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Yang C, Bai Y, Dong K, Yang J, Lai XH, Lu S, Zhang G, Cheng Y, Jin D, Zhang S, Lv X, Huang Y, Xu J. Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. isolated from wild animals and reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively. Int J Syst Evol Microbiol 2021; 71. [PMID: 33560201 DOI: 10.1099/ijsem.0.004696] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-stain-positive, catalase-negative, non-spore-forming, rod-shaped bacterial strains (zg-325T, zg329, dk561T and dk752) were isolated from the respiratory tract of marmot (Marmota himalayana) and the faeces of Tibetan gazelle (Procapra picticaudata) from the Qinghai-Tibet Plateau of PR China. The results of 16S rRNA gene sequence-based phylogenetic analyses indicated that strains zg-325T and dk561T represent members of the genus Actinomyces, most similar to Actinomyces denticolens DSM 20671T and Actinomyces ruminicola B71T, respectively. The DNA G+C contents of strains zg-325T and dk561T were 71.6 and 69.3 mol%, respectively. The digital DNA-DNA hybridization values of strains zg-325T and dk561T with their most closely related species were below the 70 % threshold for species demarcation. The four strains grew best at 35 °C in air containing 5 % CO2 on brain heart infusion (BHI) agar with 5 % sheep blood. All four strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-8 and MK-9 were the major menaquinones in zg-325T while MK-10 was predominant in dk561T. The major polar lipids included diphosphatidylglycerol and phosphatidylinositol. On the basis of several lines of evidence from phenotypic and phylogenetic analyses, zg-325T and dk561T represent novel species of the genus Actinomyces, for which the name Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. are proposed. The type strains are zg-325T (=GDMCC 1.1724T=JCM 34091T) and dk561T (=CGMCC 4.7566T=JCM 33484T). We also propose, on the basis of the phylogenetic results herein, the reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively.
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Affiliation(s)
- Caixin Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Yibo Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Kui Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yanpeng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Xianglian Lv
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- Institute of Public Health, Nankai University, Tianjin, PR China
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Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME, Holmes B, Steigerwalt AG, Villarma A, Sheth M, Batra D, Rowe LA, Burroughs M, Pryor JC, Bernardet JF, Hugo C, Kämpfer P, Newman JD, McQuiston JR. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432-4450. [PMID: 32735208 PMCID: PMC7660247 DOI: 10.1099/ijsem.0.003935] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/28/2019] [Accepted: 12/02/2019] [Indexed: 01/10/2023] Open
Abstract
The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.
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Affiliation(s)
- Ainsley C. Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher A. Gulvik
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Anne M. Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Ben W. Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Melissa E. Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Barry Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - Arnie G. Steigerwalt
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Aaron Villarma
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Lori A. Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Mark Burroughs
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jessica C. Pryor
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jean-François Bernardet
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Domaine de Vilvert, Jouy-en-Josas, France
| | - Celia Hugo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Jeffrey D. Newman
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- Biology Department, Lycoming College, Williamsport PA 17701, USA
| | - John R. McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Huang Y, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Huang Y, Ren Z, Zhu W, Meng J, Dong K, Ge Y, Zhou J, Zhang G, Zhang S, Lei W, Liang H, Xu J. Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces. Int J Syst Evol Microbiol 2019; 69:3629-3635. [PMID: 31511125 DOI: 10.1099/ijsem.0.003674] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, irregular rod-shaped (0.2-0.5×1.3-2.5 um) strains, HY056T and HY057, were isolated from the faeces of Equus kiang (the largest of the wild asses) collected at different regions from the Qinghai-Tibetan Plateau of PR China. Phylogenetic analyses indicated that strains HY056T and HY057 belong to the genus Nocardioides by sharing a similarity ranging from 96.3 to 97.0 % in the 16S rRNA gene sequence and forming a distinct cluster with Nocardioides daphniae JCM 16608T, Nocardioides houyundeii 78T, Nocardioides solisilvae Ka25T and Nocardioides gilvus XZ17T. The digital DNA-DNA hybridization value of strain HY056T was 96.9 % with strain HY057, but less than 30.0 % with the above four closest relatives. MK-8(H4) was the predominant (91.6 %) respiratory quinone. The cell wall contained ll-2,6-diaminopimelic acid as the diamino acid of the peptidoglycan. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phospholipid. The predominant fatty acids (>10.0 %) were C18 : 1ω9c and iso-C16:0. The DNA G+C contents of strains HY056T and HY057 were 68.9 and 69.1 mol%, respectively. β-Glucosidase expression was positive, and acid was produced from d-fructose. Strain HY056T (=CGMCC 4.7563T=JCM 33399T) is assigned as the type strain of a novel species within the genus Nocardioides, for which the name Nocardioidesyefusunii sp. nov is proposed.
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Xiaoxia Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Zhihong Ren
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Wentao Zhu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Jiajia Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Kui Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Yajun Ge
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Wenjing Lei
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Jianguo Xu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
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Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Wang XX, Wu XM, Li J, Wang S, Xu J. Roseomonas wenyumeiae sp. nov., isolated from faeces of Tibetan antelopes ( Pantholops hodgsonii) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2019; 69:2979-2986. [PMID: 31145678 DOI: 10.1099/ijsem.0.003479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic, motile, flagellated, and coccus-shaped strains (Z23T and Z24) were isolated from faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai-Tibet Plateau, PR China. Results of the morphological, biochemical, and phylogenetic studies indicated that they were similar to each other, but distinct from existing species of the genus Roseomonas. The proposed type strain, Z23T, had 97.8, 97.1 and 96.8 % 16S rRNA similarity to Roseomonas ludipueritiae DSM 14915T, Roseomonas aerofrigidensis JCM 31878T and Roseomonas aerophila KACC 16529T. Results from further phylogenetic analyses based on the 16S rRNA gene and 857 core genes indicated that the two strains were members of Roseomonas, but clearly separated from the currently recognized species. Strains Z23T had 43.8 %, 25.0 % DNA-DNA relatedness and 91.2, 81.3 % ANI values with R. ludipueritiae DSM 14915T and R. aerophila KACC 16529T. The genomic DNA G+C content of strain Z23T was 68.6 mol%. The major cellular fatty acids of strain Z23T were C18 : 1ω7c and/or C18 : 1ω6c and C19 : 0cyclo ω8c. The cell-wall sugars included glucose, rhamnose and ribose. Q-10 was the sole respiratory quinone, and spermidine was the major polyamine component. Polar lipids present in strain Z23T were phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, three aminolipids, two phospholipids and two unidentified lipids. Based on the distinct differences from other Roseomonas species judged from the genotypic and phenotypic data, a novel species represented by Z23T and Z24, Roseomonas wenyumeiae sp. nov., is proposed. The type strain is Z23T (=CGMCC 1.16540T=DSM 106207T).
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Affiliation(s)
- Zhi Tian
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China
| | - Xiao-Xia Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xiao-Min Wu
- Shaanxi Institute of Zoology, Xi'an, Shanxi 710032, PR China
| | - Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Jianguo Xu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
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5
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Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Bai XN, Wu XM, Li J, Wang S, Xu J. Streptococcus chenjunshii sp. nov. isolated from feces of Tibetan antelopes. Int J Syst Evol Microbiol 2019; 69:1237-1243. [PMID: 30785389 DOI: 10.1099/ijsem.0.003303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Three Gram-stain-positive, catalase-negative, α-haemolytic, chain-forming and coccus-shaped microorganisms (strains Z15T, Z1 and Z2) were isolated from feces of Tibetan antelopes collected from the Qinghai-Tibet plateau, PR China. The results of 16S rRNA gene sequence studies indicated that Z15T shared 94.5, 93.1 and 92.2 % similarity with Streptococcus pantholopis DSM 102135T, Streptococcus ursoris NUM 1615T and Streptococcus dentapri NUM 1529T, respectively. rpoB and groEL-based sequence analysis of our three novel isolates revealed interspecies divergence of 16.7 and 14.3 % from Streptococcus pantholopis DSM 102135T. The genomic DNA G+C content of Z15T is 42.48 mol%. Z15T has an average nucleotide identity (ANI) value of 81.19 % with S. pantholopis DSM 102135T and a DNA-DNA relatedness value of less than 70 % in the in-silico DNA-DNA hybridization (isDDH) with other species of genus Streptococcus deposited in the GenBank database. A whole-genome phylogenetic tree based on 246 core genes of 78 genomes of members of the genus Streptococcusindicated that Z15T represents a member of genus Streptococcus but one well separated from the currently recognized species. Z15T contains C18 : 1ω7c (25.5 %), C18 : 1ω9c (19.6 %), C16 : 0 (17.5 %) and C16 : 1ω9c (13.3 %) as its major cellular fatty acids. According to the morphological, biochemical and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus, and Streptococcus chenjunshii sp. nov. is thus proposed. The type strain is Z15T (=CGMCC 1.16529=DSM 106182).
