Soil microbial diversity in agriculture : Responses to land-use and extreme weather events

Sammanfattning: Land-use intensification of agricultural soils and increased occurrence and intensity of extreme weather events like drought periods are two of the main threats responsible for soil biodiversity declines. These changes in soil biodiversity can alter ecosystem functions performed especially by soil microbial communities that could further contribute to those threats. Microbial diversity is an essential key for the understanding of ecosystem functioning, however the diversity of functions performed by soil microorganisms and how they are linked to ecosystem functions like carbon cycling remain largely unexplored. The aim of this thesis was to understand how the taxonomic and functional diversity of soil microorganisms in agriculture are influenced by agricultural land-use intensification and extreme weather events, specifically short-term drought. Thus, a combination of field experiments across Europe and glasshouse experiments along with different molecular methods, specifically high-throughput sequencing-based omics approaches was used. Different land-use types (grassland and agricultural soils) affected soil microbial communities, particularly their response in relation to soil organic matter degradation. It was found that crop management practices, i.e., crop residue incorporation promoted gene expression in these soils, particularly in agricultural soils. These findings support the notion that careful land-use practices have the potential to mitigate losses of soil organic carbon in traditionally carbon depleted soils and can thereafter promote the functioning of soil microorganisms. Further, interactive effects of long-term agricultural management and short-term drought on the communities of plant-associated arbuscular mycorrhizal fungi (AMF) were studied. Organic and conventional long-term farming systems influenced the taxonomic composition of AMF, while the effects on their diversity were negligible. No effect of short-term drought on the diversity and composition of AMF was found. To further explore how short-term drought influence the functional diversity of soil microorganisms in agricultural soils, particularly on the gene level, functional genetic diversity was assessed. By studying the diversity of extracellular enzymes related to soil organic matter degradation, it was found that functional and taxonomic gene composition significantly differed between European agricultural fields (Sweden, Germany, and Spain). However, the effect of short-term drought was only observed in Germany. These results indicate that soil microorganisms are differently adjusted to short-term drought, either due to (a) regional adaptations of microorganisms to already dry environments or (b) differences in soil physicochemical properties like soil organic carbon content, as it has the potential to buffer drought effects. Finally, the short-term drought also affected the response of soil microbial communities in these soils, especially in their gene expression towards degrading soil organic matter. Altogether, these findings show that soil microorganisms respond differently to agricultural land-use intensification and extreme weather events such as drought. Careful land-use practices like the incorporation of crop residues, specific farming systems and increased levels of soil organic carbon have the potential to mitigate the negative effects of drought on soil health and soil microorganisms. Moreover, these findings demonstrate the importance of studying microbial responses to drought at different diversity levels, with the necessity to link taxonomic and functional diversity to soil ecosystem functions.