Microbial community composition and function in soil aggregates from a fertilized prairie

Background/Question/Methods

Soil structure affects the composition and function of microbial communities that regulate the biogeochemical cycling of carbon (C) and nutrients.  Although upland soils typically are considered oxic, the heterogeneous nature of redox conditions driven by anaerobic microsites may structure microbial community composition and function within the soil matrix.  The objective of our empirical study was to understand how soil structure affects the diversity and respiratory potential of microbial communities in prairie ecosystems.  We examined microbial community diversity and function across soil aggregate fractions that vary in C and nitrogen (N) content. Paired-end 16S rRNA amplicon and shotgun metagenomic sequencing were used to assess differences in microbial community composition and functional potential among soil aggregate fractions.  We processed our 16S rRNA data through the QIIME pipeline and quantified microbial community differences across four aggregate size classes and whole soil. The assembled metagenomic data was classified using the SEED subsystems database.  Analysis among aggregate fractions focused on subsystems that confer anaerobic capabilities to microbial communities, as we hypothesized that redox potential and therefore microbial anaerobic capacity may vary across soil aggregates.  

Results/Conclusions

In upland agricultural soils, we detected the genetic potential for anaerobic microbial metabolic pathways (e.g. denitrification, methanogenesis, sulfur oxidation, etc.) did not differ across aggregate fractions or whole soil in absolute abundance or composition (P > 0.1, permutation test for absolute abundance/diversity; P > 0.8, permutational manova for composition of contigs).  Alternatively, phylogenetic composition based on 16S rRNA varied across aggregate fractions (P=0.0001, permutational manova) following gradients of C and N availability.  Whole soil had roughly 60% less microbial OTUs than predicted by measurements from soil aggregates.  Despite these differences in community composition, there were no clear differences in anaerobic respiratory capacity among these communities, suggesting a high level of functional redundancy based on SEED subsystems. When aggregates were scaled to the relative proportions that occur in soil, large macroaggregates had the greatest potential to contribute to anaerobic respiratory processes that produce greenhouse gases via denitrification (N₂O) and methanogenesis (CH₄).  Our results suggest that deep sequencing of microbial communities can provide insights into microbial community composition and functional capacity that are not necessarily captured by whole soil sampling alone.