The differences and overlaps in the seed‐resident microbiome of four Leguminous and three Gramineous forages

Summary Given the important roles that seed‐borne endophytes can play on their plant hosts, comprehensive studies of the bacterial and fungal communities of seeds are of great importance. In this study, we assessed the seed endophytes of three gramineous (Avena sativa, Elymus sibiricus and Elymus dahuricus) and four leguminous (Vicia villosa, Trifolium repens, Trifolium pretense and Medicago sativa) forages using high‐throughput sequencing. In total, 1013 distinct bacterial operational taxonomic units (OTUs) and 922 fungal OTUs were detected, with bacteria and fungi per sample ranging from 240 to 425 and 261 to 463 respectively. These seven forages shared a high number of potentially beneficial taxa, including Bacillus, Pantoea, Candida and Helotiales, but the relative proportion of these taxa was different in each seed. Fungal communities were clustered more distinctively by host genotypes than bacterial. Some bacterial taxa may be involved in the recruitment of genera from the same phylum. Three Pantoea sp. and five Bacillus sp. were isolated from seeds, and all showed positive effects on Medicago sativa germination rate under salt stress, and of these, Bacillus subtilis Es‐1 and Pantoea agglomerans Ed‐3 performed best, but their influence was affected by the seed’s microbiome. Rather than simply promoting host plant growth directly, some taxa may also participate in organizing the assembly of plant microbiomes which will influence seed response to biological factors. This study uses a new, high‐throughput sequencing based strategy to identify beneficial strains and analyse the interactions between microorganisms and plants to maximize microbial functions in long‐term agricultural practices. These seven forages shared a high number of potentially beneficial taxa, including Bacillus, Pantoea, Candida and Helotiales. Rather than simply promoting host plant growth directly, some taxa may also participate in organizing the assembly of plant microbiomes which will influence seed response to biological factors.