Lakes, ponds, and reservoirs (hereafter: “lakes”) are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Emissions of CO2 and CH4 from 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 CO2 and CH4 measurements 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.

Muskegon Lake, a drowned river mouth and estuary of Lake Michigan, has been removed from the list of Great Lakes Areas of Concern (AOC) following decades of restoration effort. Each of the nine beneficial use impairments (BUIs) listed for the Muskegon Lake AOC contained restoration targets. However, reports that document whether those targets were being reached may hide long-term trends and underlying ecosystem dynamics. We examine the Eutrophication or Undesirable Algae BUI in depth to gain a better understanding of how Muskegon Lake water quality and restoration targets interrelate. Surface total phosphorus and chlorophyll a concentrations have declined by 61% and 46%, respectively, since the 1970s, with most of that change happening before the mid-2000s. Surface total phosphorus has remained below the BUI removal target of 30 μg/L through the 2020s, but chlorophyll a rose slightly above the 10 μg/L target. Water clarity improved with a 34% increase in Secchi depth, meeting the water quality targets for Muskegon Lake's delisting as an AOC. Decreases in soluble reactive phosphorus, ammonia, and bottom-water total phosphorus, along with increases in nitrate, offer additional insight into possible mechanisms of change during our study period even though they were not included as BUI indicators. The simultaneous decrease in nutrients and increase in chlorophyll a suggest a decoupling of algal growth and nutrients, as well as a shift in nutrient cycling dynamics. Change in the water quality drivers indicates the need for continued monitoring and adaptive management.

Historically, recreational fisheries have been managed through a single-species framework where fish species are considered in isolation. This single-species framework can lead to unintended consequences for fisheries, potentially resulting in fishery collapses or regime shifts. A common factor leading to regime shifts and the prevention of population recoveries are interspecific interactions between the collapsed species and their competitors. Increasingly, ecosystem-based management has been advocated in recreational fisheries where users have a diverse set of goals. Although, in practice, ecosystem-based management can be difficult in systems subject to non-linear dynamics. We used a modeled recreational fishery to describe how interactions between two harvested species could drive shifts in the stable state of the system and sought to understand how interactions could be leveraged for efficient management. Our experiments explored: 1) the effectiveness of single-species management actions at maintaining the desired stable state as compared to multi-species management; 2) the diversity of decision making paths that could lead to positive outcomes when leveraging certain interspecific interactions; and 3) how interspecific interactions could be leveraged to maintain a system in a safe-operating-space despite stable state drivers outside of a manager’s control. Our model demonstrated how interspecific interactions within a system could lead to non-linear outcomes, and when these interactions were unaccounted for, resulted in regime shifts. Accounting for interspecific interactions allowed decision makers to meet their goals through a diverse and cost-effective combination of direct (i.e., managing the focal species through stocking and harvest limitation) and indirect (i.e., managing the competitor) approaches.

Visual communication in fish is often shaped by their light environment, which influences both sensory (e.g., eye size, opsin gene expression) and signalling traits (e.g., body reflectance). This study explores the phenotypic variation in the visual communication traits of six species of centrarchids (Centrarchidae) inhabiting two contrasting light environments. We measured morphological, molecular and signalling traits to determine their variation across photic conditions. Our findings reveal significant interspecific variation in sensory traits but no consistent phenotypic variation between light environments. Centrarchids showed robust visual systems with green-sensitive rh2 and red-sensitive lws opsin genes representing the main chromatic channels, with their expression remaining largely unaffected between distinct light habitats. We also found significant molecular evolution in the visual opsin genes, although these changes were not associated with environmental conditions. However, body reflectance displayed species-specific responses to environmental conditions, suggesting that signalling traits may be more flexible than sensory traits. Overall, our results challenge the generality of the current paradigm in visual ecology, which portrays visual systems in fish as highly tunable owing to photic conditions. Our study highlights the potential evolutionary or developmental constraints on centrarchid visual systems and their implications for adaptability to various habitats and novel environmental threats.

