Abstract
Purpose
The objective of this study was to characterize
Bradyrhizobium
strains currently recommended as inoculants for
Arachis pintoi
in Brazil using comparative genomic and symbiotic analyses. In addition, this study aimed to expand current knowledge on the diversity, evolution, and bacterial symbiotic traits of
Arachis
-associated
Bradyrhizobium
while providing robust taxonomic evidence to support the description of a novel
Bradyrhizobium
species isolated from root nodules of
Arachis
.
Methods
Phylogenetic reconstruction was performed based on the 16S rRNA gene and by phylogenomics using 116 single- copy core gene sequences. Average Nucleotide Identity (ANI) analyses were conducted to evaluate the genomic relatedness of strains BR 1432ᵀ, BR 1433 and BR 14999 to 1,301 reference
Bradyrhizobium
genomes, including all available type strain strains. The results were validated using digital DNA–DNA hybridization (dDDH). Additional analyses included phylogenetic reconstruction of symbiotic genes (
nodC
and
nifH
) and, assessment of the denitrification pathway, and phenotypic characterization.
Results
Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome data indicated that strains BR 1432ᵀ and BR 14999 form a distinct lineage within the genus
Bradyrhizobium
, clearly separated from BR 1433, which clustered with
Bradyrhizobium brasilense
. ANI and dDDH values between BR 1432ᵀ and BR 14999 and their closest related type strains, including
B. zhanjiangense
LMG 29279ᵀ, were below the species delineation thresholds of 96% and 70%, respectively, supporting the proposal of a novel species. In addition, the publicly available RefSeq genomes
Bradyrhizobium
sp. DN5 and Rc2d were found to be closely related to BR 1432ᵀ. Phylogenetic analyses of the
nodC
and
nifH
genes revealed distinct evolutionary patterns, while genomic analyses showed that the proposed novel species harbors a complete denitrification pathway, unlike strain BR 1433. Furthermore, phenotypic characterization revealed differences in carbon source utilization and enzymatic activities.
Conclusion
Based on genomic, phylogenetic, and phenotypic evidence, strain BR 1433 was identified as a member of
B. brasilense
, whereas strains BR 1432ᵀ (= UCCC 277ᵀ = LMG 34120ᵀ = CCP577ᵀ), BR 14999, DN5 and Rc2d represent a novel species within the genus
Bradyrhizobium
, for which the name
Bradyrhizobium boddeyi
sp. nov. is proposed.