Earthworm feeding guild affects the selective activation of fermenters in the earthworm alimentary canal

The earthworm alimentary canal is an anoxic microzone in aerated soils, constituting an oasis for microorganisms capable of anaerobiosis. The feeding habits of the anecic Lumbricus terrestris and the endogeic Aporrectodea caliginosa are distinct, as the former mostly ingests large amounts of plant litter, whereas the latter mainly ingests mineral soil. Due to these contrasting ecotypes, we hypothesised that fermenters along the two alimentary canals are dissimilar and would yield contrasting processes. Fermentation products of four sections (crop/gizzard, fore-, mid-, and hindgut) of the alimentary canals of L. terrestris and A. caliginosa were analyzed. Bacterial 16S rRNA and 16S rRNA gene sequences were obtained by Illumina sequencing. L. terrestris and A. caliginosa specimens emitted H2 in vivo. Profiles of glucose and organic acids along the alimentary canal of both earthworm species were similar in quality, but dissimilar in quantity. Succinate and acetate were the predominant fermentation products, indicative of mixed acid fermentations. The alimentary canal of A. caliginosa was characterized by (1) a similar relative abundance of 16S rRNA based phylotypes across all sections, at both gene and transcript levels, (2) Bacillaceae and Bradyrhizobiaceae being the most abundant taxa in all sections, and (3) a higher relative abundance of Acidobacteria in mid- and hindgut compared to crop/gizzard and foregut. In marked contrast, the alimentary canal of L. terrestris was characterized by (1) dynamic changes in relative abundance of phylotypes on both gene and transcript level, (2) these dynamics being particularly pronounced at the transcript level, (3) Enterobacteriaceae and Pseudomonadaceae dominating the crop/gizzard and foregut, and (4) Aeromonadaceae and Flavobacteriaceae dominating the mid- and hindgut. The majority of the detected taxa are capable of facilitating mixed acid fermentations, while some are capable of facilitating denitrification and iron reduction, both processes previously detected in the gut of earthworms. The phylogenetic dissimilarity of the taxa in L. terrestris and A. caliginosa likely reflects the dissimilar microbiomes of the contrasting ingested material of these earthworms (i.e. mainly litter and mineral soil, respectively), while the detected fermentation products reflect a functional redundancy of the gut microbiota of both earthworm species. H2, a product of mixed acid fermentation, is emitted in vivo by the earthworm and could drive secondary redox processes in aerated soils.