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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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2
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Bai S, Zhang P, Zhang C, Du J, Du X, Zhu C, Liu J, Xie P, Li S. Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium. Front Microbiol 2021; 12:769012. [PMID: 34745077 PMCID: PMC8567075 DOI: 10.3389/fmicb.2021.769012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
Despite an increasing appreciation in the importance of host–microbe interactions in ecological and evolutionary processes, information on the gut microbial communities of some marine mammals is still lacking. Moreover, whether diet, environment, or host phylogeny has the greatest impact on microbial community structure is still unknown. To fill part of this knowledge gap, we exploited a natural experiment provided by an aquarium with belugas (Delphinapterus leucas) affiliated with family Monodontidae, Pacific white-sided dolphins (Lagenorhynchus obliquidens) and common bottlenose dolphin (Tursiops truncatus) affiliated with family Delphinidae, and Cape fur seals (Arctocephalus pusillus pusillus) affiliated with family Otariidae. Results show significant differences in microbial community composition of whales, dolphins, and fur seals and indicate that host phylogeny (family level) plays the most important role in shaping the microbial communities, rather than food and environment. In general, the gut microbial communities of dolphins had significantly lower diversity compared to that of whales and fur seals. Overall, the gut microbial communities were mainly composed of Firmicutes and Gammaproteobacteria, together with some from Bacteroidetes, Fusobacteria, and Epsilonbacteraeota. However, specific bacterial lineages were differentially distributed among the marine mammal groups. For instance, Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae were the dominant bacterial lineages in the gut of belugas, while for Cape fur seals, Moraxellaceae and Bacteroidaceae were the main bacterial lineages. Moreover, gut microbial communities in both Pacific white-sided dolphins and common bottlenose dolphins were dominated by a number of pathogenic bacteria, including Clostridium perfringens, Vibrio fluvialis, and Morganella morganii, reflecting the poor health condition of these animals. Although there is a growing recognition of the role microorganisms play in the gut of marine mammals, current knowledge about these microbial communities is still severely lacking. Large-scale research studies should be undertaken to reveal the roles played by the gut microbiota of different marine mammal species.
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Affiliation(s)
- Shijie Bai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Jiang Du
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | | | - Chengwei Zhu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jun Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peiyu Xie
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Khomyakova MA, Merkel AY, Slobodkin AI. Perlabentimonas gracilis gen. nov., sp. nov., a gliding aerotolerant anaerobe of the order Bacteroidales, isolated from a terrestrial mud volcano. Syst Appl Microbiol 2021; 44:126245. [PMID: 34392063 DOI: 10.1016/j.syapm.2021.126245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/15/2022]
Abstract
A novel anaerobic bacterium (strain M08_MBT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Gram-stain-negative cells were straight and slender rods with gliding motility, occasionally forming long filaments. The isolate was mesophilic, slightly halo- and alkaliphilic chemoorganoheterotroph, growing on carbohydrates (starch, dextrin, pectin, glucose, fructose, mannose, maltose, trehalose, lactose, sucrose) and proteinaceous compounds (peptone, tryptone, gelatin, casein and albumin). Strain M08_MBT tolerated 3% oxygen in the gas phase while catalase negative. The dominant cellular fatty acids of strain M08_MBT were C15:0, C15:1 and C13:0 acids. 16S rRNA gene sequence analysis revealed that strain M08_MBT belongs to the order Bacteroidales and only distantly related to other cultivated members of this order (85.12-90.01% 16S rRNA gene similarity). The genome of strain M08_MBT had a size of 4.37 Mb with a DNA G + C content of 43.5 mol% (WGS). The genes involved in gliding motility, proteolysis, central carbon metabolism, and oxygen tolerance were listed in genome annotation. Based on the phenotypic and genotypic characteristics, strain M08_MBT represents a novel species of a novel genus within family Tenuifilaceae, with proposed name Perlabentimonas gracilis gen. nov., sp. nov. The type strain is M08_ MBT (=DSM 110720 T = VKM B-3471 T). This is the first representative of Bacteroidales isolated in pure culture from a mud volcano.
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia.
