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Despite the increasing concern about the harmful effects of micro- and nanoplastics (MNPs), there are no harmonized guidelines or protocols yet available for MNP ecotoxicity testing. Current ecotoxicity studies often use commercial spherical particles as models for MNPs, but in nature, MNPs occur in variable shapes, sizes and chemical compositions. Moreover, protocols developed for chemicals that dissolve or form stable dispersions are currently used for assessing the ecotoxicity of MNPs. Plastic particles, however, do not dissolve and also show dynamic behavior in the exposure medium, depending on, for example, MNP physicochemical properties and the medium’s conditions such as pH and ionic strength. Here we describe an exposure protocol that considers the particle-specific properties of MNPs and their dynamic behavior in exposure systems. Procedure 1 describes the top-down production of more realistic MNPs as representative of MNPs in nature and particle characterization (e.g., using thermal extraction desorption-gas chromatography/mass spectrometry). Then, we describe exposure system development for short- and long-term toxicity tests for soil (Procedure 2) and aquatic (Procedure 3) organisms. Procedures 2 and 3 explain how to modify existing ecotoxicity guidelines for chemicals to target testing MNPs in selected exposure systems. We show some examples that were used to develop the protocol to test, for example, MNP toxicity in marine rotifers, freshwater mussels, daphnids and earthworms. The present protocol takes between 24 h and 2 months, depending on the test of interest and can be applied by students, academics, environmental risk assessors and industries.

Plastic debris is thought to be widespread in freshwater ecosystems globally1. However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging2,3. Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 μm) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris4. Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services.

ABSTRACTDepletion of deepwater dissolved oxygen (DO) in lakes has become increasingly prevalent and severe because of many external stressors, potentially threatening human-derived ecosystem services ranging from drinking water quality to fisheries. Using year-round, high-frequency DO data from 12 dimictic lakes, we compared 3 measures of deepwater DO depletion during winter and summer: DO depletion rate, DO minimum, and hypoxia duration. Hypoxia (DO < 3 mg L−1) occurred in over half of the lakes and persisted an average of 83% longer in summer than in winter. While we found no difference in DO depletion rates between winter versus summer, these rates were significantly related to lake morphology in winter but trophic state in summer. In assessing cross-seasonal linkages, we found limited evidence for significant legacy effects in deepwater DO availability. Only fall mixing efficacy significantly responded to the previous summer’s minimum DO saturation, but it always reached moderate to high DO replenishment levels (>65%) regardless of the previous summer’s DO depletion severity. This lack of ecological memory in deepwater DO depletion across seasons suggests that deepwater DO largely resets during spring and fall mixing periods in most years in these dimictic lakes. Understanding the patterns and drivers in deepwater DO depletion in both winter and summer is a key step forward for predicting future chemical and biological consequences of seasonal DO depletion and managing lake ecosystem health, as well as the effects that climate change may have on these patterns.

Climate‐change is rapidly and intensively altering aquatic communities and habitats. While previous work has focused on direct effects of potential drivers, indirect and interactive effects on organisms and ecosystems have received less attention. Here, we give an overview of contributions to a special issue in Limnology and Oceanographythat addresses this knowledge gap. Contributions covered diverse habitats, from polar to tropical regions, alpine streams to coral reefs. Several studies relied on time‐series to identify indirect effects, thus emphasizing our need to maintain high‐quality time‐series data. Time‐series are particularly crucial now that the pace of climate‐change on aquatic‐ecosystems is accelerating. Another common theme is the role of species‐specific characteristics in physiology, behavior or genetics in aquatic ecosystem function. The addition of inter‐ and intra‐specific variability to investigations of climate‐change may be challenging particularly since ecosystem studies typically involve a large parameter space of environmental and biological variables across spatial and temporal scales. However, the results demonstrate that inclusion of species‐specific dynamics, although challenging, can deliver mechanistic insights into aquatic ecosystem patterns and processes. Some contributions leverage habitat changes from disturbances or climate shifts to document capacity for resilience or recovery of pelagic and benthic communities. Jointly, the results in this special issue document fruitful approaches and provide urgent information needed for deciphering aquatic ecosystem responses to climate forcings. This information is foundational if we wish to tackle the combined effects of climate change and other human impacts with maximum efficacy and minimize unintended consequences for biodiversity and ecosystem functioning.

