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Hameed A, Suchithra KV, Lin SY, Stothard P, Young CC. Genomic potential for inorganic carbon sequestration and xenobiotic degradation in marine bacterium Youngimonas vesicularis CC-AMW-E T affiliated to family Paracoccaceae. Antonie Van Leeuwenhoek 2023; 116:1247-1259. [PMID: 37740842 DOI: 10.1007/s10482-023-01881-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023]
Abstract
Ecological studies on marine microbial communities largely focus on fundamental biogeochemical processes or the most abundant constituents, while minor biological fractions are frequently neglected. Youngimonas vesicularis CC-AMW-ET, isolated from coastal surface seawater in Taiwan, is an under-represented marine Paracoccaceae (earlier Rhodobacteraceae) member. The CC-AMW-ET genome was sequenced to gain deeper insights into its role in marine carbon and sulfur cycles. The draft genome (3.7 Mb) contained 63.6% GC, 3773 coding sequences and 51 RNAs, and displayed maximum relatedness (79.06%) to Thalassobius litoralis KU5D5T, a Roseobacteraceae member. While phototrophic genes were absent, genes encoding two distinct subunits of carbon monoxide dehydrogenases (CoxL, BMS/Form II and a novel form III; CoxM and CoxS), and proteins involved in HCO3- uptake and interconversion, and anaplerotic HCO3- fixation were found. In addition, a gene coding for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, form II), which fixes atmospheric CO2 was found in CC-AMW-ET. Genes for complete assimilatory sulfate reduction, sulfide oxidation (sulfide:quinone oxidoreductase, SqrA type) and dimethylsulfoniopropionate (DMSP) cleavage (DMSP lyase, DddL) were also identified. Furthermore, genes that degrade aromatic hydrocarbons such as quinate, salicylate, salicylate ester, p-hydroxybenzoate, catechol, gentisate, homogentisate, protocatechuate, 4-hydroxyphenylacetic acid, N-heterocyclic aromatic compounds and aromatic amines were present. Thus, Youngimonas vesicularis CC-AMW-ET is a potential chemolithoautotroph equipped with genetic machinery for the metabolism of aromatics, and predicted to play crucial roles in the biogeochemical cycling of marine carbon and sulfur.
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Affiliation(s)
- Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India.
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Kokkarambath Vannadil Suchithra
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, India
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 402, Taiwan.
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Cho ES, An CW, Bae SS, Chung D, Yu WJ, Kim JYH, Choi G, Kwon YM. Falsirhodobacter algicola sp. nov., a member of the Rhodobacteraceae isolated from the marine red algae Grateloupia sp. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750753 DOI: 10.1099/ijsem.0.006056] [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: 09/27/2023] Open
Abstract
A Gram-negative, pale yellow-pigmented, non-flagellated, motile, rod-shaped and aerobic bacterium, designated strain PG104T, was isolated from red algae Grateloupia sp. collected from the coastal area of Pohang, Republic of Korea. Growth of strain PG104T was observed at 15-35 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.5-8.0) and in the presence of 0-8.0 % (w/v) NaCl (optimum, 5.0 %). The predominant fatty acids included C17 : 0, C18 : 0, 11-methyl C18 : 1 ω7c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and the major respiratory quinone was Q-10. Polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain PG104T formed a phylogenetic lineage with members of the genus Falsirhodobacter and exhibited 16S rRNA gene sequence similarities of 97.1 and 96.6 % to Falsirhodobacter deserti W402T and Falsirhodobacter halotolerans JA744T, respectively. The complete genome of strain PG104T consisted of a single circular chromosome of approximately 2.8 Mbp with five plasmids. Based on polyphasic taxonomic data, strain PG104T represents a novel species in the genus Falsirhodobacter, for which the name Falsirhodobacter algicola sp. nov. is proposed. The type strain of Falsirhodobacter algicola is PG104T (=KCTC 82230T=JCM 34380T).
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Affiliation(s)
- Eun-Seo Cho
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Chang Woo An
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Seung Seob Bae
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Dawoon Chung
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Woon-Jong Yu
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Jaoon Young Hwan Kim
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Grace Choi
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101 Beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
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Jiang Y, Zheng C, Yu T, Li J, Ai J, Li M, Liu X, Deng Z. Rhodococcus yananensis sp. nov., a novel denitrification actinobacterium isolated from microbial fermentation bed material from a pig farm. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An opaque, pink-coloured, gram-positive, aerobic bacteria (designated as FBM22-1T), was isolated from microbial fermentation bed material from a pig farm in northwestern China. Optimal growth occurred at 30–37 °C, pH 7.0 and with 0.5 % NaCl (w/v). The strain had nitrification and denitrification functions. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate belonged to the genus
Rhodococcus
. Strain FBM22-1T was closely related to
Rhodococcus zopfii
NBRC 100606T and
Rhodococcus rhodochrous
NBRC 16069T, with 16S rRNA gene sequence similarities of 97.9 and 97.7 %, respectively. The predominant menaquinone in strain FBM22-1T was MK-8(H2). The cellular fatty acids consisted primarily of C16 : 1ω7c and/or C16 : 1 ω6c, C16 : 0 and 10-methyl C18 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The G+C content of strain FBM22-1T was 68.64 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic characterization results, in combination with low values of digital DNA–DNA hybridization between strain FBM22-1T and its closest neighbours, FBM22-1T represents a novel species of the genus
Rhodococcus
, for which the name Rhodococcus yananensis sp. nov. is proposed; the type strain is FBM22-1T (=KCTC 49502T=CCTCC AB2020275T).
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Affiliation(s)
- Yingying Jiang
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an 716000, PR China
- Shaanxi Key Laboratory of Research and Utilization of Resource Plants on the Loess Plateau, Yan'an University, Yan’an 716000, PR China
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Chaochao Zheng
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Tianfei Yu
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Jing Li
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Jiamin Ai
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Maiping Li
- Animal Husbandry and Veterinary Service Center, Yan’an 716000, PR China
| | - Xiaodong Liu
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an 716000, PR China
- Shaanxi Key Laboratory of Research and Utilization of Resource Plants on the Loess Plateau, Yan'an University, Yan’an 716000, PR China
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
| | - Zhenshan Deng
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an 716000, PR China
- College of Life Sciences, Yan’an University, Yan’an 716000, PR China
- Shaanxi Key Laboratory of Research and Utilization of Resource Plants on the Loess Plateau, Yan'an University, Yan’an 716000, PR China
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Yadav S, Kim JS, Lee SS. Alkanindiges hydrocarboniclasticus sp. nov. Isolated From Crude Oil Contaminated Sands and Emended Description of the Genus Alkanindiges. Curr Microbiol 2020; 78:378-382. [PMID: 33179156 DOI: 10.1007/s00284-020-02266-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022]
Abstract
The taxonomic position of strain H1T isolated from crude oil contaminated desert sands was determined. Strain H1T was Gram-stain-negative and cocci to short rod-shaped bacterium. It grew at 15-42ºC (optimum, 30-35ºC) and pH 6.5-8.8 (optimum, 7.0-7.5). No added NaCl was required for the growth. The isolate showed 98% 16S rRNA gene sequence similarity with the Alkanindiges illinoisensis GTI MVAB Hex1T, 95.5% with Alkanindiges hongkongensis HKU9T and < 95.2% with other members of the family Moraxellaceae of the phylum Proteobacteria. C10:0, C10:0 -2OH, C12:0 -3OH, C16:0, C16:0 N alcohol and C16:1ω6c/C16:1ω7c were present as major (5%) fatty acids with minor (< 5%) amounts of C12:0, C14:0, C14:1ω5c and C18:1ω9c in strain H1T. It contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified two unidentified lipids. Distinct morphological, physiological, phylogenetic, and genomic differences from the previously described taxa support the classification of strain H1T as a representative of a novel species in the genus Alkanindiges for which the name Alkanindiges hydrocarboniclasticus sp. nov. is proposed. The type strain is H1T (= JCM 31550T = KEMB 2255-480T). Emended description of the genus Alkanindiges is also proposed based on additional characteristics.