Scientific research plays a crucial role in supporting the safety and prosperity of tens of millions of people who live, work, and recreate in the Laurentian Great Lakes. Cuts to US federal funding, programs, and agencies threaten this research enterprise. As scientists and collaborators at the Cooperative Institute for Great Lakes Research, we make the case for the value of Great Lakes research in terms of human health and safety, economic prosperity, and society’s capacity to confront major challenges today and in the future. The successful track record of scientific research in the Great Lakes shows that it provides return on investment by protecting and restoring the ecosystem, supporting human well-being, and stimulating a thriving economy. Without this continued investment, the future of the Great Lakes and those depending on them is in peril.

Catch-and-release (C&R) angling is often used to maintain high catch rates but fish vulnerability to capture may decrease following hooking, thereby decreasing angler catch per unit effort (CPUE) (hyperdepletion). To determine if fish post-capture response affected recapture probability and population-level CPUE, individual capture histories of Largemouth Bass in two lakes were compared before and after doubling angling effort in a Before-After Control-Impact (BACI) analysis. Previous capture and day-of-season both affected recapture probability. Counteracting effects of previous capture and reduced late-season catch rates caused no hyperdepletion of angler CPUE. Our results highlight the complexity of fish behavioral responses to angling and suggest that hyperdepletion of angling catch rates may not be an issue in C&R fisheries.

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.

Widespread and increasing use of road deicing salt is a major driver of increasing lake chloride concentrations, which can negatively impact aquatic organisms and ecosystems. We used a simple model to explore the controls on road salt concentrations and predict equilibrium concentrations in lakes across the contiguous United States. The model suggests that equilibrium salt concentration depends on three quantities: salt application rate, road density, and runoff (precipitation minus evapotranspiration). High application combined with high road density leads to high equilibrium salt concentrations regardless of runoff. Yet if application can be held at current rates or reduced, concentrations in many lakes situated in lightly to moderately urbanized watersheds should equilibrate at levels below currently recommended thresholds. In particular, our model predicts that, given 2010–2015 road salt application rates, equilibrium chloride concentrations in the contiguous United States will exceed the current regulatory chronic exposure threshold of 230 mg L −1 in over 2000 lakes; will exceed 120 mg L −1 in over 9000 lakes; and will be below 120 mg L −1 in hundreds of thousands of lakes. Our analysis helps to contextualize current trends in road salt pollution of lakes, and suggests that stabilization of equilibrium chloride concentrations below thresholds designed to protect aquatic organisms should be an achievable goal.

Lake crustacean zooplankton densities often are negatively correlated with terrestrial dissolved organic carbon (DOC) concentrations. These reductions in zooplankton with increased DOC are hypothesised to be linked to diminished resource quantity or lower resource quality as terrestrial material is low in essential nutrients and macromolecules. The impact of DOC on lake physics also potentially reduces available habitat for zooplankton as the warm and well-oxygenated epilimnion is shallower in lakes with high DOC concentrations. Our goal was to investigate these potential mechanisms to determine the influence of DOC on drivers of zooplankton densities in a survey of north temperate lakes. We sampled crustacean zooplankton densities in 10 lakes that varied in mean DOC concentration from 6 to 27 mg L-1. We also measured resource availability as chlorophyll concentration, resource quality as essential fatty acid (EFA) concentration and the stoichiometric ratio of carbon-to-phosphorus (C:P), and habitat availability as integrated habitat temperature and dissolved oxygen to determine the strongest predictor of zooplankton densities across lakes. In addition, we quantified zooplankton habitat use through Schindler trap profiles through the water column. Zooplankton densities were most strongly related to integrated habitat temperature and were not closely related to measures of resource quantity or quality. Depth of the mix layer was negatively correlated with DOC concentration, yet there was no relationship between DOC concentration and zooplankton habitat use. Overall resource quantity and quality increased across the DOC gradient, as chlorophyll and EFA concentration were greatest in lakes with higher DOC. Our results indicate the potential for physics-mediated responses between lake DOC and zooplankton density. As lakes with greater DOC concentrations have, on average, shallower mixed layers and colder habitats, zooplankton may either be constrained to a relatively smaller proportion of the catchment or experience reduced temperatures that may delay development or feeding rates. Lake DOC concentrations are projected to increase under future climate scenarios, so accompanying changes in lake temperature profiles are likely to follow. These also may reduce food-web productivity, as shrinking mixed layers or colder total water columns resulting from steeper thermoclines may reduce habitat availability or suitability for zooplankton communities.

