Taxonomy and genomic of bradyrhizobium strains isolated from tropical legumes

Abstract

Tropical legumes have a wide geographic distribution and are extremely important for the natural balance of the environments where they are found. This group of plant species has increased taxonomic diversity and it is found under different edaphoclimatic conditions. This Family has the ability to establish symbiosis with different genus of N2-fixing bacteria. Among them, Bradyrhizobium stands out, for forming symbiosis with several species of economic and, or environmental importance including soybean. The first objective of this work was to identify at the species level strains from Bradyrhizobium genus and the second was to verify the relationship between symbiotic genes and efficiency, geographic origin, and the host plant species, in 38 Bradyrhizobium strains isolated from 3 legume species (forage peanut, soybean and lima-bean). In addition, 3 new species of Bradyrhizobium, one from soybean from the group of 38 strains and two from cowpea bean and Campsiandra Laurilifolia Benth., respectively, were described. The 38 genomas of the strains isolated from Lima bean, forage peanut, and soybean were sequenced, and the genes nodA, nodB, nodC, nodD1, nodI, nodJ, nodN, nodZ, nodW, nifA, nifB, nifD, nifE, nifH, nifK, nifN, nifQ, nifX, nifZ, fixJ, fixL were phylogenetically analyzed. The phylogenetic trees of the studied genes showed that the strains were positioned according to their host plants.To describe the three new species, genomic, phylogenetic, and phenotypic analyzes were performed (temperature, pH, salinity, assimilation of different carbon and nitrogen sources and antibiotic resistance). Based on the ANI (average nucleotide identity) ≥ 96% of the genomes of the symbiotic strains of each studied legume species, the following species of Bradyrhizobium were identified: B. japonicum e B. elkanii e B. guangdongense and B. brasilense, in soybean, e B. zhanjiagense, B. forestalis e B. pachyrhizi. in Lima bean. All forage peanut strains represented a new species. In addition to these, other possible new species were also found: one from the fava and one from soybean, the latter already described in this work (B. uflense). The concatenation of housekeeping genes (recA, gyrB, dnaK, atpD, glnII e rpoB) of the 3 possible new species showed that they were positioned in different clusters from those containing the type strains from Bradyrhizobium species already described. The ANI confirmed the three new species, and they were named as Bradyrhizobium uflense, Bradyrhizobium uaiense e Bradyrhizobium campsiandrae, whose type strains are UFLA06-05T, UFLA03-164T e UFLA 01-1174T, respectively. The nod, nif and fix genes showed that the phylogenetic position of the strains was not related to their geographic origin. It was not possible to establish a relationship between the nif genes and the efficiency in fixing N symbiotically. The studied Bradyrhizobium strains showed significant phylogenetic differences, evidencing the high diversity between strains within the species of this genus which are native to Brazilian soils and establish symbiosis with different species of native or exotic legumes.