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ARS Home » Plains Area » Brookings, South Dakota » Integrated Cropping Systems Research » Research » Publications at this Location » Publication #426022
Research Project: Combined Management Tactics for Resilient and Sustainable Crop Production

Location: Integrated Cropping Systems Research

Title: Rhizo-microbiome engineering enhances soybean resistance to soybean cyst nematode

Author
item Yin, Chuntao
item Lahr, Nathan

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/24/2025
Publication Date: 2/24/2026
Citation: Yin, C., Lahr, N.D. 2026. Rhizo-microbiome engineering enhances soybean resistance to soybean cyst nematode. Phytobiomes Journal. 10:72-82. https://doi.org/10.1094/PBIOMES-07-25-0049-R.
DOI: https://doi.org/10.1094/PBIOMES-07-25-0049-R

Interpretive Summary: Soybean is an important protein and oil crop. The U.S. is responsible for more than one-third of the world’s soybean production annually. However, crop damage from soybean cyst nematode (SCN) is one of the largest threats to soybean producers. While resistant soybean has been the primary tactic used to combat SCN, the widespread use of limited genetic resistance has led to SCN adapting and being able to reproduce on these resistant soybean plants. This study explored alternative methods to manage SCN. We transferred microbes from the roots of SCN-resistant soybean cultivars to the susceptible soybean Williams 82. As a result, we found a noticeable decrease in SCN population when Williams 82 grew in the SCN-infected soil. Our microbial analysis revealed that the roots of resistant cultivars harbored unique bacterial and fungal species, some of which have been identified as contributors to SCN disease suppression. This study demonstrated that breeding microbe-friendly soybeans is an effective tool for controlling SCN and improving plant health, and that using microbial inoculants can improve soybean resistance to SCN, complementing other SCN control strategies.

Technical Abstract: Soybean cyst nematode (SCN), caused by Heterodera glycines (Ichinohe), is a serious threat to soybean production worldwide. Genetic resistance is the primary strategy for managing SCN. However, due to limited genetic resources and the potential for SCN to rapidly overcome plant immunity, alternative measures are needed. Plant microbiomes play an important role in plant growth and health. In this study, we examined the rhizosphere microbiomes (bacteria and fungi) in ten soybean cultivars, including five SCN-resistant and five SCN-susceptible cultivars, using amplicon sequencing. We found that the rhizosphere bacterial communities in resistant cultivars exhibited a higher Shannon index and different compositions compared to those in susceptible cultivars, although a similar trend was not observed in fungal communities. Notably, the rhizosphere microbiomes in resistant cultivars enriched potential plant-beneficial microbes that may contribute to SCN disease suppression. Furthermore, rhizosphere microbial inoculants derived from the SCN-resistant cultivars significantly reduced the SCN populations in the susceptible soybean Williams 82. Overall, our study highlighted the genetic basis of the reciprocal interactions between plants and associated rhizosphere microbiomes. The engineering of plant microbiomes through microbial inoculants can improve soybean resistance to SCN, complementing other conventional crop health improvement practices.