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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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Dai W, Sun W, Fu T, Jia C, Cui H, Han Y, Shi X, Zhang XH. Marinifilum caeruleilacunae sp. nov., isolated from Yongle Blue Hole in the South China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, facultatively anaerobic and non-flagellated marine bacterium, designated JC070T was isolated from the Yongle Blue Hole in the South China Sea. The temperature, pH and NaCl ranges for growth of strain JC070T were 4–37 °C (optimum, 16 °C), pH 6.0–9.0 (optimum, pH 7.0) and 1.0 –6.0% (w/v; optimum, 3.0%). The predominant isoprenoid quinone of strain JC070T was identified as menaquinone-7. The dominant fatty acids (>10%) were iso-C15:0 (59.6%) and iso-C17:0 3-OH (17.2%). The major polar lipids were aminophospholipid, aminolipid, two unknown phospholipids and two unidentified lipids. The genomic DNA G+C content was determined to be 37.0 mol%. Based on the results of polyphasic analysis, a new species, named Marinifilum caeruleilacunae sp. nov., within the genus
Marinifilum
was proposed. The type strain is JC070T (= JCM 39045T=MCCC 1K03774T).
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Affiliation(s)
- Wei Dai
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Wen Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Tianyu Fu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Chao Jia
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Hongchang Cui
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Yanqiong Han
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, PR China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, PR China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
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Ricci F, Tandon K, Black JR, Lê Cao KA, Blackall LL, Verbruggen H. Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses. mSystems 2022; 7:e0004422. [PMID: 35253476 PMCID: PMC9045482 DOI: 10.1128/msystems.00044-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022] Open
Abstract
The success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host phylogeny and traits are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using 12 coral species representing the complex and robust clades, we explored the influence of host phylogeny, skeletal architecture, and reproductive mode on the microbiome composition, and further investigated the structure of the tissue and skeleton bacterial communities. Our results show that host phylogeny and traits explained 14% of the tissue and 13% of the skeletal microbiome composition, providing evidence that these predictors contributed to shaping the holobiont in terms of presence and relative abundance of bacterial symbionts. Based on our data, we conclude that host phylogeny affects the presence of specific microbial lineages, reproductive mode predictably influences the microbiome composition, and skeletal architecture works like a filter that affects bacterial relative abundance. We show that the β-diversity of coral tissue and skeleton microbiomes differed, but we found that a large overlapping fraction of bacterial sequences were recovered from both anatomical compartments, supporting the hypothesis that the skeleton can function as a microbial reservoir. Additionally, our analysis of the microbiome structure shows that 99.6% of tissue and 99.7% of skeletal amplicon sequence variants (ASVs) were not consistently present in at least 30% of the samples, suggesting that the coral tissue and skeleton are dominated by rare bacteria. Together, these results provide novel insights into the processes driving coral-bacterial symbioses, along with an improved understanding of the scleractinian microbiome.
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Affiliation(s)
- Francesco Ricci
- School of BioSciences, University of Melbourne, Victoria, Australia
| | - Kshitij Tandon
- School of BioSciences, University of Melbourne, Victoria, Australia
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jay R. Black
- School of Geography, Earth and Atmospheric Sciences, University of Melbourne, Victoria, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Victoria, Australia
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Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
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Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
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Chen XJ, Wang ZQ, Zhou ZY, Zeng NY, Huang QF, Wang ZW, Tang WL, Zhou HW. Characterization of Peptacetobacter hominis gen. nov., sp. nov., isolated from human faeces, and proposal for the reclassification of Clostridium hiranonis within the genus Peptacetobacter. Int J Syst Evol Microbiol 2020; 70:2988-2997. [PMID: 32369000 DOI: 10.1099/ijsem.0.003925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A novel, Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, obligately anaerobic bacterium, designated strain ZHW00191T, was isolated from human faeces and characterized by using a polyphasic taxonomic approach. Growth occurred at 25-45 °C (optimum, 37-42 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). The end products of glucose fermentation were acetic acid, isobutyric acid and isovaleric acid and a small amount of propionic acid. The dominant cellular fatty acids (>10 %) of strain ZHW00191T were C16 : 0, C18 : 1 ω9с and C18 : 2ω6,9с. Its polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and ten unidentified glycolipids. Respiratory quinones were not detected. The cell-wall peptidoglycan contained meso-2,6-diaminopimelic acid, and the whole-cell sugars were ribose and glucose. The genomic DNA G+C content was 32.8 mol%. Analysis of the 16S rRNA gene sequence indicated that ZHW00191T was most closely related to Clostridium hiranonis TO-931T (95.3 % similarity). Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses with closely related reference strains indicated that reassociation values were both well below the thresholds of 95-96% and 70 % for species delineation, respectively. Based on phenotypic, chemotaxonomic and genetic studies, a novel genus, Peptacetobacter gen. nov., is proposed. The novel isolate ZHW00191T (=JCM 33482T=GDMCC 1.1530T) is proposed as the type strain of the type species Peptacetobacter hominis gen. nov., sp. nov. of the proposed new genus. Furthermore, it is proposed that Clostridium hiranonis be transferred to this novel genus, as Peptacetobacter hiranonis comb. nov.
