1
|
Peng C, Zhang X, Li J, Yang M, Ma S, Fan H, Dai L, Cheng L. Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512751 DOI: 10.1099/ijsem.0.006292] [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: 03/23/2024] Open
Abstract
A microaerophilic, Gram-negative, motile, and spiral-shaped bacterium, designated Y-M2T, was isolated from oil sludge of Shengli oil field. The optimal growth condition of strain Y-M2T was at 25 °C, pH 7.0, and in the absence of NaCl. The major polar lipid was phosphatidylethanolamine. The main cellular fatty acid was iso-C17 : 0 3-OH. It contained Q-9 and Q-10 as the predominant quinones. The DNA G+C content was 68.1 mol%. Strain Y-M2T showed the highest 16S rRNA gene sequence similarity to Telmatospirillum siberiense 26-4bT (91.1 %). Phylogenetic analyses based on 16S rRNA gene and genomes showed that strain Y-M2T formed a distinct cluster in the order Rhodospirillales. Genomic analysis showed that Y-M2T possesses a complete nitrogen-fixation cluster which is phylogenetically close to that of methanogene. The nif cluster, encompassing the nitrogenase genes, was found in every N2-fixing strain within the order Rhodospirillales. Phylogeny, phenotype, chemotaxonomy, and genomic results demonstrated that strain Y-M2T represents a novel species of a novel genus in a novel family Oleispirillaceae fam. nov. in the order Rhodospirillales, for which the name Oleispirillum naphthae gen. nov., sp. nov. was proposed. The type strain is Y-M2T (=CCAM 827T=JCM 34765T).
Collapse
Affiliation(s)
- Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu 610213, Sichuan Province, PR China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan Province, PR China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu 610041, PR China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu 610213, Sichuan Province, PR China
| |
Collapse
|
2
|
Yang M, Zhang X, Ma S, Zhang Q, Peng C, Fan H, Dai L, Li J, Cheng L. Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis. Antonie Van Leeuwenhoek 2023; 116:1359-1374. [PMID: 37843737 DOI: 10.1007/s10482-023-01878-1] [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: 10/13/2022] [Accepted: 09/03/2023] [Indexed: 10/17/2023]
Abstract
A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0 µm in length and 0.4-0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).
Collapse
Affiliation(s)
- Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China
| | - Qiumei Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China.
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China.
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China.
| |
Collapse
|
3
|
Koziaeva VV, Sorokin DY, Kolganova TV, Grouzdev DS. Magnetospirillum sulfuroxidans sp. nov., capable of sulfur-dependent lithoautotrophy and a taxonomic reevaluation of the order Rhodospirillales. Syst Appl Microbiol 2023; 46:126406. [PMID: 36898262 DOI: 10.1016/j.syapm.2023.126406] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
A spiral-shaped, highly motile bacterium was isolated from freshwater sulfidic sediment. Strain J10T is a facultative autotroph utilizing sulfide, thiosulfate, and sulfur as the electron donors in microoxic conditions. Despite high 16S rRNA gene sequence sequence identity to Magnetospirillum gryphiswaldense MSR-1 T (99.6 %), digital DNA-DNA hybridisation homology and average nucleotide identity between the two strains was of the different species level (25 % and 83 %, respectively). Strain J10T is not magnetotactic. The DNA G + C content of strain J10T is 61.9 %. The predominant phospholipid ester-linked fatty acids are C18:1ω7, C16:1ω7, and C16:0. Strain J10T (=DSM 23205 T = VKM B-3486 T) is the first strain of the genus Magnetospirillum showing lithoautotrophic growth and is proposed here as a novel species, Magnetospirillum sulfuroxidans sp. nov. In addition, we propose to establish a framework for distinguishing genera and families within the order Rhodospirillales based on phylogenomic analysis using the threshold values for average amino acid identity at ̴ 72 % for genera and ̴ 60 % for families. According to this, we propose to divide the existing genus Magnetospirillum into three genera: Magnetospirillum, Paramagnetospirillum, and Phaeospirillum, constituting a separate family Magnetospirillaceae fam. nov. in the order Rhodospirillales. Furthermore, phylogenomic data suggest that this order should accomodate six more new family level groups including Magnetospiraceae fam. nov., Magnetovibrionaceae fam. nov., Dongiaceae fam. nov., Niveispirillaceae fam. nov., Fodinicurvataceae fam. nov., and Oceanibaculaceae fam. nov.
Collapse
Affiliation(s)
- Veronika V Koziaeva
- Skryabin Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tatiana V Kolganova
- Skryabin Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | |
Collapse
|
4
|
Pacificispira spongiicola gen. nov., sp. nov., a nitrate-reducing bacterium isolated from tropical western Pacific. Antonie van Leeuwenhoek 2021; 114:2083-2090. [PMID: 34550493 DOI: 10.1007/s10482-021-01662-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/13/2021] [Indexed: 10/20/2022]
Abstract
The Gram-stain-negative, strictly aerobic, curved-to-spiral rod-shaped bacterial strain, designated KN72T, was isolated from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain KN72T was a member of the family Rhodospirillaceae and formed a distinct lineage. Strain KN72T contained ubiquinone-10 as the major respiratory quinone. The polar lipid profiles contained phosphatidylethanolamine, phosphatidylglycerol, one aminolipid and three phospholipids. The predominant cellular fatty acids were C16:0 and summed feature 8 (comprising C18:1ω7c/C18:1ω6c). The strain KN72T displayed highest 16S rRNA gene sequence similarities with Hwanghaeella grinnelliae Gri0909T (92.3%), Marivibrio halodurans ZB80T (91.0%) and Aestuariispira insulae AH-MY2T (90.1%). The DNA G+C content of strain KN72T was 61.1%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence presented, strain KN72T represents a novel species of a novel genus of the family Rhodospirillaceae, for which the name Pacificispira spongiicola gen. nov., sp. nov. is proposed. The type strain is KN72T (= CGMCC 1.17142T = KCTC 72429T).
Collapse
|
5
|
Liao X, Lai Q, Yang J, Dong C, Li D, Shao Z. Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:4280-4284. [PMID: 32618558 DOI: 10.1099/ijsem.0.004285] [Citation(s) in RCA: 3] [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 taxonomic study was carried out on strain PA15-N-34T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0-15.0% NaCl and at temperatures of 10-45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34T belonged to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax profundi MTEO17T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %-97.0 %). The average nucleotide identity and DNA-DNA hybridization values between strain PA15-N-34T and type strains of the genus Alcanivorax were 71.46-81.78% and 18.7-25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 31.2 %), C16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34T represents a novel species within the genus Alcanivorax, for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34T (=MCCC 1A14738T=KCTC 72163T).
