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Kan Y, Zhang L, Wang Y, Ma Q, Zhou Y, Jiang X, Zhang W, Ruan Z. Endophytic Bacterium Flexivirga meconopsidis sp. nov. with Plant Growth-Promoting Function, Isolated from the Seeds of Meconopsis integrifolia. Microorganisms 2023; 11:2899. [PMID: 38138043 PMCID: PMC10745605 DOI: 10.3390/microorganisms11122899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Strain Q11T of an irregular coccoid Gram-positive bacterium, aerobic and non-motile, was isolated from Meconopsis integrifolia seeds. Strain Q11T grew optimally in 1% (w/v) NaCl, pH 7, at 30 °C. Strain Q11T is most closely related to Flexivirga, as evidenced by 16S rRNA gene analysis, and shares the highest similarity with Flexivirga aerilata ID2601ST (99.24%). Based on genome sequence analysis, the average nucleotide identity and digital DNA-DNA hybridization values of strains Q11T and D2601ST were 88.82% and 36.20%, respectively. Additionally, strain Q11T showed the abilities of nitrogen fixation and indole acetic acid production and was shown to promote maize growth under laboratory conditions. Its genome contains antibiotic resistance genes (the vanY gene in the vanB cluster and the vanW gene in the vanI cluster) and extreme environment tolerance genes (ectoine biosynthetic gene cluster). Shotgun proteomics also detected antibiotic resistance proteins (class A beta-lactamases, D-alanine ligase family proteins) and proteins that improve plant cold tolerance (multispecies cold shock proteins). Strain Q11T was determined to be a novel species of the genus Flexivirga, for which the name Flexivirga meconopsidis sp. nov. is proposed. The strain type is Q11T (GDMCC 1.3002T = JCM 36020 T).
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Affiliation(s)
- Yongtao Kan
- College of Life Sciences, Xinjiang Normal University, Urumqi 830017, China;
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China;
| | - Yan Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Qingyun Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqing Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Jiang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi 830017, China;
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Chaudhary DK, Lee H, Dahal RH, Kim DH, Cha IT, Lee KE, Kim DU. Flexivirga aerilata sp. nov., Isolated from an Automobile Air Conditioning System. Curr Microbiol 2020; 78:796-802. [PMID: 33249533 DOI: 10.1007/s00284-020-02300-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022]
Abstract
A novel light-yellow-coloured, Gram-stain-positive, nearly-coccoid, aerobic bacterium, designated strain ID2601ST was isolated from a car evaporator core collected from South Korea. Strain ID2601ST was catalase positive and oxidase negative, able to grow at pH 6.0-8.0, temperature 20-45 °C, and 0-6.0% (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain ID2601ST belonged to the genus Flexivirga, with the nearest phylogenetic neighbour being Flexivirga endophytica YIM 7505T (97.9% sequence similarity). The strain comprised diphosphatidylglycerol as the main polar lipid; MK-8(H4) as a predominant respiratory quinone; serine, alanine, glycine, glutamic acid, and lysine as main components of peptidoglycan and iso-C16:0, summed feature 9 (iso-C17:1ω9c and/or C16:0 10-methyl), anteiso-C17:0, and C17:0 10-methyl as the major fatty acids. The average nucleotide identity (ANI) values between strain ID2601ST and the closest species (Flexivirga endophytica YIM 7505T and Flexivirga caeni BO-16T) were < 78%. The in silico DNA-DNA hybridization (dDDH) values of strain ID2601ST with the closest species were < 22%. These observations were below the threshold values of 95% (for ANI) and 70% (for dDDH) used for species delineation. The DNA G+C content was 69.8 mol%. Based on the polyphasic taxonomic data, the novel species Flexivirga aerilata sp. nov. is proposed with the type strain ID2601ST (=KCTC 49353T =NBRC 114622T).
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, College of Science and Technology, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| | - Dae Hyun Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - In-Tae Cha
- National Institute of Biological Resources, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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