juntao Xia
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Hao Li
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yuming Zhen
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yanduo Yang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jiahua Guo
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Liang Zhang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Rongliang Qiu
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, School of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Feng Jiang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial International Joint Research Center on Urban Water Management and Treatment, Sun Yat-sen University, Guangzhou, China.
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2
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Zou J, Qiu YY, Li H, Jiang F. Sulfur disproportionation realizes an organic-free sulfidogenic process for sustainable treatment of acid mine drainage. WATER RESEARCH 2023; 232:119647. [PMID: 36738555 DOI: 10.1016/j.watres.2023.119647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Biological sulfidogenic processes (BSPs) have been considered effective biotechnologies for the treatment of organic-deficit acid mine drainage (AMD) and heavy metal recovery. However, high-rate sulfide production relies on the continuous addition of exogenous organic substrates as electron donors to facilitate dissimilatory sulfate reduction, which substantially increases the operational cost and CO2 emission and also limits the wide application of BSPs in AMD treatment. In this study, we proposed a novel chemoautotrophic elemental sulfur disproportionation (SD) process as an alternative to conventional BSPs for treating AMD, in which sulfur-disproportionating bacteria (SDB) disproportionates sulfur to sulfide and sulfate without organic substrate supplementation. During the 393-day lab-scale test, we observed that the sulfur-disproportionating reactor (SDR) achieved a stable high-rate sulfide production, with a maximal rate of 21.10 mg S/L-h at an organic-substrate-free condition. This high rate of sulfide production suggested that the SD process could provide sufficient sulfide to precipitate metal ions from AMD. Thermodynamics analysis and batch tests further revealed that alkalinity rather than sulfate was the critical factor influencing the SD process, suggesting that the abundant sulfate present in AMD would not inhibit the SD process. The critical condition of SD in the SDR was therefore determined. Microbial community analysis showed that Dissulfurimicrobium sp. was the dominant SDB during the long-term operation regardless of dynamic sulfate and/or alkalinity concentrations, which provides evidence that SDB can be employed for sustainable and high-rate sulfide production for engineering purposes. A multi-stage AMD treatment system equipped with a SDR removed over 99% of the influent metals (i.e., Fe, Al, Zn, Cu, Pb) from AMD except for Mn. This study demonstrated that the novel SD process is a green and promising biotechnology for the sustainable treatment of organic-deficient metal-laden wastewater, such as AMD.
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Affiliation(s)
- Jiahui Zou
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Yan-Ying Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Hao Li
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Feng Jiang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial International Joint Research Center on Urban Water Management and Treatment, Sun Yat-sen University, Guangzhou, China.
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3
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Li F, Hou W, Wang S, Zhang Y, He Q, Zhang W, Dong H. Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation. ENVIRONMENTAL MICROBIOME 2023; 18:22. [PMID: 36949539 PMCID: PMC10035157 DOI: 10.1186/s40793-023-00481-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Diverse mineralogical compositions occur in hot spring sediments, but the impact of minerals on the diversity and structure of microbial communities remains poorly elucidated. In this study, different mineral particles with various chemistries (i.e., hematite, biotite, K-feldspar, quartz, muscovite, aragonite, serpentine, olivine, barite, apatite, and pyrite) were incubated for ten days in two Tengchong hot springs, one alkaline (pH ~ 8.34) with a high temperature (~ 82.8 °C) (Gumingquan, short as GMQ) and one acidic (pH ~ 3.63) with a relatively low temperature (~ 43.3 °C) (Wenguangting, short as WGT), to determine the impacts of minerals on the microbial communities taxonomic and functional diversities. Results showed that the mineral-associated bacterial taxa differed from those of the bulk sediment samples in the two hot springs. The relative abundance of Proteobacteria, Euryarchaeota, and Acidobacteria increased in all minerals, indicating that these microorganisms are apt to colonize on solid surfaces. The α-diversity indices of the microbial communities on the mineral surfaces in the WGT were higher than those from the bulk sediment samples (p < 0.05), which may be caused by the stochastically adhering process on the mineral surface during 10-day incubation, different from the microbial community in sediment which has experienced long-term environmental and ecological screening. Chemoheterotrophy increased with minerals incubation, which was high in most cultured minerals (the relative contents were 5.8 - 21.4%). Most notably, the sulfate respiration bacteria (mainly related to Desulfobulbaceae and Syntrophaceae) associated with aragonite in the acidic hot spring significantly differed from other minerals, possibly due to the pH buffering effect of aragonite providing more favorable conditions for their survival and proliferation. By comparison, aragonite cultured in the alkaline hot spring highly enriched denitrifying bacteria and may have promoted the nitrogen cycle within the system. Collectively, we speculated that diverse microbes stochastically adhered on the surface of minerals in the water flows, and the physicochemical properties of minerals drove the enrichment of certain microbial communities and functional groups during the short-term incubation. Taken together, these findings thereby provide novel insights into mechanisms of community assembly and element cycling in the terrestrial hydrothermal system associated with hot springs.
