Excess nitrogen (N) in freshwater systems is harmful and can lead to eutrophication, loss of biodiversity and toxic cyanobacterial blooms. External loading of N is an important driver of eutrophication, however, internal processing can either exacerbate or relieve excess N through N2 fixation or denitrification, respectively. Here, we aimed to determine how variation in N loading and hydrologic setting affect internal N processing in lakes in summer by quantifying N2 saturation in 17 lakes across a land use gradient in Minnesota and Iowa. We hypothesized that lakes with the highest N loading rates would have the highest N2 saturation values, indicative of net denitrification. We observed that lakes in agricultural regions had the highest N2 saturation and all lakes showed the highest levels of supersaturation in June when runoff was maximal. Although seasonal changes affected the degree of N2 saturation, all lakes were sources of N2 to the atmosphere throughout the sample period suggesting that denitrification was more impactful to internal processing than was N2-fixation. Peaks in N2 supersaturation co-occurred with both low and high dissolved oxygen levels, the latter being somewhat paradoxical given that denitrification is an anaerobic process.

AbstractThe world's 1.4 million lakes (≥10 ha) provide many ecosystem services that are essential for human well‐being; however, only if their health status is good. Here, we reviewed common lake health issues and classified them using a simple human health‐based approach to outline that lakes are living systems that are in need of oxygen, clean water and a balanced energy and nutrient supply. The main reason for adopting some of the human health terminology for the lake health classification is to increase the awareness and understanding of global lake health issues. We show that lakes are exposed to various anthropogenic stressors which can result in many lake health issues, ranging from thermal, circulatory, respiratory, nutritional and metabolic issues to infections and poisoning. Of particular concern for human well‐being is the widespread lake drying, which is a severe circulatory issue with many cascading effects on lake health. We estimated that ∼115,000 lakes evaporate twice as much water as they gain from direct precipitation, making them vulnerable to potential drying if inflowing waters follow the drying trend, putting more than 153 million people at risk who live in close vicinity to those lakes. Where lake health issues remain untreated, essential ecosystem services will decline or even vanish, posing a threat to the well‐being of millions of people. We recommend coordinated multisectoral and multidisciplinary prevention and treatment strategies, which need to include a follow‐up of the progress and an assessment of the resilience of lakes to intensifying threats. Priority should be given to implementing sewage water treatment, mitigating climate change, counteracting introductions of non‐native species to lakes and decreasing uncontrolled anthropogenic releases of chemicals into the hydro‐, bio‐, and atmosphere.

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.

Inland waters are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Ponds have amongst the highest CO2 and CH4 fluxes of all aquatic ecosystems, yet seasonal variation in fluxes remain poorly characterized, creating challenges for accurately estimating annual emissions. Further, ponds can exhibit a range of mixing regimes, yet the impact of mixing regimes on gas emissions remains unclear. Here, we assessed annual dynamics of CO2 and CH4 in four temperate ponds (Minnesota, USA) that varied in mixing regimes. The ponds ranged from annual sinks to sources of CO2 (−1 to 15 mol m−2 yr−1) and were all significant sources of CH4 (4.3–8.2 mol m−2 yr−1), with annual fluxes in CO2 equivalents of 1.8–4.1 kg CO2-eq. m−2 yr−1. Mixing regimes impacted CO2 and CH4 dynamics, as stratified periods were associated with more anoxia, greater accumulation of gases in the bottom waters, higher emissions of CH4, and lower fluxes of CO2. Ponds with stronger summer stratification also had increased CO2 and CH4 fluxes associated with fall turnover. Overall, the two ponds with the strongest stratification had higher annual fluxes (2.6, 4.1 kg CO2-eq. m−2 yr−1) compared to the two ponds that more frequently mixed (1.8, 2.2 kg CO2-eq. m−2 yr−1).

Lakes are expected to become more active in processing dissolved organic matter (DOM), but the fate of DOM with different origins remains poorly constrained. We conducted long-term incubation experiments (similar to 1 year) with sole light, sole microbial, and combined light and microbial treatments using DOM from algal and terrestrial sources (DOMa and DOMt, respectively). Fourier transform ion cyclotron resonance mass spectrometry and 16s rRNA were used to analyze the DOM molecular composition and bacterial community, respectively. We observed that DOMa and DOMt converged toward a similar composition under the combined light and microbial treatment, driven by the removal of source-specific compositions along with the production of refractory, carboxylic-rich alicyclic molecules (CRAM). For CRAM enrichment, microbial processes played a greater role for DOMa, while phototransformation was more important for DOMt. The co-occurrence patterns between DOM molecules and bacteria showed that DOM molecular composition influenced the bacterial community. More complex DOM-bacteria interactions were observed for DOMt compared to DOMa, suggesting that greater bacterial cooperation was necessary for transforming DOMt. Collectively, these findings offer new insights into the mechanisms underlying the uniformity of DOM from various sources through prolonged environmental transformations in lakes.

