1
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Hirano S, Terahara T, Mori K, Hamada M, Matsumoto R, Kobayashi T. Vallitalea longa sp. nov., an anaerobic bacterium isolated from marine sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185279 DOI: 10.1099/ijsem.0.005882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
A novel bacterium, strain SH18-1T, was isolated from marine sediment collected near Sado Island in the Sea of Japan. This strain was strictly anaerobic, Gram-stain-negative, non-spore-forming, rod-shaped, motile, and mesophilic. It grew at 15-40 °C (optimum, 30-35 °C), at a NaCl concentration of 0.2-5.0 % (w/v; optimum, 1.5-2.5 %), and at pH 5.5-8.5 (optimum, pH 7.0). Results of 16S rRNA gene phylogenetic analysis showed a similarity value of 97.49 % between strain SH18-1T and Vallitalea guaymasensis Ra1766G1T, which was the most closely related species. The genome size of strain SH18-1T was 5.71 Mb and its G+C content was 30.2 mol%. Genome sequence analyses for comparison between strain SH18-1T and V. guaymasensis Ra1766G1T showed values lower than the threshold for species demarcation determined using the Genome-to-Genome Distance Calculator and the Average Nucleotide Identity Calculator. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, and nitrite were not used as terminal electron acceptors. The major fatty acids in strain SH18-1T were iso-C15 : 0, anteiso-C15 : 0, and C16 : 0, and the detected polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid, three unidentified phospholipids, and one unidentified polar lipid. From these results, strain SH18-1T (=NBRC 115488T=DSM 114058T) is suggested to represent a novel species of the genus Vallitalea and the name Vallitalea longa sp. nov. is proposed.
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Affiliation(s)
- Shiori Hirano
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Takeshi Terahara
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ryo Matsumoto
- Gas Hydrate Research Laboratory, Meiji University, 1-1-1 Higashi-Mita, Tama, Kawasaki, Kanagawa 214-8571, Japan
| | - Takeshi Kobayashi
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
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2
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Kawamura Y, Mori K, Amachi S. Reductive deiodination of 2,4,6-triiodophenol by Vallitalea sp. strain TIP-1 isolated from the marine sponge. J Biosci Bioeng 2021; 132:154-160. [PMID: 34024749 DOI: 10.1016/j.jbiosc.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
An anaerobic microbial consortium capable of reductively dehalogenating 2,4,6-triiodophenol (2,4,6-TIP) was enriched from the marine sponge Hymeniacidon sinapium. The enrichment reductively deiodinated 100 μM of 2,4,6-TIP to 4-iodophenol (4-IP) and 2-iodophenol (2-IP) in the presence of sterile sponge tissue as the sole carbon source and electron donor. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis revealed that bacteria closely related with Vallitalea guaymasensis and Oceanirhabdus sediminicola, both of which are members of the order Clostridiales, were predominant in the enrichment. When glucose was added to the enrichment as alternative carbon source, one of these bacteria grew predominantly, which was subsequently isolated as a pure culture. The strain, designated as TIP-1, showed 99.7% 16S rRNA gene sequence similarity with V. guaymasensis. In the presence of glucose, strain TIP-1 reductively deiodinated 2,4,6-TIP to 2-IP and 4-IP at a molar ratio of 3:1, during which 2,4-diiodophenol (2,4-DIP) and 2,6-diiodophenol (2,6-DIP) were observed as deiodinated intermediates. Glucose was required for 2,4,6-TIP deiodination, but 2,4,6-TIP was not essential for growth of strain TIP-1. The strain also deiodinated 2,4-DIP to 2-IP and 4-IP at a molar ratio of 1:1, and 2,6-DIP to 2-IP, but further deiodination of the monoiodophenols was not observed. These results suggest that strain TIP-1 removed both ortho- and para-substituted iodines equally. Such deiodinating bacteria could be applied to the mineralization or dehalogenation of triiodobenzene derivatives, which are widely used as X-ray contrast media.
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Affiliation(s)
- Yuki Kawamura
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba 271-8510, Japan
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba 271-8510, Japan.
