Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis |
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| Institution: | 1. Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India;2. Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 001, India;3. Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh,160036, India;1. The Japan Society for the Promotion of Science, Tokyo, Japan;2. Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, Japan;3. National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan;4. Technology Research Association for Single Wall Carbon Nanotubes, Tsukuba, Ibaraki, Japan;1. Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan;2. National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan;3. Institute of Molecular Biology and Biotechnology, University of Lahore Main Campus, Defense road, Lahore, Pakistan;4. Department of Bioinformatics and Biotechnology, Government College University Faisalabad 38000, Pakistan;5. Department of Soil and Environmental Sciences, The University of Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan;1. Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark;2. Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, Denmark;3. Section for Geogenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark;4. Pacific Ecoinformatics and Computational Ecology Lab, Berkeley, CA, USA;1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China;2. Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China;3. Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, 2601DA Delft, the Netherlands;4. School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China |
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| Abstract: | Three strains L3B27T, 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9–98.3% 16S rRNA similarity and 91.3–94.0% recA similarity values, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridisation (dDDH) values between L3B27T (representative of the novel strains) and its phylogenetically closest Sphingomonas species were well below the established cut-off <94% (ANI/AAI) and <70% (dDDH) for species delineation. Further, the novel strains can be distinguished from its closest relatives based on several phenotypic traits. Thus, based on the polyphasic approach, we describe a novel Sphingomonas species for which the name Sphingomonas pokkalii sp. nov (type strain L3B27T = KCTC 42098T = MCC 3001T) is proposed. In addition, the novel strains were characterised for their plant associated properties and found to possess several phenotypic traits which probably explain its plant associated lifestyle. This was further confirmed by the presence of several plant associated gene features in the genome of L3B27T. Also, we could identify gene features which may likely involve in brackish water adaptation. Thus, this study provides first insights into the plant associated lifestyle, genome and taxonomy of a novel brackish adapted plant associated Sphingomonas. |
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| Keywords: | Pokkali Brackish rice PGPR Rhizobacteria |
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