Litter-type-specific succession of microeukaryotic communities and their associations with litter decomposition

• Litter type shapes microeukaryotic succession. • Protist-related metrics increasingly predict litter mass loss over time. • Tracing microeukaryotic succession helps understand litter decomposition. Litter decomposition regulates nutrient cycling and carbon turnover, with fungi arguably being the main drivers. While protists are interacting with fungi, their role, as well as the interaction between both groups of microeukaryotes in litter decomposition, remain largely unknown. In this study, we used long-read nanopore sequencing to investigate the taxonomic and functional succession of microeukaryotes throughout one-year decomposition. To obtain more generalizable insights, we used six different litter types, spanning a wide C/N gradient (6–47) and diverse plant families (Poaceae, Brassicaceae, Fabaceae, and Asteraceae). Our results revealed that microeukaryotic succession during litter decomposition was strongly shaped by litter type. Across all litter types, taxonomic richness (Chao1) followed a unimodal trajectory, peaking at mid-decomposition, whereas Shannon diversity increased consistently over time. Microeukaryotic community composition (i.e., β-diversity) changed primarily with litter type, while temporal progression reduced within-litter dissimilarity and was associated with phase-specific indicator taxa. Microeukaryotic functional composition further diverged among litter types, with saprotroph and predator abundances showing distinct litter-dependent trajectories, highlighting strong litter-type-specific successional patterns in microeukaryotic communities. Random forest analysis indicated that protist-related metrics increased in importance over time, becoming the strongest predictors of litter mass loss by explaining 47% of the variation at the end of decomposition. Our findings highlight the importance of integrating fungal and protist dynamics to understand litter decomposition and underscore the role of litter-type-specific microeukaryotic succession in shaping carbon cycling and ecosystem functioning.