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Huang Y, Liu L, Li J, Pan J, Li M. Limibaculum sediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2022; 72. [PMID: 36269565 DOI: 10.1099/ijsem.0.005580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325T, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325T was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325T grew optimally at 37-40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325T was most similarly related to Limibaculum halophilum CAU 1123T (96.2 %), Phaeovulum vinaykumarii DSM 18714T (93.9%) and Amaricoccus solimangrovi HB 172011T (93.7 %). The major fatty acids (>10 %) were C18 : 1 ω7c (60.0 %) and 11-methyl C18 : 1 ω7c (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325T represents a novel species of the genus Limibaculum, for which the name Limibaculum sediminis sp. nov. is proposed (=MCCC 1K07397T=KCTC 92313T).
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Affiliation(s)
- Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Jiayi Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Xbiome Biotech Co. Ltd, Shenzhen, Guangdong 518058, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
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Sun H, Zheng H, Liao B, Chen B, Li A, Xiao B. Algiphilus acroporae sp. nov. and Coraliihabitans acroporae gen. nov. sp. nov., isolated from scleractinian coral Acropora digitifera. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005321] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-staining-negative, aerobic, rod-shaped bacteria NNCM1T and NNCM2T were isolated from the scleractinian coral Acropora digitifera. NNCM1T grew with 0.5–12 % (w/v) NaCl (optimum, 3–6 %), at 18–37 °C (optimum, 28 °C) and at pH 6.0–10.0 (optimum, 7.0–8.0). NNCM2T grew with 0.5–10 % (w/v) NaCl (optimum, 2 %), at 18–37 °C (optimum, 28 °C) and at pH 6.5–9.0 (optimum, 7.0). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NNCM1T formed a lineage within the genus
Algiphilus
of the family Algiphilaceae, and it was distinct from the most closely related species
Algiphilus aromaticivorans
DG1253T, with a 16S rRNA gene sequences similarity of 97.05 %. NNCM2T formed a lineage within the family Rhodobacteraceae, and it was distinct from the closely related genera
Limibaculum halophilum
CAU 1123T,
Paroceanicella profunda
D4M1T and
Pseudoruegeria aestuarii
MME-001T with 93.41, 92.78 and 91.09% identities, respectively. The major respiratory quinone was Q-8 and Q-10 for NNCM1T and NNCM2T, respectively. The predominant fatty acids (more than 10 %) were summed feature 8 (39.4 %) and C16 : 0 (19.4 %) for NNCM1T and summed feature 8 (62.8 %) and C16 : 0 (12.4 %) for NNCM2T. The DNA G+C contents of NNCM1T and NNCM2T were 63.3 and 63.4 mol% respectively. The polar lipids of NNCM1T comprised one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol and one unknown polar lipid, while those of NNCM2T comprised one phosphatidylethanolamine, one phosphatidylglycerol, one aminolipid and four unknown polar lipids. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of the two isolates. Thus, NNCM1T is considered to represent a novel species within genus
Algiphilus
, for which the name Algiphilus acroporae sp. nov. is proposed. The type strain is NNCM1T (=KCTC 82966T=MCCC 1K06445T). NNCM2T represents a novel genus and species within the family Rhodobacteraceae, for which the name Coraliihabitans acroporae gen. nov. sp. nov. is proposed. The type strain is NNCM2T (=KCTC 82967T=MCCC 1K06408T).
