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Syst Appl Microbiol. 2019 May;42(3):334-342. doi: 10.1016/j.syapm.2019.02.003. Epub 2019 Feb 15.

Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis.

Author information

1
Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 001, India.
2
Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh,160036, India.
3
Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 001, India. Electronic address: rameshkumar@niist.res.in.

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.

KEYWORDS:

Brackish rice; PGPR; Pokkali; Rhizobacteria; Sphingomonas

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