Soil microbial communities are responsible for cycling nutrients essential for bioenergy crop productivity. Thus, maximizing bioenergy yield for sustainable energy production requires an understanding of how environmental variables alter microbial community composition. Crop and soil type have both been identified as main drivers of community composition depending on the type of organism (bacteria versus fungi) and the type of community (active versus total). While metabolically active (RNA) and total (DNA) bacterial and fungal communities are compositionally different in various ecosystems, investigations of cropping systems typically report only one of the two, assuming similar responses to environmental variables. To explore soil microbial community composition changes under dominant bioenergy crops, we characterized both the active and total bacterial and fungal communities under maize and switchgrass production in two long-term experimental sites differing in soil texture (sandy versus silty). We hypothesized that composition of bacterial communities would be largely driven by soil type due to its influence over soil moisture. In contrast, we hypothesized that fungal communities would be impacted by crop type due to the wider metabolic capabilities of fungi. Simultaneous RNA and DNA amplicon sequencing allowed us to elucidate active and total microbial community composition within bioenergy cropping systems.
Results/Conclusions
We found community type (active versus total) to be the top explanatory variable, explaining 30% of bacterial and 8% of fungal community composition. Species richness differed between community types with higher richness in the active bacterial and total fungal communities. Since active and total communities were markedly different, we analyzed bacterial and fungal community types separately to identify environmental drivers of each. Soil type explained 28% of bacterial and 16% of fungal community composition while crop type explained 11% for both communities with similar R-squared values between active and total communities. Indicator species analysis revealed Glomeromycota, a fungal phylum comprised of arbuscular mycorrhizal fungi known to associate with plant roots, as abundant and indicative of early growing season perennial crops (i.e. switchgrass).Crop inputs took a backseat to edaphic variables (soil type) in shaping microbial community structure, yet influenced key members in our bioenergy cropping system. Our results show radically different active microbial communities in terms of diversity and composition compared to the total community and therefore inferring functional activity based on total community dominance is not reliable. However, total communities captured the main environmental drivers of active community composition, which is a primary goal of ecology.