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Affiliation(s)
- Xiao-Jiao Chen
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China
| | - Zhan-Qiang Wang
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China
| | - Zu-Yi Zhou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China
| | - Nian-Yi Zeng
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China
| | - Qing-Fa Huang
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China
| | - Zhong-Wei Wang
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, PR China
| | - Wen-Li Tang
- Shenzhen Fun-Poo Biotech Co., Ltd, Shenzhen 518000, PR China
| | - Hong-Wei Zhou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, PR China
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6
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Christman GD, León-Zayas RI, Zhao R, Summers ZM, Biddle JF. Novel clostridial lineages recovered from metagenomes of a hot oil reservoir. Sci Rep 2020; 10:8048. [PMID: 32415178 PMCID: PMC7229112 DOI: 10.1038/s41598-020-64904-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 12/05/2022] Open
Abstract
Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name UPetromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that UPetromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.
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Affiliation(s)
- Glenn D Christman
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
| | - Rosa I León-Zayas
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA.,Department of Biological Sciences, Willamette University, Salem, OR, USA
| | - Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
| | | | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA.
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Sun W, Fu T, Jia C, Fu L, Zhou S, Yao P, Gao X, Liu L, Yang Z, Shi X, Zhang XH. Puteibacter caeruleilacunae gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from Yongle Blue Hole in the South China Sea. Int J Syst Evol Microbiol 2020; 70:1623-1629. [DOI: 10.1099/ijsem.0.003948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blue holes are unique geomorphological units characterized by steep redox and biogeochemical gradients. Yongle Blue Hole is located on the largest atoll (Yongle Atoll) of the western Xisha Islands in the South China Sea. A Gram-stain-negative, facultatively anaerobic, non-motile, non-flagellated marine bacterium with creamy white colonies, designated JC036T, was isolated from Yongle Blue Hole. Cells were short-rod-shaped and catalase-negative. 16S rRNA gene sequence analysis showed that sequence similarities were lower than 91.6 % against all validly named species in the familyProlixibacteraceae; a reconstructed phylogenetic tree indicated that strain JC036Tformed a lineage with strains in the familyProlixibacteraceae. Growth occurred at 4–37 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum, 7.0) and in the presence of 2–6 % (w/v) NaCl (optimum, 3 %). The prevalent isoprenoid quinone of strain JC036Twas menaquinone-7 (MK-7). Iso-C15 : 0and iso-C17 : 03-OH were the predominant fatty acids. The major polar lipids included a phospholipid, phosphatidylethanolamine, an aminophospholipid and four unidentified lipids. The genomic DNA G+C content of strain JC036Twas 37.8 mol%. Based on physiological and biochemical characteristics and whole genome comparisons, we propose a new genus and species,Puteibacter caeruleilacunaegen. nov., sp. nov., within the familyProlixibacteraceae. The type strain ofPuteibacter caeruleilacunaeis JC036T(=JCM 33128T=MCCC 1K03579T). From this study, a deeper understanding of the community of the microorganism and their roles in biogeochemical cycles, especially anaerobic bacteria, is provided.
