Microniches harbor distinct bacterial communities at the soil-plant-earthworm interface

Earthworms modify soil physicochemical properties and microbial communities, although their effect on different soil microniches is unclear. Here, we aimed to elucidate the effect of the geophagous earthworm Pontoscolex corethrurus on bacterial communities in the bulk soil, rhizosphere and rhizoplane of two cultivated Coffea species. In addition, we assessed the similarity of the earthworm bacterial microbiome (anterior and posterior intestine and casts) with the soil bacterial communities. We implemented a mesocosm experiment with four treatments: 1) Coffea arabica with earthworms; 2) C. arabica without earthworms; 3) Coffea canephora with earthworms; 4) C. canephora without earthworms. We used 16S rDNA amplicon sequencing to study bacterial communities associated with soil microniches and P. corethrurus intestine content and casts. Our findings show that rhizoplane bacterial communities were markedly distinct from those of the bulk and rhizosphere soils, regardless of the coffee species or the presence of earthworms. Nonetheless, P. corethrurus influenced bacterial community composition and structure in the different soil microniches, at the phylum and genus levels. Strong differences were observed in bacterial community structure and diversity between soil and earthworm gut and cast samples, which suggests that the P. corethrurus gut bacterial microbiome is not predominantly derived from the surrounding soil. Bacterial communities from the anterior and posterior gut sections were dominated by different bacterial taxa than those in the casts. Our study is the first one to demonstrate earthworm-induced shifts in rhizoplane-associated bacterial communities and emphasizes the need to consider the earthworm gut as a complex environment with a specific bacterial community.