Our changing climate is having effects on freshwater ecosystems in all seasons, especially winter. High latitude lakes, wetlands, and rivers are experiencing shorter periods of ice cover, and lower latitudes systems that used to freeze are experiencing open water conditions throughout the winter. A 2019 AGU Chapman conference convened aquatic scientists to examine these changes and address the implications of changing winters to aquatic life, chemistry, and physics. Several studies demonstrate decreased ice cover duration than in the past. The removal of an ice “lid” from lakes and rivers impacts the exchange of gases with the atmosphere and the predominant types of metabolism occurring in the waters below, with the potential for more photosynthesis and an increase in oxic versus anoxic metabolism when the lid is removed. Multiple studies indicated an increase in the interannual variability of winters, especially in terms of ice‐cover duration and ice quality. Increased variability may simply be an outcome of a more variable winter climate or small differences in environmental conditions such as temperature that can have strong effects on gas exchange, light transmission, and turbulence when ice forms. A question that merits further consideration is whether and how winters of shorter duration and severity will change the dynamics of freshwater systems. Are there memory or legacy effects that carry over to the next season or year? There is much work to be done to understand how changing winters will impact the biogeochemical behavior of lakes and rivers in the coming decades.

Biogeochemistry patterns in shallow lakes are influenced by both in-lake factors such as ecosystem state as well as watershed-level factors such as land use, but the relative importance of in-lake versus watershed factors is poorly known. This knowledge gap makes it difficult for lake mangers to prioritize efforts on watershed versus in-lake strategies for stabilizing the clear-water state. We studied 48 shallow lakes in Minnesota, USA to assess the relative influence of lake size, land use in watersheds, and ecosystem state (turbid versus clear) on water column total nitrogen (TN) and total phosphorus (TP), as well as δ15N and δ13C in three species of fish. Our land use categories included natural areas, row crop agriculture, and all agriculture (row crops plus alfalfa). A model selection approach revealed different control mechanisms on the behavior of stable isotopes and nutrients. δ13C ratios in fish were most strongly influenced by lake size, while δ15N ratios were influenced by all agriculture in watersheds. In contrast, water column TN and TP concentrations were influenced by the in-lake factor of ecosystem state, with both nutrients lower in the clear state. We detected no effects of land use on TN or TP concentrations, likely due to strong effects of ecosystem state masking watershed effects. However, the strong relationship between agriculture and δ15N in fish indicated that watersheds did influence nutrient processing in shallow lakes, and that effects are not a legacy from past watershed events. Collectively, these observations indicate that lake managers should minimize agricultural intensity in shallow lake watersheds to facilitate the clear-water state, which will, in turn reduce water-column TN and TP relative to the turbid state.

Freshwaters are significant contributors of greenhouse gases to the atmosphere, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Small waterbodies such as ponds are now recognized to have disproportionate greenhouse gas emissions relative to their size, but measured emissions from ponds have varied by several orders of magnitude. To assess drivers of variation in pond greenhouse gas dynamics, we measured concentrations and emissions of CO2, CH4, and N2O across 26 ponds in Minnesota, United States, during the ice-free season. The studied ponds differed in land-use, from urban stormwater ponds to natural forested ponds. The ponds were all sources of greenhouse gases, driven by large CH4 emissions (mean 704 [sd 840] mg CH4-C m−2 d−1). CO2 fluxes were variable, but on average a sink (mean −25.9 [sd 862] mg CO2-C m−2 d−1), and N2O emissions were generally low (mean 0.398 [sd 0.747] mg N2O-N m−2 d−1). Duckweed coverage on the water surfaces ranged from 0% to 100% coverage, and had the largest influence on water chemistry and greenhouse gas dynamics across the ponds. Duckweed covered ponds (ponds with greater than 85% coverage) had higher phosphorus levels and increased anoxia compared to ponds without duckweed (ponds with less than 12% coverage), leading to higher CH4 concentrations and overall greenhouse gas emissions in the duckweed ponds. Duckweed ponds had a mean emission rate in CO2 equivalents of 30.9 g C m−2 d−1 compared to 11.0 g C m−2 d−1 in non-duckweed ponds.

