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Wang XW, Tan X, Dang CC, Lu Y, Xie GJ, Liu BF. Thermophilic microorganisms involved in the nitrogen cycle in thermal environments: Advances and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165259. [PMID: 37400035 DOI: 10.1016/j.scitotenv.2023.165259] [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: 12/04/2022] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Thermophilic microorganisms mediated significant element cycles and material conversion in the early Earth as well as mediating current thermal environments. Over the past few years, versatile microbial communities that drive the nitrogen cycle have been identified in thermal environments. Understanding the microbial-mediated nitrogen cycling processes in these thermal environments has important implications for the cultivation and application of thermal environment microorganisms as well as for exploring the global nitrogen cycle. This work provides a comprehensive review of different thermophilic nitrogen-cycling microorganisms and processes, which are described in detail according to several categories, including nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and dissimilatory nitrate reduction to ammonium. In particular, we assess the environmental significance and potential applications of thermophilic nitrogen-cycling microorganisms, and highlight knowledge gaps and future research opportunities.
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Affiliation(s)
- Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Gheibzadeh MS, Manyumwa CV, Tastan Bishop Ö, Shahbani Zahiri H, Parkkila S, Zolfaghari Emameh R. Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems. BIOLOGY 2023; 12:770. [PMID: 37372055 DOI: 10.3390/biology12060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023]
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.
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Affiliation(s)
- Mohammad Sadegh Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
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Muto H, Miyazaki J, Sawayama S, Takai K, Nakagawa S. A Simple and Effective Method for Solid Medium Cultivation of Strictly Hydrogen- and Sulfur-oxidizing Chemolithoautotrophs Predominant in Deep-sea Hydrothermal Fields. Microbes Environ 2023; 38:ME23072. [PMID: 38104970 PMCID: PMC10728628 DOI: 10.1264/jsme2.me23072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
Strictly hydrogen- and sulfur-oxidizing chemolithoautotrophic bacteria, particularly members of the phyla Campylobacterota and Aquificota, have a cosmopolitan distribution in deep-sea hydrothermal fields. The successful cultivation of these microorganisms in liquid media has provided insights into their physiological, evolutionary, and ecological characteristics. Notably, recent population genetic studies on Sulfurimonas (Campylobacterota) and Persephonella (Aquificota) revealed geographic separation in their populations. Advances in this field of research are largely dependent on the availability of pure cultures, which demand labor-intensive liquid cultivation procedures, such as dilution-to-extinction, given the longstanding assumption that many strictly or facultatively anaerobic chemolithoautotrophs cannot easily form colonies on solid media. We herein describe a simple and cost-effective approach for cultivating these chemolithoautotrophs on solid media. The results obtained suggest that not only the choice of gelling agent, but also the gas phase composition significantly affect the colony-forming ratio of diverse laboratory strains. The use of gellan gum as a gelling agent combined with high concentrations of H2 and CO2 in a pouch bag promoted the formation of colonies. This contrasted with the absence of colony formation on an agar-solidified medium, in which thiosulfate served as an electron donor, nitrate as an electron acceptor, and bicarbonate as a carbon source, placed in anaerobic jars under an N2 atmosphere. Our method efficiently isolated chemolithoautotrophs from a deep-sea vent sample, underscoring its potential value in research requiring pure cultures of hydrogen- and sulfur-oxidizing chemolithoautotrophs.
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Affiliation(s)
- Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
- Deep-Sea and Deep Subsurface Life Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), 5–1 Higashiyama Myodaiji, Okazaki 444–8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
- Deep-Sea and Deep Subsurface Life Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), 5–1 Higashiyama Myodaiji, Okazaki 444–8787, Japan
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Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
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Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
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In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO 2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus. Int J Mol Sci 2021; 22:ijms22062861. [PMID: 33799806 PMCID: PMC8000050 DOI: 10.3390/ijms22062861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/29/2022] Open
Abstract
Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO2 sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO2 binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn2+. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO2 sequestration agents.
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François DX, Godfroy A, Mathien C, Aubé J, Cathalot C, Lesongeur F, L'Haridon S, Philippon X, Roussel EG. Persephonella atlantica sp. nov.: How to adapt to physico-chemical gradients in high temperature hydrothermal habitats. Syst Appl Microbiol 2020; 44:126176. [PMID: 33422731 DOI: 10.1016/j.syapm.2020.126176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
A novel thermophilic, microaerophilic and anaerobic, hydrogen- sulphur- and thiosulphate-oxidising bacterium, designated MO1340T, was isolated from a deep-sea hydrothermal chimney collected from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge. Cells were short, motile rods of 1.4-2.2μm length and 0.5-0.8μm width. Optimal growth was observed for a NaCl concentration of 2.5 % (w/v) at pH 6.5. As for other members of the genus Persephonella, strain MO1340T was strictly chemolithoautotrophic and could oxidise hydrogen, elemental sulphur or thiosulphate using oxygen as electron acceptor. Anaerobic nitrate reduction using hydrogen could also be performed. Each catabolic reaction had a different optimal growth temperature (65 to 75°C) and an optimal dissolved oxygen concentration (11.4 to 119.7 μM at 70°C for aerobic reactions) that varied according to the electron donors utilised. These experimental results are consistent with the distribution of these catabolic substrates along the temperature gradient observed in active hydrothermal systems. They strongly suggest that this adaptive strategy could confer a selective advantage for strain MO1340T in the dynamic part of the ecosystem where hot, reduced hydrothermal fluid mixes with cold, oxygenated seawater. Phylogenetic analysis indicated that strain MO1340T was a member of the genus Persephonella within the order Hydrogenothermales as it shared a 16S rRNA gene sequence similarity <95.5 % and ANI respectively 75.66 % with closest described Persephonella (P. hydrogeniphila 29WT). On the basis of the physiological and genomic properties of the new isolate, the name Persephonella atlantica sp. nov. is proposed. The type strain is MO1340T (=UBOCC-M-3359T =JCM 34026T).
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Affiliation(s)
- David X François
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Clémentine Mathien
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Johanne Aubé
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Cécile Cathalot
- Ifremer, Laboratoire Cycle Géochimique et Ressources (LCG/GM/REM), F-29280, Plouzané, France
| | - Françoise Lesongeur
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Stéphane L'Haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Xavier Philippon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Erwan G Roussel
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France.
