Pyrosequencing reveals the impact of foliar fungicide application to chickpea on root fungal communities of durum wheat in subsequent year

•Fungicide application on chickpea impacts root fungi of a subsequent durum wheat.•The effect of fungicide depended on year and root type.•Fusarium is the prevalent fungus in the roots of durum wheat in Saskatchewan.•Environmental changes in 2009 vs. 2010 had a major effect on the fungal community.

Frequent application of foliar fungicide is essential for chickpea production due to the susceptibility of this plant to ascochyta blight. Chlorothalonil, pyraclostrobin, and boscalid are commonly used to control the disease in Saskatchewan. While fungicides are meant to target specific fungal pathogens, they may impact non-target organisms and alter soil microbial community structure. The effects of the typical 5-time foliar fungicide application program to chickpea CDC Vanguard on the fungal communities associated with seminal and adventitious roots of the following durum wheat crop were studied in a 2 yr field experiment. Root fungal communities were characterized through analysis of the ITS1 region of root metagenomic DNA at the genus level. One hundred and seven fungal genera were detected in durum wheat roots. Fusarium was predominant in both years. A three-way interaction of fungicide application, root type and year on fungal community structure was detected. Unlike Fusarium, the relative abundances of the genera Olpidium, Alternaria, and Cryptococcus were greater in 2010, a very wet year. Fungicide application to chickpea increased the relative abundance of Fusarium in the seminal roots of a subsequent durum crop in 2009, but did not affect the relative abundance of Fusarium in 2010. We could not detect a significant impact of fungicide application to chickpea on durum wheat yield in the subsequent year. The effect of changes in root fungal communities on durum wheat grain yield is discussed.