Microbiome dynamics during cast ageing in the earthworm Aporrectodea caliginosa

Abstract

Earthworm casts are hotspots of microbial activity playing an important role in the nutrient cycling of soil ecosystems. Cast ageing can be considered an ecological succession, where copiotrophic bacteria are replaced by oligotrophic bacteria as the ratio labile/recalcitrant substrates decreases. Here we use next-generation sequencing to describe the bacterial communities (microbiome) of fresh casts (day 0) from the earthworm Aporrectodea caliginosa and how they change over time (7, 15, 30 and 60 days) under natural conditions. We also look for the main, transitional and day-specific core microbiomes of A. caliginosa casts and assessed whether bacterial communities in each ageing stage are clearly distinct in their composition or can be merged into metacommunities. Fresh cast microbiomes were mainly comprised of Bacteroidetes and Proteobacteria (62% of the total sequences) and, in a lesser extent, of Acidobacteria, Actinobacteria Chloroflexi, Planctomycetes and Verrucomicrobia (36% of the total sequences). These fresh casts were richer in amplicon sequence variants (ASVs) than soil microbiomes, which also had lower abundances of Bacteroidetes but higher abundances of other bacterial phyla. As expected, copiotrophic bacteria (Alphaproteobacteria but not Bacteroidetes) significantly (P < 0.0001) decreased in abundance with cast ageing, while oligotrophic bacteria (Actinobacteria, Acidobacteria and Deltaproteobacteria) increased (P < 0.03) their proportion. This also resulted in a significant (P < 0.05) decrease in alpha-diversity over the first 15 days and larger differences in beta-diversity among bacterial communities of ageing casts. Despite differences in beta-diversity, microbiomes of ageing casts were grouped into two metacommunities, one comprised of younger samples collected at days 0 and 7, and another comprised of older samples collected at days 15, 30 and 60. These two metacommunities corresponded to decreased patterns in labile C and N pools in cast ageing. We found a main core microbiome comprised of eight bacterial taxa (~5% of the total sequences). Additionally, we also found transitional and day-specific core microbiomes that were richer and compositionally different from the main core microbiome. This suggests different levels of redundancy in the cast microbiomes to buffer responses to external perturbations (e.g., weather oscillations).