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Manyumwa CV, Emameh RZ, Tastan Bishop Ö. Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses. Int J Mol Sci 2020; 21:E8066. [PMID: 33138066 PMCID: PMC7662607 DOI: 10.3390/ijms21218066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
With the increase in CO2 emissions worldwide and its dire effects, there is a need to reduce CO2 concentrations in the atmosphere. Alpha-carbonic anhydrases (α-CAs) have been identified as suitable sequestration agents. This study reports the sequence and structural analysis of 15 α-CAs from bacteria, originating from hydrothermal vent systems. Structural analysis of the multimers enabled the identification of hotspot and interface residues. Molecular dynamics simulations of the homo-multimers were performed at 300 K, 363 K, 393 K and 423 K to unearth potentially thermostable α-CAs. Average betweenness centrality (BC) calculations confirmed the relevance of some hotspot and interface residues. The key residues responsible for dimer thermostability were identified by comparing fluctuating interfaces with stable ones, and were part of conserved motifs. Crucial long-lived hydrogen bond networks were observed around residues with high BC values. Dynamic cross correlation fortified the relevance of oligomerization of these proteins, thus the importance of simulating them in their multimeric forms. A consensus of the simulation analyses used in this study suggested high thermostability for the α-CA from Nitratiruptor tergarcus. Overall, our novel findings enhance the potential of biotechnology applications through the discovery of alternative thermostable CO2 sequestration agents and their potential protein design.
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Affiliation(s)
- Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6140, South Africa;
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran;
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6140, South Africa;
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Adam N, Perner M. Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents. Front Microbiol 2018; 9:2873. [PMID: 30532749 PMCID: PMC6265342 DOI: 10.3389/fmicb.2018.02873] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/08/2018] [Indexed: 11/13/2022] Open
Abstract
Deep-sea hydrothermal vents may provide one of the largest reservoirs on Earth for hydrogen-oxidizing microorganisms. Depending on the type of geological setting, hydrothermal environments can be considerably enriched in hydrogen (up to millimolar concentrations). As hot, reduced hydrothermal fluids ascend to the seafloor they mix with entrained cold, oxygenated seawater, forming thermal and chemical gradients along their fluid pathways. Consequently, in these thermally and chemically dynamic habitats biochemically distinct hydrogenases (adapted to various temperature regimes, oxygen and hydrogen concentrations) from physiologically and phylogenetically diverse Bacteria and Archaea can be expected. Hydrogen oxidation is one of the important inorganic energy sources in these habitats, capable of providing relatively large amounts of energy (237 kJ/mol H2) for driving ATP synthesis and autotrophic CO2 fixation. Therefore, hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production. So far, the specific role of hydrogen-utilizing microorganisms in deep-sea hydrothermal ecosystems has been investigated by isolating hydrogen-oxidizers, measuring hydrogen consumption (ex situ), studying hydrogenase gene distribution and more recently by analyzing metatranscriptomic and metaproteomic data. Here we summarize this available knowledge and discuss the advent of new techniques for the identification of novel hydrogen-uptake and -evolving enzymes from hydrothermal vent microorganisms.
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Affiliation(s)
| | - Mirjam Perner
- Geomicrobiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China. Sci Rep 2014; 4:7479. [PMID: 25524763 PMCID: PMC5378992 DOI: 10.1038/srep07479] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts.
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10
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Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island, Papua New Guinea. Extremophiles 2014; 18:763-78. [DOI: 10.1007/s00792-014-0657-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 05/18/2014] [Indexed: 11/30/2022]
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Kawaichi S, Ito N, Yoshida T, Sako Y. Bacterial and archaeal diversity in an iron-rich coastal hydrothermal field in Yamagawa, Kagoshima, Japan. Microbes Environ 2013; 28:405-13. [PMID: 24256999 PMCID: PMC4070711 DOI: 10.1264/jsme2.me13048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Physicochemical characteristics and archaeal and bacterial community structures in an iron-rich coastal hydrothermal field, where the temperature of the most active hot spot reaches above 100°C, were investigated to obtain fundamental information on microbes inhabiting a coastal hydrothermal field. The environmental settings of the coastal hydrothermal field were similar in some degree to those of deep-sea hydrothermal environments because of its emission of H2, CO2, and sulfide from the bottom of the hot spot. The results of clone analyses based on the 16S rRNA gene led us to speculate the presence of a chemo-synthetic microbial ecosystem, where chemolithoautotrophic thermophiles, primarily the bacterial order Aquificales, function as primary producers using H2 or sulfur compounds as their energy source and CO2 as their carbon source, and the organic compounds synthesized by them support the growth of chemoheterotrophic thermophiles, such as members of the order Thermales and the family Desulfurococcaceae. In addition, the dominance of members of the bacterial genus Herbaspirillum in the high temperature bottom layer led us to speculate the temporal formation of mesophilic zones where they can also function as primary producing or nitrogen-fixing bacteria.
