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Carr CM, Göttsch F, de Oliveira BFR, Murcia PAS, Jackson SA, Wei R, Clarke DJ, Bornscheuer UT, Dobson ADW. Identification and expression of MarCE, a marine carboxylesterase with synthetic ester-degrading activity. Microb Biotechnol 2024; 17:e14479. [PMID: 38881500 PMCID: PMC11180994 DOI: 10.1111/1751-7915.14479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Carboxylic ester hydrolases with the capacity to degrade polyesters are currently highly sought after for their potential use in the biological degradation of PET and other chemically synthesized polymers. Here, we describe MarCE, a carboxylesterase family protein identified via genome mining of a Maribacter sp. isolate from the marine sponge Stelligera stuposa. Based on phylogenetic analysis, MarCE and its closest relatives belong to marine-associated genera from the Cytophaga-Flavobacterium-Bacteroides taxonomic group and appear evolutionarily distinct to any homologous carboxylesterases that have been studied to date in terms of structure or function. Molecular docking revealed putative binding of BHET, a short-chain PET derivative, onto the predicted MarCE three-dimensional structure. The synthetic ester-degrading activity of MarCE was subsequently confirmed by MarCE-mediated hydrolysis of 2 mM BHET substrate, indicated by the release of its breakdown products MHET and TPA, which were measured, respectively, as 1.28 and 0.12 mM following 2-h incubation at 30°C. The findings of this study provide further insight into marine carboxylic ester hydrolases, which have the potential to display unique functional plasticity resulting from their adaptation to complex and fluctuating marine environmentsw.
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Affiliation(s)
- Clodagh M. Carr
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
| | - Frederike Göttsch
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | | | - Pedro A. Sánchez Murcia
- Laboratory of Computer‐Aided Molecular Design, Division of Medicinal Chemistry, Otto‐Loewi Research CenterMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Stephen A. Jackson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - David J. Clarke
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Alan D. W. Dobson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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Korponai K, Szuróczki S, Márton Z, Szabó A, Morais PV, Proença DN, Tóth E, Boros E, Márialigeti K, Felföldi T. Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326610 DOI: 10.1099/ijsem.0.005928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
The genus Belliella belongs to the family Cyclobacteriaceae (order Cytophagales, phylum Bacteroidota) and harbours aerobic chemoheterotrophic bacteria. Members of this genus were isolated from various aquatic habitats, and our analysis based on global amplicon sequencing data revealed that their relative abundance can reach up to 5-10 % of the bacterioplankton in soda lakes and pans. Although a remarkable fraction of the most frequent genotypes that we identified from continental aquatic habitats is still uncultured, five new alkaliphilic Belliella strains were characterized in detail in this study, which were isolated from three different soda lakes and pans of the Carpathian Basin (Hungary). Cells of all strains were Gram-stain-negative, obligate aerobic, rod-shaped, non-motile and non-spore-forming. The isolates were oxidase- and catalase-positive, red-coloured, but did not contain flexirubin-type pigments; they formed bright red colonies that were circular, smooth and convex. Their major isoprenoid quinone was MK-7 and the predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 containing C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipid profiles contained phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, and several unidentified lipids and aminolipids. Based on whole-genome sequences, the DNA G+C content was 37.0, 37.1 and 37.8 mol % for strains R4-6T, DMA-N-10aT and U6F3T, respectively. The distinction of three new species was confirmed by in silico genomic comparison. Orthologous average nucleotide identity (<85.4 %) and digital DNA-DNA hybridization values (<38.9 %) supported phenotypic, chemotaxonomic and 16S rRNA gene sequence data and, therefore, the following three novel species are proposed: Belliella alkalica sp. nov. (represented by strains R4-6T=DSM 111903T=JCM 34281T=UCCCB122T and S4-10), Belliella calami sp. nov. (DMA-N-10aT=DSM 107340T=JCM 34280T=UCCCB121T) and Belliella filtrata sp. nov. (U6F3T=DSM 111904T=JCM 34282T=UCCCB123T and U6F1). Emended descriptions of species Belliella aquatica, Belliella baltica, Belliella buryatensis, Belliella kenyensis and Belliella pelovolcani are also presented.
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Affiliation(s)
- Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Agricultural Institute, Centre for Agricultural Research, Brunszvik utca 2, 2462 Martonvásár, Hungary
| | - Sára Szuróczki
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms Vag 9, 750 07 Uppsala, Sweden
| | - Paula V Morais
- Department of Life Sciences, Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Diogo Neves Proença
- Department of Life Sciences, Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Emil Boros
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
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Gao P, Lu H, Phurbu D, Wu Q, Xing P. Proposal to reclassify Aquiflexum aquatile into a novel genus as Cognataquiflexum aquatile gen. nov., comb. nov., and description of Cognataquiflexum nitidum sp. nov. and Cognataquiflexum rubidum sp. nov., isolated from freshwater lakes on the Tibetan Plateau. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748472 DOI: 10.1099/ijsem.0.005653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Thousands of lakes harbouring different characteristics (pH, salinity, temperature) are located on the Tibetan Plateau, and the mining of microbial resources inhabited in these lakes has great value. Two Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LQ15WT and AIY15WT) were isolated from freshwater lakes on the Tibetan Plateau. Comparisons based on the 16S rRNA gene sequences showed that both strains LQ15WT and AIY15WT share 16S rRNA gene sequence similarities 98.4 % with Aquiflexum aquatile Z0201T, but only about 95.0 % with Aquiflexum balticum DSM 16537T. The 16S rRNA gene sequence similarity between strains LQ15WT and AIY15WT was 98.9 %. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains LQ15WT and AIY15WT take A. aquatile Z0201T as their closest neighbour and these three strains form a tight cluster. In the phylogenomic tree, the genus Aquiflexum was splited into two clusters by Mariniradius saccharolyticus. Strains LQ15WT, AIY15WT and A. aquatile Z0201T still formed a close cluster, and A. balticum DSM 16537T and Aquiflexum lacus CUG 91378T formed another cluster. The calculated OrthoANIu, average amino acid identity and digital DNA-DNA hybridization values among strains LQ15WT, AIY15WT, A. aquatile Z0201T, A. balticum DSM 16537T and A. lacus CUG 91378T were less than 91.0, 92.9 and 42.1 %, respectively. The major respiratory quinones of both strains LQ15WT and AIY15WT were MK-7 (32 %) and MK-8 (68 %), and their major fatty acids were iso-C15 : 0, C18 : 1 ω9c, summed feature 3 and summed feature 9. The predominant polar lipids of both strains were phosphatidylethanolamine, unidentified aminophospholipids, unidentified phospholipids and lipids. Strain AIY15WT also contained phosphatidylglycerol and unidentified glycolipid. Considering the distinct phylogenetic relationships and chemotaxonomic characteristics between strains A. aquatile Z0201T and A. balticum DSM 16537T, it is proposed to reclassify A. aquatile into a novel genus Cognataquiflexum gen. nov. as Cognataquiflexum aquatile comb. nov., and strains LQ15WT and AIY15WT should represent two independent novel species of the genus Cognataquiflexum, for which the names Cognataquiflexum nitidum sp. nov. (type strain: LQ15WT=CICC 24711T=JCM 34222T) and Cognataquiflexum rubidum sp. nov. (type strain: AIY15WT=CICC 24708T=JCM 34612T) are proposed.
