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Miyazaki U, Mizutani D, Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney. Antonie Van Leeuwenhoek 2024; 117:24. [PMID: 38217723 DOI: 10.1007/s10482-023-01919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
A novel mesophilic bacterial strain, designated S502T, was isolated from a deep-sea hydrothermal vent at Suiyo Seamount, Japan. Cells were Gram-positive, asporogenous, motile, and curved rods, measuring 1.6-5.6 µm in length. The strain was an obligate anaerobe that grew fermentatively on complex substrates such as yeast extract and Bacto peptone. Elemental sulfur stimulated the growth of the strain, and was reduced to hydrogen sulfide. The strain grew within a temperature range of 10-23 °C (optimum at 20 °C), pH range of 4.8-8.3 (optimum at 7.4), and a NaCl concentration range of 1.0-4.0% (w/v) (optimum at 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the class Clostridia, with Fusibacter paucivorans strain SEBR 4211T (91.1% sequence identity) being its closest relative. The total size of the genome of the strain was 3.12 Mbp, and a G + C content was 28.2 mol%. The highest values for average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) value of strain S502T with relatives were 67.5% (with Marinisporobacter balticus strain 59.4MT), 51.5% (with M. balticus strain 59.4MT), and 40.9% (with Alkaliphilus serpentinus strain LacTT), respectively. Based on a combination of phylogenetic, genomic, and phenotypic characteristics, we propose strain S502T to represent a novel genus and species, Helicovermis profundi gen. nov., sp. nov., with the type strain S502T (= DSM 112048T = JCM 39167T).
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Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daiki Mizutani
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Depertment of Marine and Earth Sciences, Marine Works Japan Ltd, 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science and 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
| | - 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
| | - 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
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, 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.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
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2
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Li XG, Lin J, Bai SJ, Dai J, Jiao ZX, Tang HZ, Qi XQ, Zhang WJ, Liu M, Xu JS, Wu LF. Crassaminicella thermophila sp. nov., a moderately thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney and emended description of the genus Crassaminicella. Int J Syst Evol Microbiol 2021; 71. [PMID: 34825884 DOI: 10.1099/ijsem.0.005112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel moderately thermophilic, anaerobic, heterotrophic bacterium (strain SY095T) was isolated from a hydrothermal vent chimney located on the Southwest Indian Ridge at a depth of 2730 m. Cells were Gram-stain-positive, motile, straight to slightly curved rods forming terminal endospores. SY095T was grown at 45-60 °C (optimum 50-55 °C), pH 6.0-7.5 (optimum 7.0), and in a salinity of 1-4.5 % (w/v) NaCl (optimum 2.5 %). Substrates utilized by SY095T included fructose, glucose, maltose, N-acetyl glucosamine and tryptone. Casamino acid and amino acids (glutamate, glutamine, lysine, methionine, serine and histidine) were also utilized. The main end products from glucose fermentation were acetate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14 : 0 (60.5%) and C16 : 0 (7.6 %). The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. No respiratory quinones were detected. The chromosomal DNA G+C content was 30.8 mol%. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that SY095T was closely related to Crassaminicella profunda Ra1766HT (95.8 % 16S rRNA gene sequence identity). SY095T exhibited 78.1 % average nucleotide identity (ANI) to C. profunda Ra1766HT. The in silico DNA-DNA hybridization (DDH) value indicated that SY095T shared 22.7 % DNA relatedness with C. profunda Ra1766HT. On the basis of its phenotypic, genotypic and phylogenetic characteristics, SY095T is suggested to represent a novel species of the genus Crassaminicella, for which the name Crassaminicella thermophila sp. nov. is proposed. The type strain is SY095T (=JCM 34213=MCCC 1K04191). An emended description of the genus Crassaminicella is also proposed.
