Divergent Diversity and Composition of Microbial Communities Between the Whole Body and Dissected Gut of Oribatid Mites Revealed by High-Throughput Sequencing

Soil microarthropods are known to harbor diverse microbial communities that play crucial roles in host physiology and ecological functions. Due to the minute size of oribatid mites, microbial studies have traditionally relied on whole body DNA extraction after surface sterilization, potentially confounding gut microbiota with microorganisms from other tissues. This study employed high-throughput Illumina sequencing to comprehensively compare bacterial and fungal communities between the whole body and dissected gut samples of the oribatid mite Eremobelba eharai. Our results revealed significantly higher bacterial α-diversity (Shannon–Wiener and Pielou evenness indices) in gut samples compared to whole body samples, while fungal richness was significantly lower in gut samples. Non-metric multidimensional scaling demonstrated significant divergence in bacterial community composition between sample types (PERMANOVA: R2 = 0.560, P = 0.010), but not for fungal communities (R2 = 0.119, P = 0.362). Taxonomic analysis identified the bacteria families Yersiniaceae and Rhizobiaceae as enriched in gut samples, potentially involved in nitrogen metabolism and plant polysaccharide degradation, whereas Mycobacteriaceae dominated whole body samples, potentially involved in lipid metabolism and antimicrobial defense. Fungal communities were predominantly pathotrophic, with minimal symbiotrophic representation. Our findings demonstrate that the choice of sample processing method (dissected gut vs. whole body) significantly influences microbial community characterization in soil microarthropods. This empirical validation highlights a critical methodological consideration for future studies of gut microbiota in soil microarthropods.