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Affiliation(s)
- Peixin Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Huibin Lu
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Dorji Phurbu
- Tibet Plateau Institute of Biology, Lhasa 850000, PR China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, 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
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Ali S, Xie J, Chen Y, Cai R, Juventus AJ, Hu Z, Zhang Y, Wang H. Penaeicolahalotolerans gen. nov., sp. nov., a novel bacterium of the family Cyclobacteriaceae isolated from a shrimp pond. Int J Syst Evol Microbiol 2021; 71. [PMID: 34623951 DOI: 10.1099/ijsem.0.005047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium (designated as LMIT005T) was isolated from shrimp ponds in Shantou, China. The new isolate was characterized taxonomically using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain LMIT005T was found to be affiliated with the family Cyclobacteriaceae of the order Cytophagales while appearing as a distinct lineage. The 16S rRNA gene sequence similarity between strain LMIT005T and Algoriphagus yeomjeoni KCTC 12309T, the closest type strain in the family, was 91.3 %. Strain LMIT005T grew optimally at 25 °C, pH 7 and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content (data from genome sequence) was 40.5 mol%. Compared with reference strain A. yeomjeoni KCTC 12309T, the average nucleotide identity (ANI) of LMIT005T was 70 %. The sole respiratory quinone of LMIT005T was menaquinone (MK-7), and the major fatty acids were summed feature 3 (C16 : 1 ω6c / C16 : 1 ω7c). The polar lipids of strain LMIT005T were mainly composed of phosphatidylethanolamine, phosphatidylcholine, two unidentified amino lipids, two unidentified lipids, one unidentified glycolipid and one unidentified phospholipid. The draft genome of strain LMIT005T comprised 3 089 781 bp (3.09 Mb) nucleotides and 2773 genes. Antimicrobial resistant-related genes (blal, mexA, and mexb) were annotated in the genome of strain LMIT005T, which indicated that it might be able to resist β-lactam antibiotics. This was further verified by antimicrobial resistant test. Given its distinct genomic, morphological, and physiological differences from previously described type strains, strain LMIT005T is proposed as a representative of a novel genus of the family Cyclobacteriaceae, with the name Penaeicola halotolerans gen. nov., sp. nov. The type strain is LMIT005T (=KCTC 82616T=CICC 25047T).
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Affiliation(s)
- Sardar Ali
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China.,Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
| | - Jianmin Xie
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China
| | - Yuerong Chen
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China
| | - Runlin Cai
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China
| | - Aweya Jude Juventus
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China
| | - Zhong Hu
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China.,Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
| | - Yueling Zhang
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China.,Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
| | - Hui Wang
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, PR China.,Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
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Song L, Liu H, Huang Y, Dai X, Zhou Y. Pararhodonellum marinum gen. nov., sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34427552 DOI: 10.1099/ijsem.0.004966] [Citation(s) in RCA: 6] [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 Gram-stain-negative, non-motile bacterial strain, designated SW124T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. SW124T was aerobic and catalase-positive. The strain grew at 4-40 °C (optimum, 30 °C), at pH 5.0-8.6 (optimum, pH 7.0) and in the presence of 0.5-9.5 % (w/v) NaCl (optimum, 3.0%). The results of comparative analyses of the 16S rRNA gene sequence indicated that SW124T was grouped in the vicinity of the genus Rhodonellum in the family Cyclobacteriaceae. The quinone system contained menaquinone MK-7. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). SW124T contained phosphatidylethanolamine (PE) as the major polar lipid. The genomic DNA G+C content of SW124T was 41.7 mol%. On the basis of its phenotypic characteristics and phylogenetic data, we propose that strain SW124T (=CGMCC 1.16171T=KCTC 82235T) represents a novel species of a novel genus, with the name Pararhodonellum marinum gen. nov., sp. nov.
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Affiliation(s)
- Lei Song
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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6
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Aquiflexum lacus sp. nov., isolated from a lake sediment sample. Arch Microbiol 2021; 203:2911-2917. [PMID: 33763765 DOI: 10.1007/s00203-021-02280-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
A novel Gram-staining negative, crescent-like or rod-shaped, non-motile bacterium, designated strain CUG 91378 T, was isolated from a sediment sample of Qinghai Lake, Qinghai Province, China. The strain was red-colored, and catalase- and oxidase-positive. Strain CUG 91378 T was able to grow at 15-37 °C (optimum, 28 °C), pH 7-9 (pH 7.0) and in the presence of up to 3.0% (w/v) NaCl (0-2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CUG 91378 T formed a well-supported monophyletic clade with Aquiflexum balticum DSM 16537 T (95.4%) and Aquiflexum aquatile Z0201T (93.2%). The DNA G + C content of CUG 91378 T was 39.0%. Low (< 87%) average nucleotide identity (ANI) and (< 26%) digital DNA-DNA hybridization (dDDH) values were observed between strain CUG 91378 T and its closest species on the phylogenetic trees. The sole respiratory quinone of strain CUG 91378 T was MK-7. The predominant fatty acids (> 5.0%) were iso-C15:0 (19.1%), iso-C16:0 (12.0%), iso-C16:1 H (10.9%), iso-C16:0 3OH (9.2%), iso-C17:0 3OH (7.7%), C17:1ω6c (6.1%) and anteiso-C15:0 (5.8%). Strain CUG 91378 T contained as phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and four unidentified lipids (L1, L2, L3 and L4). Based on the data from the current polyphasic study, the isolate represents a novel species of the genus Aquiflexum for which the name Aquiflexum lacus is proposed. The type strain of the proposed new taxon is CUG 91378 T (= KCTC 62637 T = CGMCC 1.13988 T).
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Han MX, Huang JR, Jiang HC, Fang BZ, Xie YG, Li WJ. Lunatibacter salilacus gen. nov., sp. nov., a member of the family Cyclobacteriaceae, isolated from a saline and alkaline lake sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 33406031 DOI: 10.1099/ijsem.0.004621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, Gram-staining negative, catalase- and oxidase-positive, crescent-rod shaped bacterium, designated strain CUG 91308T, was isolated from a sediment sample of Qinghai Lake, Qinghai Province, China. Colonies on OSM agar were round, smooth, flat and pinkish-orange in colour. Strain CUG 91308T could grow at 15-37 °C, pH 6-12 and in the presence of up to 7.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CUG 91308T belonged to the family Cyclobacteriaceae and formed a clade with the genus Lunatimonas in the phylogenetic tree, but separated from any species of the known genera within the family. The genomic DNA G+C content is about 42.1 %. The predominant fatty acids (>10 %) were iso-C15 : 0 (21.1 %), summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c / iso-C15 : 0 2OH) (14.3 %), iso-C17 : 0 3OH (12.3 %) and summed feature 9 (iso-C17 : 1 ω9c / C16 : 0 10-methyl) (10.6 %). The polar lipids of strain CUG 91308T were phosphatidylethanolamine (PE) and four unidentified polar lipids. Strain CUG 91308T contained MK-7 as the major respiratory quinone. On the basis of phenotypic, genotypic and phylogenetic data, strain CUG 91308T represents a novel species of a novel genus in the family Cyclobacteriaceae, for which the name Lunatibacter salilacus gen. nov., sp. nov. is proposed. The type strain of the proposed new isolate is CUG 91308T (=KCTC 62636T=CGMCC 1.13593T).
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Affiliation(s)
- Ming-Xian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Jian-Rong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yuan-Guo Xie
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.,State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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Ruiz-Lopez S, Foster L, Boothman C, Cole N, Morris K, Lloyd JR. Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site. Front Microbiol 2020; 11:587556. [PMID: 33329459 PMCID: PMC7732693 DOI: 10.3389/fmicb.2020.587556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/26/2020] [Indexed: 11/29/2022] Open
Abstract
The use of nuclear power has been a significant part of the United Kingdom’s energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 104–106 mL–1 were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.
