Soil microbiomes in three farming systems more affected by depth than farming system

Abstract

Agriculture, by its intentional design, manipulates the ecological functions of soils. It does so by altering carbon and nutrient inputs; by controlling the plant community; and in the case of tillage, by physically disrupting and redistributing the soil within the soil profile. While there are many studies that contrast soil microbiomes across farming systems, few studies have examined the effect of farming system on the vertical organization of taxa in the soil profile. We hypothesized that large effects of farming systems on edaphic factors would lead to large impacts on the microbial community that would reflect the underlying life history strategy of the microbes. For example, that tillage would increase the proportion of unicellular fungi. Our study compared farming systems that had been in place for 13 years in the mid-Atlantic region of the United States. Each system is a 3-year rotation of corn (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum), managed with either conventional no-till, conventional chisel-till, or using organic methods. We determined the relative effect of long-term farming system management on edaphic factors and the soil microbial community with depth structured sampling (0–5, 5–10, 10-Ap, Ap-30 cm). We found relatively small effects of farming system but substantial effects of depth on edaphic factors and microbial communities. For example, differences in management resulted in subtle differences in %C above the Ap horizon. Fungal gene abundance increased in the organic system relative to the no-till system, although neither fungal nor bacterial richness differed across farming systems. Farming system effects on microbial community composition were greatest in the top 10 cm but did not affect the abundance of unicellular fungi. Several groups including Pseudomonas and Mortierellomycota appear to be sensitive to redistribution by tillage in the organic system, but it is not clear to what extent this effect is due to legacy DNA from tillage.