Intra-aggregate pore structure influences phylogenetic composition of bacterial community in macroaggregates

<p>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.</p>