An oxygenated atmosphere changed life on Earth but it also provided a negative feedback to organic matter accumulation by increasing decomposition rates. Nonetheless, dissolved organic carbon (DOC) is a huge carbon pool (> 750 Pg) and it can accumulate to high concentrations (20–100 mg C L −1 ) in some freshwater aquatic systems, yet it is not clear why. Here, we examine DOC in several Greenland lakes with varying DOC concentrations and identify processes that could alter its composition to make it increasingly recalcitrant. Δ 14 C aging of DOC corresponded with increased DOC concentrations, slower degradation rates, changes in isotope ratios and optical properties, all suggesting that photochemical and microbial degradation processes contributed to recalcitrance. Young DOC degradation was stimulated by phosphorus, but older DOC was not, suggesting an important role for nutrients early in degradation. Photochemical processing coupled with decreased habitat diversity in hydrologically isolated systems may enable recalcitrant DOC to accumulate with important implications for Earth's carbon and oxygen cycles.

Where they are present in catchments, peatlands are a dominant source of dissolved organic matter (DOM) to surrounding waterways due, in part, to high production rates. Despite the preponderance of peatlands in northern latitudes and expected peatland vulnerability to climate change, little is known about peatland DOM degradation relative to a more comprehensive understanding of degradation when DOM is sourced from upland‐dominated catchments. We compared DOM biodegradability of various sources of stream water in two catchments having peatlands (22%–33% of the area) surrounded by upland forests (70%–90% of the area, either deciduous or coniferous). We measured total organic carbon (TOC), and biodegradable dissolved organic carbon concentrations; bacterial respiration rates; streamflow; and upland runoff during and after snowmelt (March to June, 2009–2011). We also explored if DOM in upland runoff stimulated biodegradation of peatland‐derived DOM (i.e., a priming effect), and if forest cover type affected DOM biodegradability. As expected, the peatlands were the largest sources of both water (72%–80%) and TOC (92%–96%) to the streams although more area in each catchment was in uplands (70%–90%). Several results were unexpected, yet revealing: (1) DOM from peatlands sometimes had the same biodegradability as DOM from uplands, (2) upland sources of DOM had negligible effects on biodegradability in the peatland and downstream, and (3) upland deciduous cover did not yield more degradable DOM than conifer cover. The most pronounced effect of upland runoff was dilution of downstream TOC concentrations when there was upland runoff. Overall, the effects of upland DOM may have been negligible due to the overriding effect of the large amount of biodegradable DOM that originated in bogs. This research highlights that peatland‐sourced DOM has important effects on downstream DOM biodegradability even in catchments where upland area is substantially larger than peatland area.

Millions of lakes worldwide are distributed at latitudes or elevations resulting in the formation of lake ice during winter. Lake ice affects the transfer of energy, heat, light, and material between lakes and their surroundings creating an environment dramatically different from open‐water conditions. While this fundamental restructuring leads to distinct gradients in ions, dissolved gases, and nutrients throughout the water column, surprisingly little is known about the resulting effects on ecosystem processes and food webs, highlighting the lack of a general limnological framework that characterizes the structure and function of lakes under a gradient of ice cover. Drawing from the literature and three novel case studies, we present the Lake Ice Continuum Concept (LICC) as a model for understanding how key aspects of the physical, chemical, and ecological structure and function of lakes vary along a continuum of winter climate conditions mediated by ice and snow cover. We examine key differences in energy, redox, and ecological community structure and describe how they vary in response to shifts in physical mixing dynamics and light availability for lakes with ice and snow cover, lakes with clear ice alone, and lakes lacking winter ice altogether. Global change is driving ice covered lakes toward not only warmer annual average temperatures but also reduced, intermittent or no ice cover. The LICC highlights the wide range of responses of lakes to ongoing climate‐driven changes in ice cover and serves as a reminder of the need to understand the role of winter in the annual aquatic cycle.

