Seasonal dynamic of the soil prokaryotes, fungi, and cercozoa

Cropland soils are dynamic habitats for microbiomes subjected to strong physical and chemical changes, as the result of agricultural managements such as the tillage practices along the seasonal variations. In order to profile the temporal dynamics of the entire soil microbiomes in terms of abundances and diversity, we sampled the soils from three neighbouring fields differed in soil types (clay vs. loam) and tillage regimes (conservative vs. conventional) from an agricultural site in the Northern Germany, via a two-week interval over two years. Microbial abundances were analysed by gene-specific qPCR, and the diversity and the composition of the microbiomes by PCR amplicon sequencing based on domain-targeted genes. We found the clay soil exhibit the highest values of soil properties and microbial abundances, among which the archaeal and fungal abundances were found to be more seasonal variable than the bacteria. Fungal and protistan communities appeared to be the most susceptible to the temporal variations, and the latter group played a pivotal role as major keystone taxa in structuring microbial community across the seasons. The frequently occurred taxa in the multi-trophic networks play a potential role in maintaining microbial co-occurrence networks, while microbial taxa that occur endemically or seasonally in multi-trophic networks are associated with a more diverse range of functional traits. Additionally, the frequently occurring edges belonged to interactions within or between trophic organisms, rather than cross-trophic interactions. These suggest that the necessity of increasing soil sample size across different seasons and years to unravel the potential feeding preferences of protists towards soil microbes. Our research sheds light on the seasonal variations of the soil microbiome through high-frequency of sampling over a two-year period in an agroecosystem. This offers valuable insights in developing sampling strategies, particularly regarding to sample sizes in croplands, and the implications for soil restoration and ecosystem service generation.