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Affiliation(s)
- Zhi Tian
- Department of Epidemiology, Shanxi Medical University School of Public Health, Shanxi 030001, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Henan 476000, PR China
| | - Xiang-Ning Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Xiao-Min Wu
- Shaanxi Institute of Zoology, Shanxi 710032, PR China
| | - Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Shanxi 030001, PR China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Shanxi 030001, PR China
| | - Jianguo Xu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Department of Epidemiology, Shanxi Medical University School of Public Health, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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6
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Dong X, Zhang G, Xiong Q, Liu D, Wang D, Liu Y, Wu G, Li P, Luo Y, Zhang R. Paracoccus salipaludis sp. nov., isolated from saline–alkaline soil. Int J Syst Evol Microbiol 2018; 68:3812-3817. [DOI: 10.1099/ijsem.0.003065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xiaoyan Dong
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Guishan Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qin Xiong
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Di Liu
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Dandan Wang
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yunpeng Liu
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Gengwei Wu
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Pan Li
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yu Luo
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ruifu Zhang
- 1Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic–based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Zhou MY, Zhang YJ, Zhang XY, Yang XD, He HL, Ning D, Du Z. Flavobacterium phocarum sp. nov., isolated from soils of a seal habitat in Antarctica. Int J Syst Evol Microbiol 2017; 68:536-541. [PMID: 29251588 DOI: 10.1099/ijsem.0.002535] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, yellow-pigmented, non-flagellated, gliding, rod-shaped, oxidase-negative and catalase-positive bacterium, designated SE14T, was isolated from soil on King George Island, South Shetland Islands, Antarctica. Strain SE14T grew at 4-25 °C (optimum, 20 °C), at pH 6.0-9.0 (optimum, pH 7.0-7.5) and with 0-3.0 % NaCl (optimum, 1.0-1.5 %), and could not produce flexirubin-type pigments. 16S rRNA gene sequence analysis showed the the isolate belonged to the genus Flavobacterium. Strain SE14T had the highest 16S rRNA gene sequence similarity to Flavobacterium antarcticum, F. tegetincola and F. degerlachei with 95.8, 95.5 and 95.2 %, respectively. The strain SE14T consisted of a clade with Flavobacteriumnoncentrifugens (16S rRNA gene sequence similarity 94.9 %) and F. qiangtangense (16S rRNA gene sequence similarity 94.2 %) and simultaneously formed a distinct phyletic lineage in the neighbour-joining phylogenetic tree. Polar lipids of the strain included phosphatidylethanolamine and four unidentified aminolipids. Strain SE14T contained anteiso-C15 : 0, iso-C15 : 0 and a mixture of iso-C15 : 0 2-OH and/or C16 : 1ω7c as the main fatty acids, and the only respiratory quinone was menaquinone-6. The genomic DNA G+C content was 42.3 mol%. The polyphasic taxonomic study revealed that strain SE14T belongs to a novel species within the genus Flavobacterium , and the name Flavobacterium phocarum sp. nov. is proposed. The type strain is SE14T (=CCTCC AB 2017225T=KCTC 52612T).
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Affiliation(s)
- Ming-Yang Zhou
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, PR China
| | - Yan-Jiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Xiao-Deng Yang
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, PR China
| | - Hai-Lun He
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, PR China
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, USA
| | - Zongjun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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8
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Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 2017; 33:3396-3404. [PMID: 29036289 PMCID: PMC5860169 DOI: 10.1093/bioinformatics/btx440] [Citation(s) in RCA: 348] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Bacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses. RESULTS We here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families. AVAILABILITY AND IMPLEMENTATION The selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de. CONTACT jan.meier-kolthoff@dsmz.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jan P Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl U. Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea. Int J Syst Evol Microbiol 2017; 67:4624-4631. [PMID: 29022541 DOI: 10.1099/ijsem.0.002344] [Citation(s) in RCA: 16] [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
Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae, designated ZGT108T and ZGT118T, were isolated from the brine-seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108T and ZGT118T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108T to its closest relative, Ruegeria conchae JCM 17315T, was 98.9 %, while the 16S rRNA gene of ZGT118T was most closely related to that of Ruegeria intermedia LMG 25539T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108T) and 4 012 109 bp (strain ZGT118T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108T) and 62.94 mol% (ZGT108T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria. This was also confirmed by low DNA-DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeriaprofundi sp. nov. (type strain ZGT108T=JCM 19518T=ACCC 19861T) and Ruegeriamarisrubri sp. nov. (type strain ZGT118T=JCM 19519T=ACCC 19862T).
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Affiliation(s)
- Guishan Zhang
- Red Sea Research Center, King Abdulah University of Science and Technology, Thuwal Jeddah 23955-6900, Saudi Arabia.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mohamed Fauzi Haroon
- Red Sea Research Center, King Abdulah University of Science and Technology, Thuwal Jeddah 23955-6900, Saudi Arabia
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoyan Dong
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Dandan Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Weibing Xun
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ulrich Stingl
- Red Sea Research Center, King Abdulah University of Science and Technology, Thuwal Jeddah 23955-6900, Saudi Arabia.,University of Florida, UF/IFAS, Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, Davie, FL 33314, USA
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10
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Zhang G, Haroon MF, Zhang R, Dong X, Liu D, Xiong Q, Xun W, Dong X, Stingl U. Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae. Int J Syst Evol Microbiol 2017; 67:4358-4364. [PMID: 28984559 DOI: 10.1099/ijsem.0.002280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol%. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).