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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5
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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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6
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Watanabe M, Kojima H, Fukui M. Labilibaculum antarcticum sp. nov., a novel facultative anaerobic, psychrotorelant bacterium isolated from marine sediment of Antarctica. Antonie Van Leeuwenhoek 2019; 113:349-355. [PMID: 31628625 DOI: 10.1007/s10482-019-01345-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/02/2019] [Indexed: 11/26/2022]
Abstract
A novel facultative anaerobic and facultative psychrophilic bacterium, designated SPP2T, was isolated from an Antarctic marine sediment. Cells of the isolate were observed to be long rods (0.5 × 5-10 μm), Gram-stain negative and to have gliding motility. For growth, the optimum NaCl concentration was found to be 2-3% and the optimum temperature to be 18-22 °C. Strain SPP2T cannot use sulfate and nitrate as electron acceptors in the presence of lactate. The G+C content of the genomic DNA was determined to be 36.0 mol%.. The major cellular fatty acids were identified as anteiso-C15:0 and iso-C15:0. MK-7 was found to be the predominant respiratory quinone. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belongs to the family Marinifilaceae and to be closely related to Labilibaculum manganireducens 59.10-2MT with 16S rRNA gene sequence identity of 98%. The OrthoANI and dDDH values between the genome sequences of strain SPP2T and its close relative were 84% and 27.3%, which are lower than the threshold values for species delineation. On the basis of phylogenetic and phenotypic characterisation, Labilibaculum antarcticum sp. nov. is proposed with the type strain SPP2T (= NBRC 111151T = CECT 9460T).
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Affiliation(s)
- Miho Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-8471, Japan.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Park S, Park JM, Yoon JH. Ancylomarina salipaludis sp. nov., isolated from a salt marsh. Int J Syst Evol Microbiol 2019; 69:2750-2754. [PMID: 31241445 DOI: 10.1099/ijsem.0.003553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and rod-shaped or filamentous bacterial strain, designated SHSM-M15T, was isolated from a salt marsh at Siheung in Republic of Korea and identified by polyphasic taxonomic study. Strain SHSM-M15T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain SHSM-M15T clusters with the type strain of Ancylomarina subtilis, showing 16S rRNA gene sequence similarity of 97.8 %. Strain SHSM-M15T had 16S rRNA gene sequence similarities of less than 93.7 % with the type strains of other recognised species. Strain SHSM-M15T contained MK-7 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipid detected in strain SHSM-M15T was phosphatidylethanolamine. The DNA G+C content of strain SHSM-M15T from genomic sequence was 36.6 %. Mean DNA-DNA relatedness value between strain SHSM-M15T and the type strain of A. subtilis was 18 % and the average nucleotide identity value between strain SHSM-M15T and the type strain of A. subtilis was 87.98 %. The phylogenetic and genetic data and differential phenotypic properties indicated that strain SHSM-M15T is separated from A. subtilis. On the basis of the polyphasic data presented, strain SHSM-M15T is considered to represent a novel species of the genus Ancylomarina, for which the name Ancylomarina salipaludis sp. nov. is proposed. The type strain is SHSM-M15T (=KACC 19862T=NBRC 113749T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, South Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, South Korea
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Zhang C, Yuan Q, Lu Y. Inhibitory effects of ammonia on syntrophic propionate oxidation in anaerobic digester sludge. WATER RESEARCH 2018; 146:275-287. [PMID: 30278382 DOI: 10.1016/j.watres.2018.09.046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/30/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
Syntrophic propionate oxidation (SPO) coupled with methanogenesis is often inhibited under high ammonium concentrations in anaerobic digesters. However, the inhibitory mechanism remains poorly understood. We conducted two independent laboratory experiments with a swine manure digester sludge. In experiment I, RNA-based stable isotope probing (SIP) was applied to determine the active players of both bacteria and methanogens involved in SPO under different ammonium concentrations (0, 3 and 7 g NH4+N L-1). In experiment II, the dynamics of the bacterial community under ammonia stress was monitored using the 16S rRNA pyrosequencing and quantitative PCR under similar conditions as in experiment I but without the addition of external propionate. An additional higher ammonium treatment (10 g NH4+N L-1) was applied in experiment II to maximize the ammonia stress. We identified that the Smithella bacteria and the Methanosaetaceae and Methanospirillaceae archaea were the most active players involved in SPO and methanogenesis. We revealed that Smithella, Methanosaetaceae and Methanospirillaceae were moderately and severely inhibited at 3 and 7-10 g NH4+N L-1, respectively. However, the fermentative bacteria appeared to be more tolerant to ammonia stress. The microbial responses were corroborated with the accumulation of VFAs and the repression of methanogenesis under high ammonium conditions.
