Rhizo-Microbiome Engineering for Enhancing Soybean Resistance to Soybean Cyst Nematode

Abstract

Soybean cyst nematode (SCN), Heterodera glycines (Ichinohe), is a serious threat to soybean production worldwide. Genetic resistance and crop rotation are the primary management strategies. However, due to limited genetic resources, long-term implementation of crop rotation, and environmental effects, alternative measures are needed. Plant microbiomes play an important role in plant health, but their contribution to SCN resistance remains unclear. In this study, we profiled the rhizosphere microbiomes in ten soybean cultivars, including five SCN-resistant and five SCN-susceptible cultivars, using amplicon sequencing. The resistant cultivars harbored distinct rhizosphere microbiomes, compared to susceptible cultivars. PERMANOVA analysis revealed that both the host genotype and SCN resistance trait significantly influenced microbial community composition, with host genotype explaining greater variation. Resistant cultivars were found to be enriched in specific microbial taxa from Phenylobacterium, Pseudoduganella, Comamonadaceae, and Arthrobotrys. Furthermore, microbial inoculants derived from resistant cultivars reduced SCN populations in the susceptible cultivar Williams 82. These results suggested that both host genotype and SCN resistance trait interacted to shape rhizosphere microbiomes and influence SCN suppression. Overall, this study highlighted the potential for engineering plant microbiomes to enhance soybean resistance to SCN, complementing traditional crop health improvement practices.