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Affiliation(s)
- Sharon Ruiz-Lopez
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Lynn Foster
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Chris Boothman
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Nick Cole
- Sellafield Ltd., Warrington, United Kingdom
| | - Katherine Morris
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
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Wang XT, Wang XM, Zheng WS, Zhang XK, Du ZJ. Aquiflexum aquatile sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2019; 69:1947-1952. [DOI: 10.1099/ijsem.0.003405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xu-Ting Wang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Xiao-Man Wang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Wei-Shuang Zheng
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Xiao-Kui Zhang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- 2State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
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10
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Effects of salinity and nitrogen source on growth and lipid production for a wild algal polyculture in produced water media. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.101406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Kruglova A, Gonzalez-Martinez A, Kråkström M, Mikola A, Vahala R. Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 605-606:291-299. [PMID: 28668740 DOI: 10.1016/j.scitotenv.2017.06.191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
In this study the influence of low-temperature (8°C), sludge retention time (SRT) and loading of spotlight wastewater micropollutants (MPs) on bacterial community of activated sludge was investigated with a special focus on nitrification. Two Sequencing batch reactors (SBR) and two membrane bioreactors (MBR) were operated with synthetic municipal-like wastewater receiving and not receiving ibuprofen, diclofenac, estrone and 17α-ethynylestradiol (EE2). Bacterial population studies were related to removal efficiencies of studied MPs. The results showed that studied bacterial communities significantly differed from all previously published nitrifying activated sludge communities. Exceptionally low concentration of autotrophic nitrifying bacteria were found (<0.5%) as well as no common heterotrophic nitrifies were presenting in activated sludge and therefore could not be related to the MPs removal. Additionally SRT had a spacious effect on the diversity of bacteria and bacterial population shifts under pressure of MPs. Growth of Firmicutes was suppressed by presence of MPs in all the reactors. Increase of MPs concentrations in wastewater improved the removal of EE2. Abundance of Delta- and Gammaproteobacteria showed positive correlation with diclofenac removal.
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Affiliation(s)
- Antonina Kruglova
- Aalto University, Department of Built Environment, P.O. Box 15200, FI-00076 AALTO Espoo, Finland.
| | | | - Matilda Kråkström
- Åbo Akademy University, Johan Gadolin Process Chemistry Centre, c/o Laboratory of Organic Chemistry, Piispankatu 8, 20500 Turku, Finland
| | - Anna Mikola
- Aalto University, Department of Built Environment, P.O. Box 15200, FI-00076 AALTO Espoo, Finland
| | - Riku Vahala
- Aalto University, Department of Built Environment, P.O. Box 15200, FI-00076 AALTO Espoo, Finland
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Yoon J, Yasumoto-Hirose M, Kasai H. Frondibacter mangrovi sp. nov., a member of the family Flavobacteriaceae isolated from seawater by in situ cultivation, and emended description of Frondibacter aureus. Int J Syst Evol Microbiol 2017; 67:5013-5018. [DOI: 10.1099/ijsem.0.002404] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Mina Yasumoto-Hirose
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
- Present address: Tropical Technology Plus, 12-75 Suzaki, Uruma, Okinawa 904-2234, Japan
| | - Hiroaki Kasai
- School of Marine Biosciences, Kitasato University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato, Iwate 022-0101, Japan
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Chen C, Su Y, Tao T, Fu G, Zhang C, Sun C, Zhang X, Wu M. Maripseudobacter aurantiacus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a sedimentation basin. Int J Syst Evol Microbiol 2017; 67:778-783. [DOI: 10.1099/ijsem.0.001580] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Can Chen
- Ocean College, Zhejiang University, Hangzhou 310058, PR China
| | - Yue Su
- Ocean College, Zhejiang University, Hangzhou 310058, PR China
| | - Tianyi Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Geyi Fu
- Ocean College, Zhejiang University, Hangzhou 310058, PR China
| | - Chongya Zhang
- Ocean College, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xinqi Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an 311300, PR China
| | - Min Wu
- Ocean College, Zhejiang University, Hangzhou 310058, PR China
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Yoon J, Adachi K, Kasai H. Aureisphaera salina sp. nov., a member of the family Flavobacteriaceae isolated from an ascidian. Int J Syst Evol Microbiol 2016; 66:2999-3004. [PMID: 27150454 DOI: 10.1099/ijsem.0.001132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic, chemoheterotrophic, pale-yellow-pigmented bacterium, designated strain A6D-50T, was isolated from an ascidian collected at Kohama Island offshore Okinawa, Japan. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (97.6 %) to Aureisphaera galaxeae 04OKA003-7T. The DNA-DNA relatedness value between strain A6D-50T and A. galaxeae 04OKA003-7T was 23.6 %. The DNA G+C content of strain A6D-50T was 40.8 mol%, MK-6 was the only menaquinone, and iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major (>10 %) cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Aureisphaera for which the name Aureisphaera salina sp. nov. is proposed. The type strain is A6D-50T (= KCTC 42975T=NBRC 111827T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Kyoko Adachi
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | - Hiroaki Kasai
- Marine Biosciences Kamaishi Research Laboratory, Kitasato University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato, Iwate 022-0101, Japan
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Wang YX, Liu YP, Huo QQ, Li YP, Feng FY, Xiao W, Ding ZG, Lai YH, Cui XL. Mongoliibacter ruber gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae isolated from a haloalkaline lake. Int J Syst Evol Microbiol 2016; 66:1088-1094. [DOI: 10.1099/ijsem.0.000836] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong-Xia Wang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Ya-Peng Liu
- Institution for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, PR China
- Inner Mongolia Yili Industrial Group, Co., Ltd, Huhhot, Inner Mongolia 010110, PR China
| | - Qing-Qing Huo
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Ya-Ping Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Fu-Ying Feng
- Institution for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, PR China
| | - Wei Xiao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Zhang-Gui Ding
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Hong Lai
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Phylogenetic and taxonomic analysis of Neptunitalea chrysea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from seawater by using an in situ cultivation technique. Antonie van Leeuwenhoek 2015; 108:537-44. [DOI: 10.1007/s10482-015-0508-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022]
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Yoon J, Adachi K, Kasai H. Isolation and characterization of a novel marine Bacteroidetes as Algitalea ulvae gen. nov., sp. nov., isolated from the green alga Ulva pertusa. Antonie van Leeuwenhoek 2015; 108:505-13. [PMID: 26063306 DOI: 10.1007/s10482-015-0504-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/05/2015] [Indexed: 01/08/2023]
Abstract
A polyphasic taxonomic investigation was performed on a bacterial strain, 38-Ka-2(T), which was isolated from the green alga Ulva pertusa Kjellman (Chlorophyta) in Hokkaido, Japan. The bacterial cells were observed to be golden-yellow coloured, Gram-negative, strictly aerobic, non-spore-forming, non-motile and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain is a member of the family Flavobacteriaceae within the phylum Bacteroidetes and that it shows high sequence similarity (94.8 %) to Aquimarina addita JC2680(T). The genomic DNA G+C content of strain 38-Ka-2(T) was determined to be 36 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, C18:0 and iso-C17:0 3-OH as the major (>10 %) cellular fatty acids. The polar lipid profile was found to consist of phosphatidylethanolamine, an unidentified glycolipid and two unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, strain 38-Ka-2(T) is considered to represent a novel genus for which the name Algitalea ulvae gen. nov., sp. nov. is proposed. The type strain of A. ulvae is 38-Ka-2(T) (=KCTC 32994(T) = NBRC 110017(T)).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, 704-701, Republic of Korea,
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Yoon J, Jo Y, Kim GJ, Choi H. Gramella lutea sp. nov., a Novel Species of the Family Flavobacteriaceae Isolated from Marine Sediment. Curr Microbiol 2015; 71:252-8. [DOI: 10.1007/s00284-015-0849-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/18/2015] [Indexed: 11/24/2022]
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19
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Zhang ZD, Gu MY, Zhu J, Li SH, Zhang LJ, Xie YQ, Shi YH, Wang W, Li WJ. Rufibacter roseus sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol 2015; 65:1572-1577. [DOI: 10.1099/ijs.0.000137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rose, Gram-stain-negative, aerobic, rod-shaped bacterium that was motile by gliding, and designated strain H359T, was isolated from radiation-polluted soil (with high Cs137) from the Xinjiang Uygur Autonomous Region of PR China and subjected to a polyphasic taxonomic analysis. The isolate grew optimally at 30 °C and pH 7.0. It grew with NaCl up to 4 % (w/v). 16S rRNA gene sequence analysis indicated that strain H359T belonged to the genus
Rufibacter
, a member of the family
Cytophagaceae
, with
Rufibacter tibetensis
CCTCC AB 208084T as its closest phylogenetic relative, having 96.1 % 16S rRNA gene sequence similarity to the type strain. Strain H359T contained menaquinone-7 (MK-7) as the predominant menaquinone, and the major fatty acids were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c. The polar lipid profile had phosphatidylethanolamine as the major component. The DNA G+C content was 43.9 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain H359T represents a novel species of the genus
Rufibacter
, for which the name Rufibacter roseus sp. nov. is proposed. The type strain is H359T ( = CPCC 100615T = KCTC 42217T).