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Affiliation(s)
- Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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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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Vandieken V, Marshall IPG, Niemann H, Engelen B, Cypionka H. Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea. Front Microbiol 2018; 8:2614. [PMID: 29354105 PMCID: PMC5760507 DOI: 10.3389/fmicb.2017.02614] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in deep subsurface sediments are challenged by the decrease in amount and quality of organic substrates with depth. In sediments of the Baltic Sea, they might additionally have to cope with an increase in salinity from ions that have diffused downward from the overlying water during the last 9000 years. Here, we report the isolation and characterization of four novel bacteria of the Bacteroidetes from depths of 14–52 m below seafloor (mbsf) of Baltic Sea sediments sampled during International Ocean Discovery Program (IODP) Expedition 347. Based on physiological, chemotaxonomic and genotypic characterization, we propose that the four strains represent two new species within a new genus in the family Marinifilaceae, with the proposed names Labilibaculum manganireducens gen. nov., sp. nov. (type strain 59.10-2MT) and Labilibaculum filiforme sp. nov. (type strains 59.16BT) with additional strains of this species (59.10-1M and 60.6M). The draft genomes of the two type strains had sizes of 5.2 and 5.3 Mb and reflected the major physiological capabilities. The strains showed gliding motility, were psychrotolerant, neutrophilic and halotolerant. Growth by fermentation of mono- and disaccharides as well as pyruvate, lactate and glycerol was observed. During glucose fermentation, small amounts of electron equivalents were transferred to Fe(III) by all strains, while one of the strains also reduced Mn(IV). Thereby, the four strains broaden the phylogenetic range of prokaryotes known to reduce metals to the group of Bacteroidetes. Halotolerance and metal reduction might both be beneficial for survival in deep subsurface sediments of the Baltic Sea.
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Affiliation(s)
- Verona Vandieken
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Ian P G Marshall
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Helge Niemann
- Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland.,CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, University of Tromsø, Tromsø, Norway.,Departments of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, and Utrecht University, Netherlands
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heribert Cypionka
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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13
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Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. ISME JOURNAL 2017; 12:367-379. [PMID: 28984846 PMCID: PMC5776450 DOI: 10.1038/ismej.2017.163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/29/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
Wood-fall ecosystems host chemosynthetic bacteria that use hydrogen sulfide as an electron donor. The production of hydrogen sulfide from decaying wood in the deep-sea has long been suspected to rely on the activity of wood-boring bivalves, Xylophaga spp. However, recent mesocosm experiments have shown hydrogen sulfide production in the absence of wood borers. Here, we combined in situ chemical measurements, amplicon sequencing and metagenomics to test whether the presence of Xylophaga spp.-affected hydrogen sulfide production and wood microbial community assemblages. During a short-term experiment conducted in a deep-sea canyon, we found that wood-fall microbial communities could produce hydrogen sulfide in the absence of Xylophaga spp. The presence of wood borers had a strong impact on the microbial community composition on the wood surface but not in the wood centre, where communities were observed to be homogeneous among different samples. When wood borers were excluded, the wood centre community did not have the genetic potential to degrade cellulose or hemicellulose but could use shorter carbohydrates such as sucrose. We conclude that wood centre communities produce fermentation products that can be used by the sulfate-reducing bacteria detected near the wood surface. We thus demonstrate that microorganisms alone could establish the chemical basis essential for the recruitment of chemolithotrophic organisms in deep-sea wood falls.
