Soil structure and agricultural management drives niche differentiation among soil microbial communities

Background/Question/Methods

The global exploration of microbial diversity has focused primarily on coarse differentiation between ecosystems. However, little emphasis has been placed on soil microbial communities in agroecosystems, despite their considerable contribution to environmental pollution.  Moreover, the majority of studies addressing soil diversity neglect structural soil micro-environments that potentially foster high levels of niche dimensionality over small spatial scales, influencing overall microbial diversity.  In order to properly scale microbial activity to global biogeochemical cycles, it is imperative to study the interactive effects of soil structure and agricultural management on soil microbes while exploring mechanisms that support these hyper-diverse communities.  We used high-throughput sequencing methods to quantify the effect of agricultural management and soil structure on microbial community diversity and composition across three bioenergy cropping systems (corn-corn, prairie, and fertilized prairie) and a series of soil aggregate fractions at the Comparison of Biofuels Site (COBS) in Boone County, Iowa during 2012.  Using the Metagenomics Analysis Server pipeline (MG-RAST) we classified sequenced amplicons into operational taxonomic units (OTUs) and higher levels of taxonomy.  Along with community analysis we generated networks of taxa co-occurence to identify assemblages that may influence biogeochemical cycling in agroecosystems.

Results/Conclusions

When considering soil fractions, OTU richness and evenness was highest in soil micro-aggregates when compared to larger fractions (P<0.002).   Differences in community measures among aggregate fractions suggested a higher level of niche dimensionality and limiting resources within micro-aggregates, while larger aggregates with possibly more resources are less speciose and dominated by certain taxa.  Surprisingly, measures of richness and beta diversity (multivariate homogeneity of group dispersions) were not significantly affected by cropping treatment (P>0.05).  Using a permutational manova, we observed distinct community composition between prairie treatments and corn (P<0.001). When observing co-occurence at the level of taxonomic order between cropping-system treatments, distinct groups of microorganisms with similar ecological niches were important in each community.  Prairie treatments support networks of co-occuring heterotrophic taxa (Myxococcales, Spirochaetales, Verrucomicrobales) able to degrade organic material at varying states of decomposition, while the corn treatment was dominated by taxa known to participate in nitrification (Nitrososphaerales and Methylococcales).  These results reflect not only the link between ammonia-oxidizing bacteria and fertilizer use, but also demonstrate the potential benefits of prairie and fertilized prairie systems as sustainable bioenergy crops.