Microbiome structure and interconnection in soil aggregates across conservation and conventional agricultural practices allow to identify main prokaryotic and fungal taxa related to soil functioning

Under conservation agriculture (CA), soil aggregates physically protect soil organic C, creating microhabitats with heterogeneities in nutrient availability. These may become rich in microbial taxa with structured interconnections, and thus maintain the equilibrium between C sources and sinks. A long-term experiment on tillage and N fertilization was used to investigate the microbiome within small macroaggregates (sM), and within occluded microaggregates (mM). At surface layer, N fertilization was the main determinant of prokaryotic and fungal alpha-diversity in sM and mM, whereas at subsurface tillage intensity was the primary driver. Moreover, although along soil profile a conserved microbial compositional core was found across managements, some taxa were uniquely found in certain treatments and microbiota structure was modified by tillage and N fertilization. Overall sM had a higher diversity of prokaryotes and a lower diversity of fungi than mM. Prokaryotic taxa, such as Actinobacteria, Chloroflexi and Thermomicrobia , and fungi, such as Agaricomycetes , Dydimellaceae , and Mortierellaceae , characterized sM, whereas others prokaryotes ( Betaproteobacteria , Sphingobacteriia , Blastocatellia ) and fungi ( Sordariales , Lasiosphaeriaceae and Glomeraceae ) characterized mM. Cross-domain networks were more complex in mM than sM at surface layer, and the opposite occurred at subsurface layer. Some prokaryotic and fungal taxa, retrieved in hubs, were positively linearly related to C cycling and soil structuring (e.g., Chloroflexi and Sordariomycetes ). Our results suggest that diversity and structure of microbiome is positively shaped by CA, and there are microbial taxa and network traits suitable as indicators of nutrient stocks and soil structuring under an agriculture focused on soil health. • N drives microbiome diversity and structure of surface soil aggregates and tillage at subsurface. • Small macroaggregates (sM) & occluded microaggregates (mM) varied in microbial structures. • A higher prokaryotic diversity was found in sM and a lower fungal diversity in mM. • Cross-domain network is more complex in mM than sM at surface, the opposite at subsurface. • Some microbes were positively linearly related to C cycling & soil structure.