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3
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Anaerotalea alkaliphila gen. nov., sp. nov., an alkaliphilic, anaerobic, fermentative bacterium isolated from a terrestrial mud volcano. Extremophiles 2021; 25:301-309. [PMID: 33891175 DOI: 10.1007/s00792-021-01229-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/12/2021] [Indexed: 02/03/2023]
Abstract
Diversity of extremophilic microorganisms in mud volcanoes is largely unexplored. Here, we report the isolation of a novel alkaliphilic, mesophilic, fermentative bacterium (strain F-3apT) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-3apT are Gram-stain-positive non-motile rods. The formation of endospores is not observed. The temperature range for growth is 14-42 °C, with an optimum at 37 °C. The pH range for growth is 7.5-11.0, with an optimum at pH 9.0. The isolate utilizes various organic polymeric substances, organic acids, carbohydrates, and proteinaceous compounds. The end products of glucose fermentation are ethanol, CO2, and H2. The major cellular fatty acids of strain F-3apT are C16:0, C16:1, and C14:0. Phylogenetic analysis reveals that strain F-3apT belongs to the order Clostridiales, with less than 91% of 16S rRNA gene sequence similarity to any species with a validly published name. The total size of the genome of strain F-3apT is 2.98 Mb, and a genomic DNA G + C content is 56.78 mol%. The whole-genome phylogenetic analysis confirms that strain F-3apT forms a distinct lineage within Clostridia. We propose to assign strain F-3apT to a new species of a novel genus Anaerotalea alkaliphila gen. nov., sp. nov. The type strain is F-3apT (= KCTC 15917 T = VKM B-3406 T).
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4
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Liu X, Lv Q, Ren H, Gao L, Zhao P, Yang X, Yang G, Xu D, Wang G, Yang W, Wang P, Wang Z, Xing S. The altered gut microbiota of high-purine-induced hyperuricemia rats and its correlation with hyperuricemia. PeerJ 2020; 8:e8664. [PMID: 32185104 PMCID: PMC7061907 DOI: 10.7717/peerj.8664] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
Some studies on the hyperuricemia (HUA) have focused on intestinal bacteria. To better understand the correlation between gut microbiota and HUA, we established a HUA rat model with high-purine diet, and used 16S rRNA genes sequencing to analyze gut microbiota changes in HUA rats. To analyze the potential role played by gut microbiota in HUA, we altered the gut microbiota of HUA rats with antibiotics, and compared the degree of uric acid elevation between HUA and antibiotic-fed HUA rats (Ab+HUA). Finally, we established a recipient rat model, in which we transplanted fecal microbiota of HUA and normal rats into recipient rats. Three weeks later, we compared the uric acid content of recipient rats. As a result, the diversity and abundance of the gut microbiota had changed in HUA rats. The Ab-fed HUA rats had significantly lower uric acid content compared to the HUA rats, and gut microbiota from HUA rats increased uric acid content of recipient rats. The genera Vallitalea, Christensenella and Insolitispirillum may associate with HUA. Our findings highlight the association between gut microbiota and HUA, and the potential role played by gut microbiota in HUA. We hope that this finding will promote the isolation and culture of HUA-related bacteria and orient HUA-related studies from being correlational to mechanistic. These steps will therefore make it possible for us to treat HUA using gut microbiota as the target.