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Affiliation(s)
- Guishan Zhang
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mohamed Fauzi Haroon
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Ruifu Zhang
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoyan Dong
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Di Liu
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qin Xiong
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Weibing Xun
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ulrich Stingl
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
- Department of Microbiology and Cell Science, University of Florida, Institute for Food and Agricultural Sciences (IFAS), Fort Lauderdale Research and Education Center, Fort Lauderdale (Davie), FL33314, USA
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11
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Zhou MY, Zhang XY, Yang XD, Zhang YJ, He HL, Ning D. Flavobacterium ardleyense sp. nov., isolated from Antarctic soil. Int J Syst Evol Microbiol 2017; 67:3996-4001. [DOI: 10.1099/ijsem.0.002241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ming-Yang Zhou
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan 250353, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Xiao-Deng Yang
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan 250353, PR China
| | - Yan-Jiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Hai-Lun He
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, PR China
| | - Daling Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Oklahoma, USA
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12
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Wang Y, Zhang H, Zhao C, Han Y, Liu Y, Zhang X. Isolation and characterization of a novel deoxynivalenol-transforming strainParadevosia shaoguanensisDDB001 from wheat field soil. Lett Appl Microbiol 2017; 65:414-422. [DOI: 10.1111/lam.12790] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/14/2017] [Accepted: 08/04/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Y. Wang
- Academy of State Administration of Grain; Beijing China
| | - H.H. Zhang
- Academy of State Administration of Grain; Beijing China
| | - C. Zhao
- Academy of State Administration of Grain; Beijing China
| | - Y.T. Han
- Academy of State Administration of Grain; Beijing China
| | - Y.C. Liu
- Academy of State Administration of Grain; Beijing China
| | - X.L. Zhang
- Academy of State Administration of Grain; Beijing China
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13
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Pechar R, Killer J, Salmonová H, Geigerová M, Švejstil R, Švec P, Sedláček I, Rada V, Benada O. Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). Int J Syst Evol Microbiol 2017; 67:2349-2356. [DOI: 10.1099/ijsem.0.001956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - P. Švec
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - I. Sedláček
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústi nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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14
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Zhao JJ, Zhang J, Sun L, Zhang RJ, Zhang CW, Yin HQ, Zhang XX. Rhizobium oryziradicis sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2017; 67:963-968. [PMID: 27959784 DOI: 10.1099/ijsem.0.001724] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, rod-shaped endophytic bacterial strains, N19T and N11-2, were isolated from fresh rice (Oryza sativa) roots during investigation of the rice endophytic bacterial diversity. The 16S rRNA gene sequence results indicated that the similarity between strains N19T and N11-2 was 100 %. Both of them belong to the genus Rhizobium, with close similarity to Rhizobium taibaishanense CCNWSX 0483T (97.7 %), followed by Rhizobium vitis NCPPB 3554T (97.5 %). The sequence similarities of the housekeeping genes recA, gyrB and glnA between the novel isolates and members of the established species of the genus Rhizobium were less than 87 %. The DNA-DNA hybridization rates between strains N19T and N11-2 were 87.9 % using the initial renaturation rate method. Based on draft genome sequences, strain N19T showed 18.2 % and 19.6 % DNA-DNA hybridization values to R. taibaishanense CCNWSX 0483T and R. vitis S4, which demonstrated that these new isolates represent a novel species in the genus Rhizobium. The main cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of strain N19T was 58.7 mol% (Tm). The polar lipid profile of N19T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown lipid, two unknown aminolipids and an unidentified aminophospholipid. According to physiological and biochemical characteristics and genotypic data, strains N19T and N11-2 are considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium oryziradicis sp. nov. is proposed, with N19T (=ACCC 19962T=KCTC 52413T) as the type strain.
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Affiliation(s)
- Juan-Juan Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lei Sun
- College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Rui-Jie Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Cai-Wen Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Microbacterium zeae sp. nov., an endophytic bacterium isolated from maize stem. Antonie Van Leeuwenhoek 2017; 110:697-704. [PMID: 28176143 DOI: 10.1007/s10482-017-0837-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
A novel Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped strain designated 1204T was isolated from surface-sterilised stem tissue of maize planted in Fangshan District of Beijing, People's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Microbacterium. High levels of 16S rRNA gene sequence similarity were found between strain 1204T and Microbacterium enclense NIO-1002T (98.8%) and Microbacterium proteolyticum RZ36T (98.4%) respectively. However, the DNA-DNA hybridization values between strain 1204T and its closely related species M. proteolyticum DSM 27100T and M. enclense DSM 25125T were 53.9 ± 1.6 and 20.9 ± 1.5% respectively. The DNA G+C content of strain 1204T was determined to be 68.0 mol%. The major fatty acids were found to consist of anteiso-C15:0 (37.6%), iso-C16:0 (28.6%) and anteiso-C17:0 (16.6%). The predominant menaquinone was MK-11 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The results of physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 1204T from the closely related species in the genus Microbacterium. Thus, it was concluded that strain 1204T represents a novel species within the genus Microbacterium, for which the name Microbacterium zeae sp. nov. is proposed, with the type strain 1204T (= CGMCC 1.15289 = DSM 100750).
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Zhao JJ, Zhang J, Zhang RJ, Zhang CW, Yin HQ, Zhang XX. Rhizobium rhizosphaerae sp. nov., a novel species isolated from rice rhizosphere. Antonie van Leeuwenhoek 2017; 110:651-656. [PMID: 28154946 DOI: 10.1007/s10482-017-0831-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022]
Abstract
Two novel, Gram-negative, motile, rod-shaped, aerobic bacterial strains, MH17T and RD15, were isolated from the sterilized root and rhizosphere soil of rice, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the similarity between strains MH17T and RD15 was 100%. The isolates exhibit high sequence similarities to Rhizobium oryzae CGMCC 1.7048T (98.7%) and Rhizobium petrolearium SL-1T (97.0% and 97.1%), which supports that they belong to a novel species in the genus Rhizobium. Strains MH17T and RD15 exhibited growth at 15-45 °C, pH 5.0-11.0, 0-2.0% sodium chloride (w/v). Sequence analysis of housekeeping genes gyrB, recA, atpD, ropB, gltA showed that these two novel strains had less than 94% similarity with the known species, indicating the distinct position of MH17T and RD15 in the genus Rhizobium. The major cellular fatty acids were identified as summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Type strain MH17T had 87.5% DNA-DNA relatedness with RD15 by using the initial renaturation rate method. Based on draft genome sequences, strain MH17T showed 30.1% DNA-DNA hybridization values to R. oryzae CGMCC 1.7048T, the closely related strain, which supported that MH17T represents a novel species in the genus Rhizobium. Average nucleotide identity (ANI) between strains MH17T and RD15 were 97.8%, and strain MH17T showed 82.2% ANI value with R. oryzae CGMCC 1.7048T. The DNA G+C content was 60.4 mol% (Tm). Based on physiological, biochemical characteristic, genotypic data, strains MH17T and RD15 are concluded to represent a new species within the genus Rhizobium, for which the name Rhizobium rhizosphaerae sp. nov. is proposed. The type strain is MH17T (=ACCC 19963T = KCTC 52414T).
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Affiliation(s)
- Juan-Juan Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Jun Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Rui-Jie Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Cai-Wen Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, People's Republic of China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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17
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Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JG. Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:4022-4026. [PMID: 27412002 DOI: 10.1099/ijsem.0.001304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated 65T, was isolated from surface-sterilized root tissue of maize, collected from Fangshan District of Beijing, People's Republic of China, and was subjected to a taxonomic study by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 65T belonged to the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter jiangsuensis CGMCC 1.12969T (99.1 %), Dyadobacter beijingensis CGMCC 1.6375T (98.8 %), Dyadobacter fermentans DSM 18053T (98.6 %) and Dyadobacter soli KCTC 22481T (98.6 %). However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to D. jiangsuensis CGMCC 1.12969T (18.2±1.3 %), D. beijingensis CGMCC 1.6375T (14.2±2.0 %), D. fermentans DSM 18053T (14.1±2.0 %) and D. soli KCTC 22481T (13.8±0.6 %). The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω5c, iso-C15 : 0 3-OH, C16 : 0 3-OH and C16 : 0. The polar lipid profile of strain 65T revealed the presence of phosphatidylethanolamine, four aminolipids and two unidentified phospholipids. The DNA G+C content was 46.6 mol%. The results of physiological and biochemical tests and the differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 65T from closely related species of the genus Dyadobacter. Strain 65T thus represents a novel species within the genus Dyadobacter, for which the name Dyadobacterendophyticus sp. nov. is proposed. The type strain is 65T (=CGMCC 1.15288T=DSM 100786T).
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Affiliation(s)
- Jun-Lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Pengbo Sun
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xu-Ming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Tian-Lei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Fan-Yang Lv
- Key Laboratory of Microbial Resource, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mei Yuan
- Key Laboratory of Microbial Resource, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ming-Ming Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resource, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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18
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Bai X, Xiong Y, Lu S, Jin D, Lai X, Yang J, Niu L, Hu S, Meng X, Pu J, Ye C, Xu J. Streptococcuspantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2016; 66:3281-3286. [PMID: 27226124 DOI: 10.1099/ijsem.0.001189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as representing a novel streptococcal species based on their morphological features, biochemical test results and phylogenomic findings. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the unknown coccus was Streptococcus ursoris NUM 1615T (93.4 % 16S rRNA gene sequence similarity). Analysis of groEL and rpoB gene sequences of the novel isolates showed interspecies divergence of 27.0 and 22.2 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. ursoris. The complete genome of strain TA 26T has been sequenced. Digital DNA-DNA hybridization studies between strain TA 26T and other species of the genus Streptococcus deposited in the GenBank database showed less than 70 % DNA-DNA relatedness, supporting a novel species status of the strain. On the basis of their genotypic and phenotypic differences from recognized Streptococcus species, the two isolates represent a novel species of the genus Streptococcus, for which the nameStreptococcus pantholopis sp. nov. (type strain TA 26T=CGMCC 1.15667T=DSM 102135T) is proposed.