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Affiliation(s)
- Wen Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Tianyu Fu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chao Jia
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha 573199, PR China
| | - Shun Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Peng Yao
- Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao 266100, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Xueyu Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Lijun Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao 266100, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
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Fu T, Cui H, Jia C, Sun W, Zhou S, Han Y, Liu L, Shi X, Zhang XH. Ancylomarina longa sp. nov., isolated from southern Okinawa Trough sediment and emended description of the family Marinifilaceae. Int J Syst Evol Microbiol 2020; 70:2531-2536. [PMID: 32100699 DOI: 10.1099/ijsem.0.004066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-CT, was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-CT was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae. Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-CT was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C15 : 0 (38.9 %) and anteiso-C15 : 0 (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-CT was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-CT is considered to represent a novel species of the genus Ancylomarina, for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-CT (=KCTC 15505T=MCCC 1K01617T).
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Affiliation(s)
- Tianyu Fu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Hongchang Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chao Jia
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wen Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Shun Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanqiong Han
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Lijun Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China.,College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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Yu HY, Meade A, Liu SJ. Phylogeny of Clostridium spp. Based on Conservative Genes and Comparisons with Other Trees. Microbiology (Reading) 2019. [DOI: 10.1134/s002626171904012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Fu T, Jia C, Fu L, Zhou S, Yao P, Du R, Sun H, Yang Z, Shi X, Zhang XH. Marinifilum breve sp. nov., a marine bacterium isolated from the Yongle Blue Hole in the South China Sea and emended description of the genus Marinifilum. Int J Syst Evol Microbiol 2018; 68:3540-3545. [PMID: 30230441 DOI: 10.1099/ijsem.0.003027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultative anaerobic, non-motile, short-clavate and non-flagellated marine bacterium strain, designated JC075T, was isolated from the Yongle Blue Hole in the South China Sea. Based on the 16S rRNA gene sequence, strain JC075T was found to be closely related to Marinifilum albidiflavum FB208T (97.10 %), Marinifilum flexuosum DSM 21950T (96.43 %) and Marinifilum fragile JCM 15579T (95.58 %), with less than 90.24 % sequence similarity to other genera of the family Marinifilaceae. The growth temperature was in the range of 10-37 °C, and the optimum temperature was 16 °C. Optimal growth occurred at pH 7.0 and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain JC075T was identified as menaquinone-7 and the predominant fatty acids (>10 %) were iso-C15 : 0 (47.9 %), summed feature 9 (C17 : 1 or/and iso-C17 : 1ω9c; 18.7 %) and iso-C17 : 0 3-OH (14.9 %). The major polar lipids were one phosphatidylethanolamine, one phospholipid, one aminophospholipid, one glycolipid, one aminolipid and two unidentified lipids. The DNA G+C content of strain JC075T was 35.8 mol%. On the basis of polyphasic analysis, strain JC075T was considered to represent a novel species of the genus Marinifilum, for which the name Marinifilumbreve sp. nov. is proposed. The type strain is JC075T (=KCTC 15646T=MCCC 1K03477T=JCM 32401T).
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Affiliation(s)
- Tianyu Fu
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chao Jia
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Liang Fu
- 2Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha 573199, PR China
| | - Shun Zhou
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Peng Yao
- 3Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.,4Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao 266100, PR China
| | - Rui Du
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Hao Sun
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Zuosheng Yang
- 5College of Marine Geosciences, Ocean University of China, Qingdao 266100, PR China
| | - Xiaochong Shi
- 6Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao 266003, PR China.,3Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.,1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.,3Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.,6Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao 266003, PR China
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11
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Ancylomarina psychrotolerans sp. nov., isolated from sediments of Fildes Peninsula and emended the description of genus Ancylomarina. Antonie van Leeuwenhoek 2018; 111:1183-1189. [DOI: 10.1007/s10482-018-1025-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/25/2018] [Indexed: 11/25/2022]
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12
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Draft Genome Sequence of Anaerobic Fermentative Bacterium
Anaeromicrobium sediminis
DY2726D. GENOME ANNOUNCEMENTS 2018; 6:6/6/e00002-18. [PMID: 29439028 PMCID: PMC5805866 DOI: 10.1128/genomea.00002-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Here, we report the draft genome sequence of Anaeromicrobium sediminis DY2726D, isolated from a west Pacific Ocean sediment sample. The genome comprises 4,710,590 bp in 56 contigs, with a G+C content of 31.2%. A total of 3,811 protein-coding sequences were predicted. The genome annotation revealed that DY2726D may represent a marine type of Clostridiaceae.
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13
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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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