Ecosystem functions, such as the nutrient cycling of soils and emissions of greenhouse gases, are highly dependent on the bacterial and fungal communities in soil and plants. These communities determine the ecosystem services these ecosystems are providing. Molecular techniques, such as meta-barcoding and functional metagenomics provide emerging tools to understand ecosystem services and ecosystem functioning alike. There are many open questions on soil functioning; for example, we do not understand the interactions between soil microbial diversity and soil functioning. Also, the role of legacy responses and the long-term impacts of disturbances on below-ground processes are not well documented. The proposed session aims to attract scientists from metagenomic research as well as from the ecosystem functioning and ecosystem service communities to bridge the current gap between metagenomics of plants and soils and ecosystem services. The work is associated with the Biodiversa+-funded MicroEco and the EU Eco2adapt projects.