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Long M, Chen D, Fan H, Tang S, Gan Z, Xia H, Lu Y. Microbulbifer bruguierae sp. nov., isolated from sediment of mangrove plant Bruguiera sexangula, and comparative genomic analyses of the genus Microbulbifer. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240737 DOI: 10.1099/ijsem.0.006209] [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: 01/23/2024] Open
Abstract
A Gram-negative, non-motile, strictly aerobic, rod-shaped bacterium, designated as H12T, was isolated from the sediments of mangrove plant Bruguiera sexangula taken from Dapeng district, Shenzhen, PR China. The pairwise 16S rRNA gene sequence analysis showed that strain H12T shared high identity levels with species of the genus Microbulbifer, with the highest similarity level of 98.5 % to M. pacificus SPO729T, followed by 98.1 % to M. donghaiensis CN85T. Phylogenetic analysis using core-genome sequences showed that strain H12T formed a cluster with type species of M. pacificus SPO729T and M. harenosus HB161719T. The complete genome of strain H12T was 4 481 396 bp in size and its DNA G+C content was 56.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values among strain H12T and type species of genus Microbulbifer were below the cut-off levels of 95-96 and 70 %, respectively. The predominant cellular fatty acids of strain H12T were iso-C15 : 0 (22.5 %) and C18 : 1 ω7c (13.9 %). Ubiquinone-8 was detected as the major respiratory quinone. The polar lipids of strain H12T comprised one phosphatidylglycerol, one phosphatidylethanolamine, one unidentified aminoglycophospholipid, one unidentified glycophospholipid, three unidentified glycolipids, two unidentified aminolipids, and one unidentified lipid. Based on polyphasic evidence, strain H12T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer bruguierae sp. nov. is proposed. The type strain is H12T (=KCTC 92859T=MCCC 1K08451T). Comparative genomic analyses of strain H12T with strains of the genus Microbulbifer reveal its potential in degradation of pectin.
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Affiliation(s)
- Meng Long
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Dakun Chen
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| | - Huimin Fan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Shaoshuai Tang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Zhen Gan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| | - Hongli Xia
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Yishan Lu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
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Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk Sea. Arch Microbiol 2022; 204:548. [PMID: 35945400 DOI: 10.1007/s00203-022-03161-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, aerobic, non-motile bacterium КMM 9862T was isolated from a deep bottom sediment sample obtained from the Okhotsk Sea, Russia. Based on the 16S rRNA gene and whole genome sequences analyses the novel strain КMM 9862T fell into the genus Microbulbifer (class Gammaproteobacteria) sharing the highest 16S rRNA gene sequence similarities of 97.4% to Microbulbifer echini AM134T and Microbulbifer epialgicus F-104T, 97.3% to Microbulbifer pacificus SPO729T, 97.1% to Microbulbifer variabilis ATCC 700307T, and similarity values of < 97.1% to other recognized Microbulbifer species. The average nucleotide identity and digital DNA-DNA hybridization values between strain КMM 9862T and M. variabilis ATCC 700307T and M. thermotolerans DSM 19189T were 80.34 and 77.72%, and 20.2 and 19.0%, respectively. Strain КMM 9862T contained Q-8 as the predominant ubiquinone and C16:0, C16:1 ω7c, C12:0, and C10:0 3-OH as the major fatty acids. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, an unidentified aminolipid, two unidentified phospholipids, phosphatidic acid, and an unidentified lipid. The DNA G+C content of 49.8% was calculated from the genome sequence. On the basis of the phylogenetic evidence and distinctive phenotypic characteristics, the marine bacterium KMM 9862T is proposed to be classified as a novel species Microbulbifer okhotskensis sp. nov. The type strain of the species is strain KMM 9862T (= KACC 22804T).
