Microbial co-occurrence analysis reveals community restructuring during organic matter degradation in millimeter-sized soil aggregates

Soil microorganisms are essential to the processes and cycles that sustain terrestrial ecosystems. They mediate the decomposition of fresh organic matter derived from plant material, driving its transformation into a complex array of microbial products that ultimately form stable soil organic matter. Despite their central role, the extent to which microbial community composition and interactions within these communities shape the transformations of organic matter remains poorly understood.

In this study, we analyse the relationship between the structure of microbial communities and the degradation state of organic matter in individual millimeter-sized soil aggregates sampled from a Beech forest. Microbial communities were characterized by sequencing the 16S rRNA gene (bacteria and archaea) and the ITS region (fungi). Using co-occurrence network analysis and relating microbial composition to biogeochemical parameters (such as C, N, δ¹⁵N, and δ¹³C), we were able to determine three groups of bacteria: generalists, whose abundance does not depend on the degradation state of organic matter, and two groups of specialists – one abundant in soils that are rich in fresh organic matter, and the other abundant in soils that are dominated by more recycled organic matter. While generalists are abundant in all aggregates, the relative abundance of specialists alternates in samples across the gradient of carbon availability. This pattern observed for bacteria is less clear for fungi, for them we distinguish generalists that appear in all samples independent on carbon availability from specialists that are abundant in carbon rich samples. Our findings reveal that the structure of microbial communities in millimeter-sized soil aggregates is closely linked to specific states of carbon recycling. Moreover, this pattern remains consistent across different seasons of the year. Our study highlights the interplay of spatial and temporal complexity of microbial dynamics within soil ecosystems, and the utility of co-occurrence analysis.