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Affiliation(s)
- Xiu Liu
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Qiulan Lv
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongyan Ren
- Shanghai Itechgene Technology Co.,Ltd, Shanghai, China
| | - Liu Gao
- Medical Department of 3SBio Group, Shanghai, China
| | - Peng Zhao
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaomin Yang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guanpin Yang
- The Key Laboratory of Mariculture of Ministry of Education, Ocean University of China, Qingdao, China
| | - Daxing Xu
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Guangtao Wang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wan Yang
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Pengjun Wang
- Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zenglan Wang
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Shichao Xing
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China.,Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Sports Medicine and Health, Qingdao, China.,School of Cardiovascular Medicine and Science, King's College London, London, United Kingdom
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5
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Lam BR, Barr CR, Rowe AR, Nealson KH. Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment. Front Microbiol 2019; 10:1979. [PMID: 31555224 PMCID: PMC6724507 DOI: 10.3389/fmicb.2019.01979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/12/2019] [Indexed: 01/21/2023] Open
Abstract
The diversity of microbially mediated redox processes that occur in marine sediments is likely underestimated, especially with respect to the metabolisms that involve solid substrate electron donors or acceptors. Though electrochemical studies that utilize poised potential electrodes as a surrogate for solid substrate or mineral interactions have shed some much needed light on these areas, these studies have traditionally been limited to one redox potential or metabolic condition. This work seeks to uncover the diversity of microbes capable of accepting cathodic electrons from a marine sediment utilizing a range of redox potentials, by coupling electrochemical enrichment approaches to microbial cultivation and isolation techniques. Five lab-scale three-electrode electrochemical systems were constructed, using electrodes that were initially incubated in marine sediment at cathodic or electron-donating voltages (five redox potentials between -400 and -750 mV versus Ag/AgCl) as energy sources for enrichment. Electron uptake was monitored in the laboratory bioreactors and linked to the reduction of supplied terminal electron acceptors (nitrate or sulfate). Enriched communities exhibited differences in community structure dependent on poised redox potential and terminal electron acceptor used. Further cultivation of microbes was conducted using media with reduced iron (Fe0, FeCl2) and sulfur (S0) compounds as electron donors, resulting in the isolation of six electrochemically active strains. The isolates belong to the genera Vallitalea of the Clostridia, Arcobacter of the Epsilonproteobacteria, Desulfovibrio of the Deltaproteobacteria, and Vibrio and Marinobacter of the Gammaproteobacteria. Electrochemical characterization of the isolates with cyclic voltammetry yielded a wide range of midpoint potentials (99.20 to -389.1 mV versus Ag/AgCl), indicating diverse metabolic pathways likely support the observed electron uptake. Our work demonstrates culturing under various electrochemical and geochemical regimes allows for enhanced cultivation of diverse cathode-oxidizing microbes from one environmental system. Understanding the mechanisms of solid substrate oxidation from environmental microbes will further elucidation of the ecological relevance of these electron transfer interactions with implications for microbe-electrode technologies.
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Affiliation(s)
- Bonita R. Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey R. Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Kenneth H. Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
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6
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Quéméneur M, Erauso G, Frouin E, Zeghal E, Vandecasteele C, Ollivier B, Tamburini C, Garel M, Ménez B, Postec A. Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov. Front Microbiol 2019; 10:1497. [PMID: 31379757 PMCID: PMC6647913 DOI: 10.3389/fmicb.2019.01497] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/14/2019] [Indexed: 01/03/2023] Open
Abstract
Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-AT. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.
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Affiliation(s)
- Marianne Quéméneur
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Gaël Erauso
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Eléonore Frouin
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Emna Zeghal
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | | | - Bernard Ollivier
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Christian Tamburini
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Marc Garel
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Bénédicte Ménez
- Université de Paris, Institut de Physique du Globe de Paris, CNRS UMR 7154, Paris, France
| | - Anne Postec
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
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7
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Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun 2019; 10:1816. [PMID: 31000700 PMCID: PMC6472368 DOI: 10.1038/s41467-019-09747-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/20/2019] [Indexed: 02/07/2023] Open
Abstract
The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism. Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.
