ALIENinSoil · Microbial community response to the invasion of a non-endemic fungal bio-inoculant in soil

Microbial community response to the invasion of a non-endemic fungal bio-inoculant in soil

Fungi and bacteria are utilised to produce microbial-based fertilisers and pesticides worldwide. These bioinoculants have a vast potential in agriculture because they can help increase crop yields and quality and reduce the application of chemicals. While the effectiveness of bio-inoculants as biofertilisers or biopesticides is widely tested for crop yield and pathogens control, little is known about the effect of bioinoculants on microbial assemblages in the non-rhizospheric soil of agroecosystems. ALIENinSoil project evaluated the impact of a fungal inoculum, the globally used biofertiliser Trichoderma afroharzianum T22, on microbial assemblages of a model soil system. The fertiliser industry has selected this fungus to be very competitive and exhibit specific functions. Like all bioinoculants, it can influence soil properties, crops and pathogens by producing hormone-like compounds, antibiotics, secondary metabolites, siderophores, and organic acids. The fungus has proven effective in supporting many crops; however, it is not known how these interactions and compounds might affect the native soil microbial biology in agroecosystems. Furthermore, the size of such a change can depend on many variables, like the initial alpha and beta diversity of the community or the bioavailability of nutrients. The project applied a rapid metagenomic approach based on long-read Oxford Nanopore Technology to assess the effects of the fungal inoculum on soil microbial communities and functions in a laboratory-based microcosms experiment. Metagenomics is based on the analysis of all DNA present in environmental samples and, thus, the genetic material belonging to all organisms present in that environment, which in the case of this project is soil. Innovative and cutting-edge techniques were used to understand 1) to what extent the native microbial community richness and relative abundance are influenced by a competitive fungal strain introduced to soil; 2) whether the keystone microbial taxa are resilient to the disturbance by the introduced fungus 3) how far the bioinoculant impacts the functions of soil microorganisms. A better knowledge of the interaction mechanisms between a massively introduced fungal species and the resident communities can stimulate innovation in soil bioinoculants and agriculture through competitive technology transfer. We showed that Oxford Nanopore sequencing has great potential for real-time diagnostics in agricultural surveys and the development of indicators for monitoring soil biodiversity and functionality.

Data: CORDIS, © European Union