Proteomes of Cold-Stenothermal Species across Temperature and Environment

Climate-change induced increases in environmental temperatures pose a considerable risk to many species, as temperatures may surpass their upper thermal tolerance limits. Aquatic, ectothermic biota inhabiting cold-stable environments are theorized to be particularly vulnerable since they may have lost the capacity to tolerate warming temperatures. However, most species can overcome adverse thermal conditions by moving to favorable habitats, evolutionary adaptation, phenotypic, and physiologic plasticity. Plastic responses enable organisms to survive adverse thermal conditions by counteracting the thermodynamic consequences of temperature increase, consisting of cell biological, physiological, behavioral, developmental, and morphological adjustments. Recent works have shown that plastic responses can be characterized and their molecular mechanisms made explicit by studying genomic, gene expression, post-transcriptional, and epigenetic changes. However, changes on these levels of molecular organization are only the introductory chapters of a complex story, as the final products of these processes are proteins, the molecular machines that enable life. Therefore, the study of the total protein complement, proteomics, is required to fully understand species’ responses to warming temperatures. This thesis consists of four chapters addressing the question of thermal tolerance in two non-model species from cold-stable freshwater springs within a proteogenomic framework. Chapters I, II, and III are experimental studies investigating proteome and phosphoproteome changes following thermal acclimation of the caddisfly Crunoecia irrorata (Trichoptera: Lepidostomatidae, Curtis 1834) and the free-living flatworm Crenobia alpina (Platyhelminthes: Tricladida, Dana, 1766)). Chapter IV looks at the relationship between environmental and proteome variation in wild populations of C. irrorata to assess how quantitative proteomics translates into “the real world” and its associated abiotic complexity. The main findings are that 1. these species exhibit signs of physiological and phenotypic flexibility to respond to temperature increases, despite occurring primarily in cold-stable habitats, 2. environmental and proteome variation shows a tractable functional relationship, suggesting that the confounding influence of abiotic variation on the proteome can be made explicit, and 3. post-translational changes play a role in thermal acclimation mechanisms, but only after crossing the fundamental thermal niche. Overall, these results contribute to our understanding of the molecular mechanisms underlying plastic responses of aquatic invertebrates to warming and help formulate hypotheses regarding mechanisms of plasticity and the involved (phospho)proteins. Overall, the results from these studies emphasize that species not currently living close to their thermal limits may benefit from future temperature increases by experiencing shifts towards their un-realized thermal optima. The studied species exhibited attenuated classical heat-stress responses, complicating the application of biomarkers of temperature stress in species from cold-stable habitats. Compared to species from thermally variable or warm environments, measuring down- regulated physiological processes associated with maintaining homeostasis at colder temperatures may be more informative. A reduction in these processes indicates relaxed demands on core cellular processes and a shift towards the species’ thermal optima