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Sun YT, Zhou N, Wang BJ, Liu XD, Jiang CY, Ge X, Liu SJ. Vallitalea okinawensis sp. nov., isolated from Okinawa Trough sediment and emended description of the genus Vallitalea. Int J Syst Evol Microbiol 2018; 69:404-410. [PMID: 30540237 DOI: 10.1099/ijsem.0.003158] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic study was conducted to characterize an obligately anaerobic bacterial strain, S15T, that was isolated from Okinawa Trough sediment. Strain S15T was Gram-stain-negative, non-motile and rod-shaped. Spores were not observed. Strain S15T grew anaerobically at 20-35 °C (optimum at 25-30 °C) and at pH range of 6.0-8.5 (optimum at 7.5). Analysis of 16S rRNA gene sequences showed that strain S15T was phylogenetically related to Vallitalea guaymasensis Ra1766G1T (94.0 %) and Vallitalea pronyensis FatNI3T (93.1 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The predominant fatty acids of strain S15T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The draft genome was 5.86 Mb with a DNA G+C content of 33.9 mol%. A total of 5285 genes were predicted and, of those, 4669 genes were annotated. The genome data supported the result that strain S15T assimilated various carbon sources. On the basis of unique phenotypic, chemotaxonomic and phylogenetic comparisons, strain S15T is proposed to represent a novel species within the genus Vallitalea, and the name Vallitaleaokinawensis sp. nov. is proposed. The type strain is S15T=CGMCC 1.5231T=KCTC 15675T.
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Affiliation(s)
- Yu-Tong Sun
- 1College of Life Science, Hebei University, Baoding 071002, PR China.,2State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Nan Zhou
- 2State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,3University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bao-Jun Wang
- 2State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao-Dong Liu
- 2State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Ying Jiang
- 2State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,4RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, PR China
| | - Xin Ge
- 1College of Life Science, Hebei University, Baoding 071002, PR China
| | - Shuang-Jiang Liu
- 1College of Life Science, Hebei University, Baoding 071002, PR China.,3University of Chinese Academy of Sciences, Beijing 100049, PR China.,2State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,4RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, PR China
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9
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Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
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Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
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10
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Ma S, Huang Y, Wang C, Fan H, Dai L, Zhou Z, Liu X, Deng Y. Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw. Int J Syst Evol Microbiol 2017; 67:1607-1612. [PMID: 27902335 PMCID: PMC5817277 DOI: 10.1099/ijsem.0.001664] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. Cells were Gram-stain-positive, slightly curved rods with a size of 0.6-1×2.5-8.2 µm, non-motile and produced terminal spores. The temperature, pH and NaCl concentration ranges for growth were 40-60 °C, 6.5-8.0 and 0-15.0 g l-1, with optimum growth noted at 50-55 °C, pH 7.5 and in the absence of NaCl, respectively. Yeast extract was required for growth. d-Glucose, maltose, d-xylose, d-galactose, d-fructose, d-ribose, lactose, raffinose, sucrose, d-arabinose, cellobiose, d-mannose and yeast extract were used as carbon and energy sources. The fermentation products from glucose were ethanol, lactate, acetate, propionate, butyrate, valerate, iso-butyrate, iso-valerate, H2 and CO2. The G+C content of the genomic DNA was 36.6 mol%. The predominant fatty acids were C16 : 0, iso-C17 : 1, C14 : 0, C16 : 1ω7c, C16 : 0 N-alcohol and C13 : 0 3-OH. Respiratory quinones were not detected. The polar lipid profile comprised phosphoglycolipids, phospholipids, glycolipids, a diphosphatidylglycerol, a phosphatidylglycerol and an unidentified lipid. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was closely related to Defluviitalea saccharophila DSM 22681T with a similarity of 96.0 %. Based on the morphological, physiological and taxonomic characterization, strain A6T is considered to represent a novel species of the genus Defluviitalea, for which the name Defluviitalea raffinosedens sp. nov. is proposed. The type strain is A6T (=DSM 28090T=ACCC 19951T).