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Affiliation(s)
- Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Jin Lin
- Hainan Tropical Ocean University, Sanya, PR China
| | - Shi-Jie Bai
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,Laboratory of Marine Viruses and Molecular Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Jie Dai
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Ze-Xi Jiao
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Hong-Zhi Tang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Min Liu
- Hainan Tropical Ocean University, Sanya, PR China
| | - Jian-Sheng Xu
- Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
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3
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Coskun ÖK, Vuillemin A, Schubotz F, Klein F, Sichel SE, Eisenreich W, Orsi WD. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. ISME JOURNAL 2021; 16:257-271. [PMID: 34312482 PMCID: PMC8692406 DOI: 10.1038/s41396-021-01066-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frieder Klein
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Susanna E Sichel
- Departamento de Geologia e Geofísica/LAGEMAR-Universidade Federal Fluminense-Brazil, Niterói, RJ, Brazil
| | - Wolfgang Eisenreich
- Department of Chemistry, Bavarian NMR Center-Structural Membrane Biochemistry, Technische Universität München, Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany. .,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.
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4
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Alou MT, Rathored J, Michelle C, Dubourg G, Andrieu C, Armstrong N, Sokhna C, Diallo A, Raoult D, Fournier PE. Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant. Antonie van Leeuwenhoek 2017; 110:737-750. [PMID: 28190153 DOI: 10.1007/s10482-017-0843-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/03/2017] [Indexed: 02/06/2023]
Abstract
A novel strain, Mt12T (=CSUR P1907 = DSM 100590), was isolated from the fecal sample of a 7-month-old girl from Senegal afflicted with severe acute malnutrition. This bacterium is a strictly anaerobic, spore-forming Gram-stain positive bacillus. The major cellular fatty acid was identified as tetradecanoic acid. Its 16S rRNA gene sequence exhibited 94.9% similarity with that of Crassaminicella profunda strain Ra1766HT, currently the closest species with a validly published name. The draft genome of strain Mt12T is 3,497,275-bp long with a 30.45% of G+C content. 3397 genes were predicted, including 3268 protein-coding genes and 129 RNAs, including eight 16S rRNAs. Genomic comparison with closely related species with an available genome showed a lower quantitative genomic content. The phylogenetic analysis alongside the dDDH values under 30% and phenotypic characteristics suggest that strain Mt12T represents a new genus within the family Clostridiaceae, for which the name Inediibacterium massiliense gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Maryam Tidjani Alou
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Jaishriram Rathored
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Caroline Michelle
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Gregory Dubourg
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Claudia Andrieu
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France.,Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal
| | - Aldiouma Diallo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France.,Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal
| | - Didier Raoult
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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5
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Zhang X, Zeng X, Li X, Alain K, Jebbar M, Shao Z. Anaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 67:1462-1467. [PMID: 27974087 DOI: 10.1099/ijsem.0.001739] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, mesophilic, heterotrophic bacterium, designated strain DY2726DT, was isolated from West Pacific Ocean sediments. Cells were long rods (0.5-0.8 µm wide, 4-15 µm long), Gram-positive and motile by means of flagella. The temperature and pH ranges for growth were 25-40 °C and pH 6.5-9.0, while optimal growth occurred at 37 °C and pH 7.5, with a generation time of 76 min. The strain required sea salts for growth at concentrations from 10 to 30 g l-1 (optimum at 20 g l-1). Substrates used as carbon sources were yeast extract, tryptone, glucose, cellobiose, starch, gelatin, dextrin, fructose, fucose, galactose, galacturonic acid, gentiobiose, glucosaminic acid, mannose, melibiose, palatinose and rhamnose. Products of fermentation were carbon dioxide, acetic acid and butyric acid. Strain DY2726DT was able to reduce amorphous iron hydroxide, goethite, amorphous iron oxides, anthraquinone-2,6-disulfonate and crotonate, but did not reduce sulfur, sulfate, thiosulfate, sulfite or nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DY2726DT was affiliated to the family Clostridiaceae and was most closely related to the type strains of Alkaliphilus transvaalensis (90.0 % similarity) and Alkaliphilus oremlandii (89.6 %). The genomic DNA G+C content was 33.4 mol%. The major cellular fatty acids of strain DY2726DT were C16 : 1, C14 : 0 and C16 : 0. On the basis of its phenotypic and genotypic properties, strain DY2726DT is suggested to represent a novel species of a new genus in the family Clostridiaceae, for which the name Anaeromicrobium sediminis gen. nov., sp. nov. is proposed. The type strain of Anaeromicrobium sediminis is DY2726DT (=JCM 30224T=MCCC 1A00776T).