Collapse
Affiliation(s)
- Xianzhi Liao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Junpeng Yang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Dengfeng Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| |
Collapse
|
6
|
Yan F, Fang J, Cao J, Wei Y, Liu R, Wang L, Xie Z. Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench. Int J Syst Evol Microbiol 2020; 70:2560-2568. [PMID: 32129736 DOI: 10.1099/ijsem.0.004069] [Citation(s) in RCA: 9] [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 piezotolerant, H2O2-tolerant, heavy-metal-tolerant, slightly halophilic bacterium (strain NBT06E8T) was isolated from a deep-sea sediment sample collected from the New Britain Trench at depth of 8900 m. The strain was aerobic, motile, Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth of the strain was observed at 4-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 8-9) and in 0.5-21 % (w/v) NaCl (optimum, 3-7 %). The optimum pressure for growth was 0.1-30 MPa with tolerance up to 60 MPa. Under optimum growth conditions, the strain could tolerate 15 mM H2O2. Resuls of 16S rRNA gene sequence analysis showed that strain NBT06E8T is closely related to Halomonas aquamarina DSM 30161T (99.5%), Halomonas meridiana DSM 5425T (99.43%) and Halomonas axialensis Althf1T (99.35%). The digital DNA-DNA hybridization values between strain NBT06E8T and the three related type strains, H. aquamarina, H. meridiana and H. axialensis, were 30.5±2.4 %, 30.7±2.5% and 31.5±2.5 %, respectively. The average nucleotide identity values between strain NBT06E8T and the three related type strains were 86.26, 86.26 and 83.63 %, respectively. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The predominant respiratory quinone detected was ubiquinone-9 (Q-9). Based on its phenotypic and phylogenetic characteristics, we conclude that strain NBT06E8T represents a novel species of the genus Halomonas, for which the name Halomonas piezotolerans sp. nov. is proposed (type strain NBT06E8T= MCCC 1K04228T=KCTC 72680T).
Collapse
Affiliation(s)
- Fangfang Yan
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yuli Wei
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Li Wang
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
| |
Collapse
|
7
|
Wang L, Lai Q, Liu X, Shao Z. Paramesonia marina gen. nov., sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2020; 70:2325-2333. [PMID: 32065576 DOI: 10.1099/ijsem.0.004041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out of strain K7T, which was isolated from deep-sea water collected from the Indian Ocean. The bacterium was Gram-stain-negative, aerobic, oxidase-negative, catalase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0.5-10 % (optimum, 3 %), at a pH range of pH 6.0-10.0 (optimum, pH 7.0) and at temperatures of 10-40 °C (optimum, 28 °C). Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain K7T belonged to the family Flavobacteriaceae, with the high sequence similarities to the genera Mesonia (92.2 %-94.4 %), Salinimicrobium (91.9 %-93.2 %), Salegentibacter (92.1 %-92.6 %), Leeuwenhoekiella (92.1 %-92.3 %), Gramella (91.9 %-92.1 %) and Zunongwangia (91.8 %-92.1 %). The principal fatty acids were iso-C15 : 0 (28.4 %), iso-C15 : 1G (14.2 %), summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl; 11.6 %), iso-C17 : 0 3-OH (10.0 %) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 9.6 %). The G+C content of the chromosomal DNA was 35.8 mol%. The respiratory quinone was determined to be MK-6 (100 %). Phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipid and four unidentified lipids were detected. The combined genotypic and phenotypic data show that strain K7T represents a novel species of a novel genus, for which the name Paramesonia marina gen. nov., sp. nov. is proposed, with the type strain K7T (=MCCC 1A01093T=KCTC 52325T).
Collapse
Affiliation(s)
- Lei Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| |
Collapse
|
8
|
Lai Q, Liu X, Yuan J, Xie S, Shao Z. Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2019; 69:932-936. [DOI: 10.1099/ijsem.0.003219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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 CIC4N-9T, which was isolated from deep-sea water of the Indian Ocean. The bacterium was Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0–9% and at temperatures of 4–41 °C. The isolate was able to degrade gelatin but not aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CIC4N-9T belonged to the genus
Pararhodobacter
, with the highest sequence similarity to the only recognized species,
Pararhodobacter aggregans
D1-19T (96.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain CIC4N-9T and
P. aggregans
D1-19T were 80.4 and 23.0 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C16 : 0, C18 : 1ω7c 11-methyl, C18 : 0 and C17 : 0. The G+C content of the chromosomal DNA was 66.8 mol%. The sole respiratory quinone was determined to be Q-10. Phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unknown phospholipids, four unknown aminolipids and one unknown polar lipid were present. The combined genotypic and phenotypic data show that strain CIC4N-9T represents a novel species within the genus
Pararhodobacter
, for which the name
Pararhodobacter
marinus sp. nov. is proposed. The type strain is CIC4N-9T (=MCCC 1A01225T=KCTC 52336T).
Collapse
Affiliation(s)
- Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Jun Yuan
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Shuchen Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| |
Collapse
|
9
|
Wei Y, Mao H, Xu Y, Zou W, Fang J, Blom J. Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:2462-2467. [DOI: 10.1099/ijsem.0.002785] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuli Wei
- 2National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
- 3The Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Haiyan Mao
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yunping Xu
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Wencai Zou
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- 4Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
- 5Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Jochen Blom
- 6Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| |
Collapse
|
10
|
Wang C, Huang Y, Zhang Z, Wang H. Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium. AMB Express 2018; 8:67. [PMID: 29696463 PMCID: PMC5918149 DOI: 10.1186/s13568-018-0594-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 04/13/2018] [Indexed: 11/15/2022] Open
Abstract
With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.
Collapse
|
11
|
Wei Y, Fang J, Xu Y, Zhao W, Cao J. Corynebacterium hadale sp. nov. isolated from hadopelagic water of the New Britain Trench. Int J Syst Evol Microbiol 2018; 68:1474-1478. [PMID: 29557772 DOI: 10.1099/ijsem.0.002695] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel heterotrophic, Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain NBT06-6T, was isolated from the deep seawater in the New Britain Trench and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 35 °C (range 22-41 °C), at pH 6 (4-8) and with 4 % (w/v) NaCl (0-10 %). The strain grew at hydrostatic pressures of 0.1-100 MPa (optimum, 0.1 MPa) at 35 °C. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain NBT06-6T belonged to the genus Corynebacterium, with the highest sequence similarity (97.9 %) to Corynebacterium imitans, and shared low 16S rRNA gene sequence similarities (<97.0 %) with other type strains. The major respiratory menaquinones were MK-8(H2) and MK-9(H2). The polar lipids were diphosphatidyglycerol, phosphatidylglycerol, phosphatidylinositol, three unidentified aminoglycolipids and four unidentified glycolipids. The major fatty acids detected were C18 : 1ω9c, C16 : 0 and C15 : 0. Strain NBT06-6T contained meso-diaminopimelic acid and mycolic acids in its cell wall, and mannose, galactose, glucose, arabinose and ribose as major whole-cell sugars. The G+C content of the genomic DNA was 65.1 mol%. The digital DNA-DNA hybridization value and the average nucleotide identity between strain NBT06-6T and C. imitans were 24.5±2.4 and 81.9 %, respectively. The combined genotypic and phenotypic data indicated that strain NBT06-6T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium hadale sp. nov. is proposed, with the type strain NBT06-6T (=MCCC 1K03347T=DSM 105365T).