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Cheng Y, Zhu S, Guo C, Xie F, Jung D, Li S, Zhang W, He S. Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment. Antonie van Leeuwenhoek 2021; 114:1033-1042. [PMID: 33844121 DOI: 10.1007/s10482-021-01574-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, named NBU-8HK146T. Strain NBU-8HK146T was able to grow at temperatures of 10-40 °C, at salinities of 0-11% (w/v) and at pH 5.5-9.5. Veoges-Proskauer, methyl red reaction and hydrolysis of Tween 20 were negative. Catalase and oxidase activities, H2S production, hydrolysis of starch, casein, Tweens 40, 60 and 80 were positive. The major cellular fatty acids were C16:0, iso-C15:0 and summed feature 9. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified glycolipids. According to 16S rRNA gene sequence similarities, strain NBU-8HK146T shared 98.0%, 97.9%, 97.7%, 97.6% and 97.3% similarities to the species with validated name Microbulbifer taiwanensis CC-LN1-12T, Microbulbifer rhizosphaerae Cs16bT, Microbulbifer marinus Y215T, Microbulbifer donghaiensis CN85T and Microbulbifer aggregans CCB-MM1T, respectively. Phylogenetic analyses indicated that strain NBU-8HK146T formed a distinct lineage with strains Microbulbifer taiwanensis CC-LN1-12T and Microbulbifer marinus Y215T. Both digital DNA-DNA hybridization values (19.5-22.7%) and average nucleotide identity values (73.2-78.9%) between strain NBU-8HK146T and related species of genus Microbulbifer were below the species delineation cutoffs. The DNA G+C content was 58.9 mol%. Many proteins involving in the adaption of osmotic stress in the salt environment of mangrove were predicted in genome of strain NBU-8HK146T. From phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain NBU-8HK146T can be regarded as a new Microbulbifer species for which the name Microbulbifer hainanensis. The type strain is NBU-8HK146T (= KCTC 82226T = MCCC 1K04737T).
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Affiliation(s)
- Yuping Cheng
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Suting Zhu
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Chaobo Guo
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Feilu Xie
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Dawoon Jung
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Weiyan Zhang
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China.
| | - Shan He
- College of Food and Pharmaceutical Sciences, Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315800, People's Republic of China.
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Huang H, Mo K, Hu Y, Liu M, Zhu J, Zou X, Bao S. Microbulbifer harenosus sp. nov., an alginate-degrading bacterium isolated from coastal sand. Int J Syst Evol Microbiol 2020; 70:1639-1643. [PMID: 32125262 DOI: 10.1099/ijsem.0.003945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped bacterium with peritrichous flagella, designated strain HB161719T, was isolated from coastal sand collected from Tanmen Port in Hainan, PR China. The isolate was found to grow with 2-11 % (w/v) NaCl, at 15-45 °C and pH 6.0-10.0, with an optima of 2-3 % NaCl, 37 °C and pH 7.0, respectively. Chemotaxonomic analysis showed that Q-8 was detected as the sole respiratory quinone and that iso-C15 : 0 and summed features 3, 8 and 9 were the major cellular fatty acids. The G+C content of the genomic DNA was 58.2 mol%. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Microbulbifer, sharing 98.7, 98.4, 97.8 and 97.8 % sequence similarities to the closest relatives of Microbulbifer okinawensis ABABA23T, Microbulbifer pacificus SPO729T, Microbulbifer taiwanensis CC-LN1-12T and Microbulbifer gwangyangensis GY2T, respectively. Low DNA-DNA hybridization values showed that it formed a distinct genomic species. The combined phenotypic and molecular features supported that strain HB161719T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer harenosus sp. nov. is proposed. The type strain is HB161719T (=CGMCC 1.13584T=JCM 32688T).
