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Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW. Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5–7.5 % NaCl (w/v, optimum, 1.0–3.0 %), at pH 6.0–8.0 (optimum, pH 6.5–7.0) and at 4–40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to
Pseudoruegeria aquimaris
JCM 13603T (97.5 %), followed by
Ruegeria conchae
TW15T (97.2%),
Shimia aestuarii
DSM 15283T (97.1 %) and
Ruegeria lacuscaerulensis
ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family
Roseobacteraceae
and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and cyclo-C19 : 0
ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2–79.0, 20.3–22.5 and 66.0–80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family
Roseobacteraceae
, belonging to the class
Alphaproteobacteria
, for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11–2T=KCTC 82723T=MCCC M20691T) is proposed.
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Affiliation(s)
- Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Li-Li Guo
- College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
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2
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Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:683109. [PMID: 34248901 PMCID: PMC8267831 DOI: 10.3389/fmicb.2021.683109] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.
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Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University Singapore, Singapore, Singapore
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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3
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Awata T, Goto Y, Kuratsuka H, Aoi Y, Ozaki N, Ohashi A, Kindaichi T. Reactor performance and microbial community structure of single-stage partial nitritation anammox membrane bioreactors inoculated with Brocadia and Scalindua enrichment cultures. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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4
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Cao WR, Shang DD, Liu BT, Hu YH, Sun XK, Sun YY, Jiang MY, Du ZJ. Ruegeria haliotis sp. nov., Isolated from the Gut of the Abalone Haliotis rubra. Curr Microbiol 2021; 78:2151-2159. [PMID: 33792761 DOI: 10.1007/s00284-021-02450-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/10/2021] [Indexed: 11/27/2022]
Abstract
A Gram-stain-negative, aerobic, non-motile, white-pigmented, short rod-shaped, and alginate-degrading bacterium, designated B1Z28T, was isolated from the gut of the abalone Haliotis rubra obtained at Weihai, China. Strain B1Z28T was found to grow at 4-35 °C, pH 6.5-9.0, and in the presence of 0.5-8.0% (w/v) NaCl. Cells were positive for oxidase and catalase activity. The 16S rRNA-based phylogenetic analysis revealed that the nearest phylogenetic neighbors of strain B1Z28T were Tritonibacter scottomollicae MCCC 1A06440T (98.1%), Ruegeria faecimaris KCTC 23044T (98.0%), and Ruegeria meonggei KCTC 32450T (97.8%). Based on phylogenomic analysis, the average nucleotide identity (ANI) values between strain B1Z28T and the neighbor strains were 71.6, 77.2, and 78.1%, respectively; the digital DNA-DNA hybridization (dDDH) values based on the draft genomes between strain B1Z28T and its closest neighbors were 20.5, 20.8, and 21.6%, respectively. Ubiquinone-10 (Q-10) was detected as the predominant respiratory quinone. The dominant cellular fatty acids were Summed feature 8 (contained C18:1 ω7c and/or C18:1 ω6c). The polar lipids included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL), aminolipid (AL), and three unidentified lipids. Based on the phylogenetic and phenotypic characteristics, strain B1Z28T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria haliotis sp. nov. is proposed. The type strain is B1Z28T (= KCTC 72686T = MCCC 1H00393T).
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Affiliation(s)
- Wen-Rui Cao
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Bang-Tao Liu
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Yi-Hao Hu
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xun-Ke Sun
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Yuan-Yuan Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
| | - Ming-Yu Jiang
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
- Marine College, Shandong University, Weihai, 264209, People's Republic of China.
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5
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Zhang S, Liu WX, Liu NH, He XY, Su HN, Li CY, Zhang YZ, Song XY, Zhang XY. Antarcticimicrobium sediminis gen. nov., sp. nov. , isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. Int J Syst Evol Microbiol 2020; 70:2624-2631. [PMID: 32134379 DOI: 10.1099/ijsem.0.004083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41T, was isolated from Antarctic intertidal sediment. The isolate grew at 0-37 °C and with 0.5-10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria, Phaeobacter, Pseudopuniceibacterium, Sulfitobacter, Puniceibacterium and Poseidonocella with 98.6-95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41T (=MCCC 1K03508T=KCTC 62793T). Moreover, the transfer of Ruegeria lutea Kim et al. 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1T=JCM 30927T=KCTC 72105T) is also proposed.
