A core microbiota of the plant-earthworm interaction conserved across soils

Abstract The core microbiota defines the fraction of microorganisms common to all individuals from the same host species regardless of the abiotic context, be they located inside (e.g. animal guts) or outside (e.g. plant rhizospheres). While the core microbiota of many host species have been documented, no study attempted to decipher how these core microbiota could be altered when their respective host species are interacting. We thus tested the hypothesis that interactions between different host species possessing external microbiota could result in a novel emerging entity: a core microbiota of an interaction. This is particularly true in soils, where such interactions are likely to occur between different host species harboring external microbiota, like plants through rhizospheres and earthworms through drilospheres. Using three contrasting soils (sand, loam or clay) and a meticulous sampling of different microhabitats (rhizospheres, casts and bulk) coupled to a “source-sink approach” derived from the meta-community theory, we evidenced the presence of a conserved core microbiota of bacterial OTUs resulting from plant-earthworm interactions in all soils. This interaction was also evidenced using a tailored network analysis, revealing the presence of signature OTUs always found in earthworms casts and plant rhizospheres, and whose co-occurrence patterns were indicative of soil type. Furthermore, qPCR abundance estimates revealed that not only bacteria, but also fungi and archeae, are affected by plant-earthworm interactions. Our findings provide a new framework to explore aboveground-belowground interactions through the prism of microbial communities.