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Affiliation(s)
- Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Xinhe Lai
- Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China.,Institute of Inflammation and Diseases, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Lina Niu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China.,School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou, PR China
| | - Shoukui Hu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Xiangli Meng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
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19
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Gao JL, Lv FY, Wang XM, Qiu TL, Yuan M, Li JW, Zhou Y, Sun JG. Paenibacillus wenxiniae sp. nov., a nifH gene -harbouring endophytic bacterium isolated from maize. Antonie van Leeuwenhoek 2015; 108:1015-22. [PMID: 26346477 DOI: 10.1007/s10482-015-0554-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/11/2015] [Indexed: 11/25/2022]
Abstract
A novel Gram-positive, aerobic, motile, endospore-forming, rod-shaped bacterium, designated 373(T) was isolated from surface-sterilised root tissue of a maize planted in Fangshan District of Beijing, Peopole's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Paenibacillus. The highest 16S rRNA gene sequence similarity was found between strain 373(T) and Paenibacillus hunanensis (98.1%), meanwhile the 16S rRNA gene sequence similarity between strain 373(T) and the type strains of other recognised members of the genus Paenibacillus were all below 95.6%. However, the DNA-DNA hybridization values between strain 373(T) and the type strain P. hunanensis DSM 22170(T) was 30.2%. The DNA G+C content of strain 373(T) was determined to be 46.0 mol%. The predominant respiratory quinone was identified as menaquinone-7 and the polar lipid profile was found to be composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were found to consist of anteiso-C15: 0 (59.6%), anteiso-C17: 0 (12.8%) and C16: 0 (6.7%). The results of physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 373(T) from the closely related species in this genus Paenibacillus. Strain 373(T) is concluded to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus wenxiniae sp. nov. is proposed, with the type strain 373(T) (= CGMCC 1.15007 (T) = DSM100576 ).
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Affiliation(s)
- Jun-lian Gao
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Fan-yang Lv
- Key Laboratory of Microbial Resources, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xu-ming Wang
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Tian-lei Qiu
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Mei Yuan
- Key Laboratory of Microbial Resources, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Ji-wei Li
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People's Republic of China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, People's Republic of China
| | - Yi Zhou
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People's Republic of China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, People's Republic of China
| | - Jian-guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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20
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Qiu T, Zuo Z, Gao J, Gao M, Han M, Sun L, Zhang L, Wang X. Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms. Int J Syst Evol Microbiol 2015; 65:2913-2918. [DOI: 10.1099/ijs.0.000353] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain, designated SL-205T, was isolated from the biofilms of a denitrifying reactor using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in Beijing, PR China. A polyphasic taxonomic characterization was performed on the novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain SL-205T is a member of the genus Diaphorobacter. High levels of 16S rRNA gene sequence similarity were found between strain SL-205T and Diaphorobacter nitroreducens NA10BT (99.4 %) and Diaphorobacter oryzae RF3T (98.5 %), respectively. However, the DNA–DNA relatedness values between strain SL-205T and D. nitroreducens NA10BT and D. oryzae RF3T were 57 ± 1 % and 45 ± 1.5 %, respectively. The G+C content of the genomic DNA of strain SL-205T was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. Ubiquinone Q-8 was the only respiratory quinone; the polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one uncharacterized phospholipid. We conclude that strain SL-205T represents a novel species of the genus Diaphorobacter for which the name Diaphorobacter polyhydroxybutyrativorans is proposed; the type strain is SL-205T ( = ACCC 19739T = DSM 29460T).
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Affiliation(s)
- Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing 100097, PR China
| | - Zhengyan Zuo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
- School of Chemical Engineering, Northeast Dianli University, Jilin 132012, PR China
| | - Junlian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
| | - Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
| | - Meilin Han
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
| | - Lijiao Sun
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
- School of Chemical Engineering, Northeast Dianli University, Jilin 132012, PR China
| | - Lanhe Zhang
- School of Chemical Engineering, Northeast Dianli University, Jilin 132012, PR China
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry, Beijing 100097, PR China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing 100097, PR China
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21
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Zhang XX, Gao JS, Cao YH, Sheirdil RA, Wang XC, Zhang L. Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots. Int J Syst Evol Microbiol 2015; 65:2931-2936. [PMID: 26016492 DOI: 10.1099/ijs.0.000358] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains ZYY136(T) and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice-rice--Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136(T) and ZYY9 showed the highest similarity, of 97.0%, to Rhizobium tarimense PL-41(T). Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA-DNA relatedness value between ZYY136(T) and ZYY9 was 82.3%, and ZYY136(T) showed 34.0% DNA-DNA relatedness with the most closely related type strain, R. tarimense PL-41(T). The DNA G+C content of strain ZYY136(T) was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136(T) and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136(T) and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136(T) = ACCC 05753(T) = KCTC 32088(T)).
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Affiliation(s)
- Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Ju-Sheng Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Qiyang, 426182, PR China
| | - Yan-Hua Cao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Rizwan Ali Sheirdil
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Department of Soil Science and Soil Water Conservation, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Xiu-Cheng Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Lei Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
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22
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Grison CM, Jackson S, Merlot S, Dobson A, Grison C. Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator. Int J Syst Evol Microbiol 2015; 65:1525-1530. [DOI: 10.1099/ijs.0.000130] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus
Rhizobium
and to be most closely related to
Rhizobium endophyticum
CCGE 2052T (98.4 %),
Rhizobium tibeticum
CCBAU 85039T (98.1 %),
Rhizobium grahamii
CCGE 502T (98.0 %) and
Rhizobium mesoamericanum
CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with
R. endophyticum
CCGE 2052T,
R. tibeticum
CCBAU 85039T,
R. mesoamericanum
CCGE 52T,
Rhizobium grahamii
CCGE 502T,
Rhizobium etli
CCBAU 85039T and
Rhizobium radiobacter
KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus
Rhizobium
. The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus
Rhizobium
with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).
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Affiliation(s)
- Claire M. Grison
- Environmental Research Institute, Lee road, University College Cork, Cork, Ireland
| | - Stephen Jackson
- Environmental Research Institute, Lee road, University College Cork, Cork, Ireland
| | - Sylvain Merlot
- Institut des Sciences du Végétal, CNRS, UPR 2355, Bât. 22, 1 avenue de la terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Alan Dobson
- Environmental Research Institute, Lee road, University College Cork, Cork, Ireland
| | - Claude Grison
- FRE 3673 – Bioinspired chemistry and ecological innovation – CNRS, University of Montpellier 2, Stratoz – Cap Alpha, Avenue de l’Europe 34830 Clapiers, France
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23
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Zhao R, Chen XY, Li XD, Chen ZL, Li YH. Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides. Int J Syst Evol Microbiol 2015; 65:71-76. [DOI: 10.1099/ijs.0.065888-0] [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 Gram-stain-negative, rod-shaped and non-endospore-forming bacterium, designated strain AG1-2T, was isolated from Takakia lepidozioides collected from the Gawalong glacier in Tibet, China and characterized using a polyphasic taxonomic approach. The predominant fatty acids of strain AG1-2T were iso-C15 : 0 (36.0 %), iso-C17 : 0 3-OH (20.2 %), summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl, 16.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 11.1 %). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Strain AG1-2T contained MK-6 as the dominant menaquinone, and the genomic DNA G+C content was 37.3 mol%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AG1-2T was affiliated to species of the genus
Chryseobacterium
, and its closest related species were
Chryseobacterium taiwanense
Soil-3-27T,
Chryseobacterium hispalense
AG13T,
Chryseobacterium camelliae
THG C4-1T and
Chryseobacterium taeanense
PHA3-4T with a sequence similarity of 98.0, 97.8, 97.3 and 97.1 %, respectively. However, the DNA–DNA relatedness values between these strains and strain AG1-2T were 29, 21, 21 and 45 %, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2T is considered to represent a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium
takakiae sp. nov. is proposed. The type strain is AG1-2T ( = CGMCC 1.12488T = DSM 26898T).
