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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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Ketchum RN, Smith EG, Vaughan GO, McParland D, Al-Mansoori N, Burt JA, Reitzel AM. Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients. Mol Ecol 2021; 30:3869-3881. [PMID: 34008895 DOI: 10.1111/mec.15990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Grace O Vaughan
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Dain McParland
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Noura Al-Mansoori
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - John A Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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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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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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Lv X, Chai J, Diao Q, Huang W, Zhuang Y, Zhang N. The Signature Microbiota Drive Rumen Function Shifts in Goat Kids Introduced to Solid Diet Regimes. Microorganisms 2019; 7:microorganisms7110516. [PMID: 31683646 PMCID: PMC6921049 DOI: 10.3390/microorganisms7110516] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 11/24/2022] Open
Abstract
The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production.
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Affiliation(s)
- Xiaokang Lv
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Jianmin Chai
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Qiyu Diao
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Wenqin Huang
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Yimin Zhuang
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
| | - Naifeng Zhang
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China.
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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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González-Siso MI. Editorial for the Special Issue: Thermophiles and Thermozymes. Microorganisms 2019; 7:microorganisms7030062. [PMID: 30818747 PMCID: PMC6463253 DOI: 10.3390/microorganisms7030062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Affiliation(s)
- María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
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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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