Implications of size-dependent predation of protists and nematodes on the composition and functionality of the prokaryotic soil microbiome

Protists and nematodes are dominant predators of prokaryotic communities in soil. Their strong difference in size suggests different feeding strategies and preferences. Here we analyzed the relevance of size-dependent predation by distinguishing in microcosm experiments the contribution of small-sized and large-sized protists and nematodes, respectively. Sterilized soils were inoculated with soil suspensions filtrated across 250 μm, 100 μm, 60 μm, 20 μm and 5 μm pore sized membranes and a non-filtrated control. After 60 days of incubation, only the soils inoculated with the 5 μm-filtrate showed lower abundances of bacteria, archaea and fungi, and a differently composed protistan community. The nematode communities were always dominated by the small-sized bacterivore genus Acrobeloides. Correlation analyses indicated that small-sized protists were associated with a wider range of prokaryotic taxa than larger sized protists. In contrast to small-sized nematodes, large-sized showed no correlation with specific prokaryotic taxa. The comparison of effects on prokaryotes at DNA and RNA levels suggested a preference of the soil predators for actively growing rather than resting cells. Small-sized protists (only Cercozoa) and nematodes had a more pronounced influence on the gene abundances of microbial groups and N cycling genetic potentials, i.e., bacterial amoA, nirS, and nosZII genes. Therefore, we conclude that the common ecological size-dependent predation theory also applies to trophic interactions of protists and nematodes with soil prokaryotes. The distinct feeding preferences can alter the prevalence of different N-functional genes, which could thus potentially modify the dynamics of the N cycling in soil.