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Affiliation(s)
- Xiaobo Zhang
- Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Collaborative Innovation Center of Deep Sea Biology, Xiamen, Fujian 361005, PR China
| | - Xiang Zeng
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xi Li
- Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China.,Collaborative Innovation Center of Deep Sea Biology, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China
| | - Karine Alain
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - Mohamed Jebbar
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China.,Collaborative Innovation Center of Deep Sea Biology, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China
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Li G, Zeng X, Liu X, Zhang X, Shao Z. Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively. Int J Syst Evol Microbiol 2016; 66:4355-4361. [DOI: 10.1099/ijsem.0.001355] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guangyu Li
- School of Life Sciences, Xiamen University, Xiamen, Fujian, PR China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Xiaobo Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, PR China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, PR China
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7
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Galperin MY, Brover V, Tolstoy I, Yutin N. Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov. Int J Syst Evol Microbiol 2016; 66:5506-5513. [PMID: 27902180 PMCID: PMC5244501 DOI: 10.1099/ijsem.0.001548] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18
species to Clostridium cluster XI, separating them
from Clostridium sensu stricto
(Clostridium cluster I). Subsequently,
most cluster XI species have been assigned to the family Peptostreptococcaceae with some species
being reassigned to new genera. However, several misclassified Clostridium species remained, creating
a taxonomic conundrum and confusion regarding their status. Here, we have re-examined
the phylogeny of cluster XI species by comparing the 16S rRNA gene-based trees with
protein- and genome-based trees, where available. The resulting phylogeny of the
Peptostreptococcaceae was consistent
with the recent proposals on creating seven new genera within this family. This
analysis also revealed a tight clustering of Clostridium litorale and
Eubacterium acidaminophilum. Based on
these data, we propose reassigning these two organisms to the new genus
Peptoclostridium as
Peptoclostridium litorale gen. nov.
comb. nov. (the type species of the genus) and Peptoclostridium acidaminophilum comb.
nov., respectively. As correctly noted in the original publications, the genera
Acetoanaerobium and
Proteocatella also fall within cluster
XI, and can be assigned to the Peptostreptococcaceae.
Clostridium sticklandii, which falls
within radiation of genus Acetoanaerobium, is
proposed to be reclassified as Acetoanaerobium sticklandii comb. nov.
The remaining misnamed members of the Peptostreptococcaceae,
[Clostridium]
hiranonis, [Clostridium]
paradoxum and [Clostridium]
thermoalcaliphilum, still remain to be properly classified.
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Affiliation(s)
- Michael Y. Galperin
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
- Correspondence Michael Y. Galperin
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
| | - Igor Tolstoy
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
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Lakhal R, Pradel N, Postec A, Ollivier B, Cayol JL, Godfroy A, Fardeau ML, Galés G. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments. Int J Syst Evol Microbiol 2015; 65:3097-3102. [PMID: 26296351 DOI: 10.1099/ijsem.0.000386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002 m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14 : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.
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Affiliation(s)
- Raja Lakhal
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Anne Postec
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Jean-Luc Cayol
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Ifremer, CNRS, UBO, 29280 Plouzané, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Grégoire Galés
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France.,Aix-Marseille Université, CEREGE, UMR 7330, Centre St Charles, Case 67, 3 Place Victor Hugo, 13331 Marseille, France
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Zeng X, Zhang Z, Li X, Zhang X, Cao J, Jebbar M, Alain K, Shao Z. Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2014; 65:710-715. [PMID: 25505345 DOI: 10.1099/ijs.0.068221-0] [Citation(s) in RCA: 15] [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 piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) ( = JCM 19466(T) = DSM 28033(T) = MCCC 1A06456(T)).
