Land-use intensification differentially affects protist community and decreases microbiome network complexity

Soil microbial communities are major drivers of biogeochemical cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land use intensification on the soil microbiome is still poorly understood. Here, we investigated in a long term field experiment the consequences of changes in land-use intensity (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) based on cropping frequency on bacterial, protist and fungal communities as well as on their co-occurrence networks. We showed that the structure and composition of bacterial, protist and fungal communities exhibited significant differences across land uses, however only the bacterial diversity was affected by the land-use type. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands and highlighted the predominance of protists, in particularly Rhizaria, in soil microbial associations, as they showed higher number of connection than bacteria and fungi in all land uses.