Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas

Rahi, P and Giram, P and Chaudhari, D and diCenzo, GC and Kiran, S and Khullar, A and Chandel, M and Gawari, S and Mohan, A and Chavan, S and Mahajan, B (2020) Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas. In: Systematic and Applied Microbiology, 43 (5).

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Abstract

Three strains of rhizobia isolated from effective root nodules of pea (Pisum sativum L.) collected from the Indian trans-Himalayas were characterized using 16S rRNA, atpD and recA genes. Phylogeny of the 16S rRNA genes revealed that the newly isolated strains were members of the genus Rhizobium with ≥99.9% sequence similarity to the members within the “Rhizobium leguminosarum” group. Phylogenetic analyses based on the concatenated sequences of atpD and recA gene, and 92 core genes extracted from the genome sequences indicated that strains JKLM 12A2T and JKLM 13E are grouped as a separate clade closely related to R. laguerreae FB206T. In contrast, the strain JKLM 19E was placed with “R. hidalgonense” FH14T. Whole-genome average nucleotide identity (ANI) values were 97.6% within strains JKLM 12A2T and JKLM 13E, and less than 94% with closely related species. The digital DNA-DNA hybridization (dDDH) values were 81.45 within the two strains and less than 54.8% to closely related species. The major cellular fatty acids were C18:1w7c in summed feature 8, C14:0 3OH/C16:1 iso I in summed feature 2, and C18:0. The DNA G + C content of JKLM 12A2T and JKLM 13E was 60.8 mol%. The data on genomic, chemotaxonomic, and phenotypic characteristics indicates that the strains JKLM 12A2T and JKLM 13E represent a novel species, Rhizobium indicum sp. nov. The type strain is JKLM 12A2T (= MCC 3961T = KACC 21380T = JCM 33658T). However, the strain JKLM 19E represents a member of “R. hidalgonense” and the symbiovar viciae.

Item Type:	Journal Article
Publication:	Systematic and Applied Microbiology
Publisher:	Elsevier GmbH
Additional Information:	The copyright for this article belongs to Elsevier GmbH.
Keywords:	fatty acid; nucleotide; RNA 16S; bacterial DNA; fatty acid; RNA 16S, Article; atpd gene; bacterial gene; bacterial genome; chemotaxonomy; cladistics; DNA base composition; DNA DNA hybridization; gene sequence; genomics; India; nodulation; nonhuman; pea; phenotype; phylogenetic tree; priority journal; RecA gene; Rhizobium; Rhizobium indicum; Rhizobium leguminosarum; whole genome sequencing; bacterium identification; classification; crop; DNA sequence; genetics; isolation and purification; microbiology; nodulation; pea; phylogeny; physiology; Rhizobium; RNA gene; symbiosis, Bacterial Typing Techniques; Crops, Agricultural; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Genes, rRNA; Genome, Bacterial; Genomics; India; Peas; Phylogeny; Rhizobium; Rhizobium leguminosarum; RNA, Ribosomal, 16S; Root Nodules, Plant; Sequence Analysis, DNA; Symbiosis
Department/Centre:	Division of Biological Sciences > Molecular Reproduction, Development & Genetics
Date Deposited:	14 Feb 2023 08:54
Last Modified:	14 Feb 2023 08:54
URI:	https://eprints.iisc.ac.in/id/eprint/80240

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