Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru

Abstract

A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of Bradyrhizobium lablabi CCBAU 23086 T . Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus Bradyrhizobium. Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus Bradyrhizobium (¡92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus Bradyrhizobium were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21 T 5DSM 18454 T 5HAMBI 2911 T ) and Bradyrhizobium icense sp. nov. (type strain LMTR 13 T 5HAMBI 3584 T 5CECT 8509 T 5CNPSo 2583 T ), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH and nodC symbiosis genes.

Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., isolated from nodules of legumes indigenous to Western Australia

“…Yet, this value needs to corroborate with more robust molecular analyses, including the evaluation of others molecular markers that enhance evolutionary information [18]. Until few years ago, the value of 70 % of DNA–DNA hybridization (DDH) between the genome of two strains was also used to discriminate species [19, 20]; however, with the development of bioinformatics tools, genomic parameters, including multilocus sequence analysis (MLSA) [21, 22], average nucleotide identity (ANI) [18], and digital DNA–DNA hybridization (dDDH) [23], have replaced the traditional methods.…”

Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus

“…Likewise, a change to the taxonomy of Agrobacterium tumefaciens has been proposed to reflect genome-enabled discovery of clade-specific traits (Lassalle et al, 2011). The ANI method has been used to assign newly discovered isolates to known plant-associated species and discover new species of plant pathogens (Dudnik et al, 2014; Durán et al, 2014; van der Wolf et al, 2014). …”

Microvirga tunisiensis sp. nov., a root nodule symbiotic bacterium isolated from Lupinus micranthus and L. luteus grown in Northern Tunisia

“…zambiensis [4], M. lupini [4], several species of Bradyrhizobium [15][16][17]19], Rhizobium giardinii [2], and Mesorhizobium plurifarium [14] (Fig. 3A).…”