Collapse
Affiliation(s)
- Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,The Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yunping Xu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Weiqiang Zhao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| |
Collapse
|
12
|
Du Y, Liu X, Lai Q, Li W, Sun F, Shao Z. Oceanibaculum nanhaiense sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:4842-4845. [PMID: 29022547 DOI: 10.1099/ijsem.0.002388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain L54-1-50T, which was isolated from surface seawater of the South China Sea. Cells of strain L54-1-50T were Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth was observed at salinities from 0 to 9 % (optimum 2 %, w/v), at pH 6.0-10.0 (optimum 8.0-9.0) and at temperatures from 10 to 45 °C (optimum 25-37 °C), but not at 4 or 50 °C. The 16S rRNA gene sequence analysis indicated that strain L54-1-50T was a member of the genus Oceanibaculum, related to Oceanibaculum indicum P24T (98.8 %) and Oceanibaculum pacificum MC2UP-L3T (97.7 %). The digital DNA-DNA hybridization values between strain L54-1-50T and the two type strains O. indicum P24T and O. pacificum MC2UP-L3T were 35.4±2.5 and 23.7±2.5 %, respectively. The average nucleotide identity values between strain L54-1-50T and two type strains were 79.7 and 88.3 %, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 1 2-OH. The respiratory quinone was Q-10. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, two unidentified phospholipids and three unidentified lipids. The G+C content of the chromosomal DNA was 65.1 mol%. The combined genotypic and phenotypic data showed that strain L54-1-50T represents a novel species of the genus Oceanibaculum, for which the name Oceanibaculumnanhaiense sp. nov. is proposed, with the type strain L54-1-50T (=KCTC 52312T=MCCC 1A05150T).
Collapse
Affiliation(s)
- Yaping Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Fujian Key Laboratory of Marine Genetic Resources, 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; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Fujian Key Laboratory of Marine Genetic Resources, 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; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Weiwei Li
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Fujian Key Laboratory of Marine Genetic Resources, 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; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Fujian Key Laboratory of Marine Genetic Resources, 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; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| |
Collapse
|
13
|
Wang C, Guo G, Huang Y, Hao H, Wang H. Salt Adaptation and Evolutionary Implication of a Nah-related PAHs Dioxygenase cloned from a Halophilic Phenanthrene Degrading Consortium. Sci Rep 2017; 7:12525. [PMID: 28970580 PMCID: PMC5624874 DOI: 10.1038/s41598-017-12979-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 09/14/2017] [Indexed: 12/05/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) pollutions often occur in marine and other saline environment, largely due to anthropogenic activities. However, study of the PAHs-degradation genotypes in halophiles is limited, compared with the mesophilic terrestrial PAHs degraders. In this study, a bacterial consortium (CY-1) was enriched from saline soil contaminated with crude oil using phenanthrene as the sole carbon source at 10% salinity. CY-1 was dominated by the moderate halophilic Marinobacter species, and its dominant PAHs ring-hydroxylating dioxygenase (RHD) genotypes shared high identity to the classic nah-related RHDs found in the mesophilic species. Further cloning of a 5.6-kb gene cluster from CY-1 unveiled the existence of a new type of PAHs degradation gene cluster (hpah), which most probably evolves from the nah-related gene clusters. Expression of the RHD in this gene cluster in E. coli lead to the discovery of its prominent salt-tolerant properties compared with two RHDs from mesophiles. As a common structural feature shared by all halophilic and halotolerant enzymes, higher abundance of acidic amino acids was also found on the surface of this RHD than its closest nah-related alleles. These results suggest evolution towards saline adaptation occurred after horizontal transfer of this hpah gene cluster into the halophiles.
Collapse
Affiliation(s)
- Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Guang Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,School of Environmental Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Yong Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Han Hao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
14
|
Fu YS, Hussain F, Habib N, Khan IU, Chu X, Duan YQ, Zhi XY, Chen X, Li WJ. Sphingobacteriumsoli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:2284-2288. [PMID: 28699577 DOI: 10.1099/ijsem.0.001946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling County, Yunnan Province, south-west China. The new isolate was characterized taxonomically by using a polyphasic approach. The strain grew optimally at 30 °C, at pH 7.0 and with 0-3 % (w/v) NaCl. It was positive for catalase and oxidase but negative for H2S production. Comparative 16S rRNA gene sequence analysis showed that strain YIM X0211T fell within the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii DSM 11724T (97.93 % similarity). The G+C content of the genomic DNA was 41.2 mol%. The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0 2-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, sphingolipid, and several unknown phospholipids or lipids. The DNA-DNA hybridization value between strain YIM X0211T and S. mizutaii DSM 11724T was 42.3±0.4 %, which is below the 70 % limit for species delineation. These chemotaxonomic data supported the affiliation of strain YIM X0211T to the genus Sphingobacterium. Based on the recorded phenotypic and genotypic characteristics, it is determined that the isolate represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium soli sp. nov. is proposed. The type strain is YIM X0211T (=KCTC 42696T=CGMCC 1.15966T).
Collapse
Affiliation(s)
- Yu-Song Fu
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Firasat Hussain
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Neeli Habib
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Inam Ullah Khan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Xiao Chu
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Xing Chen
- China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| |
Collapse
|
15
|
Coelho FJRC, Louvado A, Domingues PM, Cleary DFR, Ferreira M, Almeida A, Cunha MR, Cunha Â, Gomes NCM. Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz. Sci Rep 2016; 6:35272. [PMID: 27762306 PMCID: PMC5071872 DOI: 10.1038/srep35272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/26/2016] [Indexed: 11/16/2022] Open
Abstract
The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.
Collapse
Affiliation(s)
- Francisco J R C Coelho
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - António Louvado
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Patrícia M Domingues
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.,Department of Chemistry &CICECO, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Marina Ferreira
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Marina R Cunha
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology &CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| |
Collapse
|
16
|
Yuan CG, Jiang Z, Xiao M, Zhou EM, Kim CJ, Hozzein WN, Park DJ, Zhi XY, Li WJ. Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:4797-4802. [PMID: 27535803 DOI: 10.1099/ijsem.0.001432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, short rod, non-motile, non-spore-forming, aerobic bacterium, designated strain YIM M12096T, was isolated from deep-sea sediment collected from the Indian Ocean. Optimal growth conditions of the strain were observed at 25-30 °C, pH 6.0 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM M12096T was closely related to Nitratireductor indicus C115T (97.4 % 16S rRNA gene sequence similarity) and Mesorhizobium thiogangeticum SJTT (97.3 %). The strain, however, formed a robust clade with members of the genus Mesorhizobium in phylogenetic dendrograms generated with neighbour-joining, maximum-likelihood and maximum-parsimony trees. Analysis based on the sequence of housekeeping gene recA also gave a similar phylogenetic relationship, indicating that strain YIM M12096T is a member of the genus Mesorhizobium. DNA-DNA relatedness values between strain YIM M12096T and related type strains N. indicus CCTCC AB209298T and M. thiogangeticum DSM 17097T were 40.5 % and 36.7 %, respectively. Chemotaxonomic features of the isolate included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminophospholipid and an unidentified phospholipid as its characteristic polar lipids and Q-10 as respiratory ubiquinone. Major fatty acids (>10 %) detected were C18 : 1ω7c and/or C18 : 1ω6c, 11-methyl-C18 : 1ω7c and cyclo-C19 : 0ω8c. Based on the chemotaxonomic properties and phylogenetic analyses, strain YIM M12096T is determined to be a member of the genus Mesorhizobium. The strain could be differentiated from the closely related species by the differences in physiological and biochemical properties supported by low DNA-DNA relatedness values. It is therefore concluded that strain YIM M12096T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobiumsediminum sp. nov. is proposed. The type strain is YIM M12096T (=CCTCC AB 2014219T=KCTC 42205T).
