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

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, because of 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 10 soybean cultivars, including 5 SCN-resistant and 5 SCN-susceptible cultivars, using amplicon sequencing. The resistant cultivars harbored distinct rhizosphere microbiomes, compared with the susceptible cultivars. Permutational multivariate analysis of variance 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 suggest that 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. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.