Linking microbial metagenomes to biogeochemical cycles in biofuel cropping systems

Background/Question/Methods

A major goal of microbial and ecosystem ecology is to explore the link between microbial genetic potential and biogeochemical cycling in soil. The decomposition of soil organic matter and the transformation of nitrogen are driven largely by microbial metabolism. Therefore understanding how plant communities and agricultural management systems influence the functional composition of soil microbial communities is paramount for reducing environmental impacts associated with agroecosystems, such as greenhouse gas emissions, nitrate leaching, and loss of soil organic matter. Additionally, environmental heterogeneity as a result of soil aggregation should differentiate niches and functional profiles of microbial communities at small spatial scales within soil, causing concomitant shifts in biogeochemical cycling.  Here we investigate extracellular enzyme activity, genes encoding for enzymes and the taxonomic origin of genes among soil aggregates to link genetic and biogeochemical potential within the soil matrix. Soil samples were collected from continuous corn, prairie, and fertilized prairie plots at the Comparison of Biofuel Systems (COBS) experiment in central Iowa, USA. Soil aggregate fractions were isolated via sieving followed by biogeochemical and molecular analyses.   Deep whole genome sequencing was coupled with extracellular enzyme activity assays and analyzed using the DOE Systems biology Knowledgebase (KBase) pipeline.

Results/Conclusions

Cropping system significantly affected C and N degrading enzyme activity, with greater activity in soils under prairie compared to continuous corn (P<0.05). We also observed enzyme-specific differences in potential activity among the aggregate classes. Beta-glucosidase activity was high in all aggregate fractions and correlated with the abundance of genes encoding for this enzyme (R²= 0.30, p = 0.08).  Cellobiohydrolase and beta-xylosidase activity was 10 fold lower than beta-glucosidase, and positive correlations with gene abundance were restricted to the microaggregate fractions (R² ≥ 0.43).  These results suggest that C-cycling genes and enzymes covary at different scales within the soil habitat, possibly leading to substrate-specific decomposition rates within and across aggregate fractions.  Comparing across cropping systems and within the microaggregate fractions, we detected differences in the abundance and variation of other C and N cycling genes (e.g. denitrification genes). Overall, these data suggest that microbial function is not homogenous throughout the soil, and that cropping systems, in part through their effect on aggregate size distribution, result in differential microbial cycling of C and N within microhabitats.