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Fu ZY, Zhang DF, Huang MH, Wang HC, Chen XY, Yao YF, Yuan Y, Li WJ. Thalassospira aquimaris sp. nov. and Winogradskyella marincola sp. nov. two marine bacteria isolated from an agar-degrading co-culture. Antonie Van Leeuwenhoek 2024; 117:101. [PMID: 39008162 DOI: 10.1007/s10482-024-02000-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Two novel Gram-stain-negative, aerobic, and non-motile strains, designated FZY0004T and YYF002T, were isolated from an agar-degrading co-culture, which was obtained from seawater of the intertidal zone of Yancheng City, the Yellow Sea of China. Strain FZY0004T optimally grew at 28 °C, pH 7.0, and 2-6% NaCl, while strain YYF002T optimally grew at 28 °C, pH 7.5, and 2-4% NaCl. Strain FZY0004T possessed Q-9 as the major respiratory quinone, and its major fatty acids (> 10%) were summed feature 8 (C18:1 ω7c), C16:0, and summed feature 3 (C16:1 ω7c/C16:1 ω6c). The polar lipids identified in strain FZY0004T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and several unidentified phospholipids (PL) and lipids (L). On the other hand, strain YYF002T had MK-6 as the predominant respiratory quinone and its major fatty acids consisted of iso-C15:0, iso-C15:1 G, and iso-C15:0 3-OH. The polar lipids identified in strain YYF002T were aminolipid (AL), PE, and several unidentified lipids. Strain FZY0004T shared 99.5% 16S rRNA gene sequence similarity and 90.1% average nucleotide identity (ANI) with T. povalilytica Zumi 95T, and strain YYF002T shared 99.2% 16S rRNA gene sequence similarity and 88.2% ANI with W. poriferorum JCM 12885T. The genomic DNA G + C contents of strains FZY0004T and YYF002T were 54.5% and 33.5%, respectively. The phylogenetic, phenotypic, and physiological characteristics permitted the distinction of the two strains from their neighbors, and we thus propose the names Thalassospira aquimaris sp. nov. (type strain FZY0004T = JCM 35895T = MCCC 1K08380T) and Winogradskyella marincola sp. nov. (type strain YYF002T = JCM 35950T = MCCC 1K08382T).
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Affiliation(s)
- Zi-Yue Fu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China.
| | - Meng-Han Huang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Hong-Chuan Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Xiao-Ye Chen
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Yu-Fang Yao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China
| | - Yang Yuan
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China.
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Wen-Jun Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, People's Republic of China
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, People's Republic of China
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Goldberg SR, Haltli BA, Correa H, Kerr RG. Curvivirga aplysinae gen. nov., sp. nov., a marine bacterium isolated from the sea sponge Aplysina fistularis. Int J Syst Evol Microbiol 2021; 71. [PMID: 34228608 DOI: 10.1099/ijsem.0.004873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, motile bacterium, designated strain RKSG073T, was isolated from the sea sponge Aplysina fistularis, collected off the west coast of San Salvador, The Bahamas. Cells were curved-to-spiral rods with single, bipolar (amphitrichous) flagella, oxidase- and catalase-positive, non-nitrate-reducing and required salt for growth. RKSG073T grew optimally at 30-37 °C, pH 6-7, and with 2-3 % (w/v) NaCl. The predominant fatty acids of RKSG073T were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. Major isoprenoid quinones were identified as Q-10 and Q-9. Phylogenetic analyses of nearly complete 16S rRNA genes and genome sequences positioned strain RKSG073T in a clade with its closest relative Aestuariispira insulae AH-MY2T (92.1 % 16S rRNA gene sequence similarity), which subsequently clustered with Hwanghaeella grinnelliae Gri0909T, Marivibrio halodurans ZC80T and type species of the genera Kiloniella, Thalassospira and Terasakiella. The DNA G+C content calculated from the genome of RKSG073T was 42.2 mol%. On the basis of phylogenetic distinctiveness and polyphasic analysis, here we propose that RKSG073T (culture deposit numbers: ATCC collection = TSD-74T, BCCM collection = LMG 29869T) represents the type strain of a novel genus and species within the family Kiloniellaceae, order Rhodospirillales and class Alphaproteobacteria, for which the name Curvivirga aplysinae gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Stacey R Goldberg
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Brad A Haltli
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada
| | - Hebelin Correa
- Nautilus Biosciences Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada
| | - Russell G Kerr
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Duffy Research Center, Charlottetown, Prince Edward Island, Canada.,Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria 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 recognized as problematic long ago 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 and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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Dong C, Liu R, Lai Q, Liu Y, Shao Z. Thalassospira marina sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2018; 68:2943-2948. [PMID: 30028290 DOI: 10.1099/ijsem.0.002925] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel marine bacteria, designated strains CSC3H3T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10-40 °C, pH 5-10 and in the presence of 0-15 % (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira, and shared 97.5-98.3 % sequence similarity to all other validly type strains of the genus Thalassospira, and the highest similarity was to the type strain Thalassospira povalilyticaZumi 95T (98.3 %), followed by Thalassospira australica NP3b2T (98.2 %). The digital DNA-DNA hybridization value between the two strains was 80.4 %, while the values with T. povalilyticaZumi 95T and T. australica NP3b2T were only 20.5-20.7 % and 20.4-20.5 %, respectively. The two strains possess similar major cellular fatty acids including C18 : 1ω7c, C16 : 0, C19 : 0ω8c cyclo, C18 : 1 2-OH and C17 : 0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3T (=MCCC 1A11786T=KCTC 62333T).