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Affiliation(s)
- Subhash Yadav
- Department of Bio-Convergence, School of Life Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon, 443-760, Republic of Korea.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Jin-Soo Kim
- Department of Bio-Convergence, School of Life Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon, 443-760, Republic of Korea
| | - Sang-Seob Lee
- Department of Bio-Convergence, School of Life Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon, 443-760, Republic of Korea.
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5
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Phurbu D, Wang H, Tang Q, Lu H, Zhu H, Jiang S, Xing P, Wu QL. Tabrizicola alkalilacus sp. nov., isolated from alkaline Lake Dajiaco on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 69:3420-3425. [PMID: 31385782 DOI: 10.1099/ijsem.0.003635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Lake Dajiaco on the Tibetan Plateau. Strain DJCT grew without NaCl and tolerated up to 3 % (w/v) NaCl. Growth occurred at pH 6.0-10.0 (optimum, pH 7.0-8.0) and 15-37 °C (optimum, 25-30 °C). Vitamins were not required for growth. The main polar lipids of strain DJCT were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-10. The major fatty acid was C18 : 1ω7c. Genome sequencing revealed a genome size of 4.61 Mbp and a G+C content of 62.9 mol%. Analysis of 16S rRNA sequences showed that strain DJCT belonged to the genus Tabrizicola, with the closest neighbour Tabrizicola aquatica RCRI19T (97.5 %). DNA-DNA relatedness between strain DJCT and the closest phylogenetically related strain T. aquatica RCRI19T was 40.8 %. Stain DJCT was clearly distinguished from the type strain mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristic comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain DJCT could be classified as a representative of a novel species of the genus for which the name Tabrizicola alkalilacus sp. nov. is proposed. The type strain is DJCT (=CICC 24242T=KCTC 62173T).
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Affiliation(s)
- Dorji Phurbu
- Tibet Plateau Institute of Biology, Lhasa 850000, PR China
| | - Hui Wang
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, PR China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qian Tang
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Huibin Lu
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Han Zhu
- College of Life Sciences, Anhui Normal University, Wuhu 241002, PR China
| | - Siping Jiang
- Tibet Plateau Institute of Biology, Lhasa 850000, PR China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qinglong L Wu
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
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6
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Suresh G, Lodha TD, Indu B, Sasikala C, Ramana CV. Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter. Front Microbiol 2019; 10:2480. [PMID: 31736915 PMCID: PMC6834548 DOI: 10.3389/fmicb.2019.02480] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022] Open
Abstract
The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.
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Affiliation(s)
- G. Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Tushar D. Lodha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - B. Indu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Hyderabad, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Suman J, Zubrova A, Rojikova K, Pechar R, Svec P, Cajthaml T, Ulbrich P, Ridl J, Strnad H, Uhlik O. Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge. Int J Syst Evol Microbiol 2019; 69:2401-2407. [PMID: 31166163 DOI: 10.1099/ijsem.0.003493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The creamy white to beige, aerobic, non-motile, ovoid to rod-shaped, Gram-stain-negative strain, Cd-10T, was isolated from heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factory based on its ability to tolerate CdCl2 in the cultivation medium. In the reconstruction of its phylogeny based on 16S rRNA gene sequences, strain Cd-10T clustered with species of the genera Gemmobacter, Xinfangfangia, Tabrizicola and Rhodobacter within the family Rhodobacteraceae. Its 16S rRNA gene sequence exhibited 96.32 % pairwise similarity to the type strain of Xinfangfangia soli, 95.3 % to that of Gemmobacter intermedius, followed by Tabrizicola fusiformis (95.10 %), Rhodobacter sediminis (94.88 %), Gemmobacter nectariphilus and Rhodobacter capsulatus (both 94.81 %). The major respiratory quinone was Q-10 accompanied by Q-9, the fatty acid profile consisted predominantly of C18 : 1ω7c, C18 : 0, C16 : 0 and C16 : 1ω7c, the major polar lipids were phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and diphosphatidylglycerol. An analysis of the percentage of conserved proteins deduced from draft or complete genomic sequences of strain Cd-10T and representatives of its closest relatives suggested that strain Cd-10T is a member of a novel genus within the Rhodobacteraceae family for which we propose the name Pseudogemmobacter. Strain Cd-10T (=DSM 103618T=NCCB 100645T) is the type strain of Pseudogemmobacter bohemicus gen. nov., sp. nov., the type species of the genus Pseudogemmobacter gen. nov.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Andrea Zubrova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Katerina Rojikova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Radko Pechar
- Department of Chemistry, Microbiology and Biochemistry of Food, Food Research Institute Prague, Prague, Czech Republic.,Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czech Republic
| | - Pavel Svec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Cajthaml
- Institute of Microbiology, Czech Academy of Sciences, v.v.i., Prague, Czech Republic.,Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Ulbrich
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Jakub Ridl
- Institute of Molecular Genetics, Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics, Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
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Ren H, Ma H, Li H, Huang L, Luo Y. Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov. Int J Syst Evol Microbiol 2019; 69:2445-2451. [PMID: 31169491 DOI: 10.1099/ijsem.0.003513] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, short-rod bacterium, strain MS2-2T, was isolated from mangrove sediment sampled at Jiulong River Estuary, Fujian province, PR China. 16S rRNA gene sequence similarity analysis showed that strain MS2-2T was most closely related to Defluviimonas indica 20V17T (97.41 %) and Defluviimonas pyrenivorans PrR001T (96.18 %). Phylogenetic trees based on 16S rRNA genes and genome sequences both revealed that strain MS2-2T formed a distinct cluster with D. indica 20V17T and D. pyrenivorans PrR001T within family Rhodobacteracea, quite separate from other type species in the genus Defluviimonas. The average nucleotide identity value between strain MS2-2T and D. indica 20V17T was 78.35 %. Growth of strain MS2-2T was observed at 16-41 ° C (optimum, 34 ° C), pH 3.6-7.5 (pH 6.0) and 0.5-10.0 % (w/v) NaCl (4.0 %). The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 0. Ubiquinone 10 was the sole quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 67.9 mol%. The combined genotypic and phenotypic data show that strain MS2-2T represents a novel species of a novel genus in the family Rhodobacteraceae, for which the name Acidimangrovimonassediminis gen. nov., sp. nov. is proposed, with the type strain MS2-2T (=MCCC 1K02682T=NBRC 112978T). We also propose the reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov.
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Affiliation(s)
- Hao Ren
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.,Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.,Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Hao Li
- School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Lingfeng Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.,Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Yuanrong Luo
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
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9
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Kämpfer P, Busse HJ, McInroy JA, Criscuolo A, Clermont D, Glaeser SP. Xinfangfangia humi sp. nov., isolated from soil amended with humic acid. Int J Syst Evol Microbiol 2019; 69:2070-2075. [PMID: 31099734 DOI: 10.1099/ijsem.0.003434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two slightly beige-pigmented, Gram-stain-negative, rod-shaped bacterial strains, IMT-291T and IMT-297, were isolated from soil in a field located in Malvern, Alabama, USA. The source soil had been amended with humic acid and continuously used for the cultivation of worms used for fish bait. It is still conceivable that the source of the strains is from the humic acid amendment, although all attempts to isolate the novel phenotypes from the humic acid source have failed. The two strains were identical based on morphology, growth rate and subsequently by 16S rRNA gene sequences, but showed differences in genomic fingerprint patterns generated by rep-PCR. Phylogenetic analysis based on the 16S rRNA gene revealed a placement of the strain in a distinct cluster with Xinfangfangia soli (97.2 % 16S rRNA gene sequence similarity) and in close proximity to the genus Falsirhodobacter with highest 16S rRNA gene sequence similarity of 95.3 % to the type strain of Falsirhodobacter deserti. Sequence similarities to all other type strains were below 95.0 %. The chemotaxonomic analysis showed a clear similarity to the genus Xinfangfangia. The main cellular fatty acids of the strain were C18 : 1 ω7c, 11-methly-C18 : 1 ω7c and C16 : 0. The major quinone was ubiquinone Q-10. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine were predominant in the polar lipid profile. The polyamine pattern contained the major compound spermidine and moderate amounts of putrescine and cadaverine. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phylogenetic, chemotaxonomic and phenotypic analyses we propose a new species of the genus Xinfangfangia, with the name Xinfangfangiahumi sp. nov. and strain IMT-291T (=LMG 30636T=CIP 111625T=CCM 8858T) as type strain.
