Cropping practices impact fungal endophytes and pathogens in durum wheat roots

• More fungal antagonists were detected in wheat roots after pea than after chickpea.
• Previous year fungicide application to chickpea suppressed fungal antagonists.
• Durum wheat yield was positively correlated with fungal antagonists.
• There was a negative correlation of durum wheat yield and virulent fungal pathogens.

The benefit provided by chickpea (Cicer arietinum L.) to the following durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.] crop is smaller than that provided by pea (Pisum sativum L.) in the Great Plains of America. Rotation crops and the specific cropping practices associated with them may impact soil fungal communities, which in turn could affect the productivity of subsequent crops. Two separate field experiments were carried out to test the effect of pea and chickpea crops and of foliar fungicide use in chickpea on the community of fungi hosted in the roots of a subsequent durum wheat crop. The fungal communities in the healthy and diseased roots of durum wheat at maturity were characterized using plate culture and PCR-based identification. The effect of cropping practices on root-associated fungal communities depended on root type and varied with year. Functionally important fungal taxa were affected by specific cropping practices. Endophytic fungal antagonists were less abundant after chickpea than after pea and after fungicide-treated chickpea than after untreated chickpea. The chickpea cultivar CDC Vanguard increased the abundance of highly virulent pathogens in durum wheat roots in comparison with the chickpea cultivar CDC Luna and pea. We conclude that the negative impact of chickpea on durum wheat yield could be due in part to an increase in fungal pathogens resulting from the suppression of endophytic fungal antagonists by chickpea.