Dynamic changes in prokaryotic and eukaryotic communities and networks in a minimally managed cabbage-cultivated field soils

In this study, we used DNA metabarcoding to investigate both terrestrial prokaryotes and eukaryotes in minimally managed cabbage-cultivated and uncultivated agricultural fields from February to August 2021. Analyses of the relative abundances of prokaryotic and eukaryotic sequence variants (SVs) and their β-diversities have clarified the dynamic changes in eukaryotic communities during cultivation. We investigated taxonomic changes in fungi-, protist-, and animal-derived SVs, as well as abundant SVs in each eukaryotic phylum. The results revealed that the fractions of predatory or parasitic protists and animals increased, whereas those of fungi and earthworm Enchytraeus spp. decreased. The fractions of abundant SVs derived from diatoms, Ciliophora, the class Vampyrellidae (Cercozoa), and mites increased and subsequently decreased during this period. These findings suggest that predatory protists and animals fed on bacteria and autotrophic eukaryotes, such as diatoms, propagated in spring, followed by their propagation and parasitism to host eukaryotes. The co-occurrence networks of the top 150 SVs also changed, especially prokaryotic networks that markedly changed from April to May, and those of eukaryotes from May to June– August, supporting the observations mentioned above. These findings indicate dynamic changes in eukaryotes in fields with minimal agricultural practices and are useful for sustainable natural farming.