Plant roots are associated with a diverse microbial community of bacteria and fungi. The root microbiome communities associate with the root surface or penetrate the superficial layers of root tissues. It is of high agronomic interest to characterize root microbiomes and identify microbes with beneficial effects on plant defense against pathogens. Soybean taproot decline (TRD) is an emerging soil-borne disease caused by a fungus classified as Xylaria necrophora, challenging to control and with devastating effects on yield. Our group has initiated a study of the soybean root microbiome with three primary experiments: (I) perform a comparative study of root microbiomes and mycobiomes from healthy and TRD-affected soybean, (II) isolate, screen and (III) identify soybean root bacterial endophytes with anti-X. necrophora and anti-TRD properties. Our long-term objective is to discover and implement microbiome-based management techniques that enhance the health and yield of soybeans.