Collapse
Affiliation(s)
- Chang-Guo Yuan
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Dong-Jin Park
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| |
Collapse
|
17
|
Lai Q, Zhou Z, Li G, Li G, Shao Z. Alcanivorax nanhaiticus sp. nov., isolated from deep sea sediment. Int J Syst Evol Microbiol 2016; 66:3651-3655. [PMID: 27307296 DOI: 10.1099/ijsem.0.001247] [Citation(s) in RCA: 16] [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 taxonomic study was carried out on strain 19-m-6T, which was isolated from deep sea sediment of the South China Sea during the screening of alkane-degrading bacteria. The isolate was Gram-reaction-negative, and oxidase- and catalase- positive. On the basis of 16S rRNA gene sequence similarity, strain 19-m-6T was shown to belong to the genus Alcanivorax, related to Alcanivorax jadensis T9T (97.5 %), Alcanivorax hongdengensis A-11-3T (97.3 %), A. lcanivorax borkumensis SK2T (96.6 %) and seven other species of the genus Alcanivorax(93.9-95.4 %). Average nucleotide identity values between strain 19-m-6T and A. jadensis T9T, A. hongdengensis A-11-3T and A. borkumensis SK2T were 85.12, 85.87 and 84.35 %, respectively. The estimated DNA-DNA hybridization values between strain 19-m-6T and these three type strains were 22.0, 22.6 and 21.2 %, respectively. Four alkane hydroxylase (alkB) genes were obtained from the draft genome sequence. The G+C content of the chromosomal DNA was 56.44 mol%. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, one aminolipid, three phospholipids, two glycolipids and two aminophospholipids. According to its phenotypic features, fatty acid composition and 16S rRNA gene sequence, the novel strain fitted well into the genus Alcanivorax, but could be clearly distinguished from all other known Alcanivorax species described to date. The nameAlcanivorax nanhaiticus sp. nov. is thus proposed, with 19-m-6T (=MCCC 1A05629T=KCTC 52137T) as the type strain.
Collapse
Affiliation(s)
- 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; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Zhongwen Zhou
- 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; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Guizhen Li
- 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; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Guangyu Li
- 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; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 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; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| |
Collapse
|
18
|
Li X, Li C, Lai Q, Li G, Sun F, Shao Z. Hyphomonas pacifica sp. nov., isolated from deep sea of the Pacific Ocean. Antonie van Leeuwenhoek 2016; 109:1111-9. [DOI: 10.1007/s10482-016-0712-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/07/2016] [Indexed: 11/25/2022]
|
19
|
Ying Y, Tian XX, Wang JJ, Qu LY, Li J. Pseudoalteromonas fenneropenaei sp. nov., a marine bacterium isolated from sediment of a Fenneropenaeus chinensis pond. Int J Syst Evol Microbiol 2016; 66:2754-2759. [PMID: 27149865 DOI: 10.1099/ijsem.0.001128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, motile, oxidase- and catalase-positive, non-spore-forming, non-pigmented, aerobic bacterium, designated rzy34T, was isolated from the sediment of a pond containing farmed Fenneropenaeus chinensis Rizhao, China. The strain was able to grow at pH 6-10 (optimum pH 7), 20-40 °C (optimum 30 °C) and in the presence of 1.0-6.0 % NaCl (optimum 1.0-2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the nearest relative of strain rzy34T was Pseudoalteromonas xiamenensis Y2T, with the highest sequence similarity of 96.09 %. Within the genus Pseudoalteromonas, it showed the lowest similarity of 92.7 % to Pseudoalteromonas donghaensis. The G+C content of the chromosomal DNA of strain rzy34T was 45.3 mol%. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C17 : 1ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major respiratory quinone was Q-8. Polar lipid analysis indicated the presence of phosphatidylethanolamine and phosphatidylcholine. On the basis of the phenotypic and phylogenetic characteristics, strain rzy34T represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas fenneropenaei sp. nov. is proposed. The type strain is rzy34T (=CGMCC 1.15325T=KCTC 42730T).
Collapse
Affiliation(s)
- Yu Ying
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, PR China
| | - Xin-Xin Tian
- First Institute of Oceanography, State Oceanic Administration, 266061 Qingdao, PR China
| | - Jia-Jia Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, PR China
| | - Ling-Yun Qu
- First Institute of Oceanography, State Oceanic Administration, 266061 Qingdao, PR China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, PR China
| |
Collapse
|
20
|
Altererythrobacter estronivorus sp. nov., an Estrogen-Degrading Strain Isolated from Yundang Lagoon of Xiamen City in China. Curr Microbiol 2016; 72:634-40. [DOI: 10.1007/s00284-016-0995-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/22/2015] [Indexed: 11/26/2022]
|
21
|
Du J, Liu Y, Lai Q, Dong C, Xie Y, Shao Z. Kordia zhangzhouensis sp. nov., isolated from surface freshwater. Int J Syst Evol Microbiol 2015; 65:3379-3383. [DOI: 10.1099/ijsem.0.000424] [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
An aerobic, Gram-stain-negative, rod-shaped and non-motile bacterium, JS14SB-1T, was isolated from the surface freshwater of the Jiulong River, PR China. Strain JS14SB-1T grew at 15–38 °C (optimum, 28–35 °C), at pH 6.0–9.0 (optimum pH 7.0) and in the presence of 1.0–7.0 % (w/v) NaCl [optimum 3.0–5.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain JS14SB-1T was affiliated to the genus Kordia, sharing low similarities (95.1–97.1 %) to all type strains of species of this genus. The digital DNA–DNA hybridization (DDH) value between strain JS14SB-1T and the closely related strain Kordia jejudonensis SSK3-3T was 20.70 ± 2.33 % and far below the 70 % DDH value taken as the gold standard for delineation of bacterial species. The major fatty acids were identified as iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids were phosphatidylethanolamine, glycolipid, aminolipid, several unidentified phospholipids and lipids. The predominant menaquinone was MK-6. The G+C content of the genomic DNA was 33.8 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic distinctiveness, strain JS14SB-1T is considered to represent a novel species of the genus Kordia, for which the name Kordia zhangzhouensis sp. nov. is proposed; the type strain is JS14SB-1T ( = MCCC 1A00726T = KCTC 42140T).
