Predominant populations of indigenous soybean‐nodulating Bradyrhizobium japonicum strains obtained from organic farming systems in Minnesota

AIMS: Bradyrhizobium from organic fields in Minnesota were isolated and genotyped to assess diversity of soybean‐bradyrhizobia in organic farming systems that can be used to improve soybean productivity. METHODS AND RESULTS: Soil samples were collected from 25 organic fields in Minnesota during May to July 2012. Soybean (cv. Lambert) was used as a host to trap indigenous bradyrhizobia in each sample. Genetic diversity of Bradyrhizobium strains (n = 733) was determined using the horizontal, fluorophore‐enhanced, repetitive extragenic palindromic‐PCR (HFERP) DNA fingerprinting technique and the soybean‐bradyrhizobia were classified into 79 different genotypes. Of these, 15 dominant genotypes were found and were highly similar (>92% fingerprint similarity) to serotypes USDA 127 (40·4%), USDA 4 (31·8%) and USDA 123 (15·5%), which were the three main populations of soybean‐bradyrhizobia in organic fields. CONCLUSIONS: Bradyrhizobium japonicum serogroup USDA 4 strains were found to make up a previously unrecognized, predominant rhizobial population in the organic farming soils examined. The relative abundance of strain USDA 4 was negatively correlated with that of USDA 127 and this relationship may be influenced by the levels of NO₃‐N and other soil edaphic factors. SIGNIFICANCE AND IMPACT OF THE STUDY: The local community of bradyrhizobia can be affected by applying inoculant bacteria to organic fields. Based on these results, soybean production in organic farms may be improved by displacing strains similar to USDA 4 with those better at nitrogen fixation and competitive ability than indigenous strains.