Recruitment depensation describes elevated juvenile mortality with declining adult population size which can prevent or delay stock recovery. Understanding the factors influencing when a population undergoes depensation provides resource agencies with targets for management action. Using estimates of depensation from 28 walleye (Sander vitreus, Percidae) populations in Wisconsin identified by Sass et al., (2021), we tested for potential abiotic and biotic predictors of walleye recruitment depensation. The best fitting model contained covariates for climate, land cover, and fish community composition, all interacting with the relative abundance of largemouth bass (Micropterus salmoides, Centrarchidae). The consistent interaction effect of largemouth bass across the other covariates suggests a key role of this species in regulating walleye recruitment dynamics at low population size. The risk of depensation was negatively correlated with largemouth bass abundance in our dataset, pointing towards continued challenges for walleye populations given the increasingly favorable social and environmental conditions for largemouth bass. Using the model, vulnerability to depensation was predicted for an additional 115 walleye lakes with insufficient data to directly estimate the risk of depensation. Predictions suggested that 73 prediction lakes are vulnerable to depensatory recruitment should population sizes significantly decrease. This predictive framework could be used to prioritize lakes for different management actions based on depensation strength and average adult population size. Lakes with low walleye abundances, but low risk of depensation, may be more likely to respond positively to management efforts and are likely better candidates than those where depensation effects are likely strong when abundance is low.

The movement of water to and through aquatic ecosystems plays a major role in controlling rates and extents of biogeochemical transformations in those ecosystems. In this chapter, we describe the role of hydrology in the delivery of carbon and nutrients that fuels ecosystem processes such as lake metabolism (ecosystem respiration and primary production). We discuss how residence time ultimately controls the rates of biogeochemical processes within and across lake ecosystems. We draw on a legacy of theoretical and empirical research showing the relationship between hydrology, residence time, and lake ecosystem processes. Finally, we conclude by identifying important next steps for future work at the intersection of hydrology, ecosystem ecology, and limnology.

Lateral carbon transport (LCT), the flux of terrestrial C transported to aquatic ecosystems, displaces carbon (C) across the terrestrial‐aquatic continuum and is on the same order of magnitude as terrestrial net ecosystem production. However, few continental scale C models include LCT or the C‐hydrology linkages necessary for modeling LCT. Those that do exist, borrow processes and conceptual understanding from watershed scale models, assuming that large‐scale and small‐scale drivers of LCT are the same. We develop a conceptual framework of LCT, which focuses on lateral dissolved organic carbon (DOC) transport (LCT‐DOC), and operationalize it with a coupled terrestrial‐aquatic C and hydrology model. After comparing our model LCT‐DOC to previous estimates derived from a summation of landscape scale fluxes for the Contiguous U.S., we use model experiments to partition the importance of LCT‐DOC drivers including total annual precipitation, air temperature, and plant traits, which interact across regional and local scales. We find that climate is the strongest driver of LCT‐DOC, where LCT‐DOC is positively related to precipitation but inversely related to temperature at continental scales. However, the net effect of climate on LCT‐DOC is the product of cross‐scale interactions between climate and vegetation. Plant traits also interact strongly with climate and have a measurable influence on LCT‐DOC, with water use efficiency as the most influential plant trait because it couples terrestrial water and C cycling. We demonstrate that our conceptual framework and relatively simple linked C‐hydrology process model of LCT‐DOC can inform hypotheses and predict LCT‐DOC.