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Affiliation(s)
- Ran Zhao
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Xin Yao Chen
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Xue Dong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Zhi Ling Chen
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Yan Hong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
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24
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Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 2014; 197:359-70. [PMID: 25533848 DOI: 10.1007/s00203-014-1071-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
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25
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Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JG. Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere. Antonie van Leeuwenhoek 2014; 107:65-72. [PMID: 25504533 DOI: 10.1007/s10482-014-0304-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/13/2014] [Indexed: 11/28/2022]
Abstract
A 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, designated GXGD002(T), was isolated from the rhizosphere of banana plants cultivated in Guangxi province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GXGD002(T) is a member of the genus Variovorax. High levels of 16S rRNA gene sequence similarity are found between strain GXGD002(T) and Variovorax paradoxus DSM 30034(T) (99.4 %), Variovorax ginsengisoli KCTC 12583(T) (99.1 %), Variovorax boronicumulans KCTC 22010(T) (99.0 %), Variovorax soli DSM18216(T) (98.7 %), Variovorax defluvii DSM 27259(T) (98.1 %) and Variovorax dokdonensis KCTC 12544(T) (97.4 %) respectively. However, the DNA-DNA hybridization values between strain GXGD002(T) and its closely related species V. paradoxus DSM 30034(T), V. ginsengisoli KCTC 12583(T) and V. boronicumulans KCTC 22010(T) were found to be 40.7, 30.9 and 23.7 %, respectively. The DNA G + C content of strain GXGD002(T) was found to be 67.8 mol%. The major fatty acids of strain GXGD002(T) are C16:0 (20.3 %), C10:0 3OH (18.4 %), C17:0 cyclo (18.9 %), C18:1w7c (12.3 %) and summed feature 3 (13.9 %). The predominant respiratory quinone was identified as ubiquinone-8 (Q-8) and the major polar lipids as phosphatidylethanolamine and phosphatidylglycerol. The results of polyphasic taxonomic study including physiological and biochemical tests, whole-cell SDS-PAGE profiles and chemotaxonomic analysis allowed a clear differentiation of strain GXGD002(T) from the other species in the genus Variovorax. Based on these results, a new species, Variovorax guangxiensis, is proposed. The type strain is GXGD002(T) (=DSM 27352(T) = ACCC 05911(T)).
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Affiliation(s)
- Jun-lian Gao
- Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Science/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People's Republic of China
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26
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Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium. Antonie van Leeuwenhoek 2014; 107:403-10. [DOI: 10.1007/s10482-014-0338-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/15/2014] [Indexed: 10/24/2022]
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27
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Gu CT, Li CY, Yang LJ, Huo GC. Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov. Int J Syst Evol Microbiol 2014; 64:2650-2656. [PMID: 24824638 DOI: 10.1099/ijs.0.064709-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterial strain, 10-17(T), was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 10-17(T) was phylogenetically related to Enterobacter hormaechei CIP 103441(T), Enterobacter cancerogenus LMG 2693(T), Enterobacter asburiae JCM 6051(T), Enterobacter mori LMG 25706(T), Enterobacter ludwigii EN-119(T) and Leclercia adecarboxylata LMG 2803(T), having 99.5%, 99.3%, 98.7%, 98.5%, 98.4% and 98.4% 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17(T) ( = LMG 27195(T) = NCIMB 14836(T) = CCUG 62994(T)). Enterobacter sacchari Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1(T)( = CGMCC 1.12102(T) = LMG 26783(T)).
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Affiliation(s)
- Chun Tao Gu
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, PR China.,Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Yan Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Li Jie Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Gui Cheng Huo
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, PR China.,Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
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28
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Francis IM, Jochimsen KN, De Vos P, van Bruggen AHC. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int J Syst Evol Microbiol 2014; 64:1340-1350. [PMID: 24436067 DOI: 10.1099/ijs.0.058909-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T) = LMG 17323(T) = ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) ( = LMG 12560(T) = ATCC 51296(T)), WI4(T) ( = LMG 11032(T) = ATCC 51292(T)) and SP1(T) ( = LMG 12581(T) = ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic.
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Affiliation(s)
- Isolde M Francis
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Kenneth N Jochimsen
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Paul De Vos
- Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium
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29
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Chen XY, Zhao R, Tian Y, Kong BH, Li XD, Chen ZL, Li YH. Mucilaginibacter polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2014; 64:1395-1400. [DOI: 10.1099/ijs.0.055335-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, rod-shaped, non-spore-forming bacterium, designated strain RG4-7T, was isolated from the moss Polytrichastrum formosum collected from Gawalong glacier in Tibet, China, and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain RG4-7T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified aminolipids and one unidentified lipid. Strain RG4-7T contained MK-7 as the dominant menaquinone and the G+C content of its genomic DNA was 39.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RG4-7T was affiliated to species of the genus
Mucilaginibacter
, and its closest relative was
Mucilaginibacter jinjuensis
YC7004T (97.0 % sequence similarity). However, the DNA–DNA relatedness between this strain and strain RG4-7T was only 49.1±3.7 %. Based on phylogenetic inference and phenotypic data, strain RG4-7T is considered to represent a novel species of the genus
Mucilaginibacter
, for which the name Mucilaginibacter polytrichastri sp. nov. is proposed. The type strain is RG4-7T ( = CGMCC 1.12493T = DSM 26907T). An emended description of the genus
Mucilaginibacter
is also proposed.
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Affiliation(s)
- Xin Yao Chen
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Ran Zhao
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Yang Tian
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Bi He Kong
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Xue Dong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Zhi Ling Chen
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Yan Hong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
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30
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Wang Y, Ji B, Wu W, Wang R, Yang Z, Zhang D, Tian W. Hepatoprotective effects of kombucha tea: identification of functional strains and quantification of functional components. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:265-272. [PMID: 23716136 DOI: 10.1002/jsfa.6245] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Kombucha tea (KT), a traditional health beverage containing potential hepatoprotective agents, is fermented from sugared tea by a symbiotic culture of yeast and bacteria for 8 days. However, the functional strains that produce components for the hepatoprotective property of KT remain unclear. Multiple strains are involved in traditional KT production. Therefore, KT has not been standardized or produced commercially. This study aimed to identify the functional strains and quantify the functional components with hepatoprotective effects in kombucha tea. RESULTS Gluconacetobacter sp. A4 was one of the microorganisms in KT in which the D-saccharic acid-1,4-lactone (DSL) produced by G. sp. A4 was significantly higher than that produced by original tea fungus at 8 days of fermentation. Traditional KT (TKT, tea broth fermented by mixed tea fungus), modified KT (MKT, fermented by single G. sp. A4), and DSL significantly inhibited the acetaminophen-induced increase of alanine aminotransferase, alkaline phosphatase, triglyceride and malondialdehyde, as well as facilitating the reduction of total antioxidant capacity in mice. Furthermore, MKT and TKT are both similar to DSL in terms of protection against acetaminophen-induced liver injury in mice. These results suggested a positive relationship between DSL content and the hepatoprotective effect of TKT, MKT and DSL groups. CONCLUSION G. sp. A4 was concluded to be a potential functional strain and DSL might be the key functional component for the hepatoprotective property in KT. The stronger capability of G. sp. A4 in producing DSL makes it a better choice for the commercial production of KT.
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Affiliation(s)
- Yong Wang
- College of Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
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31
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Zhang XX, Tang X, Sheirdil RA, Sun L, Ma XT. Rhizobium rhizoryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2014; 64:1373-1377. [PMID: 24449787 DOI: 10.1099/ijs.0.056325-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (J3-AN59(T) and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59(T) and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium, and they were most closely related to Rhizobium tarimense ACCC 06128(T) (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59(T) and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59(T) and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA-DNA relatedness value between J3-AN59(T) and J3-N84 was 89 %, and strain J3-AN59(T) showed 9 % DNA-DNA relatedness to R. tarimense ACCC 06128(T), the most closely related strain. Based on this evidence, we found that J3-AN59(T) and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59(T) ( = ACCC 05916(T) = KCTC 23652(T)).
