Sustainable Agriculture: Role of Metagenomics in Exploring the Soil Microbiota

24 June 2021

The implementation of the EU Farm to Fork Strategy will require an environmentally-friendly utilization of existing natural resources to secure sustainable food production, including a fair use of agricultural land. To reach the 2030 targets, growers will need to change agronomic practices, including soil management, and minimize the use of chemical inputs, the consequences of which on soil microbial communities and plant nutrition are currently unknown.

Soil microbial communities are an important component of the agroecosystem, affecting biogeochemical cycling (e.g. mineralization of organic nitrogen into bioavailable forms and carbon storage) and, ultimately, plant productivity. Soil microbial diversity is usually considered an indicator of soil health and quality, and thus of soil fertility.

A wide range of microorganisms is involved in soil functions, but individual microbial species manipulate plant hormone levels and may cause severe inhibition of root growth. The presence of beneficial microorganisms in balanced microbial communities can, however, mitigate or reverse the adverse effect of other microbial species and positively modulate the plant microbiome. Understanding how the dynamics of soil microbial communities under changing conditions is affecting symbiotic associations of arbuscular mycorrhizal fungi and nitrogen-fixing bacteria with terrestrial plants and root colonization by commensal bacteria will also be crucial to predict the impact on plant mineral acquisition and immune system modulation.

Soil metagenomics is based on the isolation of soil DNA and the production of libraries that are amenable to massive parallel sequencing. With the depth of coverage that is now inexpensively provided by high-throughput sequencers, it is possible to detect and quantify all traces of microbial DNA in a species-specific manner and monitor how soil microbial communities change in response to changing climate, reduction of fertilizer use and replacement of chemical and more hazardous pesticides. Coupled with analyses of the root microbiome and root transcriptome, soil metagenomics is changing the way we study plant-microbe rhizosphere interactions.


Stay tuned for updates on our soil metagenomics projects!