Assembly of abundant and rare bacterial and fungal sub-communities in different soil aggregate sizes in an apple orchard treated with cover crop and fertilizer

Soil bacterial and fungal communities often comprise the “abundant biosphere” and “rare biosphere”, which co-exist in soil aggregates to form a complex system of inter-species interactions. However, the different assembly processes exhibited by abundant and rare bacterial and fungal communities due to the spatial isolation of aggregates are still unclear. In this study, the stochastic and deterministic processes associated with the assembly of abundant and rare sub-communities of bacteria and fungi were quantified in different sized soil aggregates in apple orchards treated with a cover crop and fertilizer. The importance of variable selection in the assembly of the abundant bacterial community increased from macroaggregates to small microaggregates. The assembly of the rare bacterial community followed a transition from homogeneous selection to weak homogeneous selection with decreases in the soil organic carbon and total nitrogen contents. Both the abundant and rare bacterial community assemblies in soil aggregates were not limited in terms of their dispersal. The assembly of the abundant fungal community was dominated by stochastic processes, whereas the assembly of the rare fungal community was dominated by homogeneous selection and limited dispersal in different sized soil aggregates. The compositions of the abundant and rare bacterial and fungal communities were also affected by soil aggregates and agricultural practices. Most of the top 20 operational taxonomic units (OTUs) with high abundances among bacteria and fungi were related to the macroaggregate amounts compared with rare bacteria and fungi, and some OTUs among abundant fungi were related to the microaggregate and small microaggregate amounts. This study provides a priori hypotheses for testing in future experiments, thereby facilitating a systematic approach to understand the mechanisms responsible for the changes in the fungal and bacterial community compositions in different sized soil aggregates. [Display omitted] •Abundant fungal community assembly was dominated by stochastic processes in aggregates.•Rare fungal community assembly was dominated by homogeneous selection and dispersal limitation.•Assemblies of abundant and rare bacterial communities were more affected by aggregate size fraction.•A conceptual model related to bacterial community assembly driven by fungi and aggregates was developed.