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Affiliation(s)
- Satoshi Kawaichi
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University
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Gupta RS, Lali R. Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae. Antonie Van Leeuwenhoek 2013; 104:349-68. [PMID: 23812969 DOI: 10.1007/s10482-013-9957-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 06/19/2013] [Indexed: 11/24/2022]
Abstract
We report here detailed phylogenetic and comparative analyses on 11 sequenced genomes from the phylum Aquificae to identify molecular markers that are specific for the species from this phylum or its different families (viz. Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae). In phylogenetic trees based on 16S rRNA gene or concatenated sequences for 32 conserved proteins, species from the three Aquificae families formed distinct clades. These trees also supported a strong relationship between the Aquificaceae and Hydrogenothermaceae families. In parallel, comparative analyses on protein sequences from Aquificae genomes have identified 46 conserved signature indels (CSIs) in broadly distributed proteins that are either exclusively or mainly found in members of the phylum Aquificae or its different families and subclades. Four of these CSIs, which are found in all sequenced Aquificae species, provide potential molecular markers for this phylum. Twelve, six and thirteen other CSIs that respectively are specific for the sequenced Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae species provide molecular markers and novel tools for the identification of members of these families and for genetic and biochemical studies on them. Lastly, these studies have identified 11 CSIs in divergent proteins that are uniquely shared by members of the Aquificaceae and Hydrogenothermaceae families providing strong evidence that these two groups of bacteria shared a common ancestor exclusive of all other Aquificae (bacteria). The species from these two families are also very similar in their metabolic and physiological properties and they consist of aerobic or microaerophilic bacteria, which generally obtain energy by oxidation of hydrogen or reduced sulfur compounds by molecular oxygen. Based upon their strong association in phylogenetic trees, unique shared presence of large numbers of CSIs in different proteins, and similarities in their metabolic and physiological properties, it is proposed that the order Aquificales should be emended to include only the members of the families Aquificaceae and Hydrogenothermaceae. The members of the family Desulfurobacteriaceae, which are obligate anaerobes that strictly use hydrogen as electron donor, are now transferred to a new order Desulfurobacteriales ord. nov. The emended descriptions of the phylum Aquificae and its three families incorporating information for different molecular signatures are also provided.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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Mino S, Makita H, Toki T, Miyazaki J, Kato S, Watanabe H, Imachi H, Watsuji TO, Nunoura T, Kojima S, Sawabe T, Takai K, Nakagawa S. Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific. Front Microbiol 2013; 4:107. [PMID: 23630523 PMCID: PMC3635849 DOI: 10.3389/fmicb.2013.00107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 04/13/2013] [Indexed: 11/30/2022] Open
Abstract
Deep-sea hydrothermal vent fields are areas on the seafloor with high biological productivity fueled by microbial chemosynthesis. Members of the Aquificales genus Persephonella are obligately chemosynthetic bacteria, and appear to be key players in carbon, sulfur, and nitrogen cycles in high temperature habitats at deep-sea vents. Although this group of bacteria has cosmopolitan distribution in deep-sea hydrothermal ecosystem around the world, little is known about their population structure such as intraspecific genomic diversity, distribution pattern, and phenotypic diversity. We developed the multi-locus sequence analysis (MLSA) scheme for their genomic characterization. Sequence variation was determined in five housekeeping genes and one functional gene of 36 Persephonella hydrogeniphila strains originated from the Okinawa Trough and the South Mariana Trough (SNT). Although the strains share >98.7% similarities in 16S rRNA gene sequences, MLSA revealed 35 different sequence types (ST), indicating their extensive genomic diversity. A phylogenetic tree inferred from all concatenated gene sequences revealed the clustering of isolates according to the geographic origin. In addition, the phenotypic clustering pattern inferred from whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis can be correlated to their MLSA clustering pattern. This study represents the first MLSA combined with phenotypic analysis indicative of allopatric speciation of deep-sea hydrothermal vent bacteria.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
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14
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Sakai S, Ehara M, Tseng IC, Yamaguchi T, Bräuer SL, Cadillo-Quiroz H, Zinder SH, Imachi H. Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order
Methanomicrobiales. Int J Syst Evol Microbiol 2012; 62:1389-1395. [DOI: 10.1099/ijs.0.035048-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, hydrogenotrophic methanogen, designated strain TNRT, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNRT grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l−1 (optimally at 0 g NaCl l−1). The strain utilized H2/CO2 and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNRT was related most closely to
Methanolinea tarda
NOBI-1T; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNRT and
M. tarda
NOBI-1T represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNRT is considered to represent a novel species of the genus
Methanolinea
, for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNRT ( = NBRC 105659T = DSM 23604T). In addition, we also suggest family status for the E1/E2 group within the order
Methanomicrobiales
, for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.
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Affiliation(s)
- Sanae Sakai
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Ehara
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - I-Cheng Tseng
- Department of Biology, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Suzanna L. Bräuer
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | | | - Stephen H. Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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15
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Izumi H, Nunoura T, Miyazaki M, Mino S, Toki T, Takai K, Sako Y, Sawabe T, Nakagawa S. Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough. Extremophiles 2012; 16:245-53. [PMID: 22212657 DOI: 10.1007/s00792-011-0425-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 12/13/2011] [Indexed: 11/25/2022]
Abstract
A novel heterotrophic, thermophilic bacterium, designated strain AC55(T), was isolated from a deep-sea hydrothermal vent chimney at the Hatoma Knoll in the Okinawa Trough, Japan. Cells of strain AC55(T) were non-motile, long rods (2.0- to 6.8-μm long and 0.3- to 0.6-μm wide). The strain was an obligatory anaerobic heterotroph capable of fermentative growth on complex proteinaceous substances. Elemental sulfur was reduced to hydrogen sulfide but did not stimulate growth. Growth was observed between 37 and 60°C (optimum 55°C), pH 5.5 and 8.5 (optimum pH 6.6), and in the presence of 1.5-4.5% (w/v) NaCl (optimum 2.5%, w/v). Menaquinone-7 and -8 were the major respiratory quinones. The G + C content of the genomic DNA from strain AC55(T) was 51.6 mol%. The 16S rRNA gene sequence analysis revealed that strain AC55(T) was the first cultivated representative of Acidobacteria subdivision 10. Based on the physiological and phylogenetic features of the novel isolate, the genus name Thermotomaculum gen. nov. is proposed, with Thermotomaculum hydrothermale sp. nov. as the type species. The type strain is AC55(T) (=JCM 17643(T) = DSM 24660(T) = NBRC 107904(T)).
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Affiliation(s)
- Hiroshi Izumi
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
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16
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Srinivasan V, Morowitz HJ, Huber H. What is an autotroph? Arch Microbiol 2011; 194:135-40. [DOI: 10.1007/s00203-011-0755-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 07/24/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
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17
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 324] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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18
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Meyer-Dombard DR, Swingley W, Raymond J, Havig J, Shock EL, Summons RE. Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Environ Microbiol 2011; 13:2216-31. [PMID: 21453405 DOI: 10.1111/j.1462-2920.2011.02476.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Yellowstone National Park, a small percentage of thermal features support streamer biofilm communities (SBCs), but their growth criteria are poorly understood. This study investigates biofilms in two SBC hosting, and two non-SBC springs. Sequencing of 16S rRNA clones indicates changing community structure as a function of downstream geochemistry, with many novel representatives particularly among the Crenarchaeota. While some taxonomic groups show little genetic variation, others show specialization by sample location. The transition fringe environment between the hotter chemosynthetic and cooler photosynthetic zones hosts a larger diversity of organisms in SBC bearing springs. This transition is proposed to represent an ecotone; this is the first description of an ecotone in a hydrothermal environment. The Aquificales are ubiquitous and dominate among the Bacteria in the hottest environments. However, there is no difference in species of Aquificales from SBC and non-SBC locations, suggesting they are not responsible for the formation of SBCs, or that their role in SBC formation is competitively suppressed in non-SBC sites. In addition, only SBC locations support Thermotogales-like organisms, highlighting the potential importance these organisms may have in SBC formation. Here, we present a novel view of SBC formation and variability in hydrothermal ecosystems.