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Affiliation(s)
- Zhi-Dong Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Mei-Ying Gu
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Jing Zhu
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Shan-Hui Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
- State Key Laboratory of Bio-control and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Li-Juan Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Yu-Qing Xie
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Yu-Hu Shi
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Wei Wang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, PR China
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Wen-Jun Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
- State Key Laboratory of Bio-control and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
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Wenyingzhuangia gracilariae sp. nov., a novel marine bacterium of the phylum Bacteroidetes isolated from the red alga Gracilaria vermiculophylla. Antonie van Leeuwenhoek 2015; 107:1607-13. [PMID: 25896307 DOI: 10.1007/s10482-015-0456-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/11/2015] [Indexed: 10/23/2022]
Abstract
A Gram-negative, strictly aerobic, beige-pigmented, non-motile, rod-shaped bacterial strain designated N5DB13-4(T) was isolated from the red alga Gracilaria vermiculophylla (Rhodophyta) collected at Sodegaura Beach, Chiba, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate is affiliated with the family Flavobacteriaceae within the phylum Bacteroidetes and that it showed highest sequence similarity (97.3 %) to Wenyingzhuangia heitensis H-MN17(T). The hybridization values for DNA-DNA relatedness between the strains N5DB13-4(T) and W. heitensis H-MN17(T) were 34.1 ± 3.5 %, which is below the threshold accepted for the phylogenetic definition of a novel prokaryotic species. The DNA G+C content of strain N5DB13-4(T) was determined to be 31.8 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C15:0 3-OH and iso-C17:0 3-OH as the major (>10 %) cellular fatty acids. A complex polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified glycolipids and four unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Wenyingzhuangia for which the name Wenyingzhuangia gracilariae sp. nov. is proposed. The type strain of W. gracilariae sp. nov. is N5DB13-4(T) (=KCTC 42246 (T)=NBRC 110602(T)).
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Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis. Antonie van Leeuwenhoek 2015; 107:1379-86. [PMID: 25795444 DOI: 10.1007/s10482-015-0432-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/14/2015] [Indexed: 10/23/2022]
Abstract
A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA003-7(T) was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436(T) and Aureitalea marina S1-66(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7(T) were identified as iso-C15:0 and iso-C17:0 3-OH as defined by the MIDI system. The DNA G+C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7(T) (=KCTC 32993(T) = NBRC 110018(T)).
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Yoon J, Kasai H. Wenyingzhuangia heitensis sp. nov., a new species of the family Flavobacteriaceae within the phylum Bacteroidetes isolated from seawater. Antonie van Leeuwenhoek 2014; 107:655-61. [DOI: 10.1007/s10482-014-0360-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
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Yoon J, Adachi K, Kasai H. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov. Antonie van Leeuwenhoek 2014; 107:321-8. [DOI: 10.1007/s10482-014-0330-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/04/2014] [Indexed: 11/29/2022]
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Yoon J, Adachi K, Kasai H, Lee MK. Spongiivirga citrea gen. nov., sp. nov., a New Marine Bacterium of the Family Flavobacteriaceae Isolated from a Marine Sponge. Curr Microbiol 2014; 70:51-7. [DOI: 10.1007/s00284-014-0682-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/17/2014] [Indexed: 10/24/2022]
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Yoon J, Adachi K, Kasai H. Citreitalea marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a marine red alga and emended description of the genus Gangjinia. Antonie van Leeuwenhoek 2014; 106:261-9. [PMID: 24866884 DOI: 10.1007/s10482-014-0190-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
A Gram-negative, strictly aerobic, pale-yellow pigmented, rod-shaped bacterium designated A4O-5(T) was isolated from a red coloured marine alga (Chondrus ocellatus Holmes). Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain was affiliated with the family Flavobacteriaceae and shared approximately 90 % sequence similarity with Leptobacterium flavescens YM3-0301(T) and Gangjinia marincola GJ16(T). The strain could be differentiated phenotypically from the related members of the family Flavobacteriaceae. The major fatty acids of strain A4O-5(T) were identified as iso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). A complex polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified phospholipid, three unidentified amino lipids and an unidentified lipid. The DNA G+C content of the strain was determined to be 41.9 mol% and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Citreitalea marina gen. nov., sp. nov. is proposed. The type strain of C. marina is A4O-5(T) (=KCTC 32483(T)=NBRC 109918(T)).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, 704-701, Republic of Korea,
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Srinivas T, Aditya S, Bhumika V, Kumar PA. Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity. Syst Appl Microbiol 2014; 37:10-6. [DOI: 10.1016/j.syapm.2013.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 10/25/2022]
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Bhumika V, Srinivas TNR, Ravinder K, Anil Kumar P. Mariniradius saccharolyticus gen. nov., sp. nov., a member of the family
Cyclobacteriaceae
isolated from marine aquaculture pond water, and emended descriptions of the genus
Aquiflexum
and
Aquiflexum balticum. Int J Syst Evol Microbiol 2013; 63:2088-2094. [DOI: 10.1099/ijs.0.043919-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel marine, Gram-stain-negative, oxidase- and catalase- positive, rod-shaped bacterium, designated strain AK6T, was isolated from marine aquaculture pond water collected in Andhra Pradesh, India. The fatty acids were dominated by iso-C15 : 0, iso-C17 : 1ω9c, iso-C15 : 1 G, iso-C17 : 0 3-OH and anteiso-C15 : 0. Strain AK6T contained MK-7 as the sole respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and seven unidentified lipids as polar lipids. The DNA G+C content of strain AK6T was 45.6 mol%. Phylogenetic analysis showed that strain AK6T formed a distinct branch within the family
Cyclobacteriaceae
and clustered with
Aquiflexum balticum
DSM 16537T and other members of the family
Cyclobacteriaceae
. 16S rRNA gene sequence analysis confirmed that
Aquiflexum balticum
DSM 16537T was the nearest neighbour, with pairwise sequence similarity of 90.1 %, while sequence similarity with the other members of the family was <88.5 %. Based on differentiating phenotypic characteristics and phylogenetic inference, strain AK6T is proposed as a representative of a new genus and species of the family
Cyclobacteriaceae
, as Mariniradius saccharolyticus gen. nov., sp. nov. The type strain of Mariniradius saccharolyticus is AK6T ( = MTCC 11279T = JCM 17389T). Emended descriptions of the genus
Aquiflexum
and
Aquiflexum balticum
are also proposed.
