Root rot alters the root-associated microbiome of field pea in commercial crop production systems

Abstract

Pulses are important crops that have been used to diversify cropping rotations in the Canadian prairies. With increasing cultivation intensity, pulses are becoming more susceptible to root rots. Understanding how root-associated microbiomes are affected by plant health is vital for developing sustainable crop production systems. In this study, we investigated the effect of root rot on rhizosphere and root microbiomes of healthy and root-rot infected field pea (Pisum sativum L.) plants from nine commercial fields in Saskatchewan using amplicon metagenomic sequencing. Bacterial and oomycete α-diversity was higher in diseased root and rhizosphere samples than their healthy counterparts, while fungal diversity was higher in diseased rhizosphere samples. The community structure of root and rhizosphere microbiomes were also affected by the health status of the plants, with root bacterial communities exhibiting the strongest differences. Healthy samples were associated with a higher relative abundance of Rhizobium, Olpidium and Mortierella, and lower abundance of Fusarium and Pythium. Diseased samples had a higher number of indicator genera (42 in diseased vs. 11 in healthy) and more taxa exclusively detected in the diseased core microbiome. Results from this study revealed that root rot generally increased the diversity and altered the community structure and relative abundance of key taxa of the pea root-associated microbiome. This knowledge may aid in the development of microbiome-based disease management strategies, such as identification of key microbial taxa that could help commercial pea growers assess root rot risk.