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Affiliation(s)
- Huiqin Huang
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Kunlian Mo
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Yonghua Hu
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Min Liu
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Jun Zhu
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Xiaoxiao Zou
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Shixiang Bao
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
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Chen YP, Wu HT, Wang GH, Wu DY, Hwang IE, Chien MC, Pang HY, Kuo JT, Liaw LL. Inspecting the genome sequence and agarases of Microbulbifer pacificus LD25 from a saltwater hot spring. J Biosci Bioeng 2019; 127:403-410. [DOI: 10.1016/j.jbiosc.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 09/29/2018] [Accepted: 10/02/2018] [Indexed: 12/27/2022]
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Moh TH, Furusawa G, Amirul AAA. Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest. Int J Syst Evol Microbiol 2017; 67:4089-4094. [DOI: 10.1099/ijsem.0.002258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tsu Horng Moh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Abdullah Al-Ashraf Amirul
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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Lee JY, Kim PS, Hyun DW, Kim HS, Shin NR, Jung MJ, Yun JH, Kim MS, Whon TW, Bae JW. Microbulbifer echini sp. nov., isolated from the gastrointestinal tract of a purple sea urchin, Heliocidaris crassispina. Int J Syst Evol Microbiol 2017; 67:998-1004. [PMID: 27959777 DOI: 10.1099/ijsem.0.001731] [Citation(s) in RCA: 12] [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 novel bacterium, designated as strain AM134T, was isolated from the gut of a purple sea urchin (Heliocidaris crassispina) gathered from the coastal waters of Dokdo, Korea. Strain AM134T was Gram-stain-negative, both catalase- and oxidase-positive, strictly aerobic and showed a rod-coccus cell cycle. Optimum growth occurred at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7. The 16S rRNA gene sequence analysis showed that strain AM134T belonged to the genus Microbulbifer in the family Alteromonadaceae and had high 16S rRNA gene sequence similarity (>97 %) with Microbulbifer epialgicus F-104T (98.9 % similarity) and Microbulbifer variabilis Ni-2088T (98.6 % similarity). The polar lipid profile of strain AM134T was composed of phosphatidylethanolamine, phosphatidylserine, three unidentified aminophospholipids, two unidentified phospholipids, an unidentified amino lipid and six unidentified lipids. The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major cellular fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The DNA-DNA hybridization analysis showed that the strain shared less than 28 % genomic relatedness with Microbulbifer epialgicus DSM 18651T (27±3 %) and Microbulbifer variabilis ATCC 700307T (15±1 %). The G+C content of the genomic DNA was 56.1 mol%. The results of the phylogenetic, phenotypic and genotypic analyses suggest that strain AM134T represents a novel species in the genus Microbulbifer, for which the name Microbulbifer echini is proposed. The type strain is AM134T (=KACC 18258T=JCM 30400T).
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Affiliation(s)
- June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
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Park S, Yoon SY, Ha MJ, Yoon JH. Microbulbifer aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:1436-1441. [DOI: 10.1099/ijsem.0.001831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sun Young Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Min-Ji Ha
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Zhao Y, Park HD, Park JH, Zhang F, Chen C, Li X, Zhao D, Zhao F. Effect of different salinity adaptation on the performance and microbial community in a sequencing batch reactor. BIORESOURCE TECHNOLOGY 2016; 216:808-16. [PMID: 27318158 DOI: 10.1016/j.biortech.2016.06.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 05/12/2023]
Abstract
The performance and microbial community profiles in a sequencing batch reactor (SBR) treating saline wastewater were studied over 300days from 0wt% to 3.0wt% salinity. The experimental results indicated that the activated sludge had high sensitivity to salinity variations in terms of pollutants removal and sedimentation. At 2.0wt% salinity, the system retained a good performance, and 95% removal rate of chemical oxygen demand (COD), biochemical oxygen demand (BOD), NH4(+)-N and total phosphorus (TP) could be achieved. Operation before addition salinity revealed the optimal performance and the most microbial diversity indicated by 16S rRNA gene clone library. Sequence analyses illustrated that Candidate_division_TM7 (TM7) was predominant at 2.0 wt% salinity; however, Actinobacteria was more abundant at 3.0wt% salinity.