Ponds play a larger role in the global freshwater methane (CH4) budget than predicted from surface area alone. To improve our understanding of pond CH4 dynamics, we measured summer CH4 production, concentrations, and emissions to the atmosphere in nine Alaskan wetland ponds along with potential physical, chemical, and biological regulators. Pond CH4 production (0.64, 0.086-1.3 mmol m(-2) d(-1); median, interquartile range), as assessed with slurry incubations, was positively related to water-column temperature and chlorophyll a (Chl a), negatively influenced by oxygen levels, and varied with microbial community structure. Average water-column CH4 concentrations (0.39, 0.21-0.87 mu mol L-1) were lower in deeper ponds and at higher oxygen levels, and as expected, they were correlated with diffusive emissions (0.055, 0.024-0.20 mmol m(-2) d(-1)) assessed with flux chambers. Based on a mass balance approach, 39-99% of CH4 produced in ponds was oxidized. Pond ebullition (3.7, 0.60-24 mmol m(-2) d(-1)) was higher and more variable than diffusive emissions. Additionally, pond ebullition rates were better correlated with production rates from the previous month. We also systematically compared the ratio of ebullition to diffusive CH4 emissions in our ponds and other northern lakes, which was negatively related to water depth (n = 71), but positively related to Chl a (n = 28). Our study sheds light on the factors that influence pond CH4 dynamics and demonstrates that pond ebullition is a significant CH4 source worthy of continued study.

Soil is the largest terrestrial carbon (C) reservoir and a large potential source or sink of atmospheric CO ₂ . Soil C models have usually focused on refining representations of microbe‐mediated C turnover, whereas lateral hydrologic C fluxes have largely been ignored at regional and global scales. Here, we provide large‐scale estimates of hydrologic export of soil organic carbon (SOC) and its effects on bulk soil C turnover rates. Hydrologic export of SOC ranged from nearly 0 to 12 g C m −2 yr −1 amongst catchments across the conterminous United States, and total export across this region was 14 (95% CI 4‐41) Tg C/yr. The proportion of soil C turnover attributed to hydrologic export ranged from <1% to 20%, and averaged 0.97% (weighted by catchment area; 95% CI 0.3%–2.6%), with the lowest values in arid catchments. Ignoring hydrologic export in C cycle models might lead to overestimation of SOC stocks by 0.3–2.6 Pg C for the conterminous United States. High uncertainty in hydrologic C export fluxes and potentially substantial effects on soil C turnover illustrate the need for research aimed at improving our mechanistic understanding of the processes regulating hydrologic C export.

Lake sediment microbial communities vary across ecosystems and are often differentiated across pH. Additionally, these pH-mediated differences in community composition are often correlated with changes in sediment functioning, such as methane and carbon dioxide production. However, few studies have experimentally tested pH effects on community assembly or considered how microbial community composition influences ecosystem function independent of differences in the environment. We used common garden experiments to test hypotheses about how pH influences microbial community assembly and function in lake sediments. Using inoculum from three acidic lakes and three near-neutral lakes, we found that both pH environment and inoculum source significantly influenced sediment microbial community assembly. However, inoculum source had a larger effect size for both the sediment methanogen and nonmethanogen communities, indicating important roles of dispersal and drift. Additionally, inoculum source, but not pH environment, significantly influenced sediment methane and carbon dioxide production. This research is one of the first to experimentally test the influence of pH on sediment microbial community composition, and in doing so, we show the community composition significantly influences sediment function independent of pH. Understanding how lake sediment microbial communities are influenced by environment is the first step toward mechanistically linking changes in community composition to ecosystem function, and we provide critical evidence for how changes in microbial community assembly with environmental change will likely alter carbon cycling in lake sediments.

Lake sediment microbial communities mediate carbon diagenesis. However, microbial community composition is variable across lakes, and it is still uncertain how variation in community composition influences sediment responses to environmental change. Sediment methane (CH 4 ) production has been shown to be substantially elevated by increased lake primary productivity and organic matter supply. However, the magnitude of the response of CH 4 production varies across lakes, and recent studies suggest a role for the microbial community in mediating this response. Here, we conducted sediment incubation experiments across 22 lakes to determine whether variation in sediment microbial community composition is related to the response of sediment CH 4 production to increases in organic matter. We sampled the 22 lakes across a gradient of pH in order to investigate lakes with variable sediment microbial communities. We manipulated the incubations with additions of dried algal biomass and show that variation in the response of CH 4 production to changes in organic matter supply is significantly correlated with metrics of sediment microbial community composition. Specifically, the diversity and richness of the non-methanogen community was most predictive of sediment CH 4 responses to organic matter additions. Additionally, neither metrics of microbial abundance nor preexisting organic matter availability explained meaningful variation in the response. Thus, our results provide experimental support that differences in sediment microbial communities influences CH 4 production responses to changes in organic matter availability.