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Affiliation(s)
- Peter Kämpfer
- 1Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- 2Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - John A McInroy
- 3Department of Entomology and Plant Pathology, Auburn University, AL 36849, USA
| | - Alexis Criscuolo
- 4Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, France
| | | | - Stefanie P Glaeser
- 1Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Yadav S, Vaddavalli R, Siripuram S, Eedara RVV, Yadav S, Rabishankar O, Lodha T, Chintalapati S, Chintalapati V. Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis. J Antibiot (Tokyo) 2018; 71:575-583. [PMID: 29467380 DOI: 10.1038/s41429-018-0035-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 01/05/2018] [Accepted: 01/14/2018] [Indexed: 11/09/2022]
Abstract
An antibiotic producing novel Planctomycete strain, designated JC280T, was isolated from the surface of the plant Hydrilla verticillata collected from an alkaline lake (Buffalo lake), University of Hyderabad, Hyderabad, India. The morphological and chemotaxonomic properties of strain JC280T were in agreement with the characteristics of the genus Planctopirus. The cell shape was spherical to ovoid and some were tear drop shaped. The cells were Gram-stain-negative divided by budding presenting stalks and rosette formation and were non-sporulating. Crateriform structures with a sub-polar flagellum were observed. Characteristic polyamines were putrescine and spermidine. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid (PL1), unidentified glycolipids (GL1-2), an unidentified aminophospholipid (APL), and an unidentified lipid (L3). Major (>10%) fatty acids were C16:0, C17:1ω8c, C18:1ω9c, and summed feature-3. Major (88%) respiratory quinone was MK-6 with minor amount (12%) of MK-7. Strain JC280T showed 99.7% 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. To resolve their full taxonomic position, the genome sequence was obtained and compared with the available P. limnophila DSM 3776T genome. The genome sequence of strain JC280T was 5,750,243 bp in size with a total of 4490 protein-coding genes, 66 RNA genes, and 2 CRISPR repeats. Based on whole-genome statistics, ANI value, in silico DDH, diversity of secondary metabolite biosynthetic gene clusters, distinct physiological, biochemical and chemotaxonomic differences, strain JC280T represents a new species in the genus Planctopirus, for which the name Planctopirus hydrillae sp. nov. is proposed. The type strain is JC280T (=KCTC 42880T = LMG 29153T).
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Affiliation(s)
- Subhash Yadav
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India.,Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Radha Vaddavalli
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Srinivas Siripuram
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Ramaprasad Veera Venkata Eedara
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Shivani Yadav
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad, 500085, India
| | - Ojha Rabishankar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Tushar Lodha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Sasikala Chintalapati
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad, 500085, India.
| | - VenkataRamana Chintalapati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India.
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11
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Subhash Y, Lee SS. Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand. Int J Syst Evol Microbiol 2018; 68:675-680. [PMID: 29388546 DOI: 10.1099/ijsem.0.002565] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two dark pink pigmented bacterial strains (M3T and M11) were isolated from crude oil contaminated desert sand from Kuwait. Both strains were Gram-stain-negative and small-rod to oval-shaped bacteria. Strains M3T and M11 grew at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.0 (optimum, 7.0-7.5). No additional NaCl was required for the growth of both strains. The genomic DNA G+C content of strains M3T and M11 were 69.5 and 69.0 mol%, respectively. Both strains were closely related and the mean DNA-DNA hybridization value was 92±1 %. 16S rRNA gene sequence comparisons of both strains indicated that they belong to the genus Roseomonas. Strains M3T and M11 had a sequence similarity of 97.3 and 97.4 % with Roseomonas oryzae JC288T, respectively. Both strains had <97 % 16S rRNA gene sequence similarity with other members of the genus Roseomonas. Strain M3T showed 18±2 and 13±2 % reassociation (based on DNA-DNA hybridization) with R. oryzae KCTC 42542T and Roseomonas cervicalis KACC 11686T, respectively. The major cellular fatty acids (>5 %) were identified as C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c and C16 : 0 in both strains. Both strains showed diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-ethanolamine, phosphatidylcholine and unidentified glycolipid as major polar lipids. Based on distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa, we propose the classification of strains M3T and M11 as representative of a novel species in the genus Roseomonas, for which the name Roseomonas deserti sp. nov. is suggested. The type strain is M3T (=KEMB 2255-459T=JCM 31275T).
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Affiliation(s)
- Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea.,Present address: Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea
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Jin DH, Subhash Y, Lee SS. Psedoduganella eburnea sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2017; 67:5268-5272. [PMID: 29087279 DOI: 10.1099/ijsem.0.002460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 10R5-21T was isolated from lagoon sediments. Cells of strain 10R5-21T were Gram-reaction-negative, rod-shaped and motile by means of polar flagella. The strain was obligately aerobic and positive for catalase and oxidase activity. Strain 10R5-21T was able to grow at 10-37 ˚C (optimum 25-30 ˚C), at pH 5.0-9.0 (optimum pH 6.5-7.5) and in the presence of 0-0.5 % (w/v) NaCl (optimum 0 %). C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C12 : 0 were present as predominant (>5 %) fatty acids. Q-8 was identified as the major respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were present as major polar lipids with minor amounts of unidentified aminophospholipids and unidentified aminolipids. The genomic G+C content of strain 10R5-21T was 64.1 mol%. 16S rRNA gene sequence analysis indicated that strain 10R5-21T belongs to the genus Pseudoduganella within the family Oxalobacteraceae of the class Betaproteobacteria. Strain 10R5-21T shared 98.8 % 16S rRNA gene sequence similarity with Pseudoduganella violaceinigra YIM 31327T. DNA-DNA hybridization values between strain 10R5-21T and P. violaceinigra KACC 11669T were clearly below the 70 % threshold. Distinct morphological, biochemical, chemotaxonomic and genetic differences from previously described taxa support the classification of strain 10R5-21T as a representative of a novel species in the genus Pseudoduganella, for which the name Pseudoduganella eburnea sp. nov. is proposed. The type strain is 10R5-21T (=KEMB 563-061T=JCM 31587T).
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Affiliation(s)
- Da-Hye Jin
- Department of Life Science, College of Natural Science, Kyonggi University, Gwanggyosan-ro Yeongtong-gu, Suwon-si Gyeonggi, 16227, Republic of Korea
| | - Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, Gwanggyosan-ro Yeongtong-gu, Suwon-si Gyeonggi, 16227, Republic of Korea.,Present address: Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, Gwanggyosan-ro Yeongtong-gu, Suwon-si Gyeonggi, 16227, Republic of Korea
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13
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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Characterisation of a newly isolated member of a candidatus lineage, Marispirochaeta aestuarii gen. nov., sp. nov. Int J Syst Evol Microbiol 2017; 67:3929-3936. [DOI: 10.1099/ijsem.0.002224] [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)
- Y. Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
- Present address: Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon 443-760, Republic of Korea
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Subhash Y, Kim HJ, Lee SS. Aneurinibacillus sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2017; 67:2544-2548. [PMID: 28771121 DOI: 10.1099/ijsem.0.001963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains (1-10M-8-7-50T and 1M) were isolated from lagoon sediments. The strains were obligately aerobic, Gram-stain-positive, spore-forming, rod-shaped and motile. Both strains were able to grow at 25-60 ˚C (optimum 40-42 ˚C), at pH 6.0-8.8 (optimum pH 7.0-7.5) and with 0-2.0 % (w/v) (optimum 0-0.8 %) NaCl. The predominant cellular fatty acids were iso-C15 : 0 and iso-C15 : 0 2-OH, and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid, glycine and alanine. Phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified phosphoglycolipids and three unidentified lipids were present as polar lipids. Genomic DNA G+C content was 41.9 mol%. 16S rRNA gene sequence comparisons of both strains indicated that they belong to the genus Aneurinibacillus within the family Paenibacillaceae of the class Bacilli. Both strains had a sequence similarity of 97.6 % with Aneurinibacillus migulanus B0270T, 97.6 % with Aneurinibacillus aneurinilyticus ATCC 12856T, 97.5 % with 'Aneurinibacillus humi' U33 and <97 % with other members of the genus Aneurinibacillus. The DNA-DNA reassociation value between strain 1-10M-8-7-50T and 1M was >90 %, while strains 1-10M-8-7-50T and 1M were only 35.1±1, 29.8±1 and 24.5±1 % related to A. migulanus KACC 18173T, A. aneurinilyticus KACC 18174T and 'A. humi' U33, respectively. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain 1-10M-8-7-50T as a representative of a novel species in the genus Aneurinibacillus, for which the name Aneurinibacillus sediminis sp. nov. is proposed. The type strain is 1-10M-8-7-50T (=KEMB 563-460T=JCM 31819T).