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Affiliation(s)
- D'Arcy R Meyer-Dombard
- Department of Earth, Atmospheric, and Environmental Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Yashiro Y, Sakai S, Ehara M, Miyazaki M, Yamaguchi T, Imachi H. Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge. Int J Syst Evol Microbiol 2011; 61:53-59. [DOI: 10.1099/ijs.0.014811-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methane-producing archaeon, strain SMSPT, was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0–2.6 μm long by 0.5 μm wide; cells were sometimes up to 7 μm long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5–1.0 μm in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 °C (optimum, 30–33 °C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and mcrA (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSPT was affiliated with group E1/E2 within the order Methanomicrobiales. The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8T (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSPT and Methanoregula boonei 6A8T represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSPT represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSPT (=NBRC 105244T =DSM 22288T).
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Affiliation(s)
- Yuto Yashiro
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Sanae Sakai
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Ehara
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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20
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Sakai S, Conrad R, Liesack W, Imachi H. Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil. Int J Syst Evol Microbiol 2010; 60:2918-2923. [PMID: 20097796 DOI: 10.1099/ijs.0.020883-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hydrogenotrophic methanogen, designated strain MRE50(T), was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3-2.8 μm long and 0.4-0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50(T) grew at 37-55 °C (optimally at 45 °C), at pH 6-7.8 (optimally at pH 7.0) and in the presence of 0-20 g NaCl l(-1). The isolate utilized H(2)/CO(2) and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker gene mcrA showed that strain MRE50(T) is affiliated with the order Methanocellales, previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene and mcrA gene sequences, strain MRE50(T) was related most closely to Methanocella paludicola SANAE(T). Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50(T) and Methanocella paludicola SANAE(T) represent different species within the genus Methanocella. In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genus Methanocella, strain MRE50(T) is considered to represent a novel species of the genus Methanocella, for which the name Methanocella arvoryzae sp. nov. is proposed. The type strain is MRE50(T) (=NBRC 105507(T) =DSM 22066(T)).
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Affiliation(s)
- Sanae Sakai
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany.,Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany
| | - Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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Nishimura H, Sako Y. Purification and characterization of the oxygen-thermostable hydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum camini. J Biosci Bioeng 2010; 108:299-303. [PMID: 19716518 DOI: 10.1016/j.jbiosc.2009.04.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 04/10/2009] [Accepted: 04/16/2009] [Indexed: 11/28/2022]
Abstract
Aeropyrum camini that was isolated from a deep-sea hydrothermal vent chimney, possessed two hydrogenases (161 and 85 kDa) in its soluble fraction. The 85-kDa hydrogenase was purified to homogeneity using several chromatography columns. The specific activities of the purified hydrogenase were: 14.8 micromol methyl viologen(ox)/mg/min for hydrogen oxidation, and 14.6 micromol methyl viologen(red)/mg/min for proton reduction. The oxygen stabilities of hydrogenases that were purified from A. camini and the hydrogen thermophilic bacterium Persephonella hydrogeniphila, were compared. The hydrogenase purified from P. hydrogeniphila completely lost its activity following a 96-h exposure to atmosphere; however, the A. camini hydrogenase maintained 75% of its initial activity, even after a 168 h of atmospheric exposure. A. camini hydrogenase showed a half-life of 48 h at 90 degrees C, while P. hydrogeniphila hydrogenase showed complete denaturation after a 30 min incubation at the same temperature. Nine residues of the N-terminal amino acid sequence of A. camini hydrogenases (MARLLMIPGT) correspond to the protein sequence encoded by the hypothetical soluble hydrogenase subunit gene (APE2423) from A. pernix strain K1. A. camini hydrogenase has a high thermostability and is very tolerant to oxygen; therefore, it may be used for actual H(2) production.
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22
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Imachi H, Sakai S, Nagai H, Yamaguchi T, Takai K. Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field. Int J Syst Evol Microbiol 2009; 59:800-5. [DOI: 10.1099/ijs.0.003731-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Nunoura T, Takai K. Comparison of microbial communities associated with phase-separation-induced hydrothermal fluids at the Yonaguni Knoll IV hydrothermal field, the Southern Okinawa Trough. FEMS Microbiol Ecol 2009; 67:351-70. [PMID: 19159423 DOI: 10.1111/j.1574-6941.2008.00636.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Microbial communities associated with a variety of hydrothermal emissions at the Yonaguni Knoll IV hydrothermal field, the southernmost Okinawa Trough, were analyzed by culture-dependent and -independent techniques. In this hydrothermal field, dozens of vent sites hosting physically and chemically distinct hydrothermal fluids were observed. Variability in the gas content and formation in the hydrothermal fluids was observed and could be controlled by the potential subseafloor phase-separation and -partition processes. The hydrogen concentration in the hydrothermal fluids was also variable (0.8-3.6 mmol kg(-1)) among the chimney sites, but was unusually high as compared with those in other Okinawa Trough hydrothermal fields. Despite the physical and chemical variabilities of the hydrothermal fluids, the microbial communities were relatively similar among the habitats. Based on both culture-dependent and -independent analyses of the microbial community structures, members of Thermococcales, Methanococcales and Desulfurococcales likely represent the predominant archaeal components, while members of Nautiliaceae and Thioreductoraceae are considered to dominate the bacterial population. Most of the abundant microbial components appear to be chemolithotrophs sustained by hydrogen oxidation. The relatively consistent microbial communities found in this study could have been because of the sufficient input of hydrogen from the hydrothermal fluids rather than other chemical properties.
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Affiliation(s)
- Takuro Nunoura
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan.
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24
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Imachi H, Sakai S, Hirayama H, Nakagawa S, Nunoura T, Takai K, Horikoshi K. Exilispira thermophila gen. nov., sp. nov., an anaerobic, thermophilic spirochaete isolated from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2008; 58:2258-65. [DOI: 10.1099/ijs.0.65727-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.
