How microbiome predator–prey interactions shape litter decomposition

Litter decomposition is a key ecosystem process regulating nutrient cycling, soil organic matter formation, and long-term soil fertility. Although microbial communities and litter properties are well known to affect litter decomposition, comparatively little attention has been given to microbiome predators, particularly protists and nematodes, in soil food webs. These microbiome predators exert top-down control on microbial communities while being simultaneously shaped by bottom-up factors such as litter properties. This thesis investigates how microbiome predator–prey interactions shape litter decomposition across multiple experimental contexts. Chapter 1 introduces the ecological roles of protists and nematodes and develops a conceptual framework that links predator–prey interactions to litter properties and decomposition dynamics. Subsequent chapters examine specific aspects through which microbiome predators influence litter decomposition. Chapter 2 tests whether protist species identity and diversity influence litter decomposition and plant performance using simplified microcosm experiments. Results show species-specific effects, with only Tetramitus thorntoni reducing litter mass loss. Although litter mass loss was positively related to plant biomass, protist presence did not directly affect plant growth. Chapter 3 evaluates whether protist body size mediates litter decomposition by altering bacterial community composition. Large-sized protists reduced litter mass loss while increasing microbial respiration, likely by promoting predation-resistant bacterial taxa. Chapter 4 examines the temporal succession of protist and fungal communities across six litter types in a one-year field decomposition experiment. Both fungal and protist communities displayed litter-type-specific successional patterns. Notably, protist-related indicators became the strongest predictors of litter mass loss during late-stage decomposition, explaining 47% of the observed variation and surpassing fungal predictors. Chapter 5 investigates whether co-adapted nematode–microbial communities influence decomposition using phase-matched and mismatched combinations. While overall Home-Interaction Advantage (HIA) values were close to zero, litter quality structured nematode succession, and greater community dissimilarity strengthened HIA effects in low-quality litter. Chapter 6 synthesizes these findings and proposes a framework for incorporating microbiome predator–prey interactions into decomposition theory. Overall, this thesis demonstrates that microbiome predators exert important, context-dependent effects on litter decomposition, driven by interactions between top-down trophic control and bottom-up litter properties. These results highlight the need to explicitly integrate microbiome predators into decomposition theory and soil biogeochemical models.