Assessment of Endophytic Microbiome of Soybean Seeds Under the Agricultural Ecosystem in Mississippi, USA

Seed microbiome plays an important role in seed quality, germination, and crop establishment. Soybean (Glycine max (L.) Merr.) is one of the most economically important field crops. However, information about soybean seed microbiomes is lacking, especially regarding how field environmental conditions and the prevalent seed pathogen Diaporthe longicolla across different years shape soybean seed microbiomes. In this study, we used amplicon sequencing to assess seed endophytic microbiomes of a soybean cultivar Dudley, collected in four successive years of field trials. Alpha diversity of both fungal and bacterial communities remained relatively stable across years with D. longicolla treatments. The microbial compositions were significantly influenced by years (p = 0.001), with environmental variables (air temperature, precipitation, and relative humidity) contributing to shifts in community structure. The seed core microbiome comprised bacterial members from genera Methylorubrum, Peribacillus, and Priestia, and fungal taxa from classes Dothideomycetes, Sordariomycetes, and Tremellomycetes. Pathogen inoculation altered bacterial composition, positively associated with taxa from genera Sphingomonas, Microbacterium, and Nocardioides, but did not notably affect fungal community. Soybean seed microbiome assembly appears driven primarily by interannual environmental variations. Pathogen inoculation exerts a secondary but detectable effect on the bacterial community. To the best of our knowledge, this is the first multi-year field-based study of soybean seed endophytic microbiomes and the impact of seedborne pathogen inoculation. The findings of this research advance our understanding of soybean seed microbiomes and provide insights into the potential use of seed microbes, thereby aiding development of novel microbiome-based alternatives to manage soybean seed diseases.