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Affiliation(s)
- Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xue Tang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Rizwan Ali Sheirdil
- Department of Soil Science and Soil Water Conservation, PMAS Arid Agriculture University, Rawalpindi, Pakistan.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lei Sun
- College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Xiao-Tong Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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32
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Li CY, Tian F, Zhao YD, Gu CT. Enterococcus xiangfangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2013; 64:1012-1017. [PMID: 24425824 DOI: 10.1099/ijs.0.058917-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterial strain, 11097(T), was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized using a polyphasic approach, including 16S rRNA gene sequence analysis, phenylalanyl-tRNA synthase (pheS) gene sequence analysis, RNA polymerase α subunit (rpoA) gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 11097(T) was phylogenetically related to Enterococcus devriesei, E. pseudoavium, E. viikkiensis, E. avium, E. malodoratus, E. gilvus and E. raffinosus. Strain 11097(T) had 99.1-99.9% 16S rRNA gene sequence similarities, 78.2-83.2% pheS gene sequence similarities and 93.8-96.6% rpoA gene sequence similarities with type strains of phylogenetically related species. Based upon polyphasic characterization data obtained in the present study, a novel species of the genus Enterococcus, Enterococcus xiangfangensis sp. nov., is proposed with the type strain 11097(T) ( = LMG 27495(T) = NCIMB 14834(T)).
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Affiliation(s)
- Chun Yan Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Fen Tian
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Ya Dong Zhao
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin 150030, PR China.,Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
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33
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Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough. Int J Syst Evol Microbiol 2013; 63:4698-4706. [DOI: 10.1099/ijs.0.054296-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive bacterial strains, 11050T, 7-19T and 11102T, were isolated from traditional pickle and sourdough in Heilongjiang Province, China. These bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 11050T belonged to the
Lactobacillus plantarum
species group and shared 98.0–98.4 % 16S rRNA gene sequence similarities and 84.7–88.9 % dnaK gene sequence similarities with type strains of
Lactobacillus plantarum subsp. plantarum
,
Lactobacillus plantarum subsp. argentoratensis
,
Lactobacillus pentosus
,
Lactobacillus paraplantarum
,
Lactobacillus fabifermentans
and
Lactobacillus xiangfangensis
and had 75.9–80.7 % pheS gene sequence similarities and 90.7–92.5 % rpoA gene sequence similarities with
Lactobacillus plantarum subsp. plantarum
LMG 6907T,
Lactobacillus plantarum subsp. argentoratensis
LMG 9205,
Lactobacillus pentosus
LMG 10755T,
Lactobacillus paraplantarum
LMG 16673T,
Lactobacillus fabifermentans
LMG 24284T and
Lactobacillus xiangfangensis
3.1.1T, respectively. Strain 7-19T was phylogenetically related to
Lactobacillus thailandensis
,
Lactobacillus pantheris
and
Lactobacillus sharpeae
, having 94.1–96.7 % 16S rRNA gene sequence similarities, 71.5–82.3 % pheS gene sequence similarities and 71.2–83.4 % rpoA gene sequence similarities with type strains of
Lactobacillus thailandensis
,
Lactobacillus pantheris
and
Lactobacillus sharpeae
, respectively. Strain 11102T was phylogenetically related to
Lactobacillus oligofermentans
,
Lactobacillus suebicus
,
Lactobacillus vaccinostercus
and
Lactobacillus hokkaidonensis
. Strain 11102T had 99.2 % 16S rRNA gene sequence similarity, 81.3 % pheS gene sequence similarity and 96.1 % rpoA gene sequence similarity with
Lactobacillus oligofermentans
LMG 22743T, respectively. Strain 11102T shared 96.0–96.8 % 16S rRNA gene sequence similarities, 73.3–81.0 % pheS gene sequence similarities and 74.6–76.9 % rpoA gene sequence similarities with type strains of
Lactobacillus suebicus
,
Lactobacillus vaccinostercus
and
Lactobacillus hokkaidonensis
, respectively. Based upon the data from polyphasic characterization obtained in the present study, three novel species, Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., are proposed and the type strains are 11050T ( = LMG 27194T = CCUG 62991T), 7-19T ( = LMG 27191T = NCIMB 14832T = CCUG 62990T) and 11102T ( = LMG 27192T = NCIMB 14833T), respectively.
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Affiliation(s)
- Chun Tao Gu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Yan Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Li Jie Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Gui Cheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
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34
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Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2013; 63:4094-4099. [DOI: 10.1099/ijs.0.053355-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterial strain, S4-3T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain S4-3T showed 97.9–98.7 % 16S rRNA gene sequence similarities, 84.4–94.1 % pheS gene sequence similarities and 94.4–96.9 % rpoA gene sequence similarities to the type strains of
Lactobacillus nantensis
,
Lactobacillus mindensis
,
Lactobacillus crustorum
,
Lactobacillus futsaii
,
Lactobacillus farciminis
and
Lactobacillus kimchiensis
. dnaK gene sequence similarities between S4-3T and
Lactobacillus nantensis
LMG 23510T,
Lactobacillus mindensis
LMG 21932T,
Lactobacillus crustorum
LMG 23699T,
Lactobacillus futsaii
JCM 17355T and
Lactobacillus farciminis
LMG 9200T were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3T ( = LMG 26166T = NCIMB 14701T).
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Affiliation(s)
- Chun Tao Gu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Yan Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Li Jie Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Gui Cheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
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35
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Zou XL, Li XA, Wang XM, Chen Q, Gao M, Qiu TL, Sun JG, Gao JL. Hansschlegelia
beijingensis sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic bacterium isolated from watermelon rhizosphere soil. Int J Syst Evol Microbiol 2013; 63:3715-3719. [DOI: 10.1099/ijs.0.052308-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped strain designated PG04T was isolated from the rhizosphere of watermelon plants cultivated in Beijing, China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, isolate PG04T belonged clearly to the genus
Hansschlegelia
and was most closely related to
Hansschlegelia zhihuaiae
(97.3 % similarity to the type strain). The predominant respiratory quinone was ubiquinone 10 (Q-10) and the polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids were C18 : 1ω7c (41.3 %), C19 : 0 cyclo ω8c (30.6 %) and C16 : 0 (19.1 %). The G+C content of the DNA was about 64.4 mol%. DNA–DNA hybridization experiments showed 34.4 % relatedness between strain PG04T and
H. zhihuaiae
DSM 18984T. The results of physiological and biochemical tests and differences in fatty acid profiles allowed clear phenotypic differentiation of strain PG04T from the most closely related species in the genus,
H. zhihuaiae
. Strain PG04T therefore represents a novel species within the genus
Hansschlegelia
, for which the name
Hansschlegelia
beijingensis sp. nov. is proposed, with the type strain PG04T ( = DSM 25481T = ACCC 05759T).
