Abstract
Plant and soil properties cooperatively structure soil microbial communities, with implications for ecosystem functioning. However, the extent to which each factor contributes to community structuring is not fully understood. To quantify the influence of plants and soil properties on microbial diversity and composition in an agricultural context, we conducted an experiment within a corn-based annual cropping system and a perennial switchgrass cropping system across three topographic positions. We sequenced barcoded 16S ribosomal RNA genes from whole soil three times throughout a single growing season and across two years in July. To target the belowground effects of plants, we also sampled rhizosphere soil in July. We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects (annual vs. perennial inputs) than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil. We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity. In July, cropping system and rhizosphere structured a small but specific group of microbes implying a subset of microbial taxa, rather than broad shifts in community composition, may explain previously observed differences in resource cycling between treatments. Using rank abundance analysis, we detected enrichment of Saprospirales and Actinomycetales, including cellulose and chitin degraders, in the rhizosphere soil and enrichment of Nitrospirales, Syntrophobacterales, and MND1 in the whole soil. Overall, these findings support environmental filtering for the soil microbial community first by soil and second by the rhizosphere. Across cropping systems, plants selected for a general rhizosphere community with evidence for plant-specific effects related to time of sampling.
Highlights
Soil microorganisms mediate biogeochemical transformations that underpin important ecosystem functions
We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil
We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity
Summary
Study siteWe conducted this study as part of the Landscape Biomass Project at the Uthe Research & Demonstration Farm in Boone County, Iowa, USA (41°55'N, 93°45'W), where plots of approximately 0.05 ha were established in fall 2008 and first planted in spring 2009. Soils at the site are classified as fine-loamy Hapludoll Mollisols and follow a topographic gradient with a slope of approximately 0.5% on the summit and approximately 2.5% on the side slope (back slope and toe slope), as described in detail in Wilson et al [32]. Prior to study initiation in 2008, summit and side slopes were managed under a corn-soybean rotation with corn in rotation in 2008. This history of annual-based agriculture may leave a legacy on the microbial community such that changes between microbial communities in the whole soil of annual and perennial cropping systems may be relatively slow (i.e. decades) [34]. Average rainfall was recorded at the end of summer 2011, followed by a record drought in 2012 [32]
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