Organic amendments greatly influence soil functions and biochemical processes that are driven by soil active microbiota. Yet, how organic fertilization impacts transcriptionally active microbes and impacts soil ecosystem functions is still largely unknown. In this study, the variations of RNA-based soil active bacteria and multifunctionality in response to long-term organic fertilization were investigated. We selected an experimental observation station with the application of organic fertilizers for 30 years. High-throughput sequencing and qPCR-based SmartChip assays were employed to explore the abundance, diversity, composition, and function of soil active microorganisms under different application regimes. Organic fertilization increased soil transcriptionally active bacterial abundances significantly, and changed their compositions compared to control treatment. Of the differentially active bacteria, Bacillus was the most abundant genus which was increased by organic fertilization dramatically. Unexpectedly, however, the impacts of organic fertilization on the active communities did not demonstrate a dose-dependent response at the RNA level. SmartChip analysis further indicated that organic fertilization significantly increased the abundances of 25 functional genes associated with energy metabolism, organic matter degradation, denitrification, phosphorus solubilization, sulfur oxidation, and sulfate reduction processes. In addition, soil multifunctionality was also promoted by organic fertilization, and such promotion had a strong relationship with the differentially active bacteria, suggesting that the variations of soil ecosystem functions could be mainly regulated by differentially active bacterial communities. Organic fertilization impacted the abundances and compositions of soil active bacteria, and increased soil multifunctionality. Understanding dynamic changes in soil active microbes is therefore crucial for managing application regimes of organic fertilizers in agricultural practices and evaluating element biogeochemical cycling in soil.

Dissolved oxygen controls important processes in lakes, from chemical reactions to organism community structure and metabolism. In shallow lakes, small volumes allow for large fluctuations in dissolved oxygen concentrations, and the oxygen regime can greatly affect ecosystem‐scale processes. We used high frequency dissolved oxygen measurements to examine differences in oxygen regimes between two alternative stable states that occur in shallow lakes. We compared annual oxygen regimes in four macrophyte‐dominated, clear state lakes to four phytoplankton‐dominated, turbid state lakes by quantifying oxygen concentrations, anoxia frequency, and measures of whole‐lake metabolism. Oxygen regimes were not significantly different between lake states throughout the year except for during the winter under‐ice period. During winter, clear lakes had less oxygen, higher frequency of anoxic periods, and higher oxygen depletion rates. Winter oxygen depletion rates correlated positively with peak summer macrophyte biomass. Due to lower levels of oxygen, clear shallow lakes may experience anoxia more often and for longer duration during the winter, increasing the likelihood of fish winterkills. These observations have important implications for shallow lake management, which typically focuses efforts on maintaining the clearwater state.

Little is known about the exchange of gaseous nitrogen (N2) with the atmosphere in freshwater systems. Although the exchange of N2, driven by excess or deficiencies relative to saturation values, has little relevance to the atmospheric N2 pool due to its large size, it does play an important role in freshwater and marine nitrogen (N) cycling. N-fixation converts N2 to ammonia, which can be used by microbes and phytoplankton, while denitrification/anammox effectively removes it by converting oxidized, inorganic N to N2 We examined N2 saturation to infer net biological nitrogen processes in 34 lakes across 5° latitude varying in trophic status, mixing regime, and bathymetry. Here, we report that nearly all lakes examined in the upper Midwest (USA) were supersaturated with N2 (>85% of samples, n = 248), suggesting lakes are continuously releasing nitrogen to the atmosphere. The traditional paradigm is that freshwaters compensate for N-limitation through N-fixation, but these results indicate that lakes were constantly losing N to the atmosphere via denitrification and/or anammox, suggesting that terrestrial N inputs are needed to balance the internal N cycle.

Abstract Stable isotopes 13C and 15N are often used in lake ecosystems to assess energy sources and trophic positions, respectively. However, δ13C and δ15N are also influenced by internal biogeochemical processes in epilimnetic and hypolimnetic habitats in lakes, but the extent to which biogeochemical processing mediates isotope values between these two habitats, and whether these patterns are influenced by lake productivity is not known. We sampled δ13C and δ15N in epilimnetic mussels, Chaoborus, cisco (Coregonus artedi), and seston and zooplankton in the epilimnia and hypolimnia of 22 Minnesota (USA) lakes ranging from oligotrophic to eutrophic. We also measured lake temperature–oxygen profiles and light levels to assess factors influencing isotope patterns. Isotope samples were baseline‐corrected using epilimnetic mussels in each lake (sample—mussel) to control for watershed‐level differences in isotope values. Results showed δ13C in epilimnetic and hypolimnetic zooplankton, hypolimnetic seston, Chaoborus, and cisco became more depleted in δ13C relative to epilimnetic mussels in low‐productivity lakes where light penetrated into the hypolimnion, while epilimnetic seston δ13C stayed similar to mussel δ13C in all lakes. This pattern was likely due to hypolimnetic phytoplankton in clearwater lakes incorporating more respired CO2, which is depleted in δ13C, and subsequently passing depleted δ13C values up the food chain. Results also showed habitat differences in δ15N with epilimnetic and hypolimnetic zooplankton, hypolimnetic seston, Chaoborus, and cisco becoming more enriched relative to epilimnetic mussels in low‐productivity lakes with higher O2 levels in the hypolimnion, while epilimnetic seston δ15N remained similar to mussel values. The δ15N pattern is consistent with the idea that denitrification and microbial degradation enriched hypolimnetic seston relative to epilimnetic seston in low nutrient lakes, while enhanced epilimnetic primary production enriched epilimnetic δ15N seston relative to hypolimnetic seston in high nutrient lakes. Our results indicate isotopic differences between epilimnetic and hypolimnetic organisms that change along productivity gradients and suggest that microbial processes and the light regime are important drivers.