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Affiliation(s)
- Xiao-lin Zou
- Department of Microbiology, College of Resources and Environment Science, Sichuan Agricultural University, Ya’an 625014, PR China
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Xiu-ai Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Xu-Ming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Qiang Chen
- Department of Microbiology, College of Resources and Environment Science, Sichuan Agricultural University, Ya’an 625014, PR China
| | - Miao Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization, Beijing 100081, PR China
| | - Tian-lei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
| | - Jian-guang Sun
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization, Beijing 100081, PR China
| | - Jun-lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing 100097, PR China
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Chalkiadakis E, Dufourcq R, Schmitt S, Brandily C, Kervarec N, Coatanea D, Amir H, Loubersac L, Chanteau S, Guezennec J, Dupont-Rouzeyrol M, Simon-Colin C. Partial characterization of an exopolysaccharide secreted by a marine bacterium, Vibrio neocaledonicus sp. nov., from New Caledonia. J Appl Microbiol 2013; 114:1702-12. [PMID: 23480553 DOI: 10.1111/jam.12184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/24/2013] [Accepted: 03/04/2013] [Indexed: 12/01/2022]
Abstract
AIMS Exopolysaccharides (EPS) are industrially valuable molecules with numerous useful properties. This study describes the techniques used for the identification of a novel Vibrio bacterium and preliminary characterization of its EPS. METHODS AND RESULTS Bioprospection in marine intertidal areas of New Caledonia followed by screening for EPS producing brought to selection of the isolate NC470. Phylogenetic analysis (biochemical tests, gene sequencing and DNA-DNA relatedness) permitted to identify NC470 as a new member of the Vibrio genus. The EPS was produced in batch fermentation, purified using the ultrafiltration process and analysed by colorimetry, Fourier Transform Infrared spectroscopy, gas chromatography, Nuclear Magnetic Resonance and HPLC-size exclusion chromatography. This EPS exhibits a high N-acetyl-hexosamines and uronic acid content with a low amount of neutral sugar. The molecular mass was 672 × 10(3) Da. These data are relevant for possible technological exploitation. CONCLUSIONS We propose the name Vibrio neocaledonicus sp. nov for this isolate NC470, producing an EPS with an unusual sugar composition. Comparison with other known polymers permitted to select applications for this polymer. SIGNIFICANCE AND IMPACT OF THE STUDY This study contributes to evaluate the marine biodiversity of New Caledonia. It also highlights the biotechnological potential of New Caledonia marine bacteria.
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Pelagibacterium nitratireducens sp.nov., A Marine Alphaproteobacterium Isolated from the East China Sea. Curr Microbiol 2013; 66:450-5. [DOI: 10.1007/s00284-012-0299-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
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38
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Claus D, Fahmy F, Rolf HJ, Tosunoglu N. Sporosarcina halophila sp. nov., an Obligate, Slightly Halophilic Bacterium from Salt Marsh Soils. Syst Appl Microbiol 2012. [PMID: 23194807 DOI: 10.1016/s0723-2020(83)80007-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twenty-two strains of endospore-forming sarcinae have been isolated from salt marsh soils. The isolates differ phenotypically from Sporosarcina ureae, the only species of the genus Sporosarcina which has been validly described, and are distinct from S. ureae in the composition of the cell walls of their vegetative cells. Lysine, found in the tetrapeptide of the murein of S. ureae, is replaced by ornithine in the new isolates. The interpeptide bridge consists of an aspartic acid residue instead of D-glutamylglycine as is found in S. ureae. The mol% G + C of the DNA of the new isolates is in the range of 40.1-40.9 (S. ureae 40.0-41.5). DNA hybridization studies revealed a high DNA-DNA homology within the new isolates but only a low relationship to S. ureae. The main menaquinone is of the MK-7 type as in S. ureae and other aerobic sporeformers. The spores of the new isolates are very similar to spores of S. ureae and Bacillus species in respect of their heat resistance, composition and ultrastructure. None of the new isolates grows on complex media unless supplemented with sodium, magnesium and chloride ions. Strains are slight halophiles as they grow best in the presence of 30 to 50 g NaCl/1 and 5 g MgCl(2)/l. The new isolates thus belong to a new species, for which the name Sporosarcina halophila is proposed. Strain DSM 2266 (= strain 3) is the type strain.
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Affiliation(s)
- D Claus
- Deutsche Sammlung von Mikroorganismen (DSM), Gesellschaft für Biotechnologische Forschung mbH, 3400 Göttingen, Federal Republic of Germany
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Zhao CT, Wang ET, Zhang YM, Chen WF, Sui XH, Chen WX, Liu HC, Zhang XX. Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species. Int J Syst Evol Microbiol 2012; 62:2180-2186. [DOI: 10.1099/ijs.0.031229-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four rhizobial strains representing a previously defined novel group in the genus
Mesorhizobium
and isolated from Astragalus species in China were further characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus
Mesorhizobium
, with
Mesorhizobium plurifarium
LMG 11892T as the closest neighbour sharing a sequence similarity of 99.8 %. Comparative sequence analysis of the atpD, recA, glnII, rpoB, nodC and nifH genes, SDS-PAGE of whole-cell soluble proteins, DNA–DNA hybridization, fatty acid profiles and a series of phenotypic and physiological tests differentitated the novel group from all recognized species of the genus
Mesorhizobium
. Based on the data obtained in the present and previous studies, this group represents a novel species within the genus
Mesorhizobium
, for which the name Mesorhizobium silamurunense sp. nov. is proposed. The type strain is CCBAU 01550T ( = HAMBI 3029T = LMG 24822T), and could form effective nodules on Astragalus membranaceus, Astragalus adsurgens and Caragana intermedia, and ineffective nodules on Phaseolus vulgaris in cross-nodulation tests.
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Affiliation(s)
- Chun Tian Zhao
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México DF 11340, México
| | - Yan Ming Zhang
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Zhang LH, Chen SF. Pseudacidovorax intermedius NH-1, a novel marine nitrogen-fixing bacterium isolated from the South China Sea. World J Microbiol Biotechnol 2012; 28:2839-47. [PMID: 22806723 DOI: 10.1007/s11274-012-1093-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/25/2012] [Indexed: 11/29/2022]
Abstract
We have taxonomically and phylogenetically characterized a novel nitrogen-fixing bacterial strain, NH-1, which was recently isolated from surface sediments of the South China Sea. The presence of the nifH gene was determined by PCR amplification. The strain NH-1 was found to belong to the genus Pseudacidovorax based on phenotypic characterization, 16S rDNA sequencing, G+C content and DNA-DNA hybridization. Isolate NH-1 was identified as Pseudacidovorax intermedius. In addition, we investigated the links between environmental factors and the nitrogenase activity of NH-1. We found that the nitrogen fixation capacity of NH-1 varied strongly when cells were grown with different ammonium ion and oxygen concentrations, amino acids and carbohydrates. This is the first report of the isolation of Pseudacidovorax from the ocean and the first study to explore the effects of different culture conditions on the nitrogenase activities of the isolate. This study provides evidence that marine nitrogen-fixing microorganisms are far more diverse than currently recognized.
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Affiliation(s)
- Li-hong Zhang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China.
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41
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Gu CT, Wang F, Li CY, Liu F, Huo GC. Lactobacillus
xiangfangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2012; 62:860-863. [DOI: 10.1099/ijs.0.031468-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive bacterial strain, 3.1.1T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Based upon the data obtained in the present study, a novel species,
Lactobacillus
xiangfangensis sp. nov., is proposed with the type strain 3.1.1T ( = LMG 26013T = NCIMB 14687T).
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Affiliation(s)
- Chun Tao Gu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Fang Wang
- College of Forestry, Southwest Forestry University, Kunming 650224, PR China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Chun Yan Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Fei Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
| | - Gui Cheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
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42
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Zhang YZ, Chen WF, Li M, Sui XH, Liu HC, Zhang XX, Chen WX. Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root. Int J Syst Evol Microbiol 2012; 62:359-363. [PMID: 21441377 DOI: 10.1099/ijs.0.028936-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gram-positive, aerobic, motile rod, designated strain CCBAU 05776(T), was isolated from the inner tissues of a healthy soybean (Glycine max L.) root collected from an agricultural field in the countryside of Shijiazhuang city, Hebei Province, China. Phylogenetic analysis of the 16S rRNA gene indicated that this strain was most closely related to Bacillus muralis LMG 20238(T) and Bacillus simplex NBRC 15720(T) with similarity of 96.5 % and 96.3 %, respectively, lower than the suggested threshold (97.0 %) for separating bacterial species. In phenotypic characterization, the novel strain differed from the two most related species in that it did not hydrolyse casein or starch but could grow on MacConkey agar. It grew between 15 and 45 °C and tolerated up to 7 % NaCl (w/v). Strain CCBAU 05776(T) grew in media with pH 5.5 to 10 (optimal growth at pH 7.0-8.0). The predominant cellular fatty acids were iso-C(15 : 0) (40.81 %) and C(16 : 1)ω7c alcohol (10.61 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C was 40.8 mol% (T(m)). DNA-DNA relatedness of the novel isolate with B. muralis and B. simplex was 42.4 % and 32.7 %, respectively. Based upon the consensus of phylogenetic and phenotypic analyses, strain CCBAU 05776(T) represents a novel species within the genus Bacillus, for which the name Bacillus endoradicis sp. nov. is proposed. The type strain is CCBAU 05776(T) ( = LMG 25492(T) = HAMBI 3097(T)).