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Affiliation(s)
- Isaac D Wagner
- 212 Biological Sciences Building, 1000 Cedar Street, University of Georgia, Athens, GA 30602-2605, USA
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26
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Nakagawa S, Takai K. Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 2008; 65:1-14. [DOI: 10.1111/j.1574-6941.2008.00502.x] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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27
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Takai K, Nunoura T, Ishibashi JI, Lupton J, Suzuki R, Hamasaki H, Ueno Y, Kawagucci S, Gamo T, Suzuki Y, Hirayama H, Horikoshi K. Variability in the microbial communities and hydrothermal fluid chemistry at the newly discovered Mariner hydrothermal field, southern Lau Basin. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jg000636] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval (SUGAR) Program; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Japan
| | - Takuro Nunoura
- Subground Animalcule Retrieval (SUGAR) Program; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Japan
| | - Jun-ichiro Ishibashi
- Department of Earth and Planetary Sciences, Faculty of Sciences; Kyushu University; Fukuoka Japan
| | - John Lupton
- NOAA Pacific Marine Environmental Laboratory; Hatfield Marine Science Center; Newport Oregon USA
| | - Ryohei Suzuki
- Department of Earth and Planetary Sciences, Faculty of Sciences; Kyushu University; Fukuoka Japan
| | - Hiroshi Hamasaki
- Department of Earth and Planetary Sciences, Faculty of Sciences; Kyushu University; Fukuoka Japan
| | - Yuichiro Ueno
- Global Edge Institute, Department of Earth and Planetary Sciences; Tokyo Institute of Technology; Tokyo Japan
| | - Shinsuke Kawagucci
- Department of Chemical Oceanography, Ocean Research Institute (ORI); University of Tokyo; Tokyo Japan
| | - Toshitaka Gamo
- Department of Chemical Oceanography, Ocean Research Institute (ORI); University of Tokyo; Tokyo Japan
| | - Yohey Suzuki
- Experimental Geoscience Team, Research Center for Deep Geological Environments; National Institute of Advanced Industrial Science and Technology (AIST); Ibaraki Japan
| | - Hisako Hirayama
- Subground Animalcule Retrieval (SUGAR) Program; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Program; Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Japan
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Molecular characterization of the diversity and distribution of a thermal spring microbial community by using rRNA and metabolic genes. Appl Environ Microbiol 2008; 74:4910-22. [PMID: 18539788 DOI: 10.1128/aem.00233-08] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1 degrees C and pH range of 5.75 to 6.91, were investigated by sequencing cloned PCR products and quantitative PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by three Aquificae genera--Thermocrinis, Hydrogenobaculum, and Sulfurihydrogenibium--and members of the Alpha-, Beta-, and Gammaproteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and candidate division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for carbon fixation by the rTCA cycle and nitrogen fixation were detected. All aclB sequences were phylogenetically related and spatially correlated to Sulfurihydrogenibium 16S rRNA gene sequences using qPCR (R(2) = 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of the Aquificaceae family. We briefly consider potential biochemical mechanisms that may allow Sulfurihydrogenibium and Thermocrinis to codominate some hydrothermal environments.
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Nunoura T, Miyazaki M, Suzuki Y, Takai K, Horikoshi K. Hydrogenivirga okinawensis sp. nov., a thermophilic sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough. Int J Syst Evol Microbiol 2008; 58:676-81. [PMID: 18319477 DOI: 10.1099/ijs.0.64615-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel extremely thermophilic sulfur-oxidizing bacterium, strain LS12-2(T), was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain LS12-2(T) were motile rods, 1.5-4.0 microm in length and 0.4-0.5 microm in width. Strain LS12-2(T) was an obligate chemolithoautotroph that could utilize elemental sulfur or thiosulfate as an electron donor and nitrate or oxygen as an electron acceptor. Growth was observed at 65-85 degrees C (optimum 70-75 degrees C), pH 5.8-8.3 (optimum pH 6.9-7.5), 1.0-4.0 % (w/v) NaCl (optimum 2.5 %) and 1.0-7.0 % O(2) in the gas phase (optimum 3.0 %). Fatty acids detected were C(16 : 0) (8.0 %), C(18 : 0) (9.0 %), C(18 : 1) (62.5 %) and C(20 : 1) (20.5 %). The genomic DNA G+C content was 51.3 mol%. 16S rRNA gene sequence analysis indicated that strain LS12-2(T) belonged to the genus Hydrogenivirga. Based on physiological and phylogenetic characteristics of the isolate, it is proposed that this strain represents a novel species in the genus Hydrogenivirga, Hydrogenivirga okinawensis sp. nov. The type strain of Hydrogenivirga okinawensis is LS12-2(T) (=JCM 13302(T)=DSM 17378(T)).
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Affiliation(s)
- Takuro Nunoura
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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30
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Ferrera I, Longhorn S, Banta AB, Liu Y, Preston D, Reysenbach AL. Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales. Extremophiles 2006; 11:57-64. [PMID: 16988757 DOI: 10.1007/s00792-006-0009-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 06/08/2006] [Indexed: 11/27/2022]
Abstract
The Aquificales are prevalent members of the microbial communities inhabiting many marine and terrestrial hydrothermal systems. Numerous new strains were obtained from deep-sea and terrestrial hydrothermal systems. In order to resolve the phylogenetic relationships within this group, three different phylogenetic datasets were used, namely the 16S rRNA gene, the intergenic transcribed spacer region between the 16S rRNA and 23S rRNA genes (ITS) and the gene coding for the ATP citrate lyase (aclB), a key enzyme in the reductive TCA cycle. The data were analyzed using neighbor-joining, parsimony and maximum likelihood. The resulting phylogenies appeared to be consistent between the three markers. The three genes confirmed the presence of isolates that merit further characterization and descriptions as new species and perhaps even new genera. The detailed phylogenetic interrelationships of these isolates are described here.
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Affiliation(s)
- I Ferrera
- Biology Department, Portland State University, Portland, OR 97201, USA
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31
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Miroshnichenko ML, Bonch-Osmolovskaya EA. Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents. Extremophiles 2006; 10:85-96. [PMID: 16418793 DOI: 10.1007/s00792-005-0489-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 11/02/2005] [Indexed: 10/25/2022]
Abstract
The diversity of thermophilic prokaryotes inhabiting deep-sea hot vents was actively studied over the last two decades. The ever growing interest is reflected in the exponentially increasing number of novel thermophilic genera described. The goal of this paper is to survey the progress in this field made in the years 2000-2005. In this period, representatives of several new taxa of hyperthermophilic archaea were obtained from deep-sea environments. Two of these isolates had phenotypic features new for this group of organisms: the presence of an outer cell membrane (the genus Ignicoccus) and the ability to grow anaerobically with acetate and ferric iron (the genus Geoglobus). Also, our knowledge on the diversity of thermophilic bacteria from deep-sea thermal environments extended significantly. The new bacterial isolates represented diverse bacterial divisions: the phylum Aquificae, the subclass Epsilonproteobacteria, the order Thermotogales, the families Thermodesulfobacteriaceae, Deferribacteraceae, and Thermaceae, and a novel bacterial phylum represented by the genus Caldithrix. Most of these isolates are obligate or facultative lithotrophs, oxidizing molecular hydrogen in the course of different types of anaerobic respiration or microaerobic growth. The existence and significant ecological role of some of new bacterial thermophilic isolates was initially established by molecular methods.