Heterotrophic bacteria are key biogeochemical regulators in freshwater systems. Through both decomposition and production of organic matter, bacteria link multiple biogeochemical cycles together. While there has been a significant amount of work done on understanding the role of microbes in the aquatic carbon cycle, important linkages with other biogeochemical cycles will require more information about how organic matter transformations impact other nutrients, such as phosphorus. In this study, we conducted a culture-based laboratory experiment to examine the production of dissolved organic matter (DOM) by heterotrophic bacteria under varied nutrient conditions. In addition to quantifying the production of dissolved organic carbon (DOC), we also measured the production of dissolved organic phosphorus (DOP) and characterized the microbially produced organic matter using optical properties. Results demonstrated that measurable amounts of DOC and DOP were produced by heterotrophic bacteria under nutrient regimes ranging from carbon-limitation to strong phosphorus-limitation. Additionally, optical characterization of DOM revealed that the organic matter produced by bacteria grown under high phosphorus conditions was highly aromatic with similar optical properties to terrestrially derived organic matter. Overall, these findings suggest that heterotrophic bacteria can be important producers of organic matter in freshwaters and that continued trends of increased nutrient concentrations (eutrophication) may fundamentally change the composition of microbially produced organic matter in freshwater systems.

This archive contains research data collected and/or funded by Forest Service Research and Development (FS R&D), U.S. Department of Agriculture. It is a resource for accessing both short and long-term FS R&D research data, which includes Experimental Forest and Range data. It is a way to both preserve and share the quality science of our researchers.

Justus von Liebig observed that one could greatly increase agricultural yields by adding relatively small quantities of nitrogen (N), phosphorus (P) and potassium (K) to soils. This finding led to the most recent agricultural revolution. But because most plants and microbes can be non-homeostatic with respect to their biomass elemental composition, adding nutrients can lead to disproportional increases in some macro-elements in organisms, while micronutrient content decreases. Increased CO2 in the atmosphere is an important driver of climate change, but it is also an important driver of changing biomass content and ecosystem stoichiometry. Increased CO2 has contributed to excess carbon in biomass and ecosystems, a state which could be contributing to changes in metabolism which I liken to metabolic diseases and ‘environmental obesity’. Here I defined environmental obesity as excess C accumulation relative to other elements in the environment. A warming climate is certainly motivation enough for humans to do whatever is necessary to decrease use of fossil fuels. However, increased carbon has detrimental health outcomes through effects on our food in natural and agricultural systems and suggests that CO2 is not ‘just an environmental problem’, but also a human health problem.

Groundwater exchanges with most lakes are rarely quantified because there are many technical challenges to quantification. We investigated a lakebed mapping approach to infer the relative areas of groundwater exchange in 12 prairie shallow lakes and five Laurentian mixed forest shallow lakes in Minnesota, USA in 2011. We used a relatively common approach (seepage meters) to provide baseline information on the magnitude and direction of flow at four locations in each lake. To expand from point measurements to the whole-lake scale, we explored use of specific conductivity as a cheaper and more time efficient proxy for groundwater discharge to lakes. We validated the approach at near shore stations in each lake where seepage meter measurements and specific conductivity surveys overlapped. Specific conductivity surveys provided a similar assessment of groundwater discharge compared to seepage meters for 50% of the lake-sampling period combinations. The lakebed mapping approach, when validated for a lake with a limited number of seepage meter (or alternative methods) measurements, offers the advantages of being more time and labor efficient over the use of a similar number of seepage meter monitoring locations; seepage meters (or piezometers, for example) are costlier in terms of equipment and labor, even for single-lake studies. We show the combined approach could provide useful baselines for understanding and mapping groundwater exchange in shallow lakes.