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Renju Liu
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Yang Liu
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
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Liu Y, Lai Q, Du J, Sun F, Shao Z. Thalassospira indica sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:4942-4946. [PMID: 27562239 DOI: 10.1099/ijsem.0.001449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study using a polyphasic approach was carried out on strain PB8BT, which was isolated from the deep water of the Indian Ocean. Cells of the bacterium were Gram-stain-negative, oxidase- and catalase-positive, curved rods and motile. Growth was observed at salinities of 0-15 % and at temperatures of 10-41°C. The isolate could reduce nitrate to nitrite and degrade Tween 80, but not degrade gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PB8BT belonged to the genus Thalassospira, with the highest sequence similarity to the closely related type strain Thalassospira tepidiphila 1-1BT (99.7 %), followed by Thalassospira profundimaris WP0211T (99.6 %). Multilocus sequence analysis demonstrated low similarities of 94.1 and 93.7 % between strain PB8BT and the two reference type strains. Digital DNA-DNA hybridization values between strain PB8BT and the two above-mentioned type strains were, respectively, 56.3 and 55.3 %. The principal fatty acids of strain PB8BT were C18 : 1ω6c/C18 : 1ω7c, C19 : 0 cyclo ω8c and C16 : 0. The G+C content of the chromosomal DNA was 54.9 mol%. The quinone was determined to be Q-10 (100 %). Phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids were present. Based on phenotypic and genotypic characteristics, strain PB8BT represents a novel species within the genus Thalassospira, for which the name Thalassospira indica sp. nov. is proposed. The type strain of the novel species is PB8BT (=MCCC 1A01103T=LMG 29620T).
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Affiliation(s)
- Yang Liu
- 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, The Third Institute of State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Zongze Shao
- 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, The Third Institute of State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
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6
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Thalassospira australica sp. nov. isolated from sea water. Antonie van Leeuwenhoek 2016; 109:1091-100. [DOI: 10.1007/s10482-016-0710-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
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Kim JH, Konkit M, Yoon JH, Kim W. Limibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium in the family Rhodospirillaceae isolated from reclaimed land. Int J Syst Evol Microbiol 2015; 65:3155-3161. [DOI: 10.1099/ijs.0.000346] [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 Gram-stain-negative, aerobic, non-motile, non-spore-forming and short rod-shaped bacterial strain, designated CAU 1121T, was isolated from reclaimed land in the Republic of Korea and its taxonomic position was investigated using a polyphasic approach. The bacterium grew optimally at 37 °C, at pH 6.5 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the novel isolate belonged to the family Rhodospirillaceae within the class Alphaproteobacteria and formed an independent lineage within the evolutionary radiation encompassed by the phylum Proteobacteria. Strain CAU 1121T exhibited very low levels of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pelagibius litoralis (similarity, 92.5 %), Fodinicurvata fenggangensis (similarity, 91.4 %), Fodinicurvata sediminis (similarity, 90.7 %) and Tistlia consotensis (similarity, 91.0 %). Strain CAU 1121T contained ubiquinone-10 as the only respiratory quinone and C18 : 1ω7c as the major cellular fatty acid. The DNA G+C content of the strain was 65 mol%. On the basis of phylogenetic inference, and physiological and chemotaxonomic data, it is proposed that strain CAU 1121T represents a novel genus and novel species in the family Rhodospirillaceae, for which the name Limibacillus halophilus gen. nov., sp. nov. is suggested. The type strain is CAU 1121T ( = KCTC 42420T = CECT 8803T = NBRC 110928T).
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Affiliation(s)
- Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Maytiya Konkit
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
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Gutierrez T, Biddle JF, Teske A, Aitken MD. Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments. Front Microbiol 2015. [PMID: 26217326 PMCID: PMC4493657 DOI: 10.3389/fmicb.2015.00695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [13C]-phenanthrene (PHE). The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from PHE enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled PHE and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of PHE degradation and mineralization. In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea.
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Affiliation(s)
- Tony Gutierrez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ; School of Life Sciences, Heriot-Watt University, Edinburgh UK
| | - Jennifer F Biddle
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
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Description of Thalassospira lohafexi sp. nov., isolated from Southern Ocean, Antarctica. Arch Microbiol 2015; 197:627-37. [DOI: 10.1007/s00203-015-1092-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
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10
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Lai Q, Liu Y, Yuan J, Du J, Wang L, Sun F, Shao Z. Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments. PLoS One 2014; 9:e106353. [PMID: 25198177 PMCID: PMC4157779 DOI: 10.1371/journal.pone.0106353] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/02/2014] [Indexed: 11/23/2022] Open
Abstract
Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16–97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76–97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments.
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Affiliation(s)
- Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Jun Yuan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Liping Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
- * E-mail:
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