Bradyrhizobium Neotropicale Sp. Nov., Isolated From Effective Nodules of Centrolobium Paraense

Int J Syst Evol Microbiol. 2014 Dec;64(Pt 12):3950-3957. doi: 10.1099/ijs.0.065458-0. Epub 2014 Sep 9.

Abstract

Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247(T), BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S-23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05(T) ( = LMG 24129(T)) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium. Results of DNA-DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium. Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247(T) ( = HAMBI 3599(T)).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Typing Techniques
  • Base Composition
  • Bradyrhizobium / classification*
  • Bradyrhizobium / genetics
  • Bradyrhizobium / isolation & purification
  • Brazil
  • DNA, Bacterial / genetics
  • DNA, Ribosomal Spacer / genetics
  • Fabaceae / microbiology*
  • Fatty Acids / chemistry
  • Genes, Bacterial
  • Molecular Sequence Data
  • Multilocus Sequence Typing
  • Nitrogen Fixation
  • Nucleic Acid Hybridization
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 23S / genetics
  • Root Nodules, Plant / microbiology*
  • Sequence Analysis, DNA
  • Symbiosis

Substances

  • DNA, Bacterial
  • DNA, Ribosomal Spacer
  • Fatty Acids
  • RNA, Ribosomal, 16S
  • RNA, Ribosomal, 23S

Associated data

  • GENBANK/KF927051
  • GENBANK/KF983829
  • GENBANK/KJ661686
  • GENBANK/KJ661693
  • GENBANK/KJ661700
  • GENBANK/KJ661707
  • GENBANK/KJ661714
  • GENBANK/KJ661727
  • GENBANK/KJ661728