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Affiliation(s)
- V. Bhumika
- CSIR – Institute of Microbial Technology, Microbial Type Culture Collection and Gene bank, Sector 39A, Chandigarh – 160 036, India
| | - T. N. R. Srinivas
- CSIR – National Institute of Oceanography, Regional centre, PB No. 1913, Dr. Salim Ali Road, Kochi – 682018 (Kerala), India
| | - K. Ravinder
- CSIR – Institute of Microbial Technology, Microbial Type Culture Collection and Gene bank, Sector 39A, Chandigarh – 160 036, India
| | - P. Anil Kumar
- CSIR – Institute of Microbial Technology, Microbial Type Culture Collection and Gene bank, Sector 39A, Chandigarh – 160 036, India
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Park S, Yoshizawa S, Muramatsu Y, Nakagawa Y, Yokota A, Kogure K. Aureicoccus marinus gen. nov., sp. nov., a member of the family
Flavobacteriaceae
, isolated from seawater. Int J Syst Evol Microbiol 2013; 63:1885-1890. [DOI: 10.1099/ijs.0.045104-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A coccoid and amorphous-shaped, non-gliding, proteorhodopsin-containing, yellow bacterium, designated strain SG-18T, was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and oxidase-positive. It hydrolysed aesculin but not DNA, urea, gelatin or agar. Growth occurred in the presence of 1–5 % NaCl, with optimum growth at 2 % NaCl. The strain grew at 15–37 °C with an optimum temperature of 25–30 °C. The DNA G+C content of the genomic DNA of strain SG-18T was 47.0 mol% (HPLC). The predominant isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH. Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain SG-18T belonged to the family
Flavobacteriaceae
and showed 92.7 % sequence similarity to the most closely related species,
Croceitalea eckloniae
DOKDO 025T. On the basis of phenotypic and phylogenetic features, strain SG-18T is classified as representing a novel species of a new genus within the family
Flavobacteriaceae
, for which the name Aureicoccus marinus gen. nov., sp. nov. is proposed. The type strain of the type species is SG-18T ( = NBRC 108814T = KCTC 23967T).
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Affiliation(s)
- Sanghwa Park
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Yuki Muramatsu
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, Kisarazu, Chiba 292-0818, Japan
| | - Yasuyoshi Nakagawa
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, Kisarazu, Chiba 292-0818, Japan
| | - Akira Yokota
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Indonesia, Kampus UI Depok, 16424, Indonesia
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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29
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Planktonic bacterial community composition of an extremely shallow soda pond during a phytoplankton bloom revealed by cultivation and molecular cloning. Extremophiles 2013; 17:575-84. [DOI: 10.1007/s00792-013-0540-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
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30
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Spongiimonas flava gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from an unidentified marine sponge. Antonie van Leeuwenhoek 2012; 103:625-33. [DOI: 10.1007/s10482-012-9846-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/31/2012] [Indexed: 01/19/2023]
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31
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Alegado RA, Brown LW, Cao S, Dermenjian RK, Zuzow R, Fairclough SR, Clardy J, King N. A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals. eLife 2012; 1:e00013. [PMID: 23066504 PMCID: PMC3463246 DOI: 10.7554/elife.00013] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/18/2012] [Indexed: 12/15/2022] Open
Abstract
Bacterially-produced small molecules exert profound influences on animal health, morphogenesis, and evolution through poorly understood mechanisms. In one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta, we find that rosette colony development is induced by the prey bacterium Algoriphagus machipongonensis and its close relatives in the Bacteroidetes phylum. Here we show that a rosette inducing factor (RIF-1) produced by A. machipongonensis belongs to the small class of sulfonolipids, obscure relatives of the better known sphingolipids that play important roles in signal transmission in plants, animals, and fungi. RIF-1 has extraordinary potency (femtomolar, or 10(-15) M) and S. rosetta can respond to it over a broad dynamic range-nine orders of magnitude. This study provides a prototypical example of bacterial sulfonolipids triggering eukaryotic morphogenesis and suggests molecular mechanisms through which bacteria may have contributed to the evolution of animals.DOI:http://dx.doi.org/10.7554/eLife.00013.001.
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Affiliation(s)
- Rosanna A Alegado
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Laura W Brown
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Shugeng Cao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Renee K Dermenjian
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Richard Zuzow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Stephen R Fairclough
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Nicole King
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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32
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Anil Kumar P, Srinivas TNR, Madhu S, Sravan R, Singh S, Naqvi SWA, Mayilraj S, Shivaji S. Cecembia lonarensis gen. nov., sp. nov., a haloalkalitolerant bacterium of the family
Cyclobacteriaceae
, isolated from a haloalkaline lake and emended descriptions of the genera
Indibacter
,
Nitritalea
and
Belliella. Int J Syst Evol Microbiol 2012; 62:2252-2258. [DOI: 10.1099/ijs.0.038604-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, rod-shaped, non-motile bacterium, designated strain LW9T, was isolated from a water sample collected from Lonar Lake of Buldhana district, Maharashtra, India. Colonies and broth cultures were reddish orange due to the presence of carotenoid pigments. Strain LW9T was positive for catalase, ornithine decarboxylase and lysine decarboxylase activities and negative for gelatinase, oxidase, urease and lipase activities. The predominant fatty acids were iso-C15 : 0 (31.3 %), iso-C16 : 0 (9.3 %), anteiso-C15 : 0 (7.3 %), iso-C16 : 1 H (6.1 %), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c; 5.9 %), iso-C17 : 1ω9c (5.4 %) and iso-C17 : 0 3-OH (5.0 %). Strain LW9T contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and seven unidentified lipids. The DNA G+C content of strain LW9T was 40.5 mol%. 16S rRNA gene sequence analysis indicated that the type strains of
Indibacter alkaliphilus
and
Aquiflexum balticum
, two members of the family
Cyclobacteriaceae
(phylum ‘
Bacteroidetes
’) were the most closely related strains with sequence similarities of 93.0 and 94.0 %, respectively. Other members of the family
Cyclobacteriaceae
showed sequence similarities <93.0 %. Based on these phenotypic characteristics and on phylogenetic inference, strain LW9T is proposed as the representative of novel species in a new genus, Cecembia lonarensis gen. nov., sp. nov. The type strain of the type species, Cecembia lonarensis, is LW9T ( = CCUG 58316T = KCTC 22772T). Emended descriptions of the genera
Indibacter
,
Nitritalea
and
Belliella
are also proposed.
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Affiliation(s)
- P. Anil Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - T. N. R. Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - S. Madhu
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - R. Sravan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Shashi Singh
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - S. W. A. Naqvi
- National Institute of Oceanography, Dona Paula, Goa 403004, India
| | - S. Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160036, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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33
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Shivaji S, Reddy PVV, Rao SSSN, Begum Z, Manasa P, Srinivas TNR. Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment. Int J Syst Evol Microbiol 2012; 62:2133-2139. [DOI: 10.1099/ijs.0.038661-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of
Cyclobacterium amurskyense
,
Cyclobacterium marinum
and
Cyclobacterium lianum
were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family
Cyclobacteriaceae
had sequence similarities of <92.0 %. However, DNA–DNA hybridization with
Cyclobacterium amurskyense
KCTC 12363T and
Cyclobacterium marinum
DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus
Cyclobacterium
, for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.