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Affiliation(s)
- Xiang Zeng
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Zhao Zhang
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xi Li
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xiaobo Zhang
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Junwei Cao
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China
| | - Mohamed Jebbar
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Karine Alain
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Zongze Shao
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
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10
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Song LY, Wang YQ. Investigation of microbial community structure of a shallow lake after one season copper sulfate algaecide treatment. Microbiol Res 2014; 170:105-13. [PMID: 25249310 DOI: 10.1016/j.micres.2014.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/24/2022]
Abstract
In present work we described, for the first time, the phylogenic structure of the microbial community in a shallow freshwater lake (Hawk Island Lake, located in the Lower Peninsula of the State of Michigan, U.S.A.) after one season (four times during May to August 2007) of CuSO₄ treatment for algae growth control. The microbial community structure was characterized by terminal restriction fragment length polymorphism (TRFLP), clone library and 454 pyrosequencing. The similar structure of water chemistry measured across three sampling sites suggested that the lake was well mixed. The concentration of chlorophyll a (chl-a) and turbidity was low, 3.35 ± 1.62 μg/L and 2.5 ± 1.9 NTU, respectively, implying that photosynthesis was suppressed. TRFLP profiles showed that the lake was dominated by 16 terminal fragments (TFs), accounting for 85.5-92.6% abundance. Analysis of similarity (ANOSIM) showed that the difference in microbial community structure between upper and lower depths of the water column was not significant (P=0.101). These results suggested that the microbial community structure within the lake was similar. Clone library and 454 pyrosequencing indicated that the lake was dominated by freshwater phyla, Proteobacteria, Bacteroides, and Actinobacteria. Moreover, the large number of unclassified bacteria (27.4% of total 2090,454 sequences) suggested a complex microbial community structure in the lake.
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Affiliation(s)
- Li-Yan Song
- Research Center of Environmental Microbiology and Ecology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China; Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| | - Yang-Qing Wang
- Research Center of Environmental Microbiology and Ecology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
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11
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Duncan KE, Perez-Ibarra BM, Jenneman G, Harris JB, Webb R, Sublette K. The effect of corrosion inhibitors on microbial communities associated with corrosion in a model flow cell system. Appl Microbiol Biotechnol 2013; 98:907-18. [DOI: 10.1007/s00253-013-4906-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/05/2013] [Accepted: 04/06/2013] [Indexed: 10/26/2022]
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12
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Brown BP, Brown SR, Senko JM. Microbial communities associated with wet flue gas desulfurization systems. Front Microbiol 2012; 3:412. [PMID: 23226147 PMCID: PMC3510643 DOI: 10.3389/fmicb.2012.00412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/14/2012] [Indexed: 02/01/2023] Open
Abstract
Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.
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Affiliation(s)
- Bryan P Brown
- Department of Biology, The University of Akron, Akron OH, USA
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13
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Rittmann S, Herwig C. A comprehensive and quantitative review of dark fermentative biohydrogen production. Microb Cell Fact 2012; 11:115. [PMID: 22925149 PMCID: PMC3443015 DOI: 10.1186/1475-2859-11-115] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/03/2012] [Indexed: 01/25/2023] Open
Abstract
Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.
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Affiliation(s)
- Simon Rittmann
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
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14
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de Vladar HP. Amino acid fermentation at the origin of the genetic code. Biol Direct 2012; 7:6. [PMID: 22325238 PMCID: PMC3376031 DOI: 10.1186/1745-6150-7-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/10/2012] [Indexed: 01/15/2023] Open
Abstract
There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eörs Szathmáry (nominated by Dr. Gáspár Jékely) and Dr. Ádám Kun (nominated by Dr. Sandor Pongor)
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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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Chung J, Shin S, Oh J. Influence of nitrate, sulfate and operational parameters on the bioreduction of perchlorate using an up-flow packed bed reactor at high salinity. ENVIRONMENTAL TECHNOLOGY 2010; 31:693-704. [PMID: 20540430 DOI: 10.1080/09593331003621557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this study we have investigated whether electron acceptors, such as nitrate or sulphate ions, competitively inhibit the reduction of perchlorate in brine in continuous up-flow packed bed bioreactors. The effect of pH and hydraulic retention time (HRT) on the reduction of perchlorate at high salinity has also been examined. Reduction of perchlorate was found to be only moderately influenced by nitrate (under 163 mg N L-'), implying that there was no significant microbial competition for electron acceptors. As a result of microbial diversity, there were few differences between microbial communities fed with a variety of media, suggesting that most nitrate-reducing bacteria are able to reduce perchlorate at high salinity. Reduction of perchlorate was almost complete at relatively high sulfate levels (1000 mg L(-1)), neutral pH (6-8) and relatively long HRTs (> 10 h).