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14
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Fadhlaoui K, Ben Hania W, Postec A, Hamdi M, Ollivier B, Fardeau ML. Balneicella halophila gen. nov., sp. nov., an anaerobic bacterium, isolated from a thermal spring and description of Balneicellaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:4692-4696. [DOI: 10.1099/ijsem.0.001412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Khaled Fadhlaoui
- Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France
- Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, Université de Carthage, BP 676, 1080 Tunis, Tunisia
| | - Wajdi Ben Hania
- Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France
- Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, Université de Carthage, BP 676, 1080 Tunis, Tunisia
| | - Anne Postec
- Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France
| | - Moktar Hamdi
- Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, Université de Carthage, BP 676, 1080 Tunis, Tunisia
| | - Bernard Ollivier
- Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France
| | - Marie-Laure Fardeau
- Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France
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15
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Xu ZX, Mu X, Zhang HX, Chen GJ, Du ZJ. Marinifilum albidiflavum sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2016; 66:4589-4593. [PMID: 27498985 DOI: 10.1099/ijsem.0.001395] [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 Gram-stain-negative, facultatively anaerobic, filamentous, and yellowish-white-pigmented marine bacterium, designated strain FB208T, was isolated from marine sediment obtained off the coastal area of Weihai, China. Cells of strain FB208T were filamentous during exponential growth, fragmented to rods in the stationary growth phase and became spherical in aged cultures. It grew optimally at 33 °C, at pH 7.0-7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence, strain FB208T was found to be closely related to Marinifilum flexuosum DSM 21950T (96.9 % similarity) and Marinifilum fragile JCM 15579T (96.4 %), with less than 90.0 % sequence similarity to other genera of the class Bacteroidia. Phylogenetic analysis, also based on 16S rRNA gene sequences, placed strain FB208T in the genus Marinifilum, family Marinifilaceae. The predominant isoprenoid quinone of strain FB208T was identified as menaquinone MK-7. The main cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c, and the major polar lipids were an unidentified lipid and aminophospholipid. The G+C content of the genomic DNA was 43.8 mol%. Based on these phylogenetic and phenotypic data, strain FB208T represents a novel species of the genus Marinifilum, for which the name Marinifilum albidiflavum sp. nov. is proposed. The type strain is FB208T (=KCTC 42591T=MCCC 1H00113T).
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Affiliation(s)
- Zhen-Xing Xu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Xin Mu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Heng-Xi Zhang
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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16
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Wu WJ, Zhao JX, Chen GJ, Du ZJ. Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales. Int J Syst Evol Microbiol 2016; 66:4243-4249. [PMID: 27470589 DOI: 10.1099/ijsem.0.001342] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, moderately halophilic, filamentous, non-motile bacterium, designated FA102T, was isolated from marine sediment from the coast of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FA102T formed a distinct evolutionary lineage within the family Marinifilaceae and its closest relative was Marinifilum fragile JCM 15579T (93.2 % sequence similarity). The DNA G+C content of the novel strain was 36.5 mol%. The predominant cellular fatty acids and respiratory quinone were iso-C15 : 0 and iso-C15 : 0 3-OH, and MK-7, respectively. On the basis of the phylogenetic, phenotypic and physiological data, strain FA102T represents a novel genus and species, for which the name Ancylomarina subtilis gen. nov., sp. nov. is proposed. The type strain of Ancylomarina subtilis is FA102T (=KCTC 42257T=DSM 28825T=CICC 10902T). Furthermore, a new order named Marinilabiliales is proposed to accommodate three families previously classified in the order Bacteroidales. Marinilabiliales ord. nov. encompasses the families Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae.
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Affiliation(s)
- Wen-Jie Wu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Jin-Xin Zhao
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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17
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Liu QQ, Li J, Xiao D, Lu JX, Chen GJ, Du ZJ. Saccharicrinis marinus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:3427-3432. [DOI: 10.1099/ijsem.0.000436] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated Y11T, was isolated from marine sediment at Weihai in China. Comparative analysis of 16S rRNA gene sequences demonstrated that the novel isolate showed highest similarity to Saccharicrinis fermentans DSM 9555T (94.0 %) and Saccharicrinis carchari SS12T (92.7 %). Strain Y11T was a Gram-stain-negative, rod-shaped, non-endospore-forming, yellow-pigmented bacterium and was able to hydrolyse agar weakly. It was catalase-negative, oxidase-positive, facultatively anaerobic and motile by gliding. Optimal growth occurred at 28–30 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. The DNA G+C content was 34.4 mol%. The strain contained MK-7 as the prevalent menaquinone. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C15 : 1ω6c. The predominant polar lipids were phosphatidylethanolamine and two unknown lipids. Data from the present polyphasic taxonomic study clearly place the strain as representing a novel species within the genus Saccharicrinis, for which the name Saccharicrinis marinus sp. nov. is proposed. The type strain is Y11T ( = CICC10837T = KCTC42400T).
