Zhiming Shi;Shuyu Shi;Wenwen Li;Congying Wang;Feng H

College of Environmental and Resource Sciences, Shanxi University, Taiyuan 030006 (China); Shanxi Laboratory for Yellow River, Taiyuan 030006 (China); Soil ecology laboratory, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095 (China);Soil ecology laboratory, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095 (China; Shaanxi Key Laboratory of Land Consolidation, School of Land engineering, Chang'an University, Xi'an, 710064 (China)

vermicompartments;gut;microbiomes;earthworm;bacterial community;gut conten

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 within the soil-earthworm system have not been systematically studied. Here, using two ecotype earthworms (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 (earthworm-associated compartments) compared with bulk soil, and the co-occurrence relationship of bacteria in the bulk soil and gut-compartments were assessed. Our results showed that three major vermicompartments (i.e., drilosphere, gut, and casts), including two sub-vermicompartments (i.e., gut wall and gut content), were distinctly different in hosting the bacterial community. For example, the levels of alpha diversity followed the order of drilosphere gt; cast gt; gut wall ≈ gut content. These patterns of vermicompartments along earthworms did not vary with ecotype, concluding that the vermicompartments were the prime 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.