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Affiliation(s)
- Fangru Li
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Weiguo Hou
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Yidi Zhang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Wenhui Zhang
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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Kambara H, Dinh HTT, Matsushita S, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. New microbial electrosynthesis system for methane production from carbon dioxide coupled with oxidation of sulfide to sulfate. J Environ Sci (China) 2023; 125:786-797. [PMID: 36375960 DOI: 10.1016/j.jes.2022.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/16/2023]
Abstract
Microbial electrosynthesis system (MES) is a promising method that can use carbon dioxide, which is a greenhouse gas, to produce methane which acts as an energy source, without using organic substances. However, this bioelectrical reduction reaction can proceed at a certain high applied voltage when coupled with water oxidation in the anode coated with metallic catalyst. When coupled with the oxidation of HS- to SO42-, methane production is thermodynamically more feasible, thus implying its production at a considerably lower applied voltage. In this study, we demonstrated the possibility of electrotrophic methane production coupled with HS- oxidation in a cost-effective bioanode chamber in the MES without organic substrates at a low applied voltage of 0.2 V. In addition, microbial community analyses of biomass enriched in the bioanode and biocathode were used to reveal the most probable pathway for methane production from HS- oxidation. In the bioanode, electroautotrophic SO42- production accompanied with electron donation to the electrode is performed mainly by the following two steps: first, incomplete sulfide oxidation to sulfur cycle intermediates (SCI) is performed; then the produced SCI are disproportionated to HS- and SO42-. In the biocathode, methane is produced mainly via H2 and acetate by electron-accepting syntrophic bacteria, homoacetogens, and acetoclastic archaea. Here, a new eco-friendly MES with biological H2S removal is established.
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Affiliation(s)
- Hiromi Kambara
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Ha T T Dinh
- Faculty of Environment, Ho Chi Minh City University of Natural Resources and Environment, 236 Le Van Sy, 1 Ward, Tan Binh District, Ho Chi Minh City, Vietnam
| | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute, 6869, Hara, Hachihonmatsu, Higashihiroshima, Hiroshima 739-0151, Japan
| | - Yoshiteru Aoi
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan.