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Affiliation(s)
- Qian-Qian Liu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Juan Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, PO Box 5, Changping, Beijing 102206, PR China
| | - Di Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, PO Box 5, Changping, Beijing 102206, PR China
| | - Jin-Xing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, PO Box 5, Changping, Beijing 102206, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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18
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Wu WJ, Liu QQ, Chen GJ, Du ZJ. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 2015; 65:2260-2264. [DOI: 10.1099/ijs.0.000250] [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 Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08T, was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5–8.0 and with 2–3 % (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88–90 % sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08T ( = KCTC 42261T = CICC 10901T).
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Affiliation(s)
- Wen-Jie Wu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Qian-Qian Liu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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19
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Nolla-Ardèvol V, Strous M, Tegetmeyer HE. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. Front Microbiol 2015; 6:597. [PMID: 26157422 PMCID: PMC4475827 DOI: 10.3389/fmicb.2015.00597] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/31/2015] [Indexed: 12/02/2022] Open
Abstract
A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na+). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 aquatic group” while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus.
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Affiliation(s)
- Vímac Nolla-Ardèvol
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany
| | - Marc Strous
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Department of Geoscience, University of Calgary Calgary, AB, Canada ; Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Halina E Tegetmeyer
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
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20
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Chen X, Di P, Wang H, Li B, Pan Y, Yan S, Wang Y. Bacterial community associated with the intestinal tract of Chinese mitten crab (Eriocheir sinensis) farmed in Lake Tai, China. PLoS One 2015; 10:e0123990. [PMID: 25875449 PMCID: PMC4395229 DOI: 10.1371/journal.pone.0123990] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/25/2015] [Indexed: 01/16/2023] Open
Abstract
Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species in South-East Asia that has been widely farmed in China. Characterization of the intestinal bacterial diversity of CMC will provide insights into the aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from culture-independent CMC gut bacteria, 124 out of 128 different clones reveal >95% nucleotide similarity to the species belonging to the four phyla of Tenericutes, Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence similarity to the member of TM7 (a candidate phylum without cultured representatives). Fluorescent in situ hybridization also reveals the abundance of Bacteroidetes in crab intestine. Electron micrographs show that spherical and filamentous bacteria are closely associated with the microvillus brush border of the midgut epithelium and are often inserted into the space between the microvilli using a stalk-like cell appendage. In contrast, the predominant rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient electrophoresis and metagenome library indicate that the CMC Mollicutes group 2 appears to be present in both the midgut and hindgut with no significant difference in abundance. The CMC Mollicutes group 1, however, was found mostly in the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely related to Mollicutes symbionts detected in the gut of isopods (Crustacea: Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and specific gut bacteria, which are likely to live in close relationships with the CMC host.
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Affiliation(s)
- Xiaobing Chen
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Panpan Di
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Hongming Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Bailin Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- Institute of Biochemistry and Molecular Cell Biology, University of Goettingen, Goettingen, Germany
| | - Yongjie Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- * E-mail:
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21
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Liu QQ, Li XL, Rooney AP, Du ZJ, Chen GJ. Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae. Int J Syst Evol Microbiol 2014; 64:3473-3477. [DOI: 10.1099/ijs.0.066902-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22T, was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33–35 °C, pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22T fell within the class
Bacteroidia
. Its closest phylogenetic neighbour was the recently described species
Draconibacterium orientale
, the sole member of the family
Draconibacteriaceae
, with merely 90.04 % sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family
Draconibacteriaceae
. The type strain is G22T ( = CICC 10587T = DSM 27063T).
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Affiliation(s)
- Qian-Qian Liu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Xiao-Li Li
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Alejandro P. Rooney
- National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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22
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Chan Y, Li A, Gopalakrishnan S, Shin PKS, Wu RSS, Pointing SB, Chiu JMY. Interactive effects of hypoxia and polybrominated diphenyl ethers (PBDEs) on microbial community assembly in surface marine sediments. MARINE POLLUTION BULLETIN 2014; 85:400-409. [PMID: 24878302 DOI: 10.1016/j.marpolbul.2014.04.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 06/03/2023]
Abstract
Hypoxia alters the oxidation-reduction balance and the biogeochemical processes in sediments, but little is known about its impacts on the microbial community that is responsible for such processes. In this study, we investigated the effects of hypoxia and the ubiquitously dispersed flame-retardant BDE47 on the bacterial communities in marine surface sediments during a 28-days microcosm experiment. Both hypoxia and BDE47 alone significantly altered the bacterial community and reduced the species and genetic diversity. UniFrac analysis revealed that BDE47 selected certain bacterial species and resulted in major community shifts, whereas hypoxia changed the relative abundances of taxa, suggesting slower but nonetheless significant community shifts. These two stressors targeted mostly different taxa, but they both favored Bacteroidetes and suppressed Gammaproteobacteria. Importantly, the impacts of BDE47 on bacterial communities were different under hypoxic and normoxic conditions, highlighting the need to consider risk assessments for BDE47 in a broader context of interaction with hypoxia.