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Affiliation(s)
- Yun Zeng Zhang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Mao Li
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong-Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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43
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Li HF, Zou ZT, Li BZ, Wang X, Yang JS, Yuan HL. Novosphingobium sediminis sp. nov., isolated from the sediment of a eutrophic lake. J GEN APPL MICROBIOL 2012; 58:357-62. [DOI: 10.2323/jgam.58.357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Smarda P, Bureš P, Smerda J, Horová L. Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability. THE NEW PHYTOLOGIST 2012; 193:513-21. [PMID: 22050640 DOI: 10.1111/j.1469-8137.2011.03942.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
• Knowledge of the phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including those of plants) is poor. With the use of flow cytometry (FCM), the amount of available data on the guanine + cytosine (GC) content of plants has nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. • Here, we tested the reliability of FCM for estimating GC content by comparison with the biochemical method of DNA temperature melting analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6-47.5% as measured by FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. • FCM and TMA data exhibited a high degree of correspondence which remained stable over the relatively wide range of binding lengths (3.39-4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM results and the sequence data in Oryza, although the latter GC contents were consistently lower. • Reliable estimates of the genomic base composition in plants by FCM are comparable with estimates obtained using other methods, and so wider application of FCM in future plant genomic research, although it would pose a challenge, would be supported by these findings.
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Affiliation(s)
- Petr Smarda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic.
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45
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Zhang X, Li B, Wang H, Sui X, Ma X, Hong Q, Jiang R. Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2011; 62:1871-1876. [PMID: 21984664 DOI: 10.1099/ijs.0.026880-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SL-1(T) and F11, which had the ability to decompose polycyclic aromatic hydrocarbons (PAHs), were isolated from soil samples contaminated by oil. The cells were motile by polar or lateral flagella. According to comparison of 16S rRNA gene sequences, strains SL-1(T) and F11 were identical and showed the greatest degree of similarity (96.8%) to both Rhizobium oryzae Alt505(T) and Rhizobium mesosinicum CCBAU 25010(T); however, only Rhizobium oryzae with SL-1(T) and F11 formed a separate clade. There were low similarities (<90%) between the atpD and recA sequences of the two strains and those of the genus of Rhizobium. The bacteria grew at temperatures of 10-40 °C with an optimum of 30 °C. The pH range for growth was 6.0-10.0 and optimum pH was 7.0-8.0. Growth occurred at NaCl concentrations up to 3.0% (w/v). They were catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (18:1ω7c and/or 18:1ω6c) and 16:0. The DNA G+C content was 62.2 mol%. Strain SL-1(T) showed 29 and 0% DNA-DNA relatedness, respectively, with the most related strains R. oryzae Alt505(T) and R. mesosinicum CCBAU 25010(T) according to phylogenic analysis of the 16S rRNA gene. According to physiological and biochemical characteristics and genotypic data obtained in this work, the bacteria represent a novel species of the genus Rhizobium, and the name Rhizobium petrolearium is proposed. The type strain is SL-1(T) ( = ACCC 11238(T) = KCTC 23288(T)) and it could nodulate Medicago sativa in nodulation tests.
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Affiliation(s)
- Xiaoxia Zhang
- Agricultural Culture Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Baoming Li
- Beijing Centre for Physical and Chemical Analysis, Beijing 100089, PR China
| | - Haisheng Wang
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xinhua Sui
- Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Xiaotong Ma
- Agricultural Culture Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qing Hong
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ruibo Jiang
- Agricultural Culture Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Aloui A, Tagourti J, El May A, Joseleau Petit D, Landoulsi A. The effect of methylation on some biological parameters in Salmonella enterica serovar Typhimurium. ACTA ACUST UNITED AC 2011; 59:192-8. [DOI: 10.1016/j.patbio.2009.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 03/18/2009] [Indexed: 10/20/2022]
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47
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Wen Y, Huang X, Zhou Y, Hong Q, Li S. Hansschlegelia zhihuaiae sp. nov., isolated from a polluted farmland soil. Int J Syst Evol Microbiol 2011; 61:1114-1117. [DOI: 10.1099/ijs.0.021543-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, aerobic, coccoid-shaped strain designated S 113T was isolated from a polluted-soil sample collected in Jiangsu Province, China. A polyphasic taxonomic study including phylogenetic analysis based on the 16S rRNA gene sequence and determination of phenotypic characteristics was performed on the new isolate. The highest 16S rRNA gene sequence similarity was 96.8 %, with Hansschlegelia plantiphila S1
T. The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids were C18 : 1ω7c and C16 : 0. The G+C content of the DNA was about 65.7 mol%. DNA–DNA hybridization experiments showed 44.9 % relatedness for strain S 113T with its closest relative, H. plantiphila NCIMB 14035T. The dominant phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylcholine. The results of our polyphasic taxonomic analysis indicate that strain S 113T represents a novel species within the genus Hansschlegelia, for which the name Hansschlegelia zhihuaiae sp. nov. is proposed. The type strain is S 113T ( = DSM 18984T = CCTCC AB 206143T = KCTC 12880T).
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Affiliation(s)
- Ya Wen
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xing Huang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yu Zhou
- Institute of Quality and Standard for Agricultural Products, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou, Zhejiang 310021, PR China
| | - Qing Hong
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Shunpeng Li
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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48
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Zhang RJ, Hou BC, Wang ET, Li Y, Zhang XX, Chen WX. Rhizobium tubonense sp. nov., isolated from root nodules of Oxytropis glabra. Int J Syst Evol Microbiol 2011; 61:512-517. [DOI: 10.1099/ijs.0.020156-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four rhizobial strains, designated CCBAU 85046T, CCBAU 85051, CCBAU 85048 and CCBAU 85049, isolated from root nodules of Oxytropis glabra grown in Tibet, China, were previously defined, using amplified 16S rRNA gene restriction analysis, as a novel group within the genus Rhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. The 16S rRNA gene analysis showed that the four isolates formed a distinct phylogenetic lineage in the genus Rhizobium. The isolates showed highest sequence similarity (97.8 %) to Rhizobium indigoferae CCBAU 71042T. Phenotypic and physiological tests, DNA–DNA hybridization, phylogenetic analyses of housekeeping genes recA, atpD and glnII and fatty acid profiles also indicated that these four strains constitute a novel group distinct from recognized species of the genus Rhizobium. Based on this evidence, strains CCBAU 85046T, CCBAU 85051, CCBAU 85048 and CCBAU 85049 represent a novel species in the genus Rhizobium, for which the name Rhizobium tubonense sp. nov. is proposed. The type strain is CCBAU 85046T (=LMG 25225T =HAMBI 3066T) and its DNA G+C content is 59.52 mol% (T
m). Strain CCBAU 85046T could form effective nodules on plant species Vigna unguiculata and Medicago sativa but not on its host of origin Oxytropis glabra.
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Affiliation(s)
- Rong Juan Zhang
- State Key Laboratories for Agro-Biotechnology, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Bao Chao Hou
- State Key Laboratories for Agro-Biotechnology, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D. F., Mexico
| | - Ying Li
- State Key Laboratories for Agro-Biotechnology, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xiao Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wen Xin Chen
- State Key Laboratories for Agro-Biotechnology, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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49
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Jin HJ, Tu R, Xu F, Chen SF. Identification of nitrogen-fixing Paenibacillus from different plant rhizospheres and a novel nifH gene detected in the P. stellifer. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711010097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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50
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