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5
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Zhang D, Ke T, Xiu W, Ren C, Chen G, Lloyd JR, Bassil NM, Richards LA, Polya DA, Wang G, Guo H. Quantifying sulfidization and non-sulfidization in long-term in-situ microbial colonized As(V)-ferrihydrite coated sand columns: Insights into As mobility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160066. [PMID: 36356776 DOI: 10.1016/j.scitotenv.2022.160066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Sulfide-induced reduction (sulfidization) of arsenic (As)-bearing Fe(III) (oxyhydro)oxides may lead to As mobilization in aquifer systems. However, little is known about the relative contributions of sulfidization and non-sulfidization of Fe(III) (oxyhydro)oxides reduction to As mobilization. To address this issue, high As groundwater with low sulfide (LS) and high sulfide (HS) concentrations were pumped through As(V)-bearing ferrihydrite-coated sand columns (LS-column and HS-column, respectively) being settled within wells in the western Hetao Basin, China. Sulfidization of As(V)-bearing ferrihydrite was evidenced by the increase in dissolved Fe(II) and the presence of solid Fe(II) and elemental sulfur (S0) in both the columns. A conceptual model was built using accumulated S0 and Fe(II) produced in the columns to calculate the proportions of sulfidization-induced Fe(III) (oxyhydro)oxide reduction and non-sulfidization-induced Fe(III) (oxyhydro)oxide reduction. Fe(III) reduction via sulfidization occurred preferentially in the inlet ends (LS-column, 31 %; HS-column, 86 %), while Fe(III) reduction via non-sulfidization processes predominated in the outlet ends (LS-column, 96 %; HS-column, 86 %), and was attributed to the metabolism of genera associated with Fe(III) reduction (including Shewanella, Ferribacterium, and Desulfuromonas). Arsenic was mobilized in the columns via sulfidization and non-sulfidization processes. More As was released from the solid of the HS-column than that of the LS-column due to the higher intensity of sulfidization in the presence of higher concentrations of dissolved S(-II). Overall, this study highlights the sulfidization of As-bearing Fe(III) (oxyhydro)oxides as an important As-mobilizing pathway in complex As-Fe-S bio-hydrogeochemical networks.
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Affiliation(s)
- Di Zhang
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Tiantian Ke
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China; Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom.
| | - Cui Ren
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Guangyu Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Naji M Bassil
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Laura A Richards
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - David A Polya
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology and MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China.
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Hashimoto Y, Shimamura S, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Physiological and comparative proteomic characterization of Desulfolithobacter dissulfuricans gen. nov., sp. nov., a novel mesophilic, sulfur-disproportionating chemolithoautotroph from a deep-sea hydrothermal vent. Front Microbiol 2022; 13:1042116. [PMID: 36532468 PMCID: PMC9751629 DOI: 10.3389/fmicb.2022.1042116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
In deep-sea hydrothermal environments, inorganic sulfur compounds are important energy substrates for sulfur-oxidizing, -reducing, and -disproportionating microorganisms. Among these, sulfur-disproportionating bacteria have been poorly understood in terms of ecophysiology and phylogenetic diversity. Here, we isolated and characterized a novel mesophilic, strictly chemolithoautotrophic, diazotrophic sulfur-disproportionating bacterium, designated strain GF1T, from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. Strain GF1T disproportionated elemental sulfur, thiosulfate, and tetrathionate in the presence of ferrihydrite. The isolate also grew by respiratory hydrogen oxidation coupled to sulfate reduction. Phylogenetic and physiological analyses support that strain GF1T represents the type strain of a new genus and species in the family Desulfobulbaceae, for which the name Desulfolithobacter dissulfuricans gen. nov. sp. nov. is proposed. Proteomic analysis revealed that proteins related to tetrathionate reductase were specifically and abundantly produced when grown via thiosulfate disproportionation. In addition, several proteins possibly involved in thiosulfate disproportionation, including those encoded by the YTD gene cluster, were also found. The overall findings pointed to a possible diversity of sulfur-disproportionating bacteria in hydrothermal systems and provided a refined picture of microbial sulfur disproportionation.
