A Novel Fungicide Consortium: Is It Better for Wheat Production and How Does It Affect the Rhizosphere Microbiome?

Chemical fungicides play a key role in protecting crops, but their use can result in environmental problems. We tested a novel fungicide, composed of endophytic microorganisms, for its effect on wheat yield, grain quality, plant development, and the rhizosphere microbiome, assessed by 16S and ITS metabarcoding. The fungicide increased the grain yield, the effect being similar to a well-known commercial bacterial fungicide, without affecting its quality. Ascomycota, Zygomycota and Mucoromycota together comprised 80% of the mycobiome. Mucoromycota/Mucoromycetes/Rhizopodaceae/Rhizopus arrhizus were significantly decreased. The dominant (≥10%) bacterial phyla were Pseudomonadota, Acidobacteriota, Bacteroidota and Actinomycetota, but their fungicide-related differences were small or random. Different modes of fungicide application (seeds only, seeds plus one or two foliar applications) had no effect on wheat characteristics. Neither of the fungicide’s agents (Raoultella ornithinolytica and Pantoea allii) were found in the rhizosphere. The changes in the mycobiome seemed more pronounced than in the bacteriobiome. The proposed preparation is concluded to have good prospects as a fungicide. However, the low species/strain resolution of the DNA metabarcoding did not allow us to fully interpret shifts in the microbiome diversity, both agronomically and environmentally. These aspects need more comprehensive investigation, using methodology with higher species resolution.