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Affiliation(s)
- Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea
| | - Hye-Ji Kim
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea
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15
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Subhash Y, Lee SS. Roseomonas suffusca sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2017; 67:2390-2396. [PMID: 28714843 DOI: 10.1099/ijsem.0.001966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The strains (S1T, AS3 and AS6) grew aerobically at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.1 (optimum, pH 7.0-7.5). All three strains were positive for catalase and oxidase activity, and no added NaCl was required for growth. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 0 were the predominant fatty acids (>5 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were the major polar lipids. The genomic DNA G+C content of strains S1T, AS3 and AS6 was 70.5, 70.1 and 70.8 mol%, respectively. Strain S1T showed 16S rRNA gene sequence similarity of 99.1 % with Roseomonas rubra S5T, 98.7 % with Roseomonas rhizosphaerae YW11T, 98.5 % with Roseomonas cervicalis E7107T, 97.8 % with Roseomonas aestuarii JC17T, 97.2 % with Roseomonas oryzae JC288T, 97.2 % with Roseomonas ludipueritiae 170/96Tand <97 % with other members of the genus Roseomonas. Strains AS3 and AS6 shared 99.9 % 16S rRNA gene sequence similarity with strain S1T. DNA-DNA hybridization values among strains S1T, AS3 and AS6 were >89 %, while all the three strains showed <56 % relatedness with the most closely related type strains. Distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa support the classification of strain S1T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas suffusca sp. nov. is proposed. The type strain is S1T (=KEMB 563-465T=JCM 31176T). Strains AS3 and AS6 serve as additional strains of the newly proposed species.
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Affiliation(s)
- Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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Skermanella mucosa sp. nov., isolated from crude oil contaminated soil. Antonie van Leeuwenhoek 2017; 110:1053-1060. [DOI: 10.1007/s10482-017-0878-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
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17
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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp. Int J Syst Evol Microbiol 2017; 67:87-93. [PMID: 27902290 DOI: 10.1099/ijsem.0.001574] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An antibiotic-producing, obligate anaerobic, Gram-stain-negative, catalase- and oxidase-negative strain (JC271T) was isolated from a marine habitat and identified, based on 16S rRNA gene sequence analysis, as a novel member of the family Desulfovibrionaceae. The closest phylogenetic relatives of strain JC271T were found to be Desulfovibrio marinisediminis C/L2T (99.2 %), Desulfovibrio acrylicus W218T (98.7 %), Desulfovibrio desulfuricans subsp. aestuarii (98.6 %), Desulfovibrio oceani subsp. oceani (98.0 %), Desulfovibrio oceani subsp. galatae (98.0 %) and other members of the genus Desulfovibrio (≤91.9 %). To resolve its full taxonomic position, the genomic sequence of strain JC271T was compared to available genomes of the most closely related phylogenetic members. Average Nucleotide Identity scores and DNA-DNA hybridization values confirmed that strain JC271T represents a novel genomic species. Iso-C17 : 0, iso-C17 : 1ω9c, and iso-C15 : 0 were found to be the major (comprising >10 % of the total present) fatty acids of strain JC271T. Phosphatidylglycerol, phosphatidylethanolamine and unidentified lipids (L1-8) were the polar lipids identified. The G+C content of strain JC271T was 46.2 mol%. Integrated genomic and phenotypic data supported the classification of strain JC271T as a representative of a novel genus, for which the name Halodesulfovibrio spirochaetisodalis gen. nov., sp. nov. is proposed. The type strain is JC271T (=KCTC 15474T=DSM 100016T). It is also proposed that Desulfovibrio acrylicus W218T is the latter heterotypic synonym of Desulfovibrio desulfuricans subsp. aestuarii Sylt 3T. Desulfovibrio desulfuricans subsp. aestuarii Sylt 3T should also be elevated as Halodesulfovibrio aestuarii comb. nov. and Desulfovibrio marinisediminisreclassified as Halodesulfovibrio marinisediminis comb. nov. Desulfovibrio oceani subsp. oceanishould be reclassified as Halodesulfovibrio oceani subsp. oceani comb. nov. and Desulfovibrio oceani subsp. galateae as Halodesulfovibrio oceani subsp. galateae comb. nov.
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Affiliation(s)
- Y Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Y Subhash
- Present address: Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon 443-760, Republic of Korea.,Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Description of 'Candidatus Marispirochaeta associata' and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov. Int J Syst Evol Microbiol 2016; 66:5485-5492. [PMID: 27902269 DOI: 10.1099/ijsem.0.001545] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain JC231 was isolated from a coastal saline habitat of Gujarat and was identified based on 16S rRNA gene sequence analysis as a member belonging to the genus Spirochaeta and showed highest sequence similarity (<91 %) with Spirochaeta bajacaliforniensis DSM 16054T and other members of the family Spirochaetaceae. Intensive attempts to culture strain JC231 in pure culture have failed and were associated with only one species of a Desulfovibrio. However, presence of fosmidomycin inhibited the growth of Desulfovibrio sp. and strain JC231 was characterized in its presence. Strain JC231 was an obligate anaerobe, helical shaped and Gram-stain-negative with catalase and oxidase negative. Draft genome sequence analysis of strain JC231 indicated the full complement of genes for both 2-C-methyl-d-erythritol 4-phosphate and 3-hydroxy-3-methylglutaryl-CoA pathways of terpenogenesis. C14 : 0, iso-C15 : 0, C16 : 0, iso-C15 : 1H/C13 : 0 3OH and iso-C14 : 0 are the major (>5 %) fatty acids. Strain JC231 contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and six unidentified lipids (L1-L6). G+C content of strain JC231 was 55.7 mol%. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC231 as a representative of a new genus and species in the family Spirochaetaceae, for which the name 'CandidatusMarispirochaeta associata' is proposed. Strain JC231 is deposited as a defined co-culture with Desulfovibrio sp. JC271 to DSMZ (DSM 29857) and KCTC (KCTC 15472). Based on phenotypic, genotypic and phylogenetic analyses, we also propose the reclassification of Spirochaeta bajacaliforniensis as Sediminispirochaeta bajacaliforniensis gen. nov., comb. nov., Spirochaeta smaragdinae as Sediminispirochaeta smaragdinae comb. nov. and Spirochaeta sinaica as Sediminispirochaeta sinaica comb. nov.
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Affiliation(s)
- Y Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Y Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Subhash Y, Lee SS. Skermanella rosea sp. nov., isolated from hydrocarbon-contaminated desert sands. Int J Syst Evol Microbiol 2016; 66:3951-3956. [DOI: 10.1099/ijsem.0.001293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui-dong Yeongtong-gu, Suwon 443-760, South Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui-dong Yeongtong-gu, Suwon 443-760, South Korea
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Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea. Antonie van Leeuwenhoek 2016; 110:11-18. [PMID: 27688210 DOI: 10.1007/s10482-016-0768-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/13/2016] [Indexed: 10/20/2022]
Abstract
A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1T, was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1T was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, D-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1T was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, an unidentified phospholipid and three unidentified glycolipids were found to be present in strain CHO1T. Based on 16S rRNA gene sequence analysis, strain CHO1T was found to be closely related to Microbacterium mangrovi DSM 28240T (97.81 % similarity), Microbacterium immunditiarum JCM 14034T (97.45 %), Microbacterium oryzae JCM 16837T (97.33 %) and Microbacterium ulmi KCTC 19363T (97.10 %) and to other species of the genus Microbacterium. The DNA G+C content of CHO1T was determined to be 70.1 mol %. The DNA-DNA hybridization values of CHO1T with M. mangrovi DSM 28240T, M. immunditiarum JCM 14034T, M. oryzae JCM 16837T and M. ulmi KCTC 19363T were 46.7 ± 2, 32.4 ± 2, 32.0 ± 2 and 29.2 ± 2 %, respectively. On the basis of genotypic, phenotypic and phylogenetic properties, it is concluded that strain CHO1T represents a novel species within the genus Microbacterium, for which the name Microbacterium rhizosphaerae sp. nov. is proposed. The type strain of M. rhizosphaerae is CHO1T (= KEMB 7306-513T = JCM 31396T).
