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

Syst Appl Microbiol. 2020 Sep;43(5):126127. doi: 10.1016/j.syapm.2020.126127. Epub 2020 Jul 30.


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 60.8mol%. 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.

Keywords: High altitude agriculture; Nitrogen fixation; Rhizobia; Symbiosis; nifH gene; nodC gene.

MeSH terms

  • Bacterial Typing Techniques
  • Crops, Agricultural / microbiology
  • DNA, Bacterial / genetics
  • Fatty Acids / analysis
  • Genes, Bacterial
  • Genes, rRNA
  • Genome, Bacterial
  • Genomics
  • India
  • Peas / microbiology*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Rhizobium / classification*
  • Rhizobium / genetics
  • Rhizobium / isolation & purification*
  • Rhizobium / physiology
  • Rhizobium leguminosarum / genetics
  • Root Nodules, Plant / microbiology*
  • Sequence Analysis, DNA
  • Symbiosis


  • DNA, Bacterial
  • Fatty Acids
  • RNA, Ribosomal, 16S