Abstract
Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.
Highlights
Bioenergy crop production provides a promising opportunity to decrease energy dependence on fossil fuels and limit increases in atmospheric carbon dioxide (CO2) concentrations (Gelfand et al, 2013)
After cumulative-sum scaling (CSS) normalization and removal of low counts, there were 2,258 fungal OTUs with 997 OTUs found within the live (RNA) community and 2,048 OTUs found within the total (DNA) community
Live maize communities had a higher proportion of Basidiomycota (+10.0%) and significantly more Mortierellomycota (+11.9%) compared to the switchgrass live community, which contained significantly more Glomeromycota (+23.9%; Table 1)
Summary
Bioenergy crop production provides a promising opportunity to decrease energy dependence on fossil fuels and limit increases in atmospheric carbon dioxide (CO2) concentrations (Gelfand et al, 2013). Perennials have more extensive root systems than annuals, which have been shown to sustain a more diverse, but not necessarily larger (μg biomass C g−1 soil) microbial community (Liang et al, 2012a; Dou et al, 2013; Hargreaves and Hofmockel, 2014). A higher fertilization rate can impact microbial recruitment by decreasing the necessity for plants to support nutrient-acquiring symbionts such as AMF, and thereby lowering AMF root colonization and/or diversity (Oates et al, 2016; Emery et al, 2017; Jach-Smith and Jackson, 2018). It is essential to understand the plant-microbe interactions within bioenergy cropping systems, to optimize microbial contributions to C and nutrient cycling, plant productivity, and long-term soil C storage
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