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Subhash Y, Bang JJ, You TH, Lee SS. Roseomonas rubra sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:3821-3827. [DOI: 10.1099/ijsem.0.001271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - John J. Bang
- Department of Environmental, Earth and Geospatial Science, North Carolina Central University, Durham, NC 27707, USA
| | - Taek H. You
- Department of Biological Sciences, Campbell University, Buies Creek, NC 27506, USA
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2965-2970. [DOI: 10.1099/ijsem.0.001130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Subhash Y, Lee SS. Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands. Int J Syst Evol Microbiol 2016; 66:3929-3934. [PMID: 27393556 DOI: 10.1099/ijsem.0.001290] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a novel bacterial strain, designated C3T, isolated from hydrocarbon-contaminated desert sands was determined. Strain C3T was a Gram-stain-negative, rod- to curved-rod-shaped and non-motile bacterium. It was able to grow at 4-45 °C (optima, 28- 35 °C) and at pH 6.1-8.8 (optima, 6.9-7.7). No added NaCl was required for growth of strain C3T and it tolerated up to 3.5 % (w/v) NaCl with optimal growth with 0.5-1.5 %. Catalase and oxidase were positive. C18 : 1ω6c/C18 : 1ω7c, C16 : 0, C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 0 I and C18 : 1ω7c 11-methyl were predominant fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were major polar lipids. The genomic DNA G+C content was 65.4 mol%. 16S rRNA gene sequence comparisons indicated that strain C3T represents a member of the genus Shinella within the family Rhizobiaceae of the class Alphaproteobacteria. Strain C3Tshowed a 16S rRNA gene sequence similarity of 98.39 % with Shinella kummerowiae CCBAU 25048T, 98.37 % with Shinella granuli Ch06T, 98.17 % with Shinella zoogloeoides I-16-MT, 97.74 % with Shinella fusca DC-196T, 97.46 % with Shinella yambaruensis MS4T and <96.68 % with other members of the family Rhizobiaceae. DNA-DNA hybridization values between strain C3T and the type strains of the nearest species were clearly below the 70 % threshold for species delineation. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain C3T as a representative of a novel species in the genus Shinella, for which the name Shinella curvata sp. nov. is proposed. The type strain is C3T (=KEMB 2255-446T=JCM 31239T).
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Affiliation(s)
- Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro, Yeongtong-gu, Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro, Yeongtong-gu, Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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Subhash Y, Bang JJ, You TH, Lee SS. Description of Comamonas sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2735-2739. [DOI: 10.1099/ijsem.0.001115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, Iuidong Yeongtong-gu, Suwon, South Korea
| | - John J. Bang
- Department of Environmental, Earth and Geospatial Science, North Carolina Central University, USA
| | - Taek H. You
- Department of Biological Sciences, Campbell University, USA
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, Iuidong Yeongtong-gu, Suwon, South Korea
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Mori T, Takahashi M, Tanaka R, Miyake H, Shibata T, Chow S, Kuroda K, Ueda M, Takeyama H. Falsirhodobacter sp. alg1 Harbors Single Homologs of Endo and Exo-Type Alginate Lyases Efficient for Alginate Depolymerization. PLoS One 2016; 11:e0155537. [PMID: 27176711 PMCID: PMC4866713 DOI: 10.1371/journal.pone.0155537] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/29/2016] [Indexed: 11/19/2022] Open
Abstract
Alginate-degrading bacteria play an important role in alginate degradation by harboring highly efficient and unique alginolytic genes. Although the general mechanism for alginate degradation by these bacteria is fairly understood, much is still required to fully exploit them. Here, we report the isolation of a novel strain, Falsirhodobacter sp. alg1, the first report for an alginate-degrading bacterium from the family Rhodobacteraceae. Genome sequencing reveals that strain alg1 harbors a primary alginate degradation pathway with only single homologs of an endo- and exo-type alginate lyase, AlyFRA and AlyFRB, which is uncommon among such bacteria. Subsequent functional analysis showed that both enzymes were extremely efficient to depolymerize alginate suggesting evolutionary interests in the acquirement of these enzymes. The exo-type alginate lyase, AlyFRB in particular could depolymerize alginate without producing intermediate products making it a highly efficient enzyme for the production of 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH). Based on our findings, we believe that the discovery of Falsirhodobacter sp. alg1 and its alginolytic genes hints at the potentiality of a more diverse and unique population of alginate-degrading bacteria.
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Affiliation(s)
- Tetsushi Mori
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
- * E-mail:
| | - Mami Takahashi
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Reiji Tanaka
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Mie, Japan
| | - Hideo Miyake
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Mie, Japan
| | - Toshiyuki Shibata
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Mie, Japan
| | - Seinen Chow
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Kanagawa, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Haruko Takeyama
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
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Sasi Jyothsna TS, Tushar L, Sasikala C, Ramana CV. Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii. Int J Syst Evol Microbiol 2016; 66:1268-1274. [DOI: 10.1099/ijsem.0.000874] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- T. S. Sasi Jyothsna
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad,P.O. Central University, Hyderabad 500 046,India
| | - L. Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad,P.O. Central University, Hyderabad 500 046,India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad,Kukatpally, Hyderabad 500 085,India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad,P.O. Central University, Hyderabad 500 046,India
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Abstract
Two bacterial strains (JC247T and JC248) were isolated from soil samples collected from Rann of Kutch, Gujarat, India. Colonies of both strains were creamy white. Cells were Gram-stain-positive, rods-to-curved rods (crescent-shaped), and produced centrally located oval-shaped endospores. Major (>5 %) fatty acids of both strains were iso-C16
:
0, iso-C14
:
0, iso-C15
:
0, C16
:
1ω11c and C16
:
0, with minor ( < 5 but >1 %) amounts of anteiso-C15
:
0, anteiso-C17
:
0, iso-C16
:
1 H, iso-C17
:
0, iso-C18
:
0, C14
:
0, C17
:
0, C18
:
0, C18
:
1ω9c, iso-C17
:
1ω10c and anteiso-C17
:
0B/isoI. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell-wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. The genomic DNA G+C content of strains JC247T and JC248 was 48.2 and 48.1 mol%, respectively. Both strains were closely related with mean DNA–DNA hybridization >90 %. 16S rRNA gene sequence analysis of both strains indicated that they are members of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a 16S rRNA gene sequence similarity of 96.93 % with Bacillus firmus NCIMB 9366T and < 96.92 % with other members of the genus Bacillus. Sequence similarity between strain JC247T and JC248 was 100 %. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strains JC247T and JC248 as representatives of a novel species of the genus Bacillus, for which the name Bacillus
crescens sp. nov. is proposed. The type strain is JC247T ( = KCTC 33627T = LMG 28608T).
