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Abstract Wetlands are a major source of methane emissions and contribute to the observed increase in atmospheric methane over the last 20 years. Methane production in wetlands is the final step of carbon decomposition performed by anaerobic archaea. Although hydrogen/carbon dioxide and acetate are the substrates most often attributed to methanogenesis, other substrates – such as methylated compounds – may additionally play important roles in driving methane production in wetland systems. Here we conducted mesocosm experiments combined with genome-resolved metatranscriptomics to investigate the impact of diverse methanogenic substrate amendment on methanogenesis in two high methane-emitting wetlands with distinct geochemistry, termed P7 and P8. Methanol amendment resulted in high methane production at both sites, whereas acetate and formate amendment only stimulated methanogenesis in P7 mesocosms, where aqueous sulfide concentrations were lower. In P7 sediments, formate amendment fueled acetogenic microbes that produced acetate, which was subsequently utilized by acetoclastic methanogens. In contrast to expression profiles in P7 mesocosms, active methylotrophic methanogen genomes from P8 showed increased expression of genes related to membrane remodeling and DNA damage repair, indicative of stress tolerance mechanisms to counter sulfide toxicity. Methylotrophic methanogenesis generates higher free energy yields than acetoclastic methanogenesis, which likely enables allocation of more energy towards stress responses. These findings contribute to the growing body of literature highlighting methylotrophic methanogenesis as an important methane production pathway in wetlands. By using less competitive substrates like methanol that provide greater energy yields, methylotrophic methanogens may invest in physiological strategies that provide competitive advantages across a range of environmental stresses. 

Abstract Lakes, ponds, and reservoirs (hereafter: “lakes”) are important sources of the greenhouse gases carbon dioxide (CO₂) and methane (CH₄). Emissions of CO₂and CH₄from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO₂and CH₄measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide. 

Abstract Ponds, wetlands, and shallow lakes (collectively “shallow waterbodies”) are among the most biogeochemically active freshwater ecosystems. Measurements of gross primary production (GPP), respiration (R), and net ecosystem production (NEP) are rare in shallow waterbodies compared to larger and deeper lakes, which can bias our understanding of lentic ecosystem processes. In this study, we calculated GPP, R, and NEP in 26 small, shallow waterbodies across temperate North America and Europe. We observed high rates of GPP (mean 8.4 g O₂ m⁻³ d⁻¹) and R (mean −9.1 g O₂ m⁻³ d⁻¹), while NEP varied from net heterotrophic to autotrophic. Metabolism rates were affected by depth and aquatic vegetation cover, and the shallowest waterbodies had the highest GPP, R, and the most variable NEP. The shallow waterbodies from this study had considerably higher metabolism rates compared to deeper lakes, stressing the importance of these systems as highly productive biogeochemical hotspots. 

Abstract Understanding controls on primary productivity is essential for describing ecosystems and their responses to environmental change. In lakes, pelagic gross primary productivity (GPP) is strongly controlled by inputs of nutrients and dissolved organic matter. Although past studies have developed process models of this nutrient‐color paradigm (NCP), broad empirical tests of these models are scarce. We used data from 58 globally distributed, mostly temperate lakes to test such a model and improve understanding and prediction of the controls on lake primary production. The model includes three state variables–dissolved phosphorus, terrestrial dissolved organic carbon (DOC), and phytoplankton biomass–and generates realistic predictions for equilibrium rates of pelagic GPP. We calibrated our model using a Bayesian data assimilation technique on a subset of lakes where DOC and total phosphorus (TP) loads were known. We then asked how well the calibrated model performed with a larger set of lakes. Revised parameter estimates from the updated model aligned well with existing literature values. Observed GPP varied nonlinearly with both inflow DOC and TP concentrations in a manner consistent with increasing light limitation as DOC inputs increased and decreasing nutrient limitation as TP inputs increased. Furthermore, across these diverse lake ecosystems, model predictions of GPP were highly correlated with observed values derived from high‐frequency sensor data. The GPP predictions using the updated parameters improved upon previous estimates, expanding the utility of a process model with simplified assumptions for water column mixing. Our analysis provides a model structure that may be broadly useful for understanding current and future patterns in lake primary production. 

Abstract Seasonality in environmental conditions plays a fundamental role in shaping lake ecosystems. However, patterns of seasonality vary worldwide, and these patterns are shifting over time amid global change. Thus, it is increasingly important to evaluate how seasons and seasonality are represented in lake ecosystem research. Here, we used a literature review and global data analysis to synthesize approaches for conceptualizing seasons and seasonality in lakes. We found that a wide range of criteria are used to delineate discrete seasons in published literature, including fixed dates (e.g., months, solstice/equinox), environmental thresholds (e.g., temperature and precipitation cutoffs), and lake‐specific indicators (e.g., ice cover, plankton phenology). Analyzing data from lakes worldwide, we found that using different criteria to define the same season resulted in divergent interpretations of ecosystem states. Based on our synthesis, we offer recommendations for how to incorporate seasonality into lake research and communications amid global change. 

Abstract Process‐based land surface models are important tools for estimating global wetland methane (CH₄) emissions and projecting their behavior across space and time. So far there are no performance assessments of model responses to drivers at multiple time scales. In this study, we apply wavelet analysis to identify the dominant time scales contributing to model uncertainty in the frequency domain. We evaluate seven wetland models at 23 eddy covariance tower sites. Our study first characterizes site‐level patterns of freshwater wetland CH₄fluxes (FCH₄) at different time scales. A Monte Carlo approach was developed to incorporate flux observation error to avoid misidentification of the time scales that dominate model error. Our results suggest that (a) significant model‐observation disagreements are mainly at multi‐day time scales (<15 days); (b) most of the models can capture the CH₄variability at monthly and seasonal time scales (>32 days) for the boreal and Arctic tundra wetland sites but have significant bias in variability at seasonal time scales for temperate and tropical/subtropical sites; (c) model errors exhibit increasing power spectrum as time scale increases, indicating that biases at time scales <5 days could contribute to persistent systematic biases on longer time scales; and (d) differences in error pattern are related to model structure (e.g., proxy of CH₄production). Our evaluation suggests the need to accurately replicate FCH₄variability, especially at short time scales, in future wetland CH₄model developments. 

Understanding controls on primary productivity is essential for describing ecosystems and their responses to environmental change. Lake primary production is strongly controlled by inputs of nutrients and colored dissolved organic matter. While past studies have developed mathematical models of this nutrient-color paradigm, broad empirical tests of these models are scarce. We compiled data from 58 diverse and globally distributed and mostly temperate lakes to test such a model and improve understanding and prediction of the controls on lake primary production. These lakes varied widely in size (0.02-2300 km2), pelagic gross primary production (20-8000 mg C m-2 d-1), and other characteristics. The data package includes high-frequency dissolved oxygen, water temperature, wind speed, and solar radiation data as well as daily estimates of GPP and ER derived from those data. In addition, the data package includes median in-lake and stream concentrations of dissolved organic carbon and total phosphorus for a subset of 18 of those lakes.