Intra-aggregate Pore Structure Influences Phylogenetic Composition of Bacterial Community in Macroaggregates

It is known that variability in the characteristics of soil physical microenvironments, e.g., locations and characteristics of soil pores, can have a major influence on microorganisms. This study compared the characteristics of intra-aggregate pores and their relationships with bacterial community composition in 4-to 6-mm soil macroaggregates from two contrasting agricultural systems, namely a corn (Zea mays L.)-soybean [Glycine max (L.) Merr.]-wheat (Triticum aestivum L.) rotation (i) with conventional chemical inputs and (ii) without chemical inputs but with legume cover crops. Characteristics of intra-aggregate pores and particulate organic matter (POM) were obtained from three-dimensional X-ray computed microtomography aggregate images at 13-mm resolution. Microbial community analyses were conducted using 16S rRNA pyrosequencing. We found that the aggregates from long-term (>20 yr) organic management with cover crops differed from the aggregates from conventional management in terms of intra-aggregate pore-size distribution, intra-aggregate pore variability, POM contents, as well as microbial community compositions. Relative abundances of Actinobacteria, Proteobacteria, and Firmicutes in the aggregates from cover-crop-based management were positively correlated with the presence of large (>110 mm) pores, while the presence of medium-sized pores (32-84 mm) was significantly correlated with 30 to 40% of the top 100 bacterial operational taxonomic units identified during sequencing. The results suggested that the legacy of rhizosphere presence in terms of intra-aggregate pore structure and microbial community composition can last in the studied soil for at least 4 to 9 mo. Our study demonstrated that working with bulk sieved soil samples can mask substantial differences present within distinct soil aggregate units.