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Affiliation(s)
- Yuki Chan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong; Auckland University of Technology, School of Applied Sciences, Institute for Applied Ecology New Zealand, Private Bag 92006, Auckland 1142, New Zealand
| | - Amy Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | | | - Paul K S Shin
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Rudolf S S Wu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Stephen B Pointing
- Auckland University of Technology, School of Applied Sciences, Institute for Applied Ecology New Zealand, Private Bag 92006, Auckland 1142, New Zealand
| | - Jill M Y Chiu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.
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Iino T, Mori K, Itoh T, Kudo T, Suzuki KI, Ohkuma M. Description of Mariniphaga anaerophila gen. nov., sp. nov., a facultatively aerobic marine bacterium isolated from tidal flat sediment, reclassification of the Draconibacteriaceae as a later heterotypic synonym of the Prolixibacteraceae and description of the family Marinifilaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:3660-3667. [PMID: 25096325 DOI: 10.1099/ijs.0.066274-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A mesophilic, chemoheterotrophic bacterium, strain Fu11-5(T), was isolated from tidal-flat sediment from Tokyo Bay, Chiba, Japan. Cells of strain Fu11-5(T) were facultatively aerobic, Gram-negative, non-sporulating, non-motile and rod-shaped (1.9-6.9 µm long). Strain Fu11-5(T) grew optimally at 35-37 °C and pH 6.5-7.0 and with 1-2% (w/v) NaCl. Oxygen and l-cysteine were used as an alternative electron acceptor and donor, respectively. Strain Fu11-5(T) also grew fermentatively on some pentoses, hexoses and disaccharides and soluble starch. Succinic acid was the major end product from d-glucose. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain Fu11-5(T) was affiliated with the order Bacteroidales, and its nearest neighbours were members of the genera Meniscus, Prolixibacter, Sunxiuqinia, Mangrovibacterium and Draconibacterium, with 87-91% sequence similarity. Cell morphology, optimum growth temperature and utilization of sugars of strain Fu11-5(T) distinguished the strain from phylogenetically related bacteria. On the basis of its phenotypic features and phylogenetic position, a novel genus and species are proposed to accommodate strain Fu11-5(T), with the name Mariniphaga anaerophila gen. nov., sp. nov. The type strain of Mariniphaga anaerophila is strain Fu11-5(T) ( =JCM 18693(T) =NBRC 109408(T) =DSM 26910(T)). We also propose to combine the family Draconibacteriaceae into the family Prolixibacteraceae as a later heterotypic synonym and to place the distinct sublineage of the genus Marinifilum in the family Marinifilaceae fam. nov.
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Affiliation(s)
- Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Koji Mori
- NITE Biological Resource Center (NBRC), Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Ken-Ichiro Suzuki
- NITE Biological Resource Center (NBRC), Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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Liu QQ, Wang Y, Li J, Du ZJ, Chen GJ. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans. Int J Syst Evol Microbiol 2014; 64:2204-2209. [DOI: 10.1099/ijs.0.061986-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, gliding, yellow-pigmented bacterium, designated SS12T, was isolated from shark gill homogenate and characterized using a polyphasic approach. The strain was catalase-positive and oxidase-negative. Optimal growth occurred at 28–30 °C, pH 7.0–7.5 and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The strain contained MK-7 as the prevailing menaquinone; iso-C15 : 0 and anteiso-C15 : 0 as the major cellular fatty acids; and phosphatidylethanolamine and an unknown lipid as the predominant polar lipids. Comparative analysis of 16S rRNA gene sequences demonstrated that the novel isolate showed the highest sequence similarity (94.68 %) to
Saccharicrinis fermentans
DSM 9555T and the sequence similarities among the type strains of all other species studied were less than 92 %. A phylogenetic tree, based on 16S rRNA gene sequences, showed that strain SS12T and
Saccharicrinis fermentans
DSM 9555T formed a distinct cluster within the family
Marinilabiliaceae
. On the basis of its phylogenetic position and phenotypic traits, strain SS12T represents a novel species of genus
Saccharicrinis
, for which the name Saccharicrinis
carchari sp. nov. is proposed. The type strain is SS12T ( = CICC 10590T = DSM 27040T). Emended descriptions of the genus
Saccharicrinis
and
Saccharicrinis fermentans
are also provided.