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Rahul K, Azmatunnisa M, Sasikala C, Ramana C. Hoeflea olei sp. nov., a diesel-oil-degrading, anoxygenic, phototrophic bacterium isolated from backwaters and emended description of the genus Hoeflea. Int J Syst Evol Microbiol 2015; 65:2403-2409. [DOI: 10.1099/ijs.0.000277] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, diesel-oil-degrading, rod-shaped bacterium (designated JC234T) was isolated from a water sample collected from diesel-oil-contaminated backwaters in Kerala, India. Strain JC234T was oxidase- and catalase-positive, and grew at 20–35 °C and at pH 7–9. Cells contained bacteriochlorophyll-a, hydroxydemethylspheroidene and three unidentified carotenoids. Growth occurred under aerobic, microaerobic and phototrophic anaerobic conditions. Strain JC234T could utilize diesel-oil as a sole source of carbon and energy. Based on the 16S rRNA gene sequence analysis, strain JC234T belonged to the genus Hoeflea within the family Phyllobacteriaceae, and was closely related to Hoeflea alexandrii AM1V30T (98.1 % 16S rRNA gene sequence similarity), Hoeflea halophila JG120-1T (97.6 %) and other members of the genus Hoeflea ( < 96.4 %). Strain JC234T showed 22 ± 2 % and 28 ± 1.5 % DNA–DNA hybridization with Hoeflea alexandrii KCTC 22096T and Hoeflea halophila KCTC 23107T, respectively. The DNA G+C content of strain JC234T was 54.3 mol %. The major cellular fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylglycerol were the major polar lipids. Strain JC234T contained Q10 as the predominant ubiquinone. On the basis of morphological, physiological, genetic, phylogenetic and chemotaxonomical analyses, we conclude that strain JC234T represents a novel species of the genus Hoeflea, for which the name Hoeflea
olei sp. nov. is proposed. The type strain is JC234T ( = KCTC 42071T = LMG 28200T). An emended description of the genus Hoeflea is also provided.
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Affiliation(s)
- K. Rahul
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India
| | - M. Azmatunnisa
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India
| | - Ch.V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
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Azmatunnisa M, Rahul K, Lakshmi KVNS, Sasikala C, Ramana CV. Lysinibacillus acetophenoni sp. nov., a solvent-tolerant bacterium isolated from acetophenone. Int J Syst Evol Microbiol 2015; 65:1741-1748. [DOI: 10.1099/ijs.0.000170] [Citation(s) in RCA: 15] [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 Gram-stain-positive, solvent-tolerating, aerobic, rod-shaped bacterium that formed terminal endospores was isolated from the organic solvent acetophenone. The strain, designated JC23T, was oxidase- and catalase-positive. The strain grew in the presence of a wide range of organic solvents with partition coefficients (log p values) between 1 and 4, which are exceptionally toxic to micro-organisms. Based on 16S rRNA gene sequence analysis, strain JC23T was identified as belonging to the genus
Lysinibacillus
and was most closely related to
Lysinibacillus manganicus
Mn1-7T (98.5 % similarity),
L. massiliensis
440831T (97.2 %) and
L. chungkukjangi
2RL3-2T (96.8 %). DNA–DNA relatedness of strain JC23T with the type strains of the closest species was <39 %. Strain JC23T grew chemo-organoheterotrophically with optimal growth at pH 7 (range pH 6–9) and at 35 °C (range 25–40 °C). The DNA G+C content was 41 mol%. Major cellular fatty acids of strain JC23T were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The cell-wall peptidoglycan type was determined to be A4α (l-Lys–d-Asp), which is in agreement with the cell-wall characteristics of the genus
Lysinibacillus
. The predominant quinone system was MK-7. Polar lipids of strain JC23T included diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, β-gentiobiosyldiacylglycerol, two unidentified phospholipids and two unidentified lipids. On the basis of our morphological, physiological, genetic, phylogenetic and chemotaxonomic analyses, we conclude that strain JC23T should be assigned to a novel species of the genus
Lysinibacillus
, for which the name Lysinibacillus acetophenoni sp. nov. is proposed. The type strain is strain JC23T ( = CCUG 57911T = KCTC 13605T = NBRC 105754T = DSM 23394T).
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Affiliation(s)
- M. Azmatunnisa
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad – 500 085, India
| | - K. Rahul
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad – 500 085, India
| | - K. V. N. S. Lakshmi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, PO Central University, Hyderabad – 500 046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad – 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, PO Central University, Hyderabad – 500 046, India
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Hopanoid inventory of Rhodoplanes spp. Arch Microbiol 2015; 197:861-7. [PMID: 25935452 DOI: 10.1007/s00203-015-1112-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
Abstract
Hopanoids are pentacyclic triterpenoid lipids and are important for bacterial membrane stability and functioning. These pentacyclic triterpenoids of hopane series are biomarkers for eubacteria and can be used as chemotaxonomic markers. Anoxygenic phototrophic bacteria are good producers of hopanoids, and their inventory to date is restricted to a few members. Rhodoplanes spp. are phototrophic prokaryotes which grow and thrive in subsurface and sediment environments. A study on the diversity of hopanoids of several species of Rhodoplanes revealed a rich diversity of hopanoids with carbon length of C30/C31 and C35. Hop-22(29)-ene (II), diplopterol (V), tetrahymanol (VII), 2-methyldiplopterol (VI), 2-methyltetrahymanol (VIII), bacteriohopanetetrol (IX), bacteriohopaneaminotriol (X) and bacteriohopanepolyols [BHP-492 (XIII), BHP-550 (XIV), BHP-508 (XII)] are the major hopanoids of the genus Rhodoplanes. Tetrahymanol (VII) content is high (38-60 %) among all the members, except for Rhodoplanes elegans. Hopanoid fingerprints allowed differentiation of species of the genus Rhodoplanes. Statistical analyses also indicate hopanoids as good chemotaxonomic markers to distinguish species of the genus Rhodoplanes.
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Li AH, Zhou YG. Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water. Int J Syst Evol Microbiol 2015; 65:1199-1206. [DOI: 10.1099/ijs.0.000080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-staining-negative, strictly aerobic, non-pigmented, non-motile, rod-shaped bacterial strains, SP32T ( = SLM-1T), SR68 ( = SLM-3) and SP95 ( = SLM-2), were isolated from two water samples of a cold-water lake in Xinjiang province, China. Growth was observed at 4–25 °C and pH 6.0–9.0, and optimum growth occurred at 18–20 °C and at pH 7.0–7.5. Phylogenetic analysis of 16S rRNA gene sequences revealed that these isolates belonged to the family
Rhodobacteraceae
, but formed an evolutionary lineage distinct from other species of this family with validly published names. Strain SP32T showed the highest 16S rRNA gene sequence similarity (96.7 %) to
Rhodobacter veldkampii
ATCC 35703T, and the similarity to members of the genera
Defluviimonas
,
Haematobacter
and
Pseudorhodobacter
was respectively 95.8–96.4, 96.0–96.1 and 95.3–96.1 %. The genomic DNA G+C content of strain SP32T was 67.6 mol%. The major fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and11-methyl C18 : 1ω7c. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified polar lipid were the main polar lipids. Ubiquinone 10 (Q-10) was the sole respiratory quinone. Strain SP32T did not produce photosynthetic pigments and did not contain the gene pufM, by which it differed from the phototrophic species of the family
Rhodobacteraceae
. Based on its distinct phenotypic, chemotaxonomic and phylogenetic properties, strain SP32T represents a novel species in a novel genus within the family
Rhodobacteraceae
, for which we propose the name Frigidibacter albus gen. nov., sp. nov. The type strain of Frigidibacter albus is strain SP32T ( = SLM-1T = CGMCC 1.13995T = NBRC 109671T).
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Affiliation(s)
- Ai-Hua Li
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Spirochaeta lutea sp. nov., isolated from marine habitats and emended description of the genus Spirochaeta. Syst Appl Microbiol 2015; 38:110-4. [DOI: 10.1016/j.syapm.2014.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/05/2014] [Accepted: 11/17/2014] [Indexed: 10/24/2022]
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Suresh G, Sasikala C, Ramana CV. Reclassification of Gemmobacter changlensis to a new genus as Cereibacter changlensis gen. nov., comb. nov. Int J Syst Evol Microbiol 2015; 65:794-798. [DOI: 10.1099/ijs.0.000016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We propose a new genus to accommodate the phototrophic bacterium
Gemmobacter changlensis
[Chen W. M., Cho, N. T., Huang, W. C., Young, C. C. & Sheu, S. Y. (2013) Int J Syst Evol Microbiol 63, 470–478] based on multiple strain analysis. Differences in the major diagnostic properties such as ability to grow phototrophically, the presence of internal photosynthetic membranes, the light harvesting complexes, fatty acids, carotenoids, bacterial chlorophylls, polar lipid composition and some other phenotypic properties warrant the creation of a new genus, designated Cereibacter gen. nov., to accommodate the phototrophic members of the genus
Gemmobacter
, as represented by the type species Cereibacter changlensis comb. nov.