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Affiliation(s)
- Shan Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Wei-Xiong Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
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6
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Sun YY, Dang YR, He XY, Wang JM, Liu NH, Sun ML, Li CY, Chen XL, Zhang YZ, Song XY, Yang J, Zhang XY. Fluviibacterium aquatile gen. nov., sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2020; 70:105-111. [DOI: 10.1099/ijsem.0.003722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuan-Yuan Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Jing-Mei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Mei-Ling Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Chun-Yang Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
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7
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Kim J, Kim DY, Yang KH, Kim S, Lee SS. Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea. Int J Syst Evol Microbiol 2019; 69:2854-2861. [PMID: 31274408 DOI: 10.1099/ijsem.0.003568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, short rod-shaped, aerobic bacterium designated as 318-1T was isolated from a marine sediment collected from Masan Bay, South Korea. Strain 318-1T grew optimally at pH 6-7, at 30 °C and in the presence of 2-3 % (w/v) NaCl, tolerant of up to 8 % (w/v) NaCl, and accumulated poly-β-hydroxybutyrate (PHB). A comparative analysis of 16S rRNA gene sequences revealed that strain 318-1T formed a distinct phyletic lineage in the genus Ruegeria (family Rhodobacteraceae, class Alphaproteobacteria) and showed high sequence similarity to Ruegeria halocynthiae DSM 27839T (96.5 %) and Shimia haliotis DSM 28453T (96.3 %). Comparing the genome sequence of 318-1T with those of the type strains of seven species of the genus Rugeria and two species of the genus Shimia, the values obtained were below the thresholds with analysis of average nucleotide identities (ANI, 71.6-76.8 %) and in silico DNA-DNA hybridisation, Genome-to-Genome Distance Calculator (GGDC, 18.5-20.6 %). The DNA G+C content was 65.75 mol%. Chemotaxonomic data [predominant quinone ubiquinone Q10; polar lipid profile consisting of major compounds phosphatidylcholine (PC), phosphatidylglycerol (PG), an unidentified aminolipid and an unidentified lipid; major fatty acids summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c)] supported the affiliation of strain 318-1T to the genus Ruegeria. Genomic, chemotaxonomic, and phenotypic differentiation of strain 318-1T from the members of the genus Ruegeria support it as a novel species. On the basis of the results in this study, a novel species, Ruegeria lutea sp. nov., is proposed. The type strain is 318-1T (=JCM 30927T=KEMB 7306-525T=KCTC 72105T).
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Affiliation(s)
- Jinsoo Kim
- Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea.,Research & Development Institute of Inventory Co. Ltd., 8-3, Yeoseori-gil, Daedeok-myeon Anseong-si, Gyeonggi-go 17542, Republic of Korea
| | - Da-Young Kim
- Life Science Major, Division of Bio-Convergence, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Keun-Hyeok Yang
- Department of Architectural Engineering, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Sungchul Kim
- Research & Development Institute of Inventory Co. Ltd., 8-3, Yeoseori-gil, Daedeok-myeon Anseong-si, Gyeonggi-go 17542, Republic of Korea.,Department of Environmental Energy Engineering, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Sang-Seob Lee
- Life Science Major, Division of Bio-Convergence, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea.,Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
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8
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Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393-2411. [DOI: 10.1099/ijsem.0.002833] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joseph S. Wirth
- Department of Microbiology, University of Georgia, Athens, GA, USA
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9
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Mlewski EC, Pisapia C, Gomez F, Lecourt L, Soto Rueda E, Benzerara K, Ménez B, Borensztajn S, Jamme F, Réfrégiers M, Gérard E. Characterization of Pustular Mats and Related Rivularia-Rich Laminations in Oncoids From the Laguna Negra Lake (Argentina). Front Microbiol 2018; 9:996. [PMID: 29872427 PMCID: PMC5972317 DOI: 10.3389/fmicb.2018.00996] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/27/2018] [Indexed: 11/13/2022] Open
Abstract
Stromatolites are organo-sedimentary structures that represent some of the oldest records of the early biosphere on Earth. Cyanobacteria are considered as a main component of the microbial mats that are supposed to produce stromatolite-like structures. Understanding the role of cyanobacteria and associated microorganisms on the mineralization processes is critical to better understand what can be preserved in the laminated structure of stromatolites. Laguna Negra (Catamarca, Argentina), a high-altitude hypersaline lake where stromatolites are currently formed, is considered as an analog environment of early Earth. This study aimed at characterizing carbonate precipitation within microbial mats and associated oncoids in Laguna Negra. In particular, we focused on carbonated black pustular mats. By combining Confocal Laser Scanning Microscopy, Scanning Electron Microscopy, Laser Microdissection and Whole Genome Amplification, Cloning and Sanger sequencing, and Focused Ion Beam milling for Transmission Electron Microscopy, we showed that carbonate precipitation did not directly initiate on the sheaths of cyanobacterial Rivularia, which dominate in the mat. It occurred via organo-mineralization processes within a large EPS matrix excreted by the diverse microbial consortium associated with Rivularia where diatoms and anoxygenic phototrophic bacteria were particularly abundant. By structuring a large microbial consortium, Rivularia should then favor the formation of organic-rich laminations of carbonates that can be preserved in stromatolites. By using Fourier Transform Infrared spectroscopy and Synchrotron-based deep UV fluorescence imaging, we compared laminations rich in structures resembling Rivularia to putatively chemically-precipitated laminations in oncoids associated with the mats. We showed that they presented a different mineralogy jointly with a higher content in organic remnants, hence providing some criteria of biogenicity to be searched for in the fossil record.