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Affiliation(s)
- Qian-Qian Liu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Ying Wang
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Juan Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:1690-1696. [DOI: 10.1099/ijs.0.056812-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic characteristics of two bacterial strains, FH5T and SS4, isolated from enrichment cultures obtained from two distinct marine environments, were determined. These bacteria were Gram-stain-negative, facultatively anaerobic rods. Growth occurred at 20–40 °C (optimum, 28–32 °C), pH 5.5–9.0 (optimum, pH 7.0–7.5) and in the presence of 1–7 % NaCl (optimum, 2–4 %). The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Menaquinone 7 (MK-7) was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, an unkown phospholipid and an unknown lipid. The DNA G+C contents of strains FH5T and SS4 were both determined to be 42.0 mol%. The results of DNA–DNA hybridization studies indicated that the FH5T and SS4 genomes share greater than 95 % relatedness. The strains formed a distinct phyletic line within the class
Bacteroidia
, with less than 89.4 % sequence similarity to their closest relatives with validly published names. On the basis of physiological and biochemical characteristics, 16S rRNA gene sequences and chemical properties, a novel genus and species, Draconibacterium orientale gen. nov., sp. nov., within the class
Bacteroidia
, are proposed, with strain FH5T ( = DSM 25947T = CICC 10585T) as the type strain. In addition, a new family, Draconibacteriaceae fam. nov., is proposed to accommodate Draconibacterium gen. nov.
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Huang XF, Liu YJ, Dong JD, Qu LY, Zhang YY, Wang FZ, Tian XP, Zhang S. Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov. Int J Syst Evol Microbiol 2014; 64:875-881. [DOI: 10.1099/ijs.0.052779-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A nitrogen-fixing bacterium, designated strain SCSIO N0430T, was isolated from a mangrove sediment sample. Analysis of the sequence of the nifH gene responsible for nitrogen fixation in this strain indicated a close relationship to an uncultured bacterium ZNZ-D11 (GenBank accession no. JF896696). 16S rRNA gene sequence analysis revealed that this isolate had less than 93 % similarity to its closest relative,
Sunxiuqinia elliptica
DQHS4T. A phylogenetic tree reconstructed based on 16S rRNA gene sequences revealed that strain SCSIO N0430T was a member of the phylum
Bacteroidetes
. Chemotaxonomic and physiological characteristics, including phospholipids and major fatty acids, readily distinguished the isolate from established members of the phylum
Bacteroidetes
. It is concluded that strain SCSIO N0430T represents a novel genus and species, for which the name Mangrovibacterium diazotrophicum gen. nov., sp. nov. is proposed, with the type strain of the species SCSIO N0430T ( = KCTC 32129T = DSM 27148T = JCM 19152T). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the three genera
Sunxiuqinia
,
Prolixibacter
and Mangrovibacterium are proposed to make up a novel family, Prolixibacteraceae fam. nov., in the order
Bacteroidales
.