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Affiliation(s)
- J Chung
- R&D Center, Samsung Engineering Co Ltd, 415-10 Woncheon-Dong, Youngting-Gu, Suwon, Gyeonggi-Do, 443-823, Korea
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Ogg CD, Patel BKC. Thermotalea metallivorans gen. nov., sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia aquifer. Int J Syst Evol Microbiol 2009; 59:964-71. [DOI: 10.1099/ijs.0.004218-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Chung J, Shin S, Oh J. Characterization of a microbial community capable of reducing perchlorate and nitrate in high salinity. Biotechnol Lett 2009; 31:959-66. [DOI: 10.1007/s10529-009-9960-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 02/16/2009] [Accepted: 02/18/2009] [Indexed: 11/24/2022]
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19
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Slobodkina GB, Kolganova TV, Tourova TP, Kostrikina NA, Jeanthon C, Bonch-Osmolovskaya EA, Slobodkin AI. Clostridium tepidiprofundi sp. nov., a moderately thermophilic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2008; 58:852-5. [DOI: 10.1099/ijs.0.65485-0] [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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20
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Villanueva L, Navarrete A, Urmeneta J, Geyer R, White DC, Guerrero R. Monitoring diel variations of physiological status and bacterial diversity in an estuarine microbial mat: an integrated biomarker analysis. MICROBIAL ECOLOGY 2007; 54:523-31. [PMID: 17347892 DOI: 10.1007/s00248-007-9224-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2007] [Revised: 01/07/2007] [Accepted: 02/01/2007] [Indexed: 05/14/2023]
Abstract
Microbial mats are highly productive microbial systems and a source of not-yet characterized microorganisms and metabolic strategies. In this article, we introduced a lipid biomarker/microbial isolation approach to detect short-term variations of microbial diversity, physiological and redox status, and also characterize lipid biomarkers from specific microbial groups that can be further monitored. Phospholipid fractions (PLFA) were examined for plasmalogens, indicative of certain anaerobes. The glycolipid fraction was processed for polyhydroxyalkanoates (PHA) and the neutral lipid fraction was used to evaluate respiratory quinone content. Data demonstrate an increase in the metabolic stress, unbalanced growth, proportion of anaerobic bacteria and respiratory rate after the maximal photosynthetic activity. Higher accumulation of polyhydroxyalkanoates at the same sampling point also suggested a situation of carbon storage by heterotrophs closely related to photosynthetic microorganisms. Besides, the characterization of lipid biomarkers (plasmalogens, sphingolipids) from specific microbial groups provided clues about the dynamics and diversity of less-characterized mat members. In this case, lipid analyses were complemented by the isolation and characterization of anaerobic spore formers and sulfate reducers to obtain insight into their affiliation and lipid composition. The results revealed that temporal shifts in lipid biomarkers are indicative of an intense change in the physiology, redox condition, and community composition along the diel cycle, and support the hypothesis that interactions between heterotrophs and primary producers play an important role in the carbon flow in microbial mats.
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Affiliation(s)
- Laura Villanueva
- Department of Microbiology, University of Barcelona, Barcelona, Spain.
