Wheat Straw Return Influences Soybean Root-Associated Bacterial and Fungal Microbiota in a Wheat–Soybean Rotation System

Roots hold complex microbial communities at the soil–root interface, which can affect plant nutrition, growth, and health. Although the composition of plant microbiomes has been extensively described for various plant species and environments, little is known about the effect of wheat straw return (WSR) on the soybean root microbiota. We used Illumina-based 16S rRNA and ITS amplicon sequencing to track changes in bacterial and fungal microbiota in bulk soil and soybean rhizosphere, rhizoplane, s1and endosphere during the third and fourth years after implementing WSR in a wheat–soybean rotation system. The results revealed that WSR had a greater impact on fungal communities than bacterial communities, particularly in bulk soil, rhizosphere, and rhizoplane. WSR enriched the relative abundance of cellulose-degrading fungi (e.g., Acremonium, Trichoderma, and Myrmecridium, among which Trichoderma also had antimicrobial activity), saprotroph (e.g., Exophiala), and nitrogen cycling bacteria (e.g., Chryseolinea). Furthermore, WSR depleted the relative abundance of pathogenic fungi (e.g., Fusarium and Alternaria). These data revealed for the first time that WSR had diverse effects on soybean root-associated microbial community composition, not only in soil but also in the rhizosphere, rhizoplane, and endosphere.