Investigating metabolism and greenhouse gas dynamics in lakes across space and time

Abstract

Lakes are biogeochemical hotspots that actively process, store, and emit carbon, yet predicting their contributions to the global carbon cycle remains challenging. The processes governing metabolism and greenhouse gas dynamics are variable across space and time. This dissertation investigates how physical structure, ecological context, seasonal transitions, and trophic status shape ecosystem metabolism and greenhouse gas (CO₂ and CH₄) dynamics across multiple spatial and temporal scales in temperate lakes. Using depth-resolved, spatially distributed, and year-round measurements from four years of field sampling in lakes spanning oligotrophic, dystrophic, and eutrophic conditions, this work quantifies how heterogeneity across depths, habitats, seasons, and lakes influences carbon cycling.Lake metabolism integrates physical and ecological processes, yet most metabolic estimates rely on single-depth, single-location measurements that overlook the pronounced horizontal and vertical heterogeneity within lakes. Physical structure, habitat variation, and proximity to littoral or wetlands can shape light availability, organic matter supply, and mixing, leading to strong spatial gradients in GPP, ER, and NEP. Understanding how these gradients influence metabolic balance is essential for accurately scaling metabolism to whole-lake carbon budgets. The first study of this dissertation used spatially distributed sensors and depth-resolved dissolved oxygen profiles in an oligotrophic lake. I calculated GPP, ER, and NEP across multiple depths and littoral–pelagic habitats throughout a stratified growing season. I found that metabolic rates varied strongly across space, with nearshore sites showing higher GPP and more negative ER than pelagic waters, and depth profiles revealing a shift from autotrophy at the surface to heterotrophy below. Day-to-day variability peaked during autumn mixing, demonstrating that both physical structure and ecological context shape metabolic balance. Metabolism varies not only across space but also across seasons and years as lakes transition through stratification, mixing, and ice-cover periods. Yet, year-round, depth-resolved metabolic datasets are rare, leaving substantial gaps in understanding how winter conditions, vertical structure, and trophic state jointly regulate GPP, ER, and NEP across the full annual cycle. Filling these gaps is crucial for predicting how lakes respond metabolically to climate-driven shifts in ice phenology and stratification strength. I quantified daily GPP, ER, and NEP using three years of depth-resolved dissolved oxygen and temperature profiles from three lakes spanning oligotrophic, dystrophic, and eutrophic conditions. Vertical patterns of ER and NEP showed lake specific patterns, while seasonal variability differed by trophic status, and winter metabolic rates strongly predicted spring dynamics. Ice phenology was strongly associated with winter NEP, underscoring the need to integrate winter into annual metabolic assessments. Lake CO₂ dynamics reflect the interplay between ecosystem metabolism, physical structure, and seasonal mixing, but most studies rely on surface-only measurements that miss deep-water carbon accumulation. Stratification can isolate large CO₂ pools in metalimnetic and hypolimnetic waters, while turnover and winter processes rapidly reorganize carbon storage and flux potential. Resolving these vertical and seasonal dynamics is essential for accurate estimates of CO₂ accumulation and whole-lake emissions. I combined monthly CO₂ sampling with three years of metabolism modeling in three lakes to examine how seasonal, metabolic, and winter processes structure vertical CO₂ gradients. All lakes exhibited strong differences in CO₂ concentration among layers, with large hypolimnetic pools forming during summer and redistribution after turnover. Winter imposed a pronounced reorganization of carbon storage, with CO₂ increasing under ice at the surface but declining in deep waters, revealing winter as a key controller of annual CO₂ dynamics. Methane production, oxidation, and accumulation are highly sensitive to redox structure, stratification, and trophic status, leading to strong spatial and seasonal gradients in CH₄ within lakes. Despite their importance, full-year, depth-resolved CH₄ datasets are uncommon, particularly during under-ice periods when gas accumulation and redox restructuring may be substantial. Understanding CH₄ dynamics across depth, season, and trophic state is necessary for predicting lake CH₄ emissions under changing climatic and ice-cover regimes. I I analyzed three years of CH₄ profiles collected monthly from three lakes spanning a trophic gradient, including two winters with under-ice sampling. I Ifound that CH₄ concentrations differed among lakes and depth layers, with oligotrophic Giles showing low concentrations, dystrophic Lacawac exhibiting moderate hypolimnetic buildup, and eutrophic Waynewood accumulating large and persistent deep-water CH₄ pools. Seasonal patterns revealed elevated under-ice CH₄ and incomplete fall ventilation of hypolimnetic CH₄ in Waynewood, along with a transient mid-column CH₄ maximum in Giles indicative of oxic methane production.