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Affiliation(s)
- S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - P. Vishnu Vardhan Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - S. S. S. Nageshwara Rao
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - Zareena Begum
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - Poorna Manasa
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
| | - T. N. R. Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, Andhra Pradesh, India
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34
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Liu YP, Wang YX, Li YX, Feng FY, Liu HR, Wang J. Mongoliicoccus roseus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake. Int J Syst Evol Microbiol 2012; 62:2206-2212. [DOI: 10.1099/ijs.0.035766-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two pink, non-motile, aerobic, alkaliphilic, halotolerant, Gram-negative cocci, designated MIM28T and MIM29, were isolated from the surface water of a haloalkaline lake on the Mongolia Plateau. The isolates grew optimally at 30–33 °C, at pH 8–9 and with 3–4 % (w/v) NaCl. The isolates were chemoheterotrophic and could assimilate carbohydrates, organic acids and amino acids. The major respiratory quinone was menaquinone MK-7. The major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The predominant cellular fatty acids were iso-C15 : 0 (13.8–17.5 %), anteiso-C15 : 0 (10.5–11.2 %), iso-C16 : 0 (9.9–13.0 %), C16 : 0 (4.3–4.6 %), iso-C17 : 0 (3.8–5.3 %), anteiso-C17 : 0 (3.7–7.1 %), C17 : 1ω6c (4.6–6.4 %), iso-C17 : 0 3-OH (4.6–5.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 4.0–6.4 %) and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 10.4–12.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were most closely related to
Litoribacter ruber
YIM CH208T (93.6 % 16S rRNA gene sequence similarity), the genus
Echinicola
(90.4–92 %) and other members of the family
Cyclobacteriaceae
(87.8–90 %). The DNA G+C contents of strains MIM28T and MIM29 were 62.8 and 62.2 mol%. On the basis of morphology, physiology, fatty acid composition, phylogeny and 16S rRNA gene sequence analysis, the isolates are assigned to a novel species of a new genus, for which we propose the name Mongoliicoccus roseus gen. nov., sp. nov.; the type strain of the type species is MIM28T ( = ACCC 05511T = KCTC 19808T).
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Affiliation(s)
- Ya Peng Liu
- Institution for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, PR China
| | - Yong Xia Wang
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR China
| | - Yun Xu Li
- Institution for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, PR China
| | - Fu Ying Feng
- Institution for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, PR China
| | - Hui Rong Liu
- Institution for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, PR China
| | - Jia Wang
- Department of Preventive Medicine Public Health School, Inner Mongolia Medical College, Huhhot 010110, PR China
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35
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Albuquerque L, Tiago I, Nobre MF, Veríssimo A, da Costa MS. Cecembia calidifontis sp. nov., isolated from a hot spring runoff, and emended description of the genus Cecembia. Int J Syst Evol Microbiol 2012; 63:1431-1436. [PMID: 22843720 DOI: 10.1099/ijs.0.044537-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two red-pigmented isolates, designated RQ-33(T) and TU-13, were recovered from hot spring runoffs on the Island of São Miguel in the Azores, Portugal. These organisms have an optimum growth temperature of approximately 45 °C and an optimum pH for growth between 7.5 and 8.5. Based on 16S rRNA gene sequence analysis, the novel isolates were most closely related to the type strain of Cecembia lonarensis at 96.4 % pairwise similarity. Cells of the two isolates were non-motile, rod-shaped, Gram-stain-negative, strictly aerobic, and oxidase- and catalase-positive. The major fatty acids were iso-C15 : 0 and C15 : 0, phosphatidylethanolamine was the major polar lipid, and menaquinone 7 was the major respiratory quinone. Based on phylogenetic analyses, and physiological and biochemical characteristics, these isolates from the Azores represent a novel species of the genus Cecembia for which the name Cecembia calidifontis is proposed with strain RQ-33(T) ( = DSM 21411(T) = LMG 24596(T)) as the type strain. The description of the genus Cecembia is also emended.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Igor Tiago
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - António Veríssimo
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal.,Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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36
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P. AK, R. A, K. F, V. B, C. R, P. P, T. NS. Shivajiella indica gen. nov., sp. nov., a marine bacterium of the family “Cyclobacteriaceae” with nitrate reducing activity. Syst Appl Microbiol 2012; 35:320-5. [DOI: 10.1016/j.syapm.2012.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 03/28/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
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37
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Yang CX, Liu YP, Bao QH, Feng FY, Liu HR, Zhang XJ, Zhao YL. Mongoliitalea lutea gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a haloalkaline lake. Int J Syst Evol Microbiol 2012; 62:647-653. [DOI: 10.1099/ijs.0.031286-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial isolates from the surface water of a haloalkaline lake on the Mongolia Plateau, strains MIM18T and MIM19, were characterized; their morphological, physiological and chemotaxonomic characters, and phylogenetic position based on 16S rRNA gene sequences, were determined. The two strains were alkaliphilic, halotolerant, non-motile, aerobic, Gram-negative, orange-red, rod-shaped and oxidase-positive. Growth was observed in 0–5.5 % (w/v) NaCl, with optimum growth at 1 %. The temperature range for growth was 0–41 °C, with good growth at 28–37 °C and optimum growth at 30–33 °C. The DNA G+C content was 39.8–41.2 mol%. The strains contained menaquinone MK-7 as the major respiratory quinone and phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Predominant cellular fatty acids were iso-C15 : 0 (28.1–29.3 %), iso-C17 : 0 3-OH (14.6–18.8 %), C15 : 1ω6c (5.3–8.6 %), C14 : 0 2-OH and/or iso-C15 : 0 2-OH (5.4–6.1 %), and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (5.0–6.8 %). 16S rRNA gene sequence analysis showed that Belliella and Nitritalea of the family Cyclobacteriaceae were the closest related species with sequence similarities of 91.7–92.3 % and 88.2 %, respectively, with strains of these genera; other members of the Cyclobacteriaceae had sequence similarities lower than 88 %. Phylogenetic analysis indicated that the strains formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Nitritalea, Indibacter, Aquiflexum, Echinicola, Litoribacter, Cyclobacterium and Algoriphagus. Based on the phenotypic and phylogenetic characteristics mentioned above, the two strains are representatives of a single novel species in a new genus; the name Mongoliitalea lutea gen. nov., sp. nov. is proposed, with MIM18T ( = ACCC 05421T = KCTC 23224T) as the type strain.
