Wheat rhizosphere persistence of Trichoderma gamsii A5MH during suppression of a Fusarium-Pythium root disease complex differentially impacts the soil fungal and oomycete microbiome.

Aims: Determine the impacts of inoculant strain Trichoderma gamsii A5MH and crop phenology on the structure of fungal and oomycete communities in wheat rhizosphere soil.

Methods and results: Over two consecutive wheat crops, A5MH inoculation suppressed an oomycete (Globisporangium)-fungal (Fusarium) root disease complex. Amplicon sequencing determined the impacts of A5MH treatment and crop phenology on the structure of rhizosphere soil fungal and oomycete communities. Culture-dependent (C-D) techniques quantified inoculant impacts on non-target root endophytic fungi, previously co-isolated with strain A5MH and the fungal and oomycete pathogens. Inoculant treatment differentiated the structure of the fungal microbiome in both years, primarily due to increased Trichoderma abundance and decreases in cereal pathogenic, root endophytic, and saprophytic taxa. Strain A5MH did not impact the structure of the oomycete microbiome. Crop phenology altered fungal and oomycete community structure, these impacts greater at tillering and grain harvest, respectively. A5MH-induced decreases in rhizosphere abundance (C-D) of root endophytic fungi were associated with increased crop biomass at tillering.

Conclusions: While the structure of rhizosphere soil fungal and oomycete communities altered as the wheat crop matured, only fungal communities were impacted by A5MH treatment due to increased Trichoderma and decreased abundance of recognized and emerging plant pathogenic fungi.