Collapse
Affiliation(s)
- Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; 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, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Chunming Dong
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yanrong Xie
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; 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, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| |
Collapse
|
22
|
Sun F, Du Y, Liu X, Lai Q, Shao Z. Halovulum dunhuangense gen. nov., sp. nov., isolated from a saline terrestrial spring. Int J Syst Evol Microbiol 2015; 65:2810-2816. [DOI: 10.1099/ijs.0.000332] [Citation(s) in RCA: 17] [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 bacterial strain, YYQ-30T, isolated from a mixed water–sand–sediment sample collected from a terrestrial spring located in Dunhuang, China, was characterized with respect to its morphology, physiology and taxonomy. Cells of the strain were Gram-stain-negative, aerobic, oxidase- and catalase-positive, non-flagellated, oval to rod-shaped (0.5–1.0 μm wide and 1.1–6.6 μm long) and divided by binary fission. Growth was observed in the presence of 0–10.0 % (w/v) NaCl with optimal growth at 0–3.0 %, at pH 6.0–9.0 (optimum pH 7.0–8.5) and at 10–45 °C (optimum 30–37 °C). The isolate could reduce nitrate to nitrite and hydrolyse aesculin and gelatin (weakly), but was unable to degrade Tween 80 or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YYQ-30T belongs to the family Rhodobacteraceae and forms a distinct lineage with the type strain of Albimonas donghaensis and forms a branch within a cluster constituted by the type strains of species of the genera Albimonas, Rhodovulum, Albidovulum, Haematobacter and Tropicimonas; levels of 16S rRNA gene sequence similarity between strain YYQ-30T and members of related genera ranged from 94.1 to 89.7 %. Strain YYQ-30T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 70.0 %), C18 : 0 (9.5 %), summed feature 2 (one or more of C14 : 0 3-OH, iso-C16 : 1 I and C12 : 0 aldehyde; 6.9 %) and 11-methyl C18 : 1ω7c (6.0 %) as the principal fatty acids. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids, two unidentified aminolipids and five unknown lipids. The pufLM gene was detected. The G+C content of the genomic DNA was 71.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain YYQ-30T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Halovulum dunhuangense gen. nov., sp. nov. is proposed. The type strain of Halovulum dunhuangense is YYQ-30T ( = LMG 27418T = MCCC 1A06483T).
Collapse
Affiliation(s)
- Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center and 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 Biogenetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center and 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 Biogenetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center and 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 Biogenetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center and 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 Biogenetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center and Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| |
Collapse
|
23
|
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).
Collapse
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
| |
Collapse
|
24
|
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).
Collapse
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
| |
Collapse
|
25
|
Yuan J, Lai Q, Sun F, Zheng T, Shao Z. The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge. Front Microbiol 2015; 6:853. [PMID: 26379634 PMCID: PMC4548250 DOI: 10.3389/fmicb.2015.00853] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 08/05/2015] [Indexed: 12/03/2022] Open
Abstract
The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946–4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments.
Collapse
Affiliation(s)
- Jun Yuan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University 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, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| |
Collapse
|
26
|
Du J, Lai Q, Liu Y, Dong C, Xie Y, Shao Z. Draconibacterium sediminis sp. nov., isolated from river sediment. Int J Syst Evol Microbiol 2015; 65:2310-2314. [DOI: 10.1099/ijs.0.000260] [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 Gram-reaction-negative, facultatively anaerobic and rod-shaped bacterium, designated strain JN14CK-3T, was isolated from surface sediment of the Jiulong River of China and was characterized phenotypically and phylogenetically. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain JN14CK-3T belonged to the genus Draconibacterium, with the highest sequence similarity (98.3 %) to Draconibacterium orientale FH5T. By contrast, strain JN14CK-3T shared low 16S rRNA gene sequence similarities ( < 91.0 %) with other type strains. The sole respiratory quinone was MK-7.The polar lipids were phosphatidylethanolamine and several unidentified phospholipids and lipids. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, C17:0 2-OH, iso-C16:0 3-OH and iso-C17:0 3-OH. The G+C content of the genomic DNA was 40.9 mol%. The digital DNA–DNA hybridization value and average nucleotide identity (ANI) between strain JN14CK-3T and D. orientale FH5T were 34.2 ± 2.5 % and 87.1 %, respectively. The combined genotypic and phenotypic data showed that strain JN14CK-3T represents a novel species of the genus Draconibacterium, for which the name Draconibacterium
sediminis sp. nov. is proposed, with the type strain JN14CK-3T ( = MCCC 1A00734T = KCTC 42152T).
Collapse
Affiliation(s)
- Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration Collaborative Innovation Center of Marine Biological Resources 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, The Third Institute of State Oceanic Administration Collaborative Innovation Center of Marine Biological Resources Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration Collaborative Innovation Center of Marine Biological Resources Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Chunming Dong
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration Collaborative Innovation Center of Marine Biological Resources Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yanrong Xie
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration Collaborative Innovation Center of Marine Biological Resources 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, The Third Institute of State Oceanic Administration Collaborative Innovation Center of Marine Biological Resources Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| |
Collapse
|
27
|
Du J, Dong C, Lai Q, Liu Y, Xie Y, Shao Z. Pseudobowmanella zhangzhouensis gen. nov., sp. nov., isolated from the surface freshwater of the Jiulong River in China. Antonie van Leeuwenhoek 2015; 107:741-8. [PMID: 25707905 DOI: 10.1007/s10482-014-0368-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/20/2014] [Indexed: 10/24/2022]
Abstract
A strain, JS7-9(T), which was isolated from the surface freshwater of the Jiulong River, China, was subjected to taxonomic study. The bacterium was Gram-negative, facultatively anaerobic, rod-shaped and motile by means of a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JS7-9(T) is affiliated to the family Alteromonadaceae, showing 90.5-94.2 % of 16S rRNA gene sequence similarity with the genera Bowmanella (94.0-94.2 %), Aestuariibacter (93.0-93.5 %), Glaciecola (91.0-93.1 %), Alteromonas (90.5-93.1 %) and Salinimonas (90.6-91.8 %). The major fatty acids were identified as C16:0, Sum In Feature 3 (C16:1 ω7c/ω6c), Sum In Feature 8 (C18:1 ω7c/ω6c) and C17:1 ω8c, and Q-8 as the predominant isoprenoid quinone. Based on the phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain JS7-9(T) is considered to represent a novel species of a novel genus of the family Alteromonadaceae, for which the name Pseudobowmanella zhangzhouensis gen. nov., sp. nov. is proposed, with the type strain JS7-9(T) (=MCCC 1A00758(T) = KCTC 42143(T)).
Collapse
Affiliation(s)
- Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | | | | | | | | | | |
Collapse
|
28
|
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.
