Soil mesofauna bacterial diversity: Insights from cultured collembolans, enchytraeids, and mites species

Soil fauna-associated microbial communities play crucial roles in nutrient cycling, host health, and ecosystem functioning. However, the differences and connections among microbiota of different soil fauna species under identical cultivation conditions remain poorly understood. Our study characterized bacterial communities of six soil fauna species (the collembolans Folsomia candida, Isotomiella minor and Onychiurus yodai; the enchytraeus Enchytraeus crypticus; the oribatid mite Damaeus expinosus and the predatory mite Hypoaspis aculeifer) after three years of standardized cultivation using 16S rRNA gene high-throughput sequencing. Results revealed distinct microbial community patterns across species. Proteobacteria dominated F. candida (78.4 % relative abundance), while Bacteroidetes were most abundant in I. minor (76.1 %), and Acidobacteria comprised 88.4 % of O. yodai's microbiota. The predatory mite H. aculeifer harbored twice the microbial diversity of detritivorous species like F. candida, reflecting their trophic position as generalist feeders within soil food webs. Only 0.8 % of OTUs (125 out of 36,719) were shared across all species, with H. aculeifer harboring the most unique OTUs (3143). Co-occurrence network analysis showed predominantly positive microbial interactions, suggesting cooperative relationships within host-associated communities. Our study demonstrates that soil fauna harbor highly specialized microbiota shaped by host ecology and trophic level, even under uniform environmental conditions. These findings provide new insights into soil biodiversity and highlight the potential of fauna-associated microbes as bioindicators for ecosystem health assessment.