Seasonal dynamics of gut microbiome: A study of multi-kingdom microbiota of earthworm gut in an urban park

Abstract

Earthworms play an important role in maintaining terrestrial ecosystem function. In urban areas, earthworms mainly inhabit parks where they function through feeding and excretion of soil elements and nutrient turnover. Seasonal diet strongly alters the earthworm gut microbiome and thus affects this ecological process, but the seasonal variation of eukaryotes is still poorly described. In this study, we obtained earthworm samples from three seasons: summer, autumn and winter, assessing the gut microbiome of earthworms using bacterial 16S rRNA and eukaryotic 18S rRNA gene amplicon sequencing techniques. We identified biomarkers that significantly change with seasons and analyzed eukaryotic-bacterial interactions under seasonal variation through inter-kingdom networks. The results of this study showed that season significantly influenced the diversity of earthworm gut bacterial community, while the diversity of eukaryotic community was relatively stable. Inter-kingdom molecular ecological network analysis revealed high degree of positive or negative interactions between fungi and bacteria, protists and bacteria, and fungi and protists as keystone taxonomies divided the network into several modules. In summary, the gut eukaryotic community is more stable than the bacterial community throughout the seasons, and it has shown to maintain season-long homeostasis in the earthworm gut.