Collapse
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:
| |
Collapse
|
29
|
Li C, Lai Q, Li G, Dong C, Wang J, Liao Y, Shao Z. Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov., isolated from surface seawater of the Bering Sea and Chukchi Sea. Antonie van Leeuwenhoek 2014; 106:657-65. [DOI: 10.1007/s10482-014-0236-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 07/14/2014] [Indexed: 11/28/2022]
|
30
|
Li C, Lai Q, Li G, Liu Y, Sun F, Shao Z. Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments. PLoS One 2014; 9:e101394. [PMID: 25019154 PMCID: PMC4096408 DOI: 10.1371/journal.pone.0101394] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 06/06/2014] [Indexed: 11/19/2022] Open
Abstract
Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.
Collapse
Affiliation(s)
- Chongping Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guizhen Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- * E-mail:
| |
Collapse
|
31
|
Ottowia beijingensis sp. nov., isolated from coking wastewater activated sludge, and emended description of the genus Ottowia. Int J Syst Evol Microbiol 2014; 64:963-967. [DOI: 10.1099/ijs.0.054015-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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 GCS-AN-3T, which was isolated from a phenol-degrading consortium enriched from coking wastewater activated sludge of Beijing Shougang Company Limited during the screening of phenol-degrading bacteria. Cells of strain GCS-AN-3T were Gram-stain-negative, short rods, and oxidase-/catalase-positive. Growth was observed at salinities from 0 to 2.5 % and at temperatures from 10 to 37 °C. 16S rRNA gene sequence analysis showed that strain GCS-AN-3T was most closely related to
Ottowia pentelensis
DSM 21699T (96.2 %). The principal fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 0, summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and cyclo C17 : 0. The major respiratory quinone was Q-8. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. The G+C content of the genomic DNA was 67.6 mol%. Thiosulfate could be utilized as co-substrate for aerobic growth and was oxidized to sulfate. On the basis of phenotypic, chemotaxonomic and molecular data, strain GCS-AN-3T is considered to represent a novel species of the genus
Ottowia
, for which the name Ottowia beijingensis sp. nov. is proposed (type strain GCS-AN-3T = LMG 27179T = CGMCC 1.12324T = MCCC 1A01410T). An emended description of the genus
Ottowia
is also proposed.
Collapse
|
32
|
Cao J, Lai Q, Li G, Shao Z. Pseudopedobacter beijingensis gen. nov., sp. nov., isolated from coking wastewater activated sludge, and reclassification of Pedobacter saltans as Pseudopedobacter saltans comb. nov. Int J Syst Evol Microbiol 2014; 64:1853-1858. [PMID: 24573160 DOI: 10.1099/ijs.0.053991-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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 GCS-AE-31(T), which was isolated from a phenol-degrading consortium, enriched from coking wastewater activated sludge of the Beijing Shougang Company Limited during the screening of phenol-degrading bacteria. Cells of strain GCS-AE-31(T) were Gram-stain-negative, short rods, motile by gliding, oxidase- and catalase-positive. Growth was observed at salinities of 0-3% and at temperatures of 10-37 °C. On the basis of 16S rRNA gene sequence similarity, strain GCS-AE-31(T) was most closely related to Pedobacter saltans LMG 10337(T) (96.17%), but it showed low similarity to all other species of the genus Pedobacter (89.28-92.45%). It also showed low 16S rRNA gene similarity to all other species of the family Sphingobacteriaceae (87.25-92.45%) examined. The dominant fatty acids were iso-C(15 : 0), summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c), anteiso-C(15 : 0) and iso-C(17 : 0) 3-OH. The menaquinones were MK-7 (95.5%) and MK-6 (4.5%). The polar lipids were phosphatidylethanolamine, three aminolipids and three unknown phospholipids. Sphingolipid was present. The G+C content of the chromosomal DNA was 36.2 mol%. According to its phylogenetic position and phenotypic traits, the novel strain could not be assigned to the genus Pedobacter; it should be classified as representing a novel species of a novel genus in the family Sphingobacteriaceae, for which the name Pseudopedobacter beijingensis gen. nov., sp. nov. is proposed (type strain GCS-AE-31(T) = MCCC 1A01299(T) = CGMCC 1.12329(T) = LMG 27180(T)). The misclassified species Pedobacter saltans is transferred to the novel genus as Pseudopedobacter saltans comb. nov. (type strain LMG 10337(T) = MCCC 1A06472(T) = DSM 12145(T) = CCUG 39354(T) = CIP 105500(T) = JCM 21818(T) = NBRC 100064(T)).
Collapse
Affiliation(s)
- Junwei Cao
- 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
| | - 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
| | - Guizhen Li
- 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
| |
Collapse
|
33
|
Shao R, Lai Q, Liu X, Sun F, Du Y, Li G, Shao Z. Zunongwangia atlantica sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2014; 64:16-20. [DOI: 10.1099/ijs.0.054007-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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 22II14-10F7T, which was isolated from the deep-sea water of the Atlantic Ocean with oil-degrading enrichment. The bacterium was Gram-stain-negative, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinities from 0.5 to 15 % and at temperatures from 4 to 37 °C; it was unable to hydrolyse Tween 40, 80 or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II14-10F7T represented a member of the genus
Zunongwangia
, with highest sequence similarity of 97.3 % to
Zunongwangia profunda
SM-A87T, while the similarities to other species were all below 94.0 %. The DNA–DNA hybridization estimate of the similarity between strain 22II14-10F7T and
Z. profunda
SM-A87T was 27.20±2.43 % according to their genome sequences. The principal fatty acids were iso-C15 : 0, anteiso-C15 : 0 , iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c/ω6c) and summed feature 9 (iso-C17 : 1ω9c or C16 : 0 10-methyl). The G+C content of the chromosomal DNA was 35.5 mol%. The major respiratory quinone was determined to be MK-6. Phosphatidylethanolamine (PE), two aminolipids (AL1 and AL2) and five unknown lipids (L1–L5) were present. The combined genotypic and phenotypic data show that strain 22II14-10F7T represents a novel species of the genus
Zunongwangia
, for which the name
Zunongwangia
atlantica sp. nov. is proposed, with the type strain 22II14-10F7T ( = CGMCC1.12470T = LMG 27421T = MCCC 1A06481T).
Collapse
Affiliation(s)
- Rui Shao
- Life Science College, Xiamen University, Xiamen 361005, 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
- Life Science College, Xiamen University, Xiamen 361005, 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
| | - 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
| | - 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
| | - Guangyu Li
- 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
| |
Collapse
|
34
|
Zhao CH, Luo JJ, Gong T, Huang XL, Ye DZ, Luo ZH. Pseudoalteromonas xiamenensis sp. nov., a marine bacterium isolated from coastal surface seawater. Int J Syst Evol Microbiol 2013; 64:444-448. [PMID: 24096356 DOI: 10.1099/ijs.0.050229-0] [Citation(s) in RCA: 21] [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 Gram-negative, oxidase- and catalase-positive, rod-shaped, non-spore-forming, motile, aerobic bacterium, designated Y2(T), was isolated from surface seawater of Yundang Lake, Xiamen, China. The strain was able to grow in the presence of 0.5-6.0% NaCl (optimum 1.0-1.5%), at pH 5-10 (optimum pH 8) and at 10-40 °C (optimum 25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y2(T) belongs to the genus Pseudoalteromonas, with the highest sequence similarity of 94.9% to Pseudoalteromonas tunicata D2(T); within the genus Pseudoalteromonas, it showed the lowest similarity of 92.8% to Pseudoalteromonas denitrificans ATCC 43337(T). The G+C content of the chromosomal DNA of strain Y2(T) was 45.1 mol%. The predominant fatty acids were summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c), C(16 : 0), C(12 : 0) 3-OH and summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c). The only respiratory quinone detected was Q-8. Based on the phylogenetic and phenotypic characteristics, strain Y2(T) represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas xiamenensis sp. nov. is proposed; the type strain is Y2(T) ( = CGMCC 1.12157(T) = JCM 18779(T)).
