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

Pulse crops are important from both economic and sustainable cropping systems perspective on the Canadian prairies. With increasing cultivation intensity, pulses are becoming more susceptible to various diseases, including root rots. Root rots are serious diseases of pulses, such as field pea and lentil, worldwide as well as on the Canadian prairies that can cause complete crop failure under favourable environment. These disease are caused by soil-borne pathogens and therefore, difficult to control. Soil and plant root associated microorganisms or microbiomes are extremely diverse and include species that are both harmful and beneficial to the host plant. Beneficial microorganisms can interact with soil-borne plant pathogens and improve plant health and productivity. In commercial production systems, agricultural management practices can alter key soil properties and growth environments that significantly influence composition and diversity of microbial communities. Plant health also impact plant-associated microbiomes. Understanding how root-associated microbiomes are affected by plant health is vital for developing sustainable crop production systems. Such knowledge would be useful to elucidate microbial dynamics in agricultural ecosystems and explore the potential of using microbes in plant disease management.

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. We used high throughput sequencing to target the bacterial, fungal, and oomycete communities to develop a comprehensive understanding of the impact of root rot on the root-associated microbiome.

Results showed higher bacterial and oomycete diversity 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. The relative abundance of beneficial microbes such as Rhizobium, Olpidium, and Mortierella were greater in healthy samples whereas the abundance of harmful microbes such as Fusarium and Pythium were lower in the same group of samples. Diseased samples had a higher number of microbial indicator genera (42 in diseased vs. 11 in healthy) and more taxa exclusively detected in the diseased core microbiome. 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.