Soil protist diversity enhances prokaryotic diversity, and regulates dominant prokaryotes and the abundance of key nitrogen cycling genes

Abstract

Soil protists play crucial roles in soil microbial food-webs by preying on bacteria and other microorganisms. However, the effect of protist diversity on soil prokaryotic communities remains poorly understood. This study aimed to elucidate how different protist diversity treatments affect the composition and functionality of soil prokaryotic communities. We established soil microcosms with increasingly complex protist communities, including a control without protists, a medium diversity treatment with three small bacterivorous protists, and a high diversity treatment with seven protists of diverse trophic styles and sizes. Over 21 days, we monitored changes in the prokaryotic community using 16S rRNA gene sequencing and assessed the effects on nitrifiers and denitrifiers by qPCR of nitrogen-cycling genes. Protist diversity explained 23% of the observed prokaryotic community differentiation over time, with the high-diversity treatment causing the greatest divergence from the control. The most abundant prokaryotes were preferentially predated in all protist treatments. Unexpectedly, the absolute abundance of the nirK gene, which is widely distributed among bacterial taxa and thus associated with high functional redundancy, decreased. The differential response of genes with lower distribution and redundancy, such as the bacterial and archaeal amoA and the Nitrospira-associated nxrB genes, to protist diversity indicated selective predation on archaea. High protist diversity systematically enhanced these effects compared to the medium diversity treatment. Overall, protist diversity was positively associated with prokaryotic diversity, which is crucial for maintaining ecosystem stability. These findings highlight the critical role of protist diversity and likely complementary predation in shaping soil prokaryotic communities and their functioning, and open up new avenues to explore how this role may differ across soil types.