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Affiliation(s)
- G. Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Subhash Y, Sasikala C, Ramana CV. Hymenobacter roseus sp. nov., isolated from sand. Int J Syst Evol Microbiol 2014; 64:4129-4133. [DOI: 10.1099/ijs.0.066225-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain JC245T was isolated from a sand sample, and appeared as dark pink colonies on agar plates with cells staining Gram-negative. Catalase and oxidase activities were positive. Casein was hydrolysed while chitin, gelatin and starch were not. Major (>5 %) fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c, C16 : 1ω6c/C16 : 1ω7c, anteiso-C17 : 1 B/iso-C17 : 1 I and iso-C17 : 0 3-OH. Strain JC245T contained phosphatidylethanolamine and two unidentified lipids as the major polar lipids, with minor amounts of four unidentified lipids and an unidentified amino lipid. Bacterial hopane derivatives and adenosylhopane were the major hopanoids. Hydroxyflexixanthin was identified as one of the major carotenoids of strain JC245T along with five unidentified carotenoids. The genomic DNA G+C content was 52.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC245T represents a member of the genus
Hymenobacter
within the family
Cytophagaceae
of the phylum
Bacteroidetes
. Strain JC245T shared the highest 16S rRNA gene sequence similarity with
Hymenobacter roseosalivarius
AA-718T (98.3 %) and other members of the genus
Hymenobacter
(<95.1 %). However, strain JC245T showed 21±2 % relatedness (based on DNA–DNA hybridization) with
H. roseosalivarius
DSM 11622T. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC245T as a representative of a novel species in the genus
Hymenobacter
, for which the name Hymenobacter roseus sp. nov. is proposed. The type strain is JC245T ( = KCTC 42090T = LMG 28260T).
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Affiliation(s)
- Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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35
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Wang L, Zhou Z, Wu G, Chen M, Lin M, Zhang W, Chen W. Falsirhodobacter deserti sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2014; 65:650-655. [PMID: 25424484 DOI: 10.1099/ijs.0.068262-0] [Citation(s) in RCA: 12] [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, non-motile, heterotrophic, rod-shaped bacterium, designated strain W402(T), was isolated from an enrichment culture of a Tamarix ramosissima rhizosphere soil sample from the Xinjiang desert in the PR China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to a species of the genus Falsirhodobacter, having a close relationship to Falsirhodobacter halotolerans JA744(T) (97 % similarity). However, DNA-DNA relatedness between W402(T) and F. halotolerans JA744(T) was 43.2±1.2 %. Strain W402(T) grew in 0-10 % (w/v) NaCl. The temperature and pH ranges for growth were 10-40 °C and pH 5.5-10.0, respectively. Optimal growth occurred at 1-3 % (w/v) NaCl, 30 °C and pH 7.0. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 61.4 %), C18 : 0 (9.8 %) and 11-methyl C18 : 1ω7c (8.2 %). The major quinone of strain W402(T) was Q-10. Phosphatidylethanolamine was predominant in the polar lipid profile. The DNA G+C content of strain W402(T) was 67.3 mol%. Taken together, these results confirm that W402(T) represents a novel species of the genus Falsirhodobacter, for which the name Falsirhodobacter deserti sp. nov. is proposed. The type strain is W402(T) ( = ACCC 05851(T) = KCTC 32408(T)).
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Affiliation(s)
- Lin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, PR China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Gang Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wuling Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, PR China
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36
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Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading Bacterium Isolated from Fermented Brown Algae. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00826-14. [PMID: 25146138 PMCID: PMC4153483 DOI: 10.1128/genomea.00826-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Falsirhodobacter sp. alg1 is an alginate-degrading bacterium, the second species from the nonphototrophic bacterial genus Falsirhodobacter. We report the first draft genome of a bacterium from this genus and point out possible important features related to alginate assimilation and its evolutionary aspects.
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37
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Tushar L, Sasikala C, Ramana CV. Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis. DNA Res 2014; 21:639-47. [PMID: 25117430 PMCID: PMC4263297 DOI: 10.1093/dnares/dsu026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Hopanoids are present in vast amounts as integral components of bacteria and plants with their primary function to strengthen rigidity of the plasma membrane. To establish their roles more precisely, we conducted sequencing of the whole genome of Rhodomicrobium udaipurense JA643(T) isolated from a fresh water stream of Udaipur in Himachal Pradesh, India, by using the Illumina HiSeq pair end chemistry of 2 × 100 bp platform. Determined genome showed a high degree of similarity to the genome of R. vannielii ATCC17100(T) and the 13.7 million reads generated a sequence of 3,649,277 bp possessing 3,611 putative genes. The genomic data were subsequently investigated with respect to genes involved in various features. The machinery required for the degradation of aromatic compounds and resistance to solvents as well as all that required for photosynthesis are present in this organism. Also, through extensive functional annotation, 18 genes involved in the biosynthesis of hopanoids are predicted, namely those responsible for the synthesis of diploptene, diplopterol, adenosylhopane, ribosylhopane, aminobacteriohopanetriol, glycosyl group containing hopanoids and unsaturated hopanoids. The hopanoid biosynthetic pathway was then inferred based on the genes identified and through experimental validation of individual hopanoid molecules. The genome data of R. udaipurense JA643(T) will be useful in understanding the functional features of hopanoids in this bacterium.
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Affiliation(s)
- L Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University, Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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38
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Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish. Int J Syst Evol Microbiol 2014; 64:2238-2243. [DOI: 10.1099/ijs.0.061937-0] [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
Strain JC216T was isolated from a contaminated Petri dish. Colonies were of pale yellow colour and cells were Gram-stain-negative, oxidase-positive and catalase-positive. Chitin, starch and gelatin were not hydrolysed. Strain JC216T contained C18 : 1ω7c/C18 : 1ω6c, C16 : 1ω7c/C16 : 1ω6c, C14 : 0 2-OH and C16 : 0 as the major (≥8 %) fatty acids with minor amounts of C12 : 0, C15 : 0 2-OH, C16 : 0 2-OH, C16
: 1 2-OH, C17 : 1ω6c, C17 : 1ω8c and C17 : 1ω9c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid were the major polar lipids. Minor amounts of unidentified amino lipids and unidentified lipids were also detected. The major hopanoids identified were bacterial hopane derivatives and diplopterol. Minor amounts of diploptene and an unidentified hopanoid were also present. Spermidine was the major polyamine with minor amounts of sym-homospermidine and putrescine. N-Acetylglucosamine and fructose were identified as major cell-wall sugars along with minor amounts of mannose and galactose. The genomic DNA G+C content was 55 mol%. Comparisons of the16S rRNA gene sequence indicated that strain JC216T represents a member of the genus
Sphingopyxis
in the family
Sphingomonadaceae
within the class
Alphaproteobacteria
. Strain JC216T had a sequence similarity of 97.28 % with
Sphingopyxis wooponensis
03SU3-PT and <96.71 % with other members of the family
Sphingomonadaceae
. Furthermore, strain JC216T had 33±1 % relatedness (based on DNA–DNA hybridization) with
S. wooponensis
KCTC 23340T ( = 03SU3-PT). Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC216T as a representative of a novel species in the genus
Sphingopyxis
, for which the name Sphingopyxis contaminans sp. nov. is proposed. The type strain is JC216T ( = KCTC 32445T = LMG 27671T).
