Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov.

Resumen

<i>Agrobacterium</i> strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as <i>Agrobacterium</i>, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (<i>glnII</i>, <i>gyrB</i> and <i>recA</i>) positioned the strains in four distinct clades, with <i>Agrobacterium pusense</i>, <i>Agrobacterium deltaense</i>, <i>Agrobacterium radiobacter</i> and <i>Agrobacterium</i> sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase <i>telA</i> gene, and MLSA analysis with six complete housekeeping genes (<i>atpD</i>, <i>glnII</i>, <i>gyrB</i>, <i>recA</i>, <i>rpoB</i> and <i>thrC</i>), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675^T and <i>Agrobacterium</i> sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of <i>Agrobacterium</i> are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675^T and <i>Agrobacterium</i> sp. genomospecies G1 strains as a new species, for which the name <i>Agrobacterium fabacearum</i> is proposed. The type strain is CNPSo 675^T (=UMR 1457^T=LMG 31642^T) and is also deposited in other culture collections.