From Morphology to Metabolism: Trait‑Based Insights into Protist Diversity and Soil Biogeochemical Processes

The assignment of functional traits to protistan sequence data has become central for understanding how these diverse microorganisms contribute to ecosystem processes, yet current schemes that reduce protists to “phototrophs,” “consumers,” or “parasites” vastly underrepresent their functional diversity and ecological strategies. Because traits directly reflect adaptations to environmental conditions, community‐level trait profiles offer more mechanistic insight into species interactions, niche partitioning, and responses to disturbance than taxonomy alone, especially in highly divergent protist lineages. Recently developed, ontology‑based trait frameworks for major soil protist groups now enable more detailed functional annotation and reveal striking differences in morphology and physiology among phyla such as Cercozoa/Endomyxa, Oomycota, Amoebozoa and testate amoebae, challenging the notion of a single, unified trait set for all protists.

I will first outline the breadth of morphological traits across soil protists and their implications for habitat use and trophic interactions, and then explore novel molecular methods to reveal expressed physiological traits using deeply sequenced transcriptomes of free-living Thecofilosea (Rhizaria: Cercozoa), including 12 Rhogostoma strains, Fisculla terrestris and Katarium polorum. A conserved core of orthogroups supported central carbohydrate and nucleotide metabolism, whereas amino acid and lipid pathways, particularly sterol and branched-chain amino acid metabolism, varied strongly even among closely related strains, indicating divergent resource demands and prey dependencies. Distinct orthogroup repertoires and expression profiles in two Rhogostoma clusters point to specialization in sensory, adhesion and biofilm-related functions that likely modulate interactions with bacterial prey and soil microhabitats. Together, these morphological and transcriptomic perspectives demonstrate that fine-scale trait variation among protists is essential for mechanistic links between microbial community composition and soil biogeochemical processes.