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Affiliation(s)
- C. X. Yang
- Institution for Applied and Environmental Microbiology of Life Sciences College, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Y. P. Liu
- Institution for Applied and Environmental Microbiology of Life Sciences College, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Q. H. Bao
- Key Laboratory of Dairy Biotechnology and Engineer, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - F. Y. Feng
- Institution for Applied and Environmental Microbiology of Life Sciences College, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - H. R. Liu
- Institution for Applied and Environmental Microbiology of Life Sciences College, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - X. J. Zhang
- Institution for Applied and Environmental Microbiology of Life Sciences College, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Y. L. Zhao
- Institution for Applied and Environmental Microbiology of Life Sciences College, Inner Mongolia Agricultural University, Hohhot 010018, PR China
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38
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Abaydulla G, Luo X, Shi J, Peng F, Liu M, Wang Y, Dai J, Fang C. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2011; 101:725-31. [DOI: 10.1007/s10482-011-9686-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/11/2011] [Indexed: 10/14/2022]
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39
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Yoon J, Oku N, Park S, Katsuta A, Kasai H. Tunicatimonas pelagia gen. nov., sp. nov., a novel representative of the family Flammeovirgaceae isolated from a sea anemone by the differential growth screening method. Antonie van Leeuwenhoek 2011; 101:133-40. [PMID: 21789597 DOI: 10.1007/s10482-011-9626-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 07/14/2011] [Indexed: 11/29/2022]
Abstract
A Gram-negative, strictly aerobic, reddish-pink pigmented, non-motile, rod-shaped strain designated N5DB8-4(T), was isolated from an orange-striped sea anemone Diadumene lineata by a differential growth screening method. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flammeovirgaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (89.1%) to Porifericola rhodea N5EA6-3A2B(T). The strain could be differentiated phenotypically from recognized members of the family Flammeovirgaceae. The G+C content of the DNA is 52.6 mol%, the major respiratory quinone is menaquinone 7 (MK-7) and iso-C15:0, C16:1ω5c and iso-C15:1 G (the double-bond position indicated by capital letter is unknown) were the major fatty acids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain represents a novel taxon for which the name Tunicatimonas pelagia gen. nov., sp. nov. is proposed. The type strain of Tunicatimonas pelagia is N5DB8-4(T) (=KCTC 23473(T )= NBRC 107804(T)).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 2800 Dalgubeoldaero, Dalseo-Gu, Daegu, Republic of Korea.
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40
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Porifericola rhodea gen. nov., sp. nov., a new member of the phylum Bacteroidetes isolated by the bait-streaked agar technique. Antonie van Leeuwenhoek 2011; 100:145-53. [PMID: 21416335 DOI: 10.1007/s10482-011-9575-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/04/2011] [Indexed: 10/18/2022]
Abstract
A strictly aerobic, gram-negative, non-motile, reddish-pink pigmented, rod-shaped strain designated N5EA6-3A2B(T), was isolated from an unidentified marine sponge by use of a bait-streaked agar technique. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate represented a distinct and deep evolutionary lineage of descent in the family Flammeovirgaceae within the phylum Bacteroidetes and clustered with as yet uncultured bacteria. The most closely related established species was Roseivirga spongicola UST030701-084(T) (89% sequence similarity) in the family of Flammeovirgaceae. The strain could be differentiated phenotypically and physiologically from recognized members of the family Flammeovirgaceae. The G+C content of DNA was 43 mol%, the major respiratory quinone was menaquinone 7 (MK-7) and iso-C15:0, C16:1ω5c and iso-C17:0 3-OH were the major fatty acids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the name Porifericola rhodea gen. nov., sp. nov. is proposed. The type strain of Porifericola rhodea is N5EA6-3A2B(T) (=MBIC08357(T) = NBRC 107748(T)).
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41
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Tian SP, Wang YX, Hu B, Zhang XX, Xiao W, Chen Y, Lai YH, Wen ML, Cui XL. Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment. Int J Syst Evol Microbiol 2010; 60:2996-3001. [DOI: 10.1099/ijs.0.021626-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1
ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c; 10.7 %) and C17 : 1
ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).
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Affiliation(s)
- Shi-Ping Tian
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Xia Wang
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Bin Hu
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Wei Xiao
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yun Chen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Hong Lai
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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42
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Anil Kumar P, Srinivas TNR, Pavan Kumar P, Madhu S, Shivaji S. Nitritalea halalkaliphila gen. nov., sp. nov., an alkaliphilic bacterium of the family ‘Cyclobacteriaceae’, phylum Bacteroidetes. Int J Syst Evol Microbiol 2010; 60:2320-2325. [DOI: 10.1099/ijs.0.020230-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7T, was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids were dominated by large amounts of iso-C15 : 0 (59.6 %) and iso-C17 : 0 3-OH (8.9 %). Strain LW7T contained MK-4 and MK-5 as the major respiratory quinones and phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. 16S rRNA gene sequence analysis indicated that Belliella baltica, a member of family ‘Cyclobacteriaceae’ (phylum Bacteroidetes), is the closest related species, with a sequence similarity of 94.0 % to the type strain. Other members of the family ‘Cyclobacteriaceae’ had sequence similarities of <93.3 %. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain LW7T is proposed as a representative of a new genus and species, Nitritalea halalkaliphila gen. nov., sp. nov. The type strain of Nitritalea halalkaliphila is LW7T (=CCUG 57665T =JCM 15946T =NCCB 100279T). The genomic DNA G+C of strain LW7T is 49 mol%.
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Affiliation(s)
- P. Anil Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India
| | - T. N. R. Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India
| | - P. Pavan Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India
| | - S. Madhu
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India
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43
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Kämpfer P, Young CC, Chen WM, Rekha PD, Fallschissel K, Lodders N, Chou JH, Shen FT, Frischmann A, Busse HJ, Arun AB. Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring. Int J Syst Evol Microbiol 2010; 60:2066-2070. [DOI: 10.1099/ijs.0.017210-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1
ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, IFZ – Heinrich-Buff-Ring 26–32, D35392 Giessen, Germany
| | - Chiu-Chung Young
- Department of Soil Environmental Science, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - P. D. Rekha
- Yenepoya Research Center, Yenepoya University, Nityanada Nagar, Deralakatte, Mangalore 575 018, Karnataka, India
| | - Kerstin Fallschissel
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, IFZ – Heinrich-Buff-Ring 26–32, D35392 Giessen, Germany
| | - Nicole Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, IFZ – Heinrich-Buff-Ring 26–32, D35392 Giessen, Germany
| | - Jui-Hsing Chou
- Department of Soil Environmental Science, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Fo-Ting Shen
- Department of Soil Environmental Science, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Alexa Frischmann
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität Wien, Wien, Austria
| | - A. B. Arun
- Yenepoya Research Center, Yenepoya University, Nityanada Nagar, Deralakatte, Mangalore 575 018, Karnataka, India
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44
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Yoon JH, Kang SJ, Lee SY, Lee JS, Park S. Ohtaekwangia koreensis gen. nov., sp. nov. and Ohtaekwangia kribbensis sp. nov., isolated from marine sand, deep-branching members of the phylum Bacteroidetes. Int J Syst Evol Microbiol 2010; 61:1066-1072. [PMID: 20511453 DOI: 10.1099/ijs.0.025874-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strains, designated 3B-2(T) and 10AO(T), were isolated from a sand sample collected from the west coast of the Korean peninsula by using low-nutrient media, and their taxonomic positions were investigated in a polyphasic study. The strains did not grow on marine agar. They grew optimally at 30 °C and pH 6.5-7.5. Strains 3B-2(T) and 10AO(T) shared 97.5 % 16S rRNA gene sequence similarity and mean level of DNA-DNA relatedness of 12 %. In phylogenetic trees based on 16S rRNA gene sequences, strains 3B-2(T) and 10AO(T), together with several uncultured bacterial clones, formed independent lineages within the evolutionary radiation encompassed by the phylum Bacteroidetes. Strains 3B-2(T) and 10AO(T) contained MK-7 as the predominant menaquinone and iso-C(15 : 0) and C(16 : 1)ω5c as the major fatty acids. The DNA G+C contents of strains 3B-2(T) and 10AO(T) were 42.8 and 44.6 mol%, respectively. Strains 3B-2(T) and 10AO(T) exhibited very low levels of 16S rRNA gene sequence similarity (<85.0 %) to the type strains of recognized bacterial species. These data were sufficient to support the proposal that the novel strains should be differentiated from previously known genera of the phylum Bacteroidetes. On the basis of the data presented, we suggest that strains 3B-2(T) and 10AO(T) represent two distinct novel species of a new genus, for which the names Ohtaekwangia koreensis gen. nov., sp. nov. (the type species; type strain 3B-2(T) = KCTC 23018(T) = CCUG 58939(T)) and Ohtaekwangia kribbensis sp. nov. (type strain 10AO(T) = KCTC 23019(T) = CCUG 58938(T)) are proposed.