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Affiliation(s)
- Estela C Mlewski
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Cordoba, Argentina
| | - Céline Pisapia
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France.,Synchrotron SOLEIL, DISCO Beamline, Saint Aubin, France
| | - Fernando Gomez
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Cordoba, Argentina
| | - Lena Lecourt
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Eliana Soto Rueda
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Cordoba, Argentina
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR Centre National de la Recherche Scientifique 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, IRD UMR 206, Paris, France
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Stephan Borensztajn
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | | | | | - Emmanuelle Gérard
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
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10
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Li G, Lai Q, Du Y, Liu X, Sun F, Shao Z. Marinibacterium profundimaris gen. nov., sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2015; 65:4175-4179. [PMID: 26303913 DOI: 10.1099/ijsem.0.000557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain 22II1-22F33T, which was isolated from deep seawater of the Atlantic Ocean. The bacterium was Gram-stain-negative, oxidase-positive and weakly catalase-positive, oval in shape without flagellum. Growth was observed at salinities of 0-12 % and at temperatures of 4-41 °C. The isolate was capable of hydrolysing aesculin and Tween 80 and reduction of nitrate to nitrite, but unable to hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II1-22F33T belongs to the family Rhodobacteraceae, with highest sequence similarity to Pseudooceanicola marinus AZO-CT (96.5 %). The principal fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ω6c) (73.8 %). The G+C content of the genomic DNA was 66.2 mol%. The respiratory quinone was Q-10 (100 %). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids (ALs), six unidentified phospholipids (PLs) and one unidentified lipid (L) were present. The combined genotypic and phenotypic data show that strain 22II1-22F33T represents a novel species within a new genus, for which the name Marinibacterium profundimaris gen. nov., sp. nov. is proposed. The type strain of Marinibacterium profundimaris is 22II1-22F33T ( = LMG 27151T = MCCC 1A09326T).
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Affiliation(s)
- Guizhen Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yaping Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Xiupian Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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Park S, Won SM, Kim H, Park DS, Yoon JH. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2969-2974. [DOI: 10.1099/ijs.0.062406-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, BS-B2T, which was isolated from a tidal flat sediment at Boseong in South Korea, was characterized taxonomically. Strain BS-B2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The novel strain exhibited highest 16S rRNA gene sequence similarity (97.4 %) to
Marivita geojedonensis
DPG-138T. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain BS-B2T is closely related to
Primorskyibacter sedentarius
KMM 9018T, showing 96.5 % sequence similarity. Strain BS-B2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain BS-B2T comprised phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, and differentiated it from the type strains of
P. sedentarius
and
M. geojedonensis
. The DNA G+C content of strain BS-B2T was 62.2 mol%. Differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrated that strain BS-B2T can be distinguished from phylogenetically related genera as well as
P. sedentarius
and
M. geojedonensis
. On the basis of the data presented, strain BS-B2T is considered to represent a novel species of a new genus, for which the name Aestuariivita boseongensis gen. nov., sp. nov. is proposed. The type strain of Aestuariivita boseongensis is BS-B2T ( = KCTC 42052T = CECT 8532T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sung-Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Hyangmi Kim
- Microbiological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Doo-Sang Park
- Microbiological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.060285-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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