Bacterial community characteristics in epigeic and anecic earthworm vermicompartments within soil-earthworm systems

Abstract

Earthworms are crucial to soil ecosystems as keystone species. They perform various ecological functions through their associated microbiomes. However, the characteristics of these microbiomes in various vermicompartments (earthworm-associated compartments) within soil-earthworm systems have not been systematically studied. Here, using earthworms of two ecotypes (i.e., epigeic Eisenia fetida and anecic Metaphire guillelmi) as models, we conducted a full and comprehensive exploration of the bacterial community in several potential distinct compartments, including bulk soil, drilosphere, gut wall, gut content, and casts, through 2D-terraria incubation technology and high-throughput sequencing approaches. Bacterial diversity, community structures in each compartment, differential OTUs in vermicompartments compared with bulk soil, and the co-occurrence relationship of bacteria in bulk soil and gut-compartments (i.e., gut wall and gut content) were assessed. Results showed that three major vermicompartments, i.e., drilosphere, gut, and casts, were distinctly different in hosting the bacterial community. The levels of alpha diversity followed the order of drilosphere > casts > gut wall ≈ gut content. These patterns of vermicompartments along earthworms did not vary with ecotype, implying that the vermicompartments were the primary factors influencing the bacterial community. Finally, based on the difference in microbiomes in gut-compartments and the state-of-the-art use of the term “gut microbiomes”, it is recommended to establish a unified definition of gut microbes that encompasses microbiomes residing in both the gut wall and gut content, which could provide a clear and consistent understanding of gut microbiomes. This work provides a comprehensive overview of earthworm-associated microbiomes, enhancing our understanding of fundamental earthworm ecology and soil biology.