Soil aggregate size mediates the responses of microbial communities to crop rotation

Soil microorganisms play an essential role in the redistribution of soil aggregate sizes due to the microenvironmental changes. Yet, little is known regarding how individual microbial taxa within different-sized aggregates respond to agronomic practice. This study integrated physical, chemical, and molecular techniques (i.e., high-throughput DNA sequencing and qPCR) to assess the influence of corn-tobacco rotation on the soil microbial community at the soil microenvironment scale, i.e., within mega- (>2 mm), macro- (0.25-2 mm) and micro-aggregate (<0.25 mm) fractions. The soil samples (0-20 cm) analyzed in this study originated from corn and tobacco, which were cultivated under three different fertilization regimes. The results demonstrate that corn-tobacco rotation substantially impacted the distribution of aggregate sizes, and the shift in soil microbial communities associated with soil aggregates was related to changes in soil total carbon (TC), the C/N ratio and pH. The indicator microbial taxa (i.e., those were sensitive to crop rotation) varied with aggregate size. When compared with tobacco soil, the corn soil showed higher relative abundances of probably more copiotrophic taxa across large-sized aggregates, also with more bacteria in mega-aggregates and more fungi in macro-aggregates. Changes in total microbial communities associated with mega- and macro-aggregates in response to crop rotation were driven mainly by alterations in bacterial and fungal communities, respectively. Overall, the results of this study demonstrate that soil aggregate size strongly affected the microbial community composition on agricultural fields, promoting the differential responses between bacteria and fungi to crop rotation in specific size of aggregates.