Collapse
Affiliation(s)
- Chang-Hui Zhao
- Department of Life Science and Chemical Engineering, Hunan University of Science and Engineering, Yongzhou 425100, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, PR China
| | - Jing-Jing Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, PR China
| | - Ting Gong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, PR China
| | - Xiang-Ling Huang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, PR China
| | - De-Zan Ye
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, PR China
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, PR China
| |
Collapse
|
35
|
Li G, Lai Q, Liu X, Sun F, Du Y, Li G, Shao Z. Maricoccus atlantica gen. nov. sp. nov., isolated from deep sea sediment of the Atlantic Ocean. Antonie van Leeuwenhoek 2013; 104:1073-81. [DOI: 10.1007/s10482-013-0029-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
|
36
|
Rubiano-Labrador C, Bland C, Miotello G, Guérin P, Pible O, Baena S, Armengaud J. Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring. J Proteomics 2013; 97:36-47. [PMID: 23727365 DOI: 10.1016/j.jprot.2013.05.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 04/30/2013] [Accepted: 05/16/2013] [Indexed: 01/18/2023]
Abstract
UNLABELLED Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions. At low salinity general stress proteins (chaperons, proteases and proteins associated with oxidative stress protection), were detected in higher amounts, probably linked to difficulties for proper protein folding and metabolism. Proteogenomics and comparative genomics pointed at the CrgA transcriptional regulator as a key-factor for the proteome remodeling upon low osmolarity. In hyper-osmotic condition, T. consotensis produced in larger amounts proteins involved in the sensing of changes in salt concentration, as well as a wide panel of transport systems for the transport of organic compatible solutes such as glutamate. We have described here a straightforward procedure in making a new environmental isolate quickly amenable to proteomics. BIOLOGICAL SIGNIFICANCE The bacterium Tistlia consotensis was isolated from a saline spring in the Colombian Andes and represents an interesting environmental model to be compared with extremophiles or other moderate organisms. To explore the halotolerance molecular mechanisms of the bacterium T. consotensis, we developed an innovative proteogenomic strategy consisting of i) genome sequencing, ii) quick annotation of the genes whose products were detected by mass spectrometry, and iii) comparative proteomics of cells grown in three salt conditions. We highlighted in this manuscript how efficient such an approach can be compared to time-consuming genome annotation when pointing at the key proteins of a given biological question. We documented a large number of proteins found produced in greater amounts when cells are cultivated in either hypo-osmotic or hyper-osmotic conditions. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
Collapse
Affiliation(s)
- Carolina Rubiano-Labrador
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá D.C., Colombia; Colombian Center for Genomics and Bioinformatics of Extreme Environments, GeBiX, Colombia
| | - Céline Bland
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Guylaine Miotello
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Philippe Guérin
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá D.C., Colombia; Colombian Center for Genomics and Bioinformatics of Extreme Environments, GeBiX, Colombia
| | - Jean Armengaud
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
| |
Collapse
|
37
|
Amoozegar MA, Makhdoumi-Kakhki A, Ramezani M, Nikou MM, Fazeli SAS, Schumann P, Ventosa A. Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae. Int J Syst Evol Microbiol 2012; 63:1562-1567. [PMID: 22904212 DOI: 10.1099/ijs.0.041236-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16(T), was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16(T) were not motile. Growth occurred with 2.5-5.2 M NaCl (optimum 3.4 M), at pH 6.0-8.0 (optimum pH 7.0) and at 30-50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16(T) belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895(T) (91.6 % sequence similarity), Rhodovibrio salinarum NCIMB 2243(T) (91.2 %), Pelagibius litoralis CL-UU02(T) (88.9 %) and Fodinicurvata sediminis YIM D82(T) (88.7 %). The novel strain's major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16(T) contained the ubiquinone Q-10. The G+C content of the novel strain's genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16(T) and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16(T) ( = IBRC-M 10018(T) = DSM 25584(T)).
Collapse
Affiliation(s)
- Mohammad Ali Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre, Academic Centre for Education, Culture and Research, Tehran, Iran.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology, and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohadaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre, Academic Centre for Education, Culture and Research, Tehran, Iran
| | - Mahdi Moshtaghi Nikou
- Microorganisms Bank, Iranian Biological Resource Centre, Academic Centre for Education, Culture and Research, Tehran, Iran
| | | | - Peter Schumann
- Genetic Department, Rojan Insititute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Antonio Ventosa
- Leibniz-Institut-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| |
Collapse
|
38
|
Luo G, Shi Z, Wang H, Wang G. Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus
Skermanella. Int J Syst Evol Microbiol 2012; 62:1271-1276. [DOI: 10.1099/ijs.0.033746-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22T, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C18 : 1ω7c (63.5 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I, 10.8 %) and C16 : 0 (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22T was most closely related to
Skermanella aerolata
5416T-32T (97.3 %),
Skermanella parooensis
ACM 2042T (95.8 %) and
Skermanella xinjiangensis
10-1-101T (92.9 %). The DNA–DNA hybridization value between strain SB22T and
S. aerolata
KACC 11604T ( = 5416T-32T) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22T and related species, it is considered that the isolate represents a novel species of the genus
Skermanella
, for which the name Skermanella stibiiresistens sp. nov. is proposed. The type strain is SB22T ( = CGMCC 1.10751T = KCTC 23364T). An emended description of the genus Skermanella is provided.
Collapse
Affiliation(s)
- Guosheng Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zunji Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hui Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| |
Collapse
|
39
|
Desertibacter roseus gen. nov., sp. nov., a gamma radiation-resistant bacterium in the family Rhodospirillaceae, isolated from desert sand. Int J Syst Evol Microbiol 2011; 61:1109-1113. [DOI: 10.1099/ijs.0.021246-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, strictly aerobic bacterium, strain 2622T, was isolated from gamma-irradiated soil sampled from the Taklimakan desert in Xinjiang, China. Phylogenetic analyses showed that strain 2622T formed a distinct lineage in the family Rhodospirillaceae and shared 91.7 and 90.1 % 16S rRNA gene sequence similarity with its closest relatives, the type strains of Skermanella xinjiangensis and Skermanella aerolata, respectively. The DNA G+C content of strain 2622T was 71.4 mol% and the isoprenoid quinone was ubiquinone Q-10. Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 2622T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Desertibacter roseus gen. nov., sp. nov. is proposed. The type strain of Desertibacter roseus is strain 2622T ( = CCTCC AB 208152T = KCTC 22436T).