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Takai K, Nakagawa S, Reysenbach AL, Hoek J. Microbial ecology of mid-ocean ridges and back-arc basins. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/166gm10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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34
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Nakagawa S, Takai K, Inagaki F, Chiba H, Ishibashi JI, Kataoka S, Hirayama H, Nunoura T, Horikoshi K, Sako Y. Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation. FEMS Microbiol Ecol 2005; 54:141-55. [PMID: 16329980 DOI: 10.1016/j.femsec.2005.03.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/10/2005] [Accepted: 03/16/2005] [Indexed: 11/26/2022] Open
Abstract
Phase-separation and -segregation (boiling/distillation of subseafloor hydrothermal fluids) represent the primary mechanisms causing intra-field variations in vent fluid compositions. To determine whether this geochemical process affects the formation of microbial communities, we examined the microbial communities at three different vent sites located within a few tens meters of one another. In addition to chimney structures, colonization devices capturing subseafloor communities entrained by the vent fluids were studied, using culture-dependent and -independent methods. Microbiological analyses demonstrated the occurrence of distinctive microbial communities in each of the hydrothermal niches. Within a chimney structure, there was a transition from a mixed community of mesophiles and thermophiles in the exterior parts to thermophiles in the interior. Beside the transition within a chimney structure, intra-field variations in microbial communities in vent fluids were apparent. Geochemical analysis demonstrated that different vent fluids have distinctive end-member compositions as a consequence of subseafloor phase-separation and -segregation, which were designated gas-depleted, normal and gas-enriched fluids. In comparison to gas-depleted and normal fluids, gas-enriched fluids harbored more abundant chemolithoautotrophs with gaseous component-dependent energy metabolism, such as hydrogenotrophic methanogenesis. Subseafloor phase-separation and -segregation may play a key role in supplying energy and carbon sources to vent-associated chemolithoautotrophs and subvent microbial communities.
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Japan.
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35
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Nakagawa S, Shtaih Z, Banta A, Beveridge TJ, Sako Y, Reysenbach AL. Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense. Int J Syst Evol Microbiol 2005; 55:2263-2268. [PMID: 16280480 DOI: 10.1099/ijs.0.63708-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, sulfur-oxidizing Gram-negative bacterium, designated strain SS-5T, was isolated from the Calcite Hot Springs in Yellowstone National Park, USA. The cells were motile rods (1·2–2·8 μm long and 0·6–0·8 μm wide). The new isolate was a facultative heterotroph capable of using elemental sulfur or thiosulfate as an electron donor and O2 (1–18 %; optimum 6 %, v/v) as an electron acceptor. Hydrogen did not support growth. The isolate grew autotrophically with CO2. In addition, strain SS-5T utilized various organic carbon sources such as yeast extract, tryptone, sugars, amino acids and organic acids. Growth was observed between 55 and 78 °C (optimum 70 °C; 3·5 h doubling time), pH 6·0 and 8·0 (optimum pH 7·5), and 0 and 0·6 % (w/v) NaCl (optimum 0 %). The G+C content of the genomic DNA was 32 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate was a member of the genus Sulfurihydrogenibium. On the basis of the physiological and molecular characteristics of the new isolate, we propose the name Sulfurihydrogenibium yellowstonense sp. nov. with SS-5T (=JCM 12773T=OCM 840T) as the type strain. In addition, emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense are proposed.
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Affiliation(s)
- S Nakagawa
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Z Shtaih
- Department of Biology, Portland Sate University, PO Box 751, Portland, OR 97207-0751, USA
| | - A Banta
- Department of Biology, Portland Sate University, PO Box 751, Portland, OR 97207-0751, USA
| | - T J Beveridge
- Department of Microbiology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Y Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - A-L Reysenbach
- Department of Biology, Portland Sate University, PO Box 751, Portland, OR 97207-0751, USA
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Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K, Sako Y. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol 2005; 7:1619-32. [PMID: 16156735 DOI: 10.1111/j.1462-2920.2005.00856.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epsilon-Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon-Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon-Proteobacteria. Energy metabolism of epsilon-Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon-Proteobacteria. Nevertheless, culturability of epsilon-Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon-Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes.
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Kyoto 606-8502, Japan.
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Nakagawa S, Nakamura S, Inagaki F, Takai K, Shirai N, Sako Y. Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field. Int J Syst Evol Microbiol 2005; 54:2079-2084. [PMID: 15545438 DOI: 10.1099/ijs.0.03031-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain IBSK3(T), was isolated from a coastal hot spring in Ibusuki, Kagoshima Prefecture, Japan. The cells were motile, straight to slightly curved rods (1.2-3.0 microm long and 0.3-0.4 microm wide). Strain IBSK3(T) was an obligate chemolithoautotroph growing by respiratory nitrate reduction with H(2), forming N(2)O as an end product. Low concentrations of O(2) (0.4-7.7 %, v/v; optimum 2.0 %, v/v) could serve as an alternative electron acceptor to growth. In addition, strain IBSK3(T) was able to utilize elemental sulfur as a sole electron donor with either nitrate or low concentrations of O(2) as an electron acceptor. Growth was observed between 55 and 77.5 degrees C (optimum 75 degrees C; 2 h doubling time), pH 5.5 and 8.3 (optimum pH 6.5-7.0), and in the presence of 0.5 and 4.0 % NaCl (optimum 2.0 %). The G+C content of the genomic DNA was 49.2 mol%. On the basis of 16S rRNA gene sequence analysis, strain IBSK3(T) belonged to the family Aquificaceae, but it only demonstrated a distant phylogenetic relationship with any recognized species within the family (sequence similarity was less than 92 %). On the basis of the physiological and molecular characteristics of the novel isolate, a new genus and novel species are proposed: the type strain of Hydrogenivirga caldilitoris gen. nov., sp. nov. is IBSK3(T) (=JCM 12173(T)=ATCC BAA-821(T)).
