Distinct seasonal and annual variability of prokaryotes, fungi and protists in cropland soil under different tillage systems and soil texture

A sustainable use of croplands should utilize beneficial services provided by their resident soil microbiome. To identify potentially adverse environmental effects on soil microbiomes in the future, a better understanding of their natural variability is fundamental. Here, we characterized the abundance and diversity of soil microbial communities over 2 years at two-week intervals on three neighboring fields at an operational farm in Northern Germany. Field soils differed in texture (clay, loam) and tillage (soil conservation vs. conventional). PCR-amplicon analyses of soil DNA revealed distinct temporal variations of bacteria, archaea, fungi, and protists (Cercozoa and Endomyxa). Annual differences and seasonal effects on all microbial groups were detected. In addition to soil pH, prokaryotic communities varied with total soil C and N, but fungi with temperature and precipitation. The C/N ratio had contrasting effects on prokaryotic phyla and protistan classes, but all fungal phyla responded positively. Irrespective of the sampling date, prokaryotic and fungal but not protistan community compositions from the three soils were distinct. Compositional turnover rates were higher for fungi and protists than for prokaryotes and, for all, lower in clay. Conventional tillage had the strongest effect on protist diversity. In co-occurrence networks, most nodes were provided by prokaryotes, but highly connected nodes by predatory protists in the first, and by saprotrophic fungi in the second year. The temporal variation established here can provide insights of what is natural and thus below the limits of concern in detecting adverse effects on the soil microbiome.