Soil aggregate modulates microbial ecological adaptations and community assemblies in agricultural soils

Soil aggregates provide spatially heterogeneous microenvironments for soil microbiome and ecological processes. Revealing the nuances of assembly processes in aggregates is critical for understanding the fine-scale organization of the soil microbiome and associated biogeochemistry. However, the effect of aggregate sizes on microbial assemblies remains poorly explored. In this study, we investigated the mechanism underlying the assembly processes of microbial communities within three different aggregates sizes across five long-term fertilization experimental stations throughout eastern China. Our results showed that although geographic sites explained most of the variations in microbial composition in aggregates, aggregates of the same size selected phylogenetically closely related microbial species with similar ecological preferences for specific nutrient variables. Null model analysis showed that environmental selection and dispersal limitation primarily governed the assembly of aggregate bacterial and fungal communities, respectively. The relative importance of deterministic processes on microbial communities increased with the increasing aggregate size across all sites. Multiple stepwise regression analysis indicated that nutrient variables associated with community assembly are distinct in different aggregate-size fractions. Bacterial assembly is mainly affected by total carbon and soil organic carbon in macro- and micro-aggregates, whereas it is influenced by the C/P ratio in the silt + clay fraction. For fungal community assembly, the C/N ratio was the major factor in macroaggregate and silt + clay fractions, while N/P ratio had stronger effects in the microaggregates. Furthermore, fertilization effects on the microbial community assembly processes varied across aggregate sizes. Organic fertilization led to a decrease for bacteria while an increase for fungi in the sorting/dispersal effect ratio. The magnitude of such an impact was higher for macro- and micro-aggregates. GeoChip and enzymatic results further demonstrated the regulation of ecological clusters and functions by nutrient variables across aggregates. Our findings highlight that microbial assembly and functional traits in large aggregate-size fractions are susceptible to nutrient changes, and thus can act as potential biological indicators for sustainable management of agricultural soils.