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Affiliation(s)
- Xiao-Fang Huang
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Yu Juan Liu
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Ling-Yun Qu
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Fa-Zuo Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
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Ruvira MA, Lucena T, Pujalte MJ, Arahal DR, Macián MC. Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009. Syst Appl Microbiol 2013; 36:155-9. [DOI: 10.1016/j.syapm.2012.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 10/27/2022]
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Fagervold SK, Galand PE, Zbinden M, Gaill F, Lebaron P, Palacios C. Sunken woods on the ocean floor provide diverse specialized habitats for microorganisms. FEMS Microbiol Ecol 2012; 82:616-28. [PMID: 22703298 DOI: 10.1111/j.1574-6941.2012.01432.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 05/09/2012] [Accepted: 06/11/2012] [Indexed: 11/30/2022] Open
Abstract
Marine waterlogged woods on the ocean floor provide the foundation for an ecosystem resulting in high biomass and potentially high macrofaunal diversity, similarly to other large organic falls. However, the microorganisms forming the base of wood fall ecosystems remain poorly known. To study the microbial diversity and community structure of sunken woods, we analyzed over 2800 cloned archaeal and bacterial 16S rRNA gene sequences from samples with different geographic locations, depths, and immersion times. The microbial communities from different wood falls were diverse, suggesting that sunken woods provide wide-ranging niches for microorganisms. Microorganisms dwelling at sunken woods change with time of immersion most likely due to a change in chemistry of the wood. We demonstrate, for the first time in sunken woods, the co-occurrence of free-living sulfate-reducing bacteria and methanogens and the presence of sulfide oxidizers. These microorganisms were similar to those of other anaerobic chemoautotrophic environments suggesting that large organic falls can provide similar reduced habitats. Furthermore, quantification of phylogenetic patterns of microbial community assembly indicated that environmental forces (habitat filtering) determined sunken wood microbial community structure at all degradation phases of marine woodfalls. We also include a detailed discussion on novel archaeal and bacterial phylotypes in this newly explored biohabitat.
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Qu L, Zhu F, Hong X, Gao W, Chen J, Sun X. Sunxiuqinia elliptica gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment in a sea cucumber farm. Int J Syst Evol Microbiol 2011; 61:2885-2889. [DOI: 10.1099/ijs.0.026971-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel aerobic, elliptic bacteria, designated DQHS4T, DQHS8 and DQHS15, were isolated from sediment of a seashore pond for sea cucumber culture in Jimo, Qingdao, on the east coast of China. Cells were Gram-, oxidase- and catalase-negative. All three strains grew at 15–42 °C, pH 5–9 and NaCl concentrations between 0.5 and 10 %. DNA–DNA hybridization experiments revealed high (>85 %) relatedness among the three novel isolates and suggested that the strains constitute a single species. Comparative 16S rRNA gene sequence analysis indicated that these bacteria had less than 90 % similarity to all described species of the phylum Bacteroidetes; the closest relative of the three isolates was Prolixibacter bellariivorans F2T, sharing only 89.6 % sequence similarity. The major cellular fatty acids were iso-C17 : 0 3-OH (19.8–20.0 %), iso-C15 : 0 (16.9–17.3 %), anteiso-C17 : 1 B and/or iso-C17 : 1 I (7.4–8.7 %), C17 : 0 2-OH (8.4 %), anteiso-C15 : 0 (8.2–8.6 %) and C17 : 1ω6c (5.6–6.0 %). The major respiratory quinone was menaquinone-7 (MK-7) and the DNA G+C content was 41.8–43.5 mol%. Based on the distinct phylogenetic position and the combination of genotypic, phenotypic and chemotaxonomic characteristics, these three strains were considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Sunxiuqinia elliptica gen. nov., sp. nov. is proposed. The type strain of Sunxiuqinia elliptica is DQHS4T ( = CGMCC 1.9156T = NCCB 100301T = LMG 25367T).
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Affiliation(s)
- Lingyun Qu
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Fengling Zhu
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Xuguang Hong
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Wei Gao
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Junhui Chen
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Xiuqin Sun
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
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Miyazaki M, Koide O, Kobayashi T, Mori K, Shimamura S, Nunoura T, Imachi H, Inagaki F, Nagahama T, Nogi Y, Deguchi S, Takai K. Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment. Int J Syst Evol Microbiol 2011; 62:1075-1080. [PMID: 21705444 DOI: 10.1099/ijs.0.032326-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, facultatively anaerobic bacterium (strain JAM-BA0501(T)) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501(T) were gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501(T) indicated a distant relationship to strains representing genera within the order Bacteroidales, such as Alkaliflexus imshenetskii Z-7010(T) (91.1 % similarity), Marinilabilia salmonicolor ATCC 19041(T) (86.2 %) and Anaerophaga thermohalophila Fru22(T) (89.3 %). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501(T) is considered to represent a novel species of a new genus within the family Marinilabiliaceae, for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501(T) ( = JCM 15548(T) = NCIMB 14482(T)).
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Affiliation(s)
- Masayuki Miyazaki
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Osamu Koide
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Tohru Kobayashi
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kozue Mori
- Marine Bioresource Exploration Research Team and Institute of Biogeosciences (BioGeos), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Shimamura
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takuro Nunoura
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takahiko Nagahama
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yuichi Nogi
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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