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Affiliation(s)
- Shichun Ma
- Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Present address: Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nan Road, Chengdu 610041, Sichuan, P.R. China.,Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Yan Huang
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Cong Wang
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, Sichuan, P.R. China.,Present address: College of Light Industry, Textile and Food Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, Sichuan, P.R. China
| | - Hui Fan
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Lirong Dai
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Zheng Zhou
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Xing Liu
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Yu Deng
- Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China
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11
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Postec A, Ollivier B, Fardeau ML. Objection to the proposition of the new genus Abyssivirga. Int J Syst Evol Microbiol 2017; 67:174. [PMID: 27902224 DOI: 10.1099/ijsem.0.001601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anne Postec
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, cedex 09, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, cedex 09, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288, Marseille, cedex 09, France
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12
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Ji SQ, Wang B, Lu M, Li FL. Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae. Appl Environ Microbiol 2016; 82:868-77. [PMID: 26590273 PMCID: PMC4725288 DOI: 10.1128/aem.03297-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
Brown algae are one of the largest groups of oceanic primary producers for CO2 removal and carbon sinks for coastal regions. However, the mechanism for brown alga assimilation remains largely unknown in thermophilic microorganisms. In this work, a thermophilic alginolytic community was enriched from coastal sediment, from which an obligate anaerobic and thermophilic bacterial strain, designated Alg1, was isolated. Alg1 shared a 16S rRNA gene identity of 94.6% with Defluviitalea saccharophila LIND6LT2(T). Phenotypic, chemotaxonomic, and phylogenetic studies suggested strain Alg1 represented a novel species of the genus Defluviitalea, for which the name Defluviitalea phaphyphila sp. nov. is proposed. Alg1 exhibited an intriguing ability to convert carbohydrates of brown algae, including alginate, laminarin, and mannitol, to ethanol and acetic acid. Three gene clusters participating in this process were predicted to be in the genome, and candidate enzymes were successfully expressed, purified, and characterized. Six alginate lyases were demonstrated to synergistically deconstruct alginate into unsaturated monosaccharide, followed by one uronic acid reductase and two 2-keto-3-deoxy-d-gluconate (KDG) kinases to produce pyruvate. A nonclassical mannitol 1-phosphate dehydrogenase, catalyzing D-mannitol 1-phosphate to fructose 1-phosphate in the presence of NAD(+), and one laminarase also were disclosed. This work revealed that a thermophilic brown alga-decomposing system containing numerous novel thermophilic alginate lyases and a unique mannitol 1-phosphate dehydrogenase was adopted by the natural ethanologenic strain Alg1 during the process of evolution in hostile habitats.
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Affiliation(s)
- Shi-Qi Ji
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Bing Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, People's Republic of China
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13
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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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14
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Ben Aissa F, Postec A, Erauso G, Payri C, Pelletier B, Hamdi M, Ollivier B, Fardeau ML. Vallitalea pronyensis sp. nov., isolated from a marine alkaline hydrothermal chimney. Int J Syst Evol Microbiol 2014; 64:1160-1165. [DOI: 10.1099/ijs.0.055756-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermotolerant, anaerobic, Gram-stain-positive, spore-forming bacterium was isolated from a hydrothermal chimney in Prony Bay, New Caledonia. This strain, designated FatNI3T, grew at 15–55 °C (optimum 30 °C) and at pH 5.8–8.9 (optimum 7.7). It was slightly halophilic, requiring at least 0.5 % NaCl for growth (optimum 2.5–3.0 %), and was able to grow at up to 6 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Growth of strain FatNI3T was inhibited in the presence of sulfite (2 mM) or nitrite (2 mM). Strain FatNI3T fermented cellobiose, glucose, mannose, maltose, sucrose, galactose, lactose, ribose, fructose, rhamnose, raffinose, xylose, yeast extract, peptone and biotrypticase. The main fermentation products from glucose metabolism were acetate, ethanol, H2 and CO2. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, and unknown glycolipids and phospholipids. The G+C content of the genomic DNA was 36.6 mol%. On the basis of phylogenetic and physiological properties, strain FatNI3T ( = DSM 25904 = JCM 18391) belonging to the phylum
Firmicutes
, class
Clostridia
, order
Clostridiales
, is proposed as the type strain of a novel species of the genus
Vallitalea
, for which the name Vallitalea pronyensis sp. nov. is proposed.
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Affiliation(s)
- Fatma Ben Aissa
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia
- 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
| | - Gaël Erauso
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Claude Payri
- Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5 – 98848 Nouméa cedex, New Caledonia
| | - Bernard Pelletier
- Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5 – 98848 Nouméa cedex, New Caledonia
| | - Moktar Hamdi
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288, Marseille, cedex 09, France
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