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Affiliation(s)
- Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Akihiro Tame
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Department of Marine and Earth Sciences, Marine Works Japan Ltd., Yokosuka, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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Alain K, Aronson HS, Allioux M, Yvenou S, Amend JP. Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents. Environ Microbiol 2022; 24:2210-2219. [PMID: 35315563 DOI: 10.1111/1462-2920.15975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/02/2022] [Accepted: 03/12/2022] [Indexed: 11/28/2022]
Abstract
Sulfur is abundant in different oxidation states in hydrothermal ecosystems, where it plays a central role in microbial energy production. The contribution of microbially catalyzed disproportionation of elemental sulfur (S0 ) to the energy fluxes of this ecosystem is unknown. Indeed, within the current knowledge it is impossible to study this process in a global way due to the lack of specific genetic markers and because of the difficulties in unraveling the isotopic signals from the different reactions of the sulfur cycle. In this context, calculations of the Gibbs energy (∆Gr) of sulfur disproportionation can identify whether this process is thermodynamically favorable and provides sufficient energy yields for growth at the temperatures, pressures, and chemical compositions found in the various niches of the hydrothermal ecosystem. Herein, free energy yield calculations were performed using internally consistent thermodynamic properties and geochemical data from four different hydrothermal systems. These calculations showed that S0 -disproportionation is sufficiently exergonic to allow growth in most niches of the hydrothermal ecosystems, regardless of the geological and geochemical context, and depth; it is most favorable at elevated temperatures and alkaline pH, at low sulfide and sulfate concentrations, and in the presence of sulfide-chelating minerals, which are common in these environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Karine Alain
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
| | - Heidi S Aronson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089
| | - Maxime Allioux
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
| | - Stéven Yvenou
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, 90089
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism. Microorganisms 2021; 10:microorganisms10010060. [PMID: 35056509 PMCID: PMC8780430 DOI: 10.3390/microorganisms10010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/22/2021] [Accepted: 12/25/2021] [Indexed: 12/12/2022] Open
Abstract
The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S0-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO2 assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68T is conserved in the genomes of a large panel of other S0-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S0 is poorly soluble and unable to cross the cytoplasmic membrane in this form.
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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11
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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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12
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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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13
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Wilkins LGE, Ettinger CL, Jospin G, Eisen JA. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Sci Rep 2019; 9:3059. [PMID: 30816235 PMCID: PMC6395817 DOI: 10.1038/s41598-019-39576-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.
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Affiliation(s)
- Laetitia G E Wilkins
- Department of Environmental Sciences, Policy & Management, University of California, Berkeley, CA, 94720, USA. .,Genome Center, University of California, Davis, CA, 95616, USA.
| | | | | | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, 95616, USA.,Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.,Department of Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA
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14
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Gureeva MV, Belousova EV, Dubinina GA, Novikov AA, Kopitsyn DS, Grabovich MY. Thioflexithrix psekupsensis gen. nov., sp. nov., a filamentous gliding sulfur bacterium from the family Beggiatoaceae. Int J Syst Evol Microbiol 2019; 69:798-804. [PMID: 30657444 DOI: 10.1099/ijsem.0.003240] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A sulfur-oxidizing, filamentous, gliding micro-organism, strain D3T, was isolated from a sulfidic spring in Goryachy Klyuch, Krasnodar, Russia. The cell walls were Gram-negative. The new isolate was a microaerophilic facultative anaerobe and an obligate chemolithoautotroph. The pH range for growth was pH 6.8-7.6, with an optimum at pH 7.2. The temperature range for growth was 10-46 °C, with an optimum at 32 °C. The G+C content of DNA was 42.1 mol%. Phylogenetic analysis of the 16S rRNA gene showed that strain D3T belongs to the family Beggiatoaceae, order Thiotrichales and was distantly related to the genera of the family Beggiatoaceae(86-88 % sequence similarity). The major respiratory quinone was ubiquinone-6. Major fatty acids were C18:1 ω7 (37.6 %), C16 : 0 (34.7 %) and C16: 1 ω7 (27.7 %). On the basis of its physiological properties and the results of phylogenetic analysis, strain D3T is considered to represent a novel species of a new genus, for which the name Thioflexithrix psekupsensis gen. nov., sp. nov. is proposed. The type strain is D3T (=KCTC 62399=UNIQEM U981).