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Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu Y. Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system. Int J Syst Evol Microbiol 2014; 64:1257-1263. [DOI: 10.1099/ijs.0.059576-0] [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 Gram-negative bacterium, strain CZ-AM5T, was isolated from an aerated biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated by using a polyphasic approach. Cells of strain CZ-AM5T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–2.0 µm long, and motile by means of one or two polar or lateral flagella. Strain CZ-AM5T was strictly aerobic, heterotrophic, oxidase-negative and catalase-positive. Growth occurred at 15–40 °C (optimum, 30–35 °C), at pH 6.5–10.5 (optimum, pH 7.0–7.5) and in the presence of 0–12.0 % (w/v) NaCl (optimum, 4.0 %). The predominant fatty acid was C18 : 1ω7c (80.3 %). Ubiquinone 10 (Q-10) was the sole respiratory quinone. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. The DNA G+C content was 60.4 mol%. Strain CZ-AM5T showed the highest 16S rRNA gene sequence similarity (96.5 %) to
Phaeobacter caeruleus
LMG 24369T; it exhibited 16S rRNA gene sequence similarity of 95.0–96.5, 95.2–96.3, 96.2, 94.6–95.7 and 94.8–95.8 % to members of the genera
Phaeobacter
,
Ruegeria
,
Citreimonas
,
Leisingera
and
Donghicola
, respectively. However, phylogenetic trees based on 16S rRNA gene sequences showed that strain CZ-AM5T did not join any of the above genera, but formed a distinct lineage in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain CZ-AM5T is considered to represent a novel genus and species of the family
Rhodobacteraceae
, for which the name Cribrihabitans marinus gen. nov., sp. nov. is proposed. The type strain of Cribrihabitans marinus is CZ-AM5T ( = CGMCC 1.13219T = JCM 19401T).
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Affiliation(s)
- Zhu Chen
- R&D Center of Marine Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Liang-Zi Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Ping Zhong
- 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
| | - Ying Liu
- R&D Center of Marine Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
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40
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Subhash Y, Sasikala C, Ramana CV. Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:984-988. [DOI: 10.1099/ijs.0.058149-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain JC207T was isolated from a deep (265 m) sea sediment, and appeared as dark yellow colonies on agar plates with cells staining Gram-negative. Catalase, oxidase and caseinase were positive, while chitinase, gelatinase and amylase were negative. Major (>5 %) fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, iso-C14 : 0 and iso-C15 : 1G. Strain JC207T contained phosphatidylethanolamine as the major polar lipid, with minor amounts of five unidentified lipids. A bacterial hopane derivative, diplopterol and adenosylhopane were the major hopanoids. Genomic DNA G+C content was 47.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC207T represented a member of the genus
Salinimicrobium
within the family
Flavobacteriaceae
of the phylum
Bacteroidetes
. Strain JC207T had sequence similarity with
Salinimicrobium terrae
YIM-C338T (98 %),
Salinimicrobium xinjiangense
BH206T (97.6 %) and other members of the genus
Salinimicrobium
(<96.8 %). However, strain JC207T showed an average of 23.6±4 and 37±4 relatedness (based on DNA–DNA hybridization) with
Salinimicrobium terrae
CGMCC 1.6308T ( = YIM-C338T) and
Salinimicrobium xinjiangense
KCTC 12883T ( = BH206T), respectively. Morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC207T as a representative of a novel species in the genus
Salinimicrobium
, for which the name Salinimicrobium sediminis sp. nov. is proposed. The type strain is JC207T ( = KCTC 32444T = CGMCC 1.12641T).
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Affiliation(s)
- Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Post Office Central University, Hyderabad 500 046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, Jawaharlal Nehru Technological University, Kukatpally, Hyderabad 500 085. India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Post Office Central University, Hyderabad 500 046, India
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41
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Subhash Y, Sasikala C, Ramana CV. Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov., isolated from the desert. Int J Syst Evol Microbiol 2014; 64:1006-1011. [DOI: 10.1099/ijs.0.058842-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of bacteria, JC213T and JC215T, were isolated from desert soil. Colonies were red to pink and cells Gram-stain-negative. Both strains were oxidase- and catalase-positive and hydrolysed casein. In both strains, phosphatidylethanolamine was the major polar lipid, iso-C15 : 0 was the major fatty acid and the bacteriohopane derivative, BHD1, was the major hopanoid. The genomic DNA G+C contents of strains JC213T and JC215T were 52.7 and 46.3 mol%, respectively. 16S rRNA gene sequence comparisons indicated that both strains belong to the genus
Pontibacter
within the family
Cytophagaceae
and the phylum
Bacteroidetes
. Strain JC213T showed the highest sequence similarity to
Pontibacter populi
HLY7-15T (96.6 %) and with other species of the genus
Pontibacter
sequence similarity was less than 96 %. Strain JC215T exhibited highest sequence similarity with
Pontibacter lucknowensis
DM9T (95.1 %) and shared 95 % or less sequence similarity with other species of the genus
Pontibacter
. The sequence similarity between strains JC213T and JC215T was 95.8 %. Distinct morphological, physiological and genotypic differences from previously described taxa support JC213T and JC215T being representatives of two novel species of the genus
Pontibacter
, for which the names Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov. are proposed and the type strains are JC213T ( = KCTC 32442T = LMG 27669T) and JC215T ( = KCTC 32443T = LMG 27670T), respectively.
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Affiliation(s)
- Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085. India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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42
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Subhash Y, Sasikala C, Ramana CV. Bacillus luteus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1580-1586. [PMID: 24478212 DOI: 10.1099/ijs.0.053504-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5%) were anteiso-C15:0, iso-C16:0, iso-C15:0, anteiso-C17:0, iso-C14:0 and C16:0 with minor (<5 but >1%) amounts of iso-C17:0, anteiso-C17:0 B/iso-C17:0 I and C16:1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were L-alanine, D-alanine, D-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA-DNA hybridization>90%). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a sequence similarity of 97.6% with Bacillus saliphilus 6AGT and <96.8% with other members of the genus Bacillus. Sequence similarity between strain JC167T and 168 was 100%. Strain JC167T showed 25.8±1% reassociation (based on DNA-DNA hybridization) with B. saliphilus DSM 15402T (=6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T (=KCTC 33100T=LMG 27257T).
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Affiliation(s)
- Y Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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43
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Subhash Y, Sasikala C, Ramana CV. Flavobacterium
aquaticum sp. nov., isolated from a water sample of a rice field. Int J Syst Evol Microbiol 2013; 63:3463-3469. [DOI: 10.1099/ijs.0.050047-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain JC164T was isolated from a water sample from a rice field at Jamdih, Mau, Uttar Pradesh, India. Colonies of strain JC164T were brown–yellow and cells were Gram-stain-negative. Catalase, oxidase and amylase were present. iso-C15 : 0, iso-C16 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C14 : 0 were the predominant fatty acids with minor amounts of iso-C16 : 0 3-OH, anteiso-C15 : 0, C16 : 0, iso-C16 : 1 H, iso-C14 : 0 3-OH and iso-C13 : 0. Strain JC164T contained phosphatidylethanolamine and a few unidentified lipids (L1, L3 and L6) as major polar lipids. Bacteriohopane derivative 1 (BHD1) and diplopterol (DPL) were the major hopanoids. β-Carotene was one among the several spirilloxanthin series carotenoids present in strain JC164T. Genomic DNA G+C content was 39.6 mol%. 16S rRNA gene sequence comparisons indicated that strain JC164T represents a member of the genus
Flavobacterium
(family
Flavobacteriaceae
, class
Flavobacteriia
). The most closely related taxa to strain JC164T were
Flavobacterium sasangense
YC6274T (98.5 %),
Flavobacterium cucumis
R2A45-3T (98.1 %),
Flavobacterium cheniae
NJ-26T (97.2 %) and the novel strain possessed <95.1 % sequence similarity with other members of the genus
Flavobacterium
. However, strain JC164T showed 12.5±2, 13.6±1 and 17.4±2 % genomic DNA association (based on DNA–DNA hybridization) with
Flavobacterium sasangense
KCTC 22246T,
Flavobacterium cucumis
DSM 18830T and
Flavobacterium cheniae
CGMCC 1.6844T, respectively. The distinct genomic difference and morphological, physiological and chemotaxonomic differences from the previously described taxa support the classification of strain JC164T as a representative of a novel species of the genus
Flavobacterium
, for which the name
Flavobacterium
aquaticum sp. nov. is proposed. The type strain is JC164T ( = KCTC 32196T = CGMCC 1.12398 = LMG 27251T).
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Affiliation(s)
- Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
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