Multilocus sequence analysis of the genus Bradyrhizobium

Area of Science:

• Microbiology
• Genomics
• Taxonomy

Background:

• Accurate bacterial taxonomy is crucial for understanding microbial ecology and evolution.
• Bradyrhizobium species are important nitrogen-fixing symbionts of legumes.
• Previous taxonomic studies relied heavily on DNA-DNA hybridization, which has limitations.

Purpose of the Study:

• To evaluate the effectiveness of multilocus sequence analysis (MLSA) for Bradyrhizobium taxonomy.
• To compare MLSA phylogenies with existing DNA-DNA hybridization data.
• To identify Bradyrhizobium species among new isolates from Spanish legumes.

Main Methods:

• Partial gene sequencing of five housekeeping genes (atpD, recA, gyrB, rpoB, dnaK).
• Phylogenetic analysis of individual and concatenated gene datasets.
• Comparison of sequence-based phylogenies with DNA-DNA hybridization results.
• Identification of novel Bradyrhizobium isolates from Lupinus albus, Arachis hypogaea, and Ornithopus compressus.

Main Results:

• Individual gene phylogenies partially reflected DNA-DNA hybridization, especially high values.
• Concatenated five-gene phylogeny provided a more comprehensive representation of overall genome similarity.
• A high sequence similarity (>99%) allowed for species identification, but clear cut-off levels for species delineation were not established.
• Most new isolates were identified as Bradyrhizobium canariense; four strains from L. albus formed a distinct group near Bradyrhizobium japonicum.
• Evidence of horizontal gene transfer and recombination was observed for some housekeeping genes.

Conclusions:

• MLSA, particularly using a concatenated dataset of five genes, is a valuable tool for Bradyrhizobium taxonomy.
• Using multiple genes is recommended to account for horizontal gene transfer and recombination events.
• The study confirmed the identity of most isolates as Bradyrhizobium canariense and identified a distinct group of strains.