Abstract Variation in traits related to foraging and locomotion in benthic and limnetic habitats has been observed in many fishes. Benthic and limnetic food chain productivity in lakes is strongly influenced by the concentration of dissolved organic carbon (DOC) in the water, suggesting that DOC might indirectly impose selection on these traits and lead to classic benthic forms at low DOC concentrations and limnetic forms at high DOC concentrations. We tested this hypothesis via geometric morphometric and meristic analyses of bluegill sunfish (Lepomis macrochirus, Centrarchidae) from 14 lakes with DOC concentrations ranging from 4 to 24 mg/L. These lakes, located in close proximity to each other, straddle the drainage divide between the Mississippi River and Laurentian Great Lakes basins in northern Wisconsin, USA. Bluegill morphology was consistently related to lake DOC concentration in both drainage basins, despite differences in morphology between basins. Fish from higher DOC lakes had deeper bodies and smaller heads, among other differences, though the proportion of shape variation described by DOC was low. Gill raker length and inter‐raker spacing were positively related to DOC concentration. Although some traits were thus related to DOC concentration, the directions of these relationships did not match the predicted benthic–limnetic patterns. Further, no relationships were evident between DOC and gill raker number, eye width, pectoral fin dimensions, or pectoral fin insertion angle in univariate analyses. These variable outcomes suggest that selection linked to DOC does not map neatly onto the classic benthic–limnetic axis, that high DOC favors a benthic–limnetic generalist rather than a limnetic specialist, or that the benthic–limnetic morphological dichotomy is less clear and universal than is often suggested.

Abstract Chlorophyll and total phosphorus (TP) concentrations are key indicators of lake water quality and the relationship between them is a common tool for assessing lake trophic status. Despite the application of the chlorophyll–TP relationship in management settings, there is still an absence of a mechanistic understanding underlying its shape. We leveraged a process‐based model that focuses primarily on biogeochemical and physiological mechanisms to develop a framework that reconciles interactions between multiscale drivers of the chlorophyll–TP relationship, such as hydrologic P loads, lake shape, and algal physiology. We found that combinations of lake shape and hydrologic P load induce broad shifts in algal limitation status that underly the shape of the chlorophyll–TP relationship. Furthermore, we highlight the importance of algal traits in controlling shifts in limitation. Our framework ties key landscape and ecosystem features to biological limitation and provides a synthetic and process‐based understanding of the chlorophyll–TP relationship.

In commercial and recreational fisheries, catch rate is often assumed to be proportional to stock size and is used by managers and fishers as an indicator of fishery sustainability. If catch rate is proportional to stock size, it can signal a decline of stocks and managers can impose restrictive harvest policies or recreational anglers can move to a new system and allow the over-exploited system to rebound. A growing literature has documented catch rates remaining high even as fish stocks decline (i.e., hyperstability of catch rates) leading to delayed management intervention and overexploitation. Although recent evidence has indicated the presence of hyperstability of catch rates in recreational fisheries, whether hyperstability differs across species or system types remains unknown. To investigate whether catch rate hyperstability varies amongst species or systems, we first tested whether electrofishing catch per unit effort (efCPUE) was an appropriate proxy for true abundance. We then compared the relationship between angler catch rate and fish abundance for common freshwater sport fishes across gradients of habitat availability. We found significant differences in the strength of hyperstability amongst species. We did not identify a consistent influence of habitat on hyperstability of catch rates. Angler preferences and behavior may explain some of the variance in non-proportional catch rates. Future research investigating angler behavior, population size structure, and population dynamics in these systems may identify key interactions that create differences in vulnerability to population collapse.