A core microbiota of plant and earthworm interaction? Phylogenetic and functional aspects

International audienceThe core microbiota concept has been proposed to describe the subset of a microbiota (e.g. the rhizosphere microbial community) associated with a given host (e.g. a plant) going beyond macroenvironment differences (e.g. soil type), and characterized by taxonomic markers (e.g. 16S rRNA gene sequences). Its existence has been questioned by geographical studies, showing the overruling soil type effect in shaping microbial communities. As far as biotic determinants are concerned, several “hosts” or macroorganisms are impacting a given habitat and its specific microbial community. In soils, there is an overlap between the so-called rhizosphere and the drilosphere, defined as the functional domains under the influence of plant roots and earthworms respectively. Plants and earthworms have been sharing the same soils over geological times, thus microbial communities living at the congruence of rhizosphere and drilosphere could be specific of plant-earthworm interaction, as a consequence of their coevolution. Here we tested the hypothesis of a specific core microbiota at the interface of two interacting macroorganisms, in three different soils. We grew barley in microcosms in the presence/absence of the endogeic earthworm Aporrectodea caliginosa. We investigated the structure of microbial communities and quantified their abundance. Because interactions between earthworms and plants have been proposed tobe mediated through the mineralization of organic matter and the release of nutrients, we also studied the abundance of genes involved in nitrogen cycling in different micro environments (bulk soil, rhizosphere and earthworm casts). 16S rRNA gene amplicon sequencing revealed the presence of microsites core microbiota over the three soil types. Despite an expected strong influence of soil type on microbial community composition (59% of explained variance), significant effects of both microsites (13%) and macro-organisms presence (7%) were observed. Many genes of the nitrogen cycle were influenced by soil type, whereas earthworms were only responsible for an increase in the abundance of the ureC gene. The interaction between plant and soil type was modifying the abundance of nosZ, nifH and narG, in the rhizosphere suggesting a strong control of the nitrogen cycle by the plant dependent on soil fertility. A refined analysis on each soil separately revealed a significant interaction between plant and earthworm presence on the structure of the rhizosphere and drilosphere microbiota. This suggests that assembly of microbial community in plant rhizospheres and earthworm casts was dependent on the mutual presence of earthworm and plant respectively. Several bacterial species were significantly enriched at the interface of plant rhizosphere and earthworm casts, suggesting that direct/indirect relationships between macroorganisms associated microbiota resulted in recruiting and promoting specific members