Sampling the control bulk soil for rhizosphere and drilosphere microbial studies

Abstract

Microbial communities dwelling in biogenic structures shaped by soil macroorganisms (e.g. rhizosphere of plants, drilosphere of earthworms) are often compared to communities in the bulk soil taken as a control. Two strategies are currently applied, by sampling either bulk soil surrounding the biogenic structures inside the same experimental unit (“surrounding bulk”) or soil from a distinct control unit without macroorganism (“pristine bulk”). While surrounding bulk is commonly used, no studies explicitly compared these two bulk types. Moreover, the potential effect of plants and earthworms on microbial communities in the surrounding bulk could depend on soil properties. In controlled conditions, we exposed three soils with contrasting properties to either a plant, earthworms, both, or without macroorganisms (pristine bulk). Root-adhering soil, casts and their surrounding bulk were retrieved by meticulous sampling. We found that molecular abundances of bacteria, fungi and archaea were modified in surrounding compared to pristine bulk. In a non-trivial manner, bacterial community structure from surrounding bulk was significantly altered by plants in all soils, while the influence of earthworms was soil-dependent, in a way related to C and N contents rather than texture. When comparing macroorganism influenced versus non-influenced soils, the pristine bulk should thus be preferred, whereas the surrounding bulk is appropriate to characterize the sphere of influence of biogenic structures.