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MESH Headings
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Gram-Negative Bacteria/classification
- Gram-Negative Bacteria/cytology
- Gram-Negative Bacteria/isolation & purification
- Gram-Negative Bacteria/metabolism
- Hot Springs/microbiology
- Hot Temperature
- Hydrogen/metabolism
- Hydrogen-Ion Concentration
- Inorganic Chemicals/metabolism
- Japan
- Molecular Sequence Data
- Movement
- Nitrates/metabolism
- Nitrous Oxide/metabolism
- Oxidation-Reduction
- Oxygen/metabolism
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic
- Sequence Analysis, DNA
- Sulfur/metabolism
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Sachiko Nakamura
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency of Marine-Earth Science and Technology 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency of Marine-Earth Science and Technology 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Nobuaki Shirai
- Industrial Research Center of Shiga Prefecture, Kamitoyama 232, Ritto 520-3004, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Hosoya R, Hamana K, Niitsu M, Itoh T. Polyamine analysis for chemotaxonomy of thermophilic eubacteria: Polyamine distribution profiles within the orders Aquificales, Thermotogales, Thermodesulfobacteriales, Thermales, Thermoanaerobacteriales, Clostridiales and Bacillales. J GEN APPL MICROBIOL 2005; 50:271-87. [PMID: 15747232 DOI: 10.2323/jgam.50.271] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cellular polyamines of 45 thermophilic and 8 related mesophilic eubacteria were investigated by HPLC and GC analyses for the thermophilic and chemotaxonomic significance of polyamine distribution profiles. Spermidine and a quaternary branched penta-amine, N4-bis(aminopropyl)norspermidine, were the major polyamine in Thermocrinis, Hydrogenobacter, Hydrogenobaculum, Aquifex, Persephonella, Sulfurihydrogenibium, Hydrogenothermus, Balnearium and Thermovibrio, located in the order Aquificales. Thermodesulfobacterium and Thermodesulfatator belonging to the order Thermodesulfobacteriales contained another quaternary penta-amine, N4-bis(aminopropyl)spermidine. In the order Thermotogales, Thermotoga contained spermidine, norspermidine, caldopentamine and homocaldopentamine. The latter two linear penta-amines were not found in Marinitoga and Petrotoga. In the order Thermales, Thermus and Marinithermus contained homospermidine, norspermine and the linear penta-amines. Meiothermus lacked penta-amines. Vulcanithermus contained linear penta-amines and hexa-amines but not homospermidine. Oceanithermus contained spermine alone. Within the order Thermoanaerobacteriales, the two quaternary branched penta-amines were found in Thermanaeromonas and Thermoanaerobacter. Caldanaerobacter contained N4-bis(aminopropyl)spermidine. Thermoanaerobacterium lacked penta-amines. Thermaerobacter of the order Clostridiales contained N4-bis(aminopropyl)spermidine and agmatine. Thermosyntropha, Thermanaerovibrio, Thermobrachium ( the order Clostridiales), Sulfobacillus, Alicyclobacillus, Anoxybacillus, Ureibacillus, Thermicanus ( the order Bacillales), Desulfotomaculum, Desulfitobacterium and Pelotomaculum (the family Peptococcaceae) ubiquitously contained spermine. Some thermophiles of Bacillales added linear and branched penta-amines.
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Affiliation(s)
- Ryuichi Hosoya
- Gunma University School of Health Sciences, Maebashi, Gunma 371-8514, Japan
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Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sako Y. Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the ε-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 2005; 55:925-933. [PMID: 15774687 DOI: 10.1099/ijs.0.63480-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel denitrifying bacteria, designated strains MI55-1Tand E9I37-1T, were isolated from deep-sea hydrothermal vent chimney structures at the Iheya North hydrothermal field in the Mid-Okinawa Trough, Japan. Both isolates were strict chemolithoautotrophs growing by respiratory nitrate reduction with H2, forming N2as a metabolic product. Oxygen (at low concentrations) could serve as an alternative electron acceptor for growth of the isolates. Growth of strain MI55-1Twas observed at temperatures between 40 and 57 °C (optimum, 55 °C; doubling time, 2 h), at pH values between 5·4 and 6·9 (optimum, pH 6·4) and in the presence of between 1·5 and 4·0 % (w/v) NaCl (optimum, 2·5 %). Growth of strain E9I37-1Twas observed at temperatures between 28 and 40 °C (optimum, 37 °C; doubling time, 2·5 h), at pH values between 5·6 and 7·6 (optimum, pH 7·0) and in the presence of between 1·5 and 3·5 % (w/v) NaCl (optimum, 3·0 %). The G+C contents of the genomic DNA of strains MI55-1Tand E9I37-1Twere 29·6 and 35·5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MI55-1Tand E9I37-1Tbelonged to groups A and F of theε-Proteobacteria, but that they had distant phylogenetic relationships with any species, within the phylogenetic groups, that had validly published names (sequence similarities were less than 91 %). On the basis of the physiological and molecular characteristics of the novel isolates, it is proposed that they should each be classified in a novel genus:Nitratiruptor tergarcusgen. nov., sp. nov., with MI55-1T(=JCM 12459T=DSM 16512T) as the type strain, andNitratifractor salsuginisgen. nov., sp. nov., with E9I37-1T(=JCM 12458T=DSM 16511T) as the type strain.
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Nakagawa S, Inagaki F, Takai K, Horikoshi K, Sako Y. Thioreductor micantisoli gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the ε-Proteobacteria isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 2005; 55:599-605. [PMID: 15774631 DOI: 10.1099/ijs.0.63351-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, hydrogen-oxidizing, sulfur-reducing bacterium, designated strain BKB25Ts-YT, was isolated from hydrothermal sediments at Iheya North in the Mid-Okinawa Trough, Japan. Cells were Gram-negative, motile rods (1·8–2·1 μm long and 0·5–0·7 μm wide). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Elemental sulfur and nitrate served as electron acceptors, respectively yielding hydrogen sulfide and ammonium. Growth was observed at 20–42 °C (optimum 32 °C; 3 h doubling time), pH 5·0–6·5 (optimum 6·0) and in the presence of 2·0–4·0 % NaCl (optimum 2·5 %) via respiratory S0 reduction with H2. The G+C content of the genomic DNA was 37·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate represented the first strain for which taxonomic properties have been characterized within the previously uncultivated ε-Proteobacteria Group G. On the basis of the physiological and molecular properties of the novel isolate, the genus name Thioreductor gen. nov. is proposed, with Thioreductor micantisoli sp. nov. as the type species. The type strain is BKB25Ts-YT (=JCM 12457T=DSM 16661T).