Collapse
|
40
|
Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov. Int J Syst Evol Microbiol 2011; 61:969-973. [DOI: 10.1099/ijs.0.022970-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [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 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T = LMG 25227T = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T = KCTC 22740T = JCM 16344T).
Collapse
|
41
|
Abstract
A taxonomic study was carried out on a novel bacterial strain, designated C115T, isolated from a crude-oil-degrading consortium, enriched from deep-sea water of the Indian Ocean. Cells were Gram-negative short rods, mobile by means of a monopolar flagellum. Growth was observed at salinities of 0–7 % and at 10–43 °C. It was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence analysis showed that strain C115T was related most closely to Nitratireductor aquibiodomus NL21T (96.5 % similarity), Nitratireductor kimnyeongensis KY 101T (96.4 %) and Nitratireductor basaltis J3T (96.2 %). The predominant fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c, 81.8 %) and C18 : 0 (7.0 %). The G+C content of the chromosomal DNA of strain C115T was 59 mol%. Based on its morphology, physiology and fatty acid composition together with 16S rRNA gene sequence comparisons, the novel strain most appropriately belongs to the genus Nitratireductor, but can be distinguished readily from recognized species of the genus. Strain C115T is therefore considered to represent a novel species of the genus Nitratireductor, for which the name Nitratireductor indicus sp. nov. is proposed. The type strain is C115T (=RC92-7T =CCTCC AB 209298T =LMG 25540T =MCCC 1A01260T).
Collapse
|
42
|
Liu Y, Jin JH, Liu YH, Zhou YG, Liu ZP. Dongia mobilis gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a sequencing batch reactor for treatment of malachite green effluent. Int J Syst Evol Microbiol 2010; 60:2780-2785. [DOI: 10.1099/ijs.0.020347-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, strictly aerobic and heterotrophic, non-spore-forming bacterial strain, designated LM22T, was isolated from activated sludge of a sequencing batch reactor for the treatment of malachite green effluent. Cells of strain LM22T were slightly curved to straight rods (0.3–0.5×0.6–1.0 μm) and motile by a single polar flagellum. Strain LM22T was negative for oxidase and catalase activities and phototrophic growth. An internal membrane system and bacteriochlorophyll a were absent. Growth occurred at 20–40 °C (optimum 30–35 °C) and pH 6.0–10.0 (optimum pH 7.0–7.5). Strain LM22T did not require NaCl for growth and tolerated up to 2.0 % NaCl (optimum 0.5 %). The major ubiquinone was Q-10. The major fatty acids (>10 % of the total) were C18 : 1
ω7c (32.9 %), C19 : 0 cyclo ω8c (18.7 %), C16 : 0 (12.1 %) and C16 : 0 2-OH (10.5 %). Phylogenetic analysis of 16S rRNA gene sequences showed that Inquilinus limosus AU0476T was the closest relative (90.4 % 16S rRNA gene sequence similarity). The DNA G+C content was 65.6 mol%. On basis of phenotypic, chemotaxonomic and phylogenetic data, strain LM22T was considered to represent a novel genus and species of the family Rhodospirillaceae, for which the name Dongia mobilis gen. nov., sp. nov. is proposed. The type strain of Dongia mobilis is LM22T (=CGMCC 1.7660T =JCM 15798T).
Collapse
Affiliation(s)
- Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jing-Hua Jin
- Environmental Protection Research Institute of Light Industry, Beijing 100089, PR China
| | - Ying-Hao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| |
Collapse
|
43
|
Fu Y, Tang X, Lai Q, Zhang C, Zhong H, Li W, Liu Y, Chen L, Sun F, Shao Z. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2010; 61:205-209. [PMID: 20190020 DOI: 10.1099/ijs.0.018846-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [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 F44-8(T), which was isolated from a crude-oil-degrading consortium, enriched from marine sediment of the Beibu Gulf, PR China. The 16S rRNA gene sequence of strain F44-8(T) showed highest similarities to those of Flavobacterium frigoris LMG 21922(T) (93.3 %), Flavobacterium terrae R2A1-13(T) (93.3 %) and Flavobacterium gelidilacus LMG 21477(T) (93.1 %). Sequence similarities to other members of the genus Flavobacterium were <93.0 %. The dominant fatty acids of strain F44-8(T) were iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c), iso-C(15 : 1) G and iso-C(17 : 0) 3-OH. The DNA G+C content of strain F44-8(T) was 38.6 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. Strain F44-8(T) could, however, be readily distinguished from all known Flavobacterium species by a number of phenotypic features. Therefore, according to the phenotypic and 16S rRNA gene sequence data, strain F44-8(T) represents a novel species in the genus Flavobacterium, for which the name Flavobacterium beibuense sp. nov. is proposed (type strain F44-8(T) =CCTCC AB 209067(T) =LMG 25233(T) =MCCC 1A02877(T)).
Collapse
Affiliation(s)
- Yuanyuan Fu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Xixiang Tang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Chunhua Zhang
- Marine Environmental Monitor Center of Beihai, State Oceanic Administration, Beihai 536000, PR China
| | - Huanzi Zhong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Weiwei Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Yuhui Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Liang Chen
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Centre of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Fengqin Sun
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| |
Collapse
|
44
|
Lai Q, Yuan J, Shao Z. Altererythrobacter marinus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2009; 59:2973-6. [PMID: 19628597 DOI: 10.1099/ijs.0.008193-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [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 H32(T), which was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. The 16S rRNA gene sequence of strain H32(T) showed highest similarity to that of Altererythrobacter luteolus SW-109(T) (96.7 %); lower similarities were observed with other members of the genus Altererythrobacter (94.7-95.7 %) and with members of the genera Erythrobacter (94.5-96.3 %), Erythromicrobium (94.9 %) and Porphyrobacter (94.3-95.3 %). Phylogenetic analyses of all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that strain H32(T) formed a clade within the genus Altererythrobacter. The dominant fatty acids were C(16 : 0) (6.7 %), C(18 : 1)omega7c (44.3 %) and 11-methyl C(18 : 1)omega7c (25.4 %). The major respiratory quinone was ubiquinone 10. The DNA G+C content was 66.5 mol%. Strain H32(T) did not contain bacteriochlorophyll a. These characteristics are in good agreement with those of members of the genus Altererythrobacter. Therefore, according to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain H32(T) belongs to the genus Altererythrobacter, but can be readily distinguished from known Altererythrobacter species. It is therefore proposed that strain H32(T) represents a novel species, Altererythrobacter marinus sp. nov., with H32(T) (=CCTCC AB 208229(T) =LMG 24629(T) =MCCC 1A01070(T)) as the type strain.
Collapse
Affiliation(s)
- Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | | | | |
Collapse
|