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Affiliation(s)
- Yuanyuan Zhao
- School of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Jeong-Hoon Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Fushuang Zhang
- School of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Chen Chen
- School of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Xiangkun Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Dan Zhao
- School of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Fangbo Zhao
- School of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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Camacho M, del Carmen Montero-Calasanz M, Redondo-Gómez S, Rodríguez-Llorente I, Schumann P, Klenk HP. Microbulbifer rhizosphaerae sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. Int J Syst Evol Microbiol 2016; 66:1844-1850. [DOI: 10.1099/ijsem.0.000955] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Maria Camacho
- IFAPA-Instituto de Investigación y Formación Agraria y Pesquera, Centro Las Torres-Tomejil, Ctra. Sevilla-Cazalla de la Sierra, Km 12.2, 41200 Alcalá del Río, Sevilla, Spain
| | - Maria del Carmen Montero-Calasanz
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Susana Redondo-Gómez
- Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes s/n, ., Sevilla, Spain
| | | | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
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Spring S, Scheuner C, Göker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281. [PMID: 25914684 PMCID: PMC4391266 DOI: 10.3389/fmicb.2015.00281] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/21/2015] [Indexed: 11/13/2022] Open
Abstract
In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Carmen Scheuner
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; School of Biology, Newcastle University Newcastle upon Tyne, UK
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Cheng H, Zhang S, Huo YY, Jiang XW, Zhang XQ, Pan J, Zhu XF, Wu M. Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. Int J Syst Evol Microbiol 2014; 65:562-569. [PMID: 25392347 DOI: 10.1099/ijs.0.065078-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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 YN3(T), which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0-10.0 and 4-32 °C in the presence of 0-9.0 % (w/v) NaCl. Strain YN3(T) was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3(T) should be assigned to the genus Gilvimarinus. 'Gilvimarinus agarilyticus' KCTC 23325 and Gilvimarinus chinensis QM42(T) had the closest phylogenetic relationship to strain YN3(T), and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA-DNA hybridization studies, we propose that strain YN3(T) represents a novel species of the genus Gilvimarinus, for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3(T) ( = KCTC 32438(T) = JCM 19198(T)). An emended description of the genus Gilvimarinus is also presented.
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Affiliation(s)
- Hong Cheng
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Shun Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xia-Wei Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, PR China
| | - Xin-Qi Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Linan 311300, PR China
| | - Jie Pan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Math RK, Jin HM, Jeong SH, Jeon CO. Defluviimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus Defluviimonas Foesel et al. 2011. Int J Syst Evol Microbiol 2013; 63:2895-2900. [PMID: 23334880 DOI: 10.1099/ijs.0.048389-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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, strictly aerobic bacterium, designated BS14(T), was isolated from a marine tidal flat of the South Sea in Korea. Colonies were opaque, white, smooth and circular on marine agar. Cells were moderately halophilic, non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain BS14(T) was observed at 5-40 °C (optimum: 30 °C), pH 6.5-9.5 (optimum: 7.0-7.5) and 0-10 % (w/v) NaCl (optimum: 1-1.5 %). The G+C content of the genomic DNA was 61.6 mol%. Strain BS14(T) contained ubiquinone-10 (Q-10) as the sole respiratory quinone and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 3-OH, C10 : 0 3-OH and C18 : 0 as the major fatty acids. The polar lipid pattern comprised phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BS14(T) formed a tight phylogenetic lineage with Defluviimonas denitrificans D9-3(T) with a bootstrap value of 100 %. The 16S rRNA gene sequence similarity between strain BS14(T) and D. denitrificans D9-3(T) was 97.4 % and their DNA-DNA relatedness was 19.1 ± 3.6 %. Based on the phenotypic and genotypic studies, strain BS14(T) represents a novel species of the genus Defluviimonas, for which the name Defluviimonas aestuarii sp. nov. is proposed. The type strain is BS14(T) (= KACC 16442(T) = JCM 18630(T)). An emended description of the genus Defluviimonas Foesel et al. 2011 is also proposed.
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Affiliation(s)
- Renukaradhya K Math
- Department of Life Science & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hyun Mi Jin
- Department of Life Science & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Sang Hyeon Jeong
- Department of Life Science & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science & Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
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