Ito Sentaro, Murakami Junya, Suzuki Mio, Hirose Yuu, Yamauchi Takahiro, Eki Toshihiko
Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580, Japan.
Laboratory of Genomics and Photobiology, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8580, Japan.
Genes (Basel). 2025 Apr 24;16(5):482. doi: 10.3390/genes16050482.
BACKGROUND/OBJECTIVES: Taxonomic profiling of soil microbial communities is useful for assessing and monitoring the biological status of agricultural land. In this study, we aimed to investigate changes in the taxonomic structure of soil organisms in minimally managed agricultural fields.
We used DNA metabarcoding to investigate both terrestrial prokaryotes and eukaryotes in cabbage-cultivated and uncultivated sites in a minimally managed agricultural field in central Japan from February to August 2021. Analyses of the relative abundances of prokaryotic and eukaryotic sequence variants (SVs) and their β-diversities, and the subsequent redundancy analysis (RDA) clarified the dynamic changes in eukaryotic communities during cultivation. We further investigated taxonomic changes in fungi-, protist-, and animal-derived SVs, abundant SVs in each eukaryotic phylum, as well as the co-occurrence networks of the top 150 SVs.
The results revealed that the fractions of predatory or parasitic protists and animals increased, whereas those of fungi and earthworm 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 networks 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 the dynamic and sequential changes in soil communities in fields with minimal agricultural practices and could be useful for sustainable natural farming.
背景/目的：土壤微生物群落的分类学分析有助于评估和监测农田的生物状况。在本研究中，我们旨在调查极少管理的农田中土壤生物分类结构的变化。
2021年2月至8月，我们采用DNA宏条形码技术，对日本中部一块极少管理的农田中种植卷心菜和未种植卷心菜的地块的陆生原核生物和真核生物进行了调查。通过分析原核生物和真核生物序列变体（SVs）的相对丰度及其β-多样性，以及随后的冗余分析（RDA），明确了种植期间真核生物群落的动态变化。我们进一步研究了真菌、原生生物和动物来源的SVs的分类变化、每个真核生物门中的丰富SVs，以及前150个SVs的共现网络。
结果显示，捕食性或寄生性原生生物和动物的比例增加，而真菌和蚯蚓属的比例下降。在此期间，硅藻、纤毛虫纲、 Vampyrellidae 类（Cercozoa）和螨类来源的丰富SVs比例先增加后下降。这些发现表明，捕食性原生生物和动物以春季繁殖的细菌和自养真核生物（如硅藻）为食，随后它们繁殖并寄生于宿主真核生物。网络也发生了变化，特别是原核生物网络在4月至5月显著变化，真核生物网络在5月至6 - 8月变化，支持了上述观察结果。
这些发现表明了极少农业活动的农田中土壤群落的动态和顺序变化，可能对可持续自然农业有用。
