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

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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 nosZ II 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.