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

Project description

Making sure native soil microbes are not adversely affected by fungal fertilisers

The use of microorganisms from nature to combat agricultural pests and provide essential nutrients for growth is an important way to reduce the use of harsher chemical pesticides and fertilisers. However, while it is known that introducing non-native species affects ecosystems on a macroscale, the effect of these microorganisms on the endemic microbial species and local community functions in soil has not been studied in depth. The EU-funded ALIENinSoil project is investigating the effects of a fungus, widely used as biofertiliser, on microbial communities in a model soil system. Utilising Oxford Nanopore Technologies sequencing, which enables the direct, real-time analysis of long DNA fragments, the team will evaluate if the presence of this foreign fungus affects the growth and functioning of the native microorganisms.


Fungi and bacteria are utilised for the production of microbial-based fertilisers and pesticides worldwide. These bioinoculants have a huge potential in agriculture because they can help to increase crop yields and quality and allow a reduction in the application of chemicals. While the effectiveness of bio-inoculants as bio fertilisers 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. A sudden artificial introduction of a fungal species in soil could create a substantial impact on the biodiversity of endemic microbial species and local community functions, as well as lead to changes in the food webs and nutrients availability. ALIENinSoil will, therefore, assess the impact of a fungal inoculum, the globally-used biofertiliser Trichoderma afroharzianum T22, on microbial assemblages of a model soil system. The project will apply an innovative 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. Thus, this project will use innovative and cutting-edge techniques to understand 1) to what extent the native microbial community richness and relative abundance is influenced by a competitive fungal strain introduced to soil; 2) whether or not the keystone microbial taxa are resilient to the disturbance by the introduced fungus 3) how far the bioinoculant impacts the functions of soil microorganisms. With this action, I want to acquire new in-depth knowledge necessary to stimulate innovation in the field of soil bioinoculants and agriculture by way of competitive technology transfer. Oxford Nanopore sequencing has great potential to be used for real-time diagnostics in agricultural surveys and the development of indicators for monitoring soil biodiversity and functionality.


Net EU contribution
€ 224 933,76
SW7 5BD London
United Kingdom

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London Inner London — West Kensington & Chelsea and Hammersmith & Fulham
Activity type
Public bodies (excluding Research Organisations and Secondary or Higher Education Establishments)
Total cost
€ 224 933,76