Increasing the frequency of pulses in crop rotations reduces soil fungal diversity and increases the proportion of fungal pathotrophs in a semiarid agroecosystem

In the Canadian Prairies, the production of pulse crops has increased considerably since the 1980's, including agronomically important crops such as field peas (Pisum sativum L.), lentils (Lens culinaris Medik.), and chickpeas (Cicer arietinum L.). As producers increase and intensify the use of pulse crops, more knowledge is needed to understand the impact these crops have on important soil biological resources. In this study, we used a high-throughput sequencing approach (454 amplicon sequencing) to determine if increasing the frequency of pulses in crop rotations affects the diversity and composition of soil and root-associated fungal communities and the proportion of functional guilds such as pathogens, saprophytes, and mutualists. This study was conducted in a semiarid region of the Canadian Prairies with nine different 4-year rotations including field pea, lentil, and chickpea grown once, twice, three times or not at all with wheat (Triticum aestivum L.). Soil fungal communities were assessed following the third year of the rotations and root-associated fungal communities were assessed during the fourth year when all of the rotations were seeded to wheat. Our results revealed that the inclusion of two or more pulses into 4-year crop rotations caused a significant shift in the composition of the soil fungal community, a decrease in fungal diversity, and an increase in the proportion of fungal pathotrophs compared to continuous wheat or rotations with only one pulse crop. Several important pathogens of pulse crops increased two to three-fold in pulse intensified rotations including Fusarium avenaceum, F. redolens, and Alternaria alternata, and crop-specific pathogens such as Didymella pinodella and F. solani increased in field pea intensified rotations. The build-up of fungal pathogens in the soil indicates that farmers in this region should avoid growing pulse crops in consecutive years or in close succession to avoid developing disease problems. This study also revealed that rotation sequence explained more of the variation in the fungal community compared to the previous crop and affected the relative abundance of several important fungal pathogens. This highlights the importance of crop selection in rotations and provides a tool that farmers can use to manage soil fungal communities to ensure the sustainability and productivity of agricultural systems.