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Crapart S, Fardeau ML, Cayol JL, Thomas P, Sery C, Ollivier B, Combet-Blanc Y. Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2007; 57:287-292. [PMID: 17267965 DOI: 10.1099/ijs.0.64639-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, halotolerant, moderately thermophilic and non-sporulating bacterium, designated strain 10C(T), was isolated from deep-sea hydrothermal vent samples collected on the 13 degrees N East Pacific Rise at a depth of approximately 2600 m. Cells of strain 10C(T) were Gram-positive, motile rods, and grew optimally at 45 degrees C (range 12-49 degrees C), pH 7.0 (range pH 5.5-9.5) and 0-2 % NaCl (range 0-11 %). (+)-L-Lactate was the main organic acid detected from carbohydrate fermentation with traces of formate, acetate and ethanol. Strain 10C(T) was catalase-positive, oxidase-negative and reduced nitrate to nitrite under anaerobic conditions. The DNA G+C content was 50.4 mol%. Its closest phylogenetic relatives were Exiguobacterium aestuarii TF-16(T) and Exiguobacterium marinum TF-80(T) (16S rRNA gene sequence similarity >99 %). However, strain 10C(T) differed genotypically from these two Exiguobacterium species as indicated by DNA-DNA relatedness data. Therefore, on the basis of phenotypic, genotypic and phylogenetic characteristics, strain 10C(T) is considered to represent a novel species of the genus Exiguobacterium, for which the name Exiguobacterium profundum sp. nov. is proposed. The type strain is 10C(T) (=CCUG 50949(T)=DSM 17289(T)).
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Affiliation(s)
- Sylvaine Crapart
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Marie-Laure Fardeau
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Jean-Luc Cayol
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Pierre Thomas
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Christian Sery
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Bernard Ollivier
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Yannick Combet-Blanc
- IRD, UMR180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
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L'Haridon S, Miroshnichenko ML, Kostrikina NA, Tindall BJ, Spring S, Schumann P, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C. Vulcanibacillus modesticaldus gen. nov., sp. nov., a strictly anaerobic, nitrate-reducing bacterium from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 2006; 56:1047-1053. [PMID: 16627653 DOI: 10.1099/ijs.0.64012-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, moderately thermophilic, spore-forming bacterium, designated strain BRT, was isolated from deep-sea hydrothermal core samples collected at the Rainbow vent field on the Mid-Atlantic Ridge (36 degrees 14' N 33 degrees 54' W). The cells were found to be rod-shaped, non-motile, Gram-positive and spore-forming. The organism grew in the temperature range 37-60 degrees C, with an optimum at 55 degrees C, and at pH values in the range 6-8.5, with an optimum around pH 7. NaCl concentrations for growth were in the range 10-40 g l(-1), with an optimum at 20-30 g l(-1). Strain BRT grew chemo-organoheterotrophically with carbohydrates, proteinaceous substrates and organic acids with nitrate as electron acceptor. The novel isolate was not able to ferment. The G+C content of the genomic DNA was 34.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain BRT in the Bacillaceae within the class 'Bacilli'. On the basis of the phenotypic and phylogenetic data, this isolate should be described as a member of a novel genus, for which the name Vulcanibacillus gen. nov. is proposed. The type species is Vulcanibacillus modesticaldus sp. nov., with the type strain BRT (=DSM 14931T=JCM 12998T).
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MESH Headings
- Atlantic Ocean
- Bacillaceae/classification
- Bacillaceae/cytology
- Bacillaceae/isolation & purification
- Bacillaceae/physiology
- Base Composition
- Carbohydrate Metabolism
- Carboxylic Acids/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Fermentation
- Genes, rRNA
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- Movement
- Nitrates/metabolism
- Phylogeny
- Proteins/metabolism
- Quinones/analysis
- Quinones/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic
- Seawater/microbiology
- Spores, Bacterial
- Temperature
- Water Microbiology
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Affiliation(s)
- S L'Haridon
- UMR 6197, Centre National de la Recherche Scientifique, IFREMER and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
| | - M L Miroshnichenko
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabraya 7/2, 117811 Moscow, Russia
| | - N A Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabraya 7/2, 117811 Moscow, Russia
| | - B J Tindall
- German Collection of Microorganisms and Cell Cultures (DSMZ), Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - S Spring
- German Collection of Microorganisms and Cell Cultures (DSMZ), Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - P Schumann
- German Collection of Microorganisms and Cell Cultures (DSMZ), Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - E Stackebrandt
- German Collection of Microorganisms and Cell Cultures (DSMZ), Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - E A Bonch-Osmolovskaya
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabraya 7/2, 117811 Moscow, Russia
| | - C Jeanthon
- UMR 6197, Centre National de la Recherche Scientifique, IFREMER and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
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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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