Colonization of Bacillus altitudinis on the Compatible Soybean Varieties to Provide Seed Rot Resistance

Seed health is crucial for plant growth and agricultural productivity. Recent studies have illustrated the importance of plant microbiome in disease resistance, however, it remains unclear whether the seed microbiome confers seed rot resistance against fungal pathogens. In this study, the application of antibiotics on the seeds of eight soybean varieties showed that seed-associated bacteria were involved in the seed rot resistance caused by Calonectria ilicicola, but this resistance cannot be carried to withstand root rot. Using PacBio 16S rDNA full-length sequencing and microbiome analyses, the seed microbiome was shown to mainly dependent on the soybean variety, and there was no consistent community network associated with seed rot resistance across soybean varieties. Instead, the seed-associated Bacillus altitudinis was identified through the differential abundance analysis and culture-dependent isolation. Moreover, qPCR confirmed the persistence of B. altitudinis on apical shoots till 21 days post-inoculation, but not on roots by 9 days post-inoculation. The short-term colonization of B. altitudinis on roots may explain the absence of root rot resistance. Furthermore, seed treated with B. altitudinis restored seed rot resistance, but only in the compatible soybean varieties. For the incompatible soybean varieties, B. altitudinis showed lower bacterial density and provided no seed protection. Collectively, this study advances the insight of B. altitudinis conferring seed rot resistance. These findings highlight the potential of using seed-associated bacteria for seed protection and underscore the importance of considering bacterial compatibility with plant genotypes and tissues.