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Soo-Young Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Sooyeon Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
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45
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Anil Kumar P, Srinivas TNR, Madhu S, Manorama R, Shivaji S. Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake. Int J Syst Evol Microbiol 2010. [DOI: 10.1099/ijs.0.014076-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, non-motile bacterium, strain LW1T, was isolated from a water sample collected at a depth of 3.5 m from Lonar Lake, Buldhana district, Maharashtra, India. The cell suspension was reddish-orange due to the presence of carotenoids. Strain LW1T was positive for catalase, oxidase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase, urease and lipase. Fatty acids were dominated by branched-chain fatty acids (>76 %), with a high abundance of iso-C15 : 0 (48 %), anteiso-C15 : 0 (7 %) and iso-C17 : 0 3-OH (11 %). Strain LW1T contained MK-4 and MK-7 as the major respiratory quinones and phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as the major phospholipids. A blast sequence similarity search based on 16S rRNA gene sequences indicated that members of the genera Belliella and Aquiflexum were the nearest phylogenetic neighbours with similarities of 91.8–92.3 %. Phylogenetic analyses indicated that strain LW1T formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Aquiflexum, Cyclobacterium, Echinicola and Algoriphagus. Based on the above-mentioned phenotypic and phylogenetic characteristics, it is proposed that strain LW1T represents a novel species in a new genus, Indibacter alkaliphilus gen. nov., sp. nov. (type strain LW1T=KCTC 22604T=CCUG 57479T). The genomic DNA G+C content of strain LW1T is 42.7±1 mol%.
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Affiliation(s)
- P. Anil Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - T. N. R. Srinivas
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - S. Madhu
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - R. Manorama
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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46
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Sahu AK, Conneely T, Nüsslein K, Ergas SJ. Hydrogenotrophic denitrification and perchlorate reduction in ion exchange brines using membrane biofilm reactors. Biotechnol Bioeng 2009; 104:483-91. [DOI: 10.1002/bit.22414] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Liu QM, Ten LN, Yu HS, Jin FX, Im WT, Lee ST. Emticicia ginsengisoli sp. nov., a species of the family 'Flexibacteraceae' isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008; 58:1100-5. [DOI: 10.1099/ijs.0.65386-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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48
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Yoon J, Ishikawa S, Kasai H, Yokota A. Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family ‘Flexibacteraceae’, isolated from seawater in Japan. Int J Syst Evol Microbiol 2007; 57:1014-1017. [PMID: 17473250 DOI: 10.1099/ijs.0.64792-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately aerobic, Gram-negative, non-motile, pale-pink-pigmented, rod-shaped strain, designated Shu-9-SY12-35CT, was isolated from seawater in Jodogahama, Iwate, Japan, and was subjected to a polyphasic taxonomic examination. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family ‘Flexibacteraceae’ of the phylum Bacteroidetes and that it showed highest sequence similarity (86.4 %) with Dyadobacter hamtensis HHS 11T. The novel isolate is phenotypically and physiologically different from strains described previously. The G+C content of the DNA was 56.3 mol%, MK-7 was the major menaquinone and iso-C15 : 0, C16 : 1
ω7c and iso-C17 : 0 3-OH were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain Shu-9-SY12-35CT represents a new genus and species of the family ‘Flexibacteraceae’, for which the name Persicitalea jodogahamensis gen. nov., sp. nov. is proposed. The type strain of Persicitalea jodogahamensis is Shu-9-SY12-35CT (=MBIC07417T=IAM 15412T=KCTC 12866T).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- Cytophagaceae/chemistry
- Cytophagaceae/classification
- Cytophagaceae/isolation & purification
- Cytophagaceae/physiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA/genetics
- Japan
- Microscopy, Phase-Contrast
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Vitamin K 2/analysis
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Affiliation(s)
- Jaewoo Yoon
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Shu Ishikawa
- Marine Biotechnology Institute Co. Ltd, 3-75-1, Heita, Kamaishi, Iwate 026-0001, Japan
| | - Hiroaki Kasai
- Marine Biotechnology Institute Co. Ltd, 3-75-1, Heita, Kamaishi, Iwate 026-0001, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
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49
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Zhou Y, Wang X, Liu H, Zhang KY, Zhang YQ, Lai R, Li WJ. Pontibacter akesuensis sp. nov., isolated from a desert soil in China. Int J Syst Evol Microbiol 2007; 57:321-325. [PMID: 17267972 DOI: 10.1099/ijs.0.64716-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, rod-shaped bacterium, designated strain AKS 1T, was isolated from a desert soil sample collected from Akesu, XinJiang Province, China. A taxonomic study, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was performed on the novel isolate. The predominant menaquinone of strain AKS 1T was MK-7. The major fatty acids included i-C15 : 0, ai-C17 : 1 B/i-C17 : 1 I and i-C17 : 0 3-OH. The G+C content of the DNA was 51.4 mol%. Based on the results of phenotypic and genotypic characteristics, strain AKS 1T should be assigned as representing a novel species of the genus Pontibacter, for which the name Pontibacter akesuensis is proposed. The type strain is AKS 1T (=KCTC 12758T=CCTCC AB 206086T).
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MESH Headings
- Base Composition
- China
- Cytophagaceae/classification
- Cytophagaceae/cytology
- Cytophagaceae/isolation & purification
- Cytophagaceae/physiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Desert Climate
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Phylogeny
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- Yu Zhou
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Xu Wang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Huan Liu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Ke-Yun Zhang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology and Yunnan University, Kunming, Yunnan 650091, People's Republic of China
| | - Ren Lai
- Biotoxin Department of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, People's Republic of China
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Wen-Jun Li
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology and Yunnan University, Kunming, Yunnan 650091, People's Republic of China
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50
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Ying JY, Wang BJ, Yang SS, Liu SJ. Cyclobacterium lianum sp. nov., a marine bacterium isolated from sediment of an oilfield in the South China Sea, and emended description of the genus Cyclobacterium. Int J Syst Evol Microbiol 2006; 56:2927-2930. [PMID: 17159000 DOI: 10.1099/ijs.0.64510-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The marine bacterial strain HY9T was isolated from sediment from the South China Sea. Strain HY9T is aerobic, heterotrophic and rose-pigmented. The cells are non-motile and curved, i.e. ring-like or horseshoe-shaped. The 16S rRNA gene sequence of strain HY9T was determined and blast searches revealed that it possessed significant sequence similarities with respect to Cyclobacterium species (92.8–93.6 %). Phylogenetic analysis confirmed that strain HY9T was tightly clustered with members of the genus Cyclobacterium. The cellular morphology and chemotaxonomic and phenotypic properties of strain HY9T showed that it should be classified as a member of the genus Cyclobacterium. Significant evolutionary distances and a range of phenotypic features distinguished strain HY9T from previously described Cyclobacterium species. Hence, strain HY9T represents a novel species in the genus Cyclobacterium, for which the name Cyclobacterium lianum sp. nov. is proposed. The type strain is HY9T (=CGMCC 1.6102T=JCM 14011T). On the basis of this study and previously described properties of Cyclobacterium species, an emended description of the genus Cyclobacterium is proposed.
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Affiliation(s)
- Jiao-Yan Ying
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, People's Republic of China
- College of Biological Sciences, China Agricultural University, Beijing 100094, People's Republic of China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, People's Republic of China
| | - Su-Sheng Yang
- College of Biological Sciences, China Agricultural University, Beijing 100094, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, People's Republic of China
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