Alterations in soil structural properties created by agricultural management practices have a significant influence on soil aggregation, which manages the chemical and physical heterogeneity of soil properties, and, consequently, the distribution of microorganisms and their activity among aggregates of different sizes. Despite the essential role of soil microbial communities in C sequestration, green house gas emission and formation of soil aggregates, attempts to determinemicrobial community distribution within various size aggregates have received little attention. This study evaluated bacterial diversity of different aggregate size classes of soil samples using bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rDNA gene. Soil samples (clay loam, 38% clay, pH of 7.5) were collected from the 0-5cm depth from a long-term (8 years) study with 5 integrated crop and livestock (beef cattle) systems. A wet-sieving fractionation method on field-moist soil was used to separate the bulk soil into macroaggregates (>250 um), microaggregates (53-250 um) and silt+clay (< 53 um). Distance-based redundancy analysis (db-RDA) using relative abundances of the predominant 29 phyla/ subphyla and also using 1000+ species was used to test for differences in overall bacterial community composition.
Based on phyla level data, the soil bacterial community composition was significantly impacted by the system treatment and by location within the soil microenvironment (i.e., soil fraction). No significant interaction was observed. For both phyla and species level information, differences between aggregate fractions were significant, indicating that soil aggregates represent a distinctive microenvironment capable of selecting for specific microbial lineages. Microaggregate fractions were distinguished by higher abundance of Rubrobacteriales, Chloroflexi phyla, while macroaggregate samples indicated a large quantity of TM7 phyla. Actinobacteria, although dominant phyla in all fractions, has relatively larger occurrence in microaggregate fractions. Though silt/clay fractions contain equivalent arrays of diverse bacterial phyla this fraction is dominated by the numerous Proteobacteria subphyla as well as Firmicutes and Verrucomicrobia phyla. To our knowledge, this is the first study that investigates bacterial community composition within the soil microenvironment using pyrosequencing technology, which revealed differences in bacterial diversity across aggregates that may affect C sequestration.