Protist-mediated microbiome governance: Integrating trophic ecology, rhizosphere biology, and biotechnological potential.

Soil protists - a phylogenetically diverse group of unicellular eukaryotes, encompassing bacterivorous flagellates, predatory amoebae, fungivorous vampyrellids, and parasitic plasmodiophorids - exist at densities ranging from 10⁴ to 10⁸ cells per gram of soil, yet are systematically underrepresented in microbiome research compared to bacteria and fungi. This review presents soil protists as active regulators of microbial community structure, nutrient biogeochemistry, and functional ecosystem resilience, rather than just passive dwellers of the soil. Three interconnected mechanistic aspects are integrated. Initially, by selectively preying on bacteria, fungi, and microbial eukaryotes, protists impose top-down trophic regulation that alters community composition, enhances nutrient mineralisation through density- and trait-mediated cascades, and governs organic carbon turnover within soil aggregates. Second, in the rhizosphere, protists engineer plant-microbiome interactions through selective enrichment of plant growth-promoting rhizobacteria, modulation of auxin biosynthesis via tryptophan-dependent pathways, regulation of endophytic colonization, and suppression of soil-borne pathogens - including through mechanistically documented positive feedback loops between predatory Cercomonas and Bacillus biocontrol strains. Third, protist diversity - particularly among rare taxa within Cercozoa, Ochrophyta, and Chlorophyta - functions as a principal determinant of soil multifunctionality, with its erosion under land-use intensification and climate-driven drought producing measurable losses in phosphorus mineralization, nitrification capacity, and pathogen suppression. Emerging tools including metabarcoding, single-cell multi-omics, and predictive network modeling are beginning to resolve longstanding gaps in protist functional ecology. We evaluate the biotechnological potential of protist-informed strategies across biofertilizer innovation, biocontrol enhancement, and soil health assessment - priorities with direct relevance to sustainable agriculture in the developing world.