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Affiliation(s)
- Hao Sun
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Huina Zheng
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Baolin Liao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Bogui Chen
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Aihua Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Baohua Xiao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, PR China
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
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Pan X, Li Z, Li F, Huang Y, Wang Q, Huang S, Hu W, Jiang M. Thermohalobaculum xanthum gen. nov., sp. nov., a moderately thermophilic bacterium isolated from mangrove sediment. Antonie van Leeuwenhoek 2021; 114:1819-1828. [PMID: 34424448 DOI: 10.1007/s10482-021-01641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/08/2021] [Indexed: 11/24/2022]
Abstract
A novel moderately thermophilic and halophilic bacterium, designated strain M0105T, was isolated from mangrove sediment collected in the Beibu Gulf, south China. The isolate is Gram-negative, non-motile and rod-shaped bacterium with smooth colonies of pale-yellow appearance. Growth occurs at 15-46 °C (optimum 37-40 °C) and pH range of 6.0-10.0 (optimum pH 8.0-9.0). It required 1-7% NaCl (optimum 3-5%) for growth. Strain M0105T was affiliated to the family 'Rhodobacteraceae', sharing the highest 16S rRNA gene sequence similarity with Limibaculum halophilum CAU 1123T (96.8%). The major menaquinone Q-10 and the dominant unsaturated fatty acid (C18:1ω7) in this family were also detected in the strain M0105T. The genome sequence possesses a circular 4.1 Mb chromosome with a G + C content of 67.9%. Strain M0105T encoded many genes for cellular stress resistance and nutrient utilization, which could improve its adaptive capacity to the mangrove environment. Values of conserved proteins (POCP), average nucleotide identity, average amino acid identity (AAI) and DNA-DNA hybridization (dDDH) between the isolate and closely related species were below the proposed threshold for species discrimination. Information from phenotypic, chemotaxonomic and phylogenetic analyses proposed that strain M0105T should be assigned to a novel genus within the family 'Rhodobacteraceae'. Thus, we suggested that the strain M0105T represents a novel species in a new genus, for which the name Thermohalobaculum xanthum gen. nov., sp. nov. is proposed. The type strain of the type species is M0105T (= BGMRC 2019T = KCTC 52118T = MCCC 1K03767T = NBRC 112057T).
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Affiliation(s)
- Xinli Pan
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Zhe Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Fei Li
- Guangxi Key Laboratory of Marine Environmental Science, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Yuanlin Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Qiaozhen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Wenjin Hu
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Bioscience and Technology Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China.
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530008, People's Republic of China.
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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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Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK. The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions. Front Microbiol 2019; 10:659. [PMID: 31001232 PMCID: PMC6454203 DOI: 10.3389/fmicb.2019.00659] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae, we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter, Paracoccus, and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae-OTUs assigned as "uncultured" were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae-OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.
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Affiliation(s)
- Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Group “Biology of Geological Processes”, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - Heath Mills
- Rhodium Scientific LLC, San Antonio, TX, United States
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States
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Ji X, Zhang C, Zhang X, Xu Z, Ding Y, Zhang Y, Song Q, Li B, Zhao H. Pelagivirga sediminicola gen. nov., sp. nov. isolated from the Bohai Sea. Int J Syst Evol Microbiol 2018; 68:3494-3499. [PMID: 30222096 DOI: 10.1099/ijsem.0.003015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, strain BH-SD19T, that was isolated from a marine sediment sample collected from the Bohai Sea, was subjected to a polyphasic taxonomic study. Cells of BH-SD19T are non-flagellated, non-gliding, oval-shaped rods, 0.5-1.0 µm wide and 1.0-2.0 µm long. BH-SD19T is strictly aerobic, and oxidase- and catalase-positive. Growth occurs at 15-40 °C (optimum 35 °C), at pH 6.0-8.5 (optimum 7.0-7.5) and with 1-10 % (w/v) NaCl (optimum 2 %). The predominant fatty acids are C19 : 0cyclo ω8c (46.5 %), C16 : 0 (20.3 %) and C18 : 1ω7c and/or C18 : 1ω6c (10.6 %). The major respiratory quinone is Q-10. The major polar lipids are phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content is 64.0 mol%. BH-SD19T shows the highest 16S rRNA sequence similarity to Pontibaca methylaminivorans (95.2 %) and strains of species of the genus Roseovarius(93.4-95.2 %). Sequence similarity values between BH-SD19T and other phylogenetically related species are all below 95.0 %. Phylogenetic trees based on 16S rRNA gene sequences indicate that BH-SD19T forms a distinct lineage and does not join any known genera in the trees. Phenotypic, chemotaxonomic and phylogenetic data indicate that BH-SD19T represents a novel genus and species in the family Rhodobacteraceae, for which the name Pelagivirga sediminicola gen. nov., sp. nov. is proposed. The type strain is BH-SD19T (=CCTCC AB 2017074T=KCTC 62202T).
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Affiliation(s)
- Xiaofei Ji
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
| | - Cong Zhang
- 2Shandong Province Key Laboratory of Applied Mycology, School of Life Science, Qingdao Agricultural University, Qingdao, PR China
| | - Xiying Zhang
- 3State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, PR China
| | - Zheng Xu
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
| | - Yunfei Ding
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
| | - Yimei Zhang
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
| | - Qing Song
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
| | - Boqing Li
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
| | - Huilin Zhao
- 1Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, PR China
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