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Trait-based approaches provide a mechanistic framework crossing scales from cellular traits to community dynamics, while ecological stoichiometry applies first principles to understand how the balance of energy and elements shape ecological interactions. However, few studies have explicitly linked both frameworks. In this study, we tested the stoichiometric regulation of a number of carbon (C) based (e.g., extracellular polysaccharides and colony formation) and nitrogen (N) containing traits (i.e., chlorophyll a, phycocyanin, and gas vesicle content) in cyanobacteria in laboratory experiments and in the field. We exposed the cosmopolitan colony forming freshwater cyanobacterium Microcystis sp. in batch experiments to light, N and phosphorus (P) limitation, and enhanced CO2 levels, and assessed the regulation of these traits. Cyanobacterial traits followed stoichiometrically predictable patterns, where N containing traits increased with cellular N content, and decreased with increasing C : N ratios. C-based traits increased with cellular C content and C : N ratios under nutrient, particularly N, limitation. The pattern of colony formation was confirmed with field data from Lake Taihu (China), showing an increase in colony size when N was limiting and N : P ratios were low. These findings demonstrate how an explicit coupling of trait-based approaches to ecological stoichiometry can support our mechanistic understanding of responses of cyanobacteria toward shifts in resource availability. Changes in the global environment are expected to strongly affect the structure and functioning of aquatic ecosystems worldwide (Paerl and Huisman 2009; Huisman et al. 2018). Understanding and predicting the implications of shifts in resource availability are major challenges in aquatic ecology (Litchman et al. 2015), including the scaling across spatial and temporal dimensions. Functional traits of a species determine its growth, survival, and population dynamics under changing biotic and abiotic environmental conditions (McGill et al. 2006). Consequently, trait-based approaches allow scaling, from fundamental processes at the cellular level to dynamics at the population and community level (Edwards et al. 2013; Weithoff and Beisner 2019). Functional traits reflect a combination of distinct metabolic processes with specific underlying chemical and structural properties (Peñuelas et al. 2019), and may be inherently linked to the elemental composition of an organism (Meunier et al. 2017). Ecological stoichiometry addresses the balance of elements in organisms and their interaction with the environment (Sterner and Elser 2002). Specifically, ecological stoichiometry allows the coupling of distinct elemental ratios to biochemistry, and thereby provides a mechanistic basis for understanding the regulation of traits (Meunier et al. 2017). The linkage of elemental composition to functional traits, and functional traits to population and community interactions allows scaling from impacts of changing resource availabilities on cellular processes to altered community dynamics (Fig. 1). Phytoplankton form the base of many aquatic food webs, and account for approximately half of the global primary production (Falkowski et al. 1998). Some species can produce toxic metabolites and under favorable conditions may proliferate to form harmful algal blooms (Smith 2003; Wells *Correspondence: [email protected] (X.T.); [email protected] (D.B.V.d.W.) This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. Additional Supporting Information may be found in the online version of this article. Author Contribution Statement: Z.D. and D.B.V.d.W. designed the experiment; Z.D. acquired the data; Z.D., X.T., and D.B.V.d.W. performed the data analysis; and all authors contributed to data interpretation; Z.D. and D.B.V.d.W. wrote a first version of the manuscript; H.W.P. performed careful editing of versions of the manuscript; and all authors contributed to the final revision of the manuscript.