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Affiliation(s)
- M V Gureeva
- 1Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
| | - E V Belousova
- 1Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
| | - G A Dubinina
- 2Federal State Institution 'Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences', Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - A A Novikov
- 3Gubkin University, 65/1 Leninsky Prospekt, Moscow 119991, Russia
| | - D S Kopitsyn
- 3Gubkin University, 65/1 Leninsky Prospekt, Moscow 119991, Russia
| | - M Y Grabovich
- 1Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
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15
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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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16
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Frolova AA, Slobodkina GB, Baslerov RV, Novikov AA, Bonch-Osmolovskaya EA, Slobodkin AI. Thermosulfurimonas marina sp. nov., an Autotrophic Sulfur-Disproportionating and Nitrate-Reducing Bacterium Isolated from a Shallow-Sea Hydrothermal Vent. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Slobodkina GB, Reysenbach AL, Kolganova TV, Novikov AA, Bonch-Osmolovskaya EA, Slobodkin AI. Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a thermophilic, chemolithoautotrophic bacterium capable of respiratory ammonification of nitrate with elemental sulfur. Int J Syst Evol Microbiol 2017; 67:3474-3479. [DOI: 10.1099/ijsem.0.002142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Galina B. Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Anna-Louise Reysenbach
- Department of Biology and Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA
| | - Tatyana V. Kolganova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | | | - Elizaveta A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Alexander I. Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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18
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Merkel AY, Pimenov NV, Rusanov II, Slobodkin AI, Slobodkina GB, Tarnovetckii IY, Frolov EN, Dubin AV, Perevalova AA, Bonch-Osmolovskaya EA. Microbial diversity and autotrophic activity in Kamchatka hot springs. Extremophiles 2016; 21:307-317. [DOI: 10.1007/s00792-016-0903-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/27/2016] [Indexed: 12/26/2022]
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19
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Mardanov AV, Beletsky AV, Kadnikov VV, Slobodkin AI, Ravin NV. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria. Front Microbiol 2016; 7:950. [PMID: 27379079 PMCID: PMC4911364 DOI: 10.3389/fmicb.2016.00950] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022] Open
Abstract
Thermosulfurimonas dismutans S95T, isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5′-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood–Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents.
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Affiliation(s)
- Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexander I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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20
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Slobodkina GB, Kolganova TV, Kopitsyn DS, Viryasov MB, Bonch-Osmolovskaya EA, Slobodkin AI. Dissulfurirhabdus thermomarina gen. nov., sp. nov., a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent. Int J Syst Evol Microbiol 2016; 66:2515-2519. [PMID: 27082267 DOI: 10.1099/ijsem.0.001083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain SH388T, was isolated from a shallow, submarine hydrothermal vent (Kuril Islands, Russia). Cells of strain SH388T were Gram-stain-negative short rods, 0.2-0.4 µm in diameter and 1.0-2.5 µm in length, and motile with flagella. The temperature range for growth was 25-58 °C (optimum 50 °C), and the pH range for growth was pH 5.0-7.0 (optimum pH 6.0-6.5). Growth of strain SH388T was observed in the presence of NaCl concentrations ranging from 0.5 to 4.0 % (w/v) (optimum 2.0-2.5 %). The strain grew chemolithoautotrophically with molecular hydrogen as electron donor, sodium sulfite as electron acceptor and bicarbonate/CO2 as a carbon source. It was also able to grow by disproportionation of sulfite and elemental sulfur but not thiosulfate. Sulfate, Fe(III) and nitrate were not used as electron acceptors either with H2 or organic electron donors. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the class Deltaproteobacteria and was most closely related to Dissulfuribacter thermophilus and Dissulfurimicrobium hydrothermale (91.6 % and 90.4 % sequence similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain SH388T is considered to represent a novel species of a new genus, for which the name Dissulfurirhabdus thermomarina gen. nov., sp. nov. is proposed. The type strain of the species is SH388T (=DSM 100025T=VKM B-2960T). It is the first thermophilic disproportionator of sulfur compounds isolated from a shallow-sea environment.
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Affiliation(s)
- Galina B Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33, bld. 2, 119071 Moscow, Russia
| | - Tatyana V Kolganova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy 33, bld. 2, 119071 Moscow, Russia
| | - Dmitry S Kopitsyn
- Gubkin Russian State University of Oil and Gas, Leninsskiy Prospect 65, 117485, Moscow, Russia
| | - Mikhail B Viryasov
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1, 119899 Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33, bld. 2, 119071 Moscow, Russia
| | - Alexander I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33, bld. 2, 119071 Moscow, Russia
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