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Mori K, Kakegawa T, Higashi Y, Nakamura KI, Maruyama A, Hanada S. Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount. Int J Syst Evol Microbiol 2004; 54:1561-1566. [PMID: 15388711 DOI: 10.1099/ijs.0.02962-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain St55BTwas isolated from a sulfide chimney in the hydrothermal field of Suiyo Seamount (Izu-Bonin Arc, Western Pacific). Cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. The isolate was a chemoheterotroph requiring yeast extract for growth. Although strain St55BTused oxygen as an electron acceptor, it could not form colonies in an oxygen concentration of more than 5 % (v/v). The isolate also used nitrate, nitrite or elemental sulfur in the absence of oxygen. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related toOceanithermus profundus, belonging to the phylum ‘Deinococcus–Thermus’ (sequence similarity 99·5 %). However, strain St55BTdiffered fromO. profundusin terms of usage of electron donors, cellular fatty acid profile and DNA G+C content. In addition, a DNA–DNA hybridization test indicated low relatedness between the isolate andO. profundus. For the reasons given above, the nameOceanithermus desulfuranssp. nov. is proposed for strain St55BT(=NBRC 100063T=DSM 15757T).
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Affiliation(s)
- Koji Mori
- Biological Resource Centre (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Takeshi Kakegawa
- Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Yowsuke Higashi
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Ko-Ichi Nakamura
- Institute for Marine Resource and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Akihiko Maruyama
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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Takai K, Gamo T, Tsunogai U, Nakayama N, Hirayama H, Nealson KH, Horikoshi K. Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles 2004; 8:269-82. [PMID: 15309563 DOI: 10.1007/s00792-004-0386-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Accepted: 02/18/2004] [Indexed: 10/26/2022]
Abstract
Subsurface microbial communities supported by geologically and abiologically derived hydrogen and carbon dioxide from the Earth's interior are of great interest, not only with regard to the nature of primitive life on Earth, but as potential analogs for extraterrestrial life. Here, for the first time, we present geochemical and microbiological evidence pointing to the existence of hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) dominated by hyperthermophilic methanogens beneath an active deep-sea hydrothermal field in the Central Indian Ridge. Geochemical and isotopic analyses of gaseous components in the hydrothermal fluids revealed heterogeneity of both concentration and carbon isotopic compositions of methane between the main hydrothermal vent (0.08 mM and -13.8 per thousand PDB, respectively) and the adjacent divergent vent site (0.2 mM and -18.5 per thousand PDB, respectively), representing potential subsurface microbial methanogenesis, at least in the divergent vent emitting more 13C-depleted methane. Extremely high abundance of magmatic energy sources such as hydrogen (2.5 mM) in the fluids also encourages a hydrogen-based, lithoautotrophic microbial activity. Both cultivation and cultivation-independent molecular analyses suggested the predominance of Methanococcales members in the superheated hydrothermal emissions and chimney interiors along with the other major microbial components of Thermococcales members. These results imply that a HyperSLiME, consisting of methanogens and fermenters, occurs in this tectonically active subsurface zone, strongly supporting the existence of hydrogen-driven subsurface microbial communities.
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Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science and Technology Center (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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Nakagawa T, Ishibashi JI, Maruyama A, Yamanaka T, Morimoto Y, Kimura H, Urabe T, Fukui M. Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific. Appl Environ Microbiol 2004; 70:393-403. [PMID: 14711668 PMCID: PMC321305 DOI: 10.1128/aem.70.1.393-403.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5 degrees C and natural vent fluids at 7 degrees C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and gamma- and epsilon-Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with "Nanoarchaeota." The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300 degrees C were affiliated with the delta-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4 degrees C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments.
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Affiliation(s)
- Tatsunori Nakagawa
- Department of Biological Science, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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Nakagawa S, Takai K, Horikoshi K, Sako Y. Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2004; 54:329-335. [PMID: 15023940 DOI: 10.1099/ijs.0.02826-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic archaeon, designated strain SY1T, was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cells were irregular cocci (1·2 to 2·1 μm in diameter), occurring singly or in pairs, and stained Gram-negative. Growth was observed between 70 and 97 °C (optimum, 85 °C; 220 min doubling time), pH 6·5 and 8·8 (optimum, pH 8·0), and salinity of 2·2 and 5·3 % (optimum, 3·5 %). It was a strictly aerobic heterotroph capable of growing on complex proteinaceous substrates such as yeast extract and tryptone. The G+C content of the genomic DNA was 54·4 mol%. Phylogenetic analysis based on the 16S rDNA sequence of the isolate indicated that the isolate was closely related toAeropyrum pernixstrain K1T. However, no significant genetic relatedness was observed between them by DNA–DNA hybridization. On the basis of the molecular and physiological traits of the new isolate, the nameAeropyrum caminisp. nov. is proposed, with the type strain SY1T(=JCM 12091T=ATCC BAA-758T).
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ken Takai
- Subground Animalcules Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcules Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Takai K, Kobayashi H, Nealson KH, Horikoshi K. Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer. Int J Syst Evol Microbiol 2003; 53:823-827. [PMID: 12807207 DOI: 10.1099/ijs.0.02506-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study was performed on a novel facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotroph recently isolated from subsurface hot aquifer water in a Japanese gold mine. The cells were straight to slightly curved rods, with a single polar flagellum. Growth was observed at 40-70 degrees C (optimum 60-65 degrees C; 80 min doubling time) and at pH 6.4-8.8 (optimum pH 7.5). The isolate was unable to use complex organic compounds, carbohydrates, amino acids or organic acids as sole energy and carbon sources. The G + C content of the genomic DNA was 31.3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was closely related to an uncultivated group of micro-organisms within the order Aquificales obtained from Icelandic and Japanese hot spring microbial mats, but distantly related to previously identified genera of the Aquificales such as Persephonella, Aquifex and Hydrogenobacter. The name Sulfurihydrogenibium subterraneum gen. nov., sp. nov. is proposed for this novel species; the type strain is HGMK1(T) (= JCM 11477(T) = ATCC BAA-562(T) = DSM 15120(T)).
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Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hideki Kobayashi
- The DEEPSTAR Group, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kenneth H Nealson
- NASA Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109-8099, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- The DEEPSTAR Group, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Japan Marine Science & Technology Center, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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