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Abstract Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long‐term whole‐ecosystem warming experiment at a boreal peatland to answer how temperature and CO₂jointly influence communities of abundant, diverse, yet poorly understood, non‐fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high‐throughput fluid imaging and 18S amplicon sequencing, we report large climate‐induced, community‐wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO₂with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO₂and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO₂levels could alter the structure and function of peatland microbial food webs—a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation. 

Summary Trade‐offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade‐offs typically fall along a productive growth to conservative, bet‐hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade‐off framework is not well understood.We examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database.We demonstrate that storage is actively accumulated, as part of a conservative, bet‐hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the speciesPopulus trichocarpa, genetic trade‐offs show that for each additional unit of wood area growth (in cm² yr⁻¹) that genotypes invest in, they lose 1.2 to 1.7 units (mg g⁻¹NSC) of storage. Across species, for each additional unit of area growth (in cm² yr⁻¹), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots.Our findings impact our understanding of basic plant biology, fit storage into a widely used growth‐survival trade‐off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.