Increasing evidence suggests that fungal communities are key components of biogeochemical cycles in coastal ecosystems. However, at a regional scale, the major drivers of the seasonal and spatial distribution of fungi in areas impacted by mariculture remain largely unknown. Intensive aquaculture takes place in Dongshan Bay of Fujian, China, a typical subtropical marine ecosystem with multiple environmental gradients extensively perturbed by anthropogenic activities. To better understand the consequences of mariculture on fungal community composition and activities, we simultaneously evaluated the temporal (four different seasons) and spatial dynamics in total (DNA) and active (RNA) fungal communities of Dongshan Bay in relation to several major physicochemical properties. Our results revealed that fungal communities in the Bay were highly diverse, but showed the ubiquitous dominance of Dikarya and the occasional predominance of Glomeromycota, Mucoromycota, Mortierellomycota, Chytridiomycota, Olpidiomycota, and Rozellomycota. Fungal diversity varied much more with season than with the degree of aquaculture activity, for both total and active communities. This notion is supported by co‐occurrence networks exhibiting a clear seasonal pattern. Furthermore, fungal community structure in coastal waters showed distinct relationships with environmental factors varying both with season and in space. For both total and active fungal communities, a combination of environmental variables including temperature, dissolved oxygen, and nitrite exhibited the greatest impact on community structure. Our study demonstrates a distinct spatiotemporal dynamics of both total and active fungi and provides a foundation to better understand the ecological roles of marine fungi in coastal ecosystems in relation to mariculture activities.

Plastic debris is an established environmental menace affecting aquatic systems globally. Recently, microplastics (MP) and plastic leachates (PL) have been detected in vital human organs, the vascular system, and in vitroanimal studies positing severe health hazards. MP and PL have been found in every conceivable aquatic ecosystem─from open oceans and deep sea floors to supposedly pristine glacier lakes and snow covered mountain catchment sites. Many studies have documented the MP and PL impacts on a variety of aquatic organisms, whereby some exclusively focus on aquatic microorganisms. Yet, the specific MP and PL impacts on primary producers have not been systematically analyzed. Therefore, this review focuses on the threats posed by MP, PL, and associated chemicals on phytoplankton, their comprehensive impacts at organismal, community, and ecosystem scales, and their endogenous amelioration. Studies on MP- and PL-impacted individual phytoplankton species reveal the production of reactive oxygen species, lipid peroxidation, physical damage of thylakoids, and other physiological and metabolic changes, followed by homo- and heteroaggregations, ultimately eventuating in decreased photosynthesis and primary productivity. Likewise, analyses of the microbial community in the plastisphere show a radically different profile compared to the surrounding planktonic diversity. The plastisphere also enriches multidrug-resistant bacteria, cyanotoxins, and pollutants, accelerating microbial succession, changing the microbiome, and thus, affecting phytoplankton diversity and evolution. These impacts on cellular and community scales manifest in changed ecosystem dynamics with widespread bottom-up and top-down effects on aquatic biodiversity and food web interactions. These adverse effects─through altered nutrient cycling─have “knock-on” impacts on biogeochemical cycles and greenhouse gases. Consequently, these impacts affect provisioning and regulating ecosystem services. Our citation network analyses (CNA) further demonstrate dire effects of MP and PL on all trophic levels, thereby unsettling ecosystem stability and services. CNA points to several emerging nodes indicating combined toxicity of MP, PL, and their associated hazards on phytoplankton. Taken together, our study shows that ecotoxicity of plastic particles and their leachates have placed primary producers and some aquatic ecosystems in peril.

The smallest fraction of plastic pollution, submicron plastics (SMPs <1 μm) are expected to be ubiquitous in the environment. No information is available about SMPs in peatlands, which have a key role in sequestering carbon in terrestrial ecosystems. It is unknown how these plastic particles might behave and interact with (micro)organisms in these ecosystems. Here, we show that the chemical composition of polystyrene (PS) and poly(vinyl chloride) (PVC)-SMPs influenced their adsorption to peat. Consequently, this influenced the accumualtion of SMPs by Sphagnummoss and the composition and diversity of the microbial communities in peatland. Natural organic matter (NOM), which adsorbs from the surrounding water to the surface of SMPs, decreased the adsorption of the particles to peat and their accumulation by Sphagnummoss. However, the presence of NOM on SMPs significantly altered the bacterial community structure compared to SMPs without NOM. Our findings show that peatland ecosystems can potentially adsorb plastic particles. This can not only impact mosses themselves but also change the local microbial communities.

Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4emissions to the atmosphere. Until recently, aquatic biogenic CH4production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom‐bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4emissions and thus to substantially reduce current uncertainties when estimating global CH4emissions from aquatic ecosystems.

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28?S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

Pelagic bacteria can be classified into free‐living and particle‐attached life modes, which either dwell in the water column or attach to suspended particles. Bacteria with a generalist life style, however, can actively shift between these two habitats. Globally increasing densities of natural and artificial particles enhance habitat heterogeneity, with potential consequences for system stability and trophic transfer through aquatic food webs. To better decipher the dynamics of microbial communities, we investigated the influence of adaptive vs. fixed habitat choice on species coexistence for a simplified bacterial community by analyzing a corresponding food web model, consisting of two specialist bacterial prey species (free and attached), a generalist bacterial prey species with the ability to shift between both habitats, and two protist predators, specialized on either water or particle compartment. For simplicity we assume a shared resource pool, considering particles only for colonization but not as a source for nutrients or carbon, that is, inert particles like microplastics or inorganic sediments. The model predicts coexistence on a cyclic attractor between fixed and flexible bacteria, if the costs for adaptive habitat choice can be balanced by adaptation speed. The presence of adaptive prey dampens predator–prey cycle amplitudes, contributing to system stabilization resulting in higher mean predator biomass compared to specialist prey only. Thus, in pelagic microbial systems, flexible habitat choice at the prey level has important implications for system stability and magnitude of energy flow through the microbial loop.

Fungi in marine ecosystems play crucial roles as saprotrophs, parasites, and pathogens. The definition of marine fungi has evolved over the past century. Currently, “marine fungi” are defined as any fungi recovered repeatedly from marine habitats that are able to grow and/or sporulate in marine environments, form symbiotic relationships with other marine organisms, adapt and evolve at the genetic level, or are active metabolically in marine environments. While there are a number of recent reviews synthesizing our knowledge derived from over a century of research on marine fungi, this review article focuses on the state of knowledge on planktonic marine fungi from the coastal and open ocean, defined as fungi that are in suspension or attached to particles, substrates or in association with hosts in the pelagic zone of the ocean, and their roles in remineralization of organic matter and major biogeochemical cycles. This review differs from previous ones by focusing on biogeochemical impacts of planktonic marine fungi and methodological considerations for investigating their diversity and ecological functions. Importantly, we point out gaps in our knowledge and the potential methodological biases that might have contributed to these gaps. Finally, we highlight recommendations that will facilitate future studies of marine fungi. This article first provides a brief overview of the diversity of planktonic marine fungi, followed by a discussion of the biogeochemical impacts of planktonic marine fungi, and a wide range of methods that can be used to study marine fungi. Fungi are an important yet often overlooked member of marine food webs, especially in the water column. This review highlights the important ecological roles fungi play in the ocean water column, such as the recycling of dead organic matter and acting as parasites of microalgae in the ocean. We provide a summary of state‐of‐the‐art methods for studying planktonic marine fungi and making discoveries in the future. Planktonic marine fungi play key roles in the cycling of carbon, nitrogen, phosphorus, sulfur, and metals in the oceanThere is a large potential for discovering novel lineages and functions of planktonic marine fungi, particularly in the open oceanThe ecological roles of planktonic marine fungi should be studied by combining multi‐omics and biochemical tools Planktonic marine fungi play key roles in the cycling of carbon, nitrogen, phosphorus, sulfur, and metals in the ocean There is a large potential for discovering novel lineages and functions of planktonic marine fungi, particularly in the open ocean The ecological roles of planktonic marine fungi should be studied by combining multi‐omics and biochemical tools

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

To determine the drivers of phytoplankton biomass, we collected standardized morphometric, physical, and biological data in 230 lakes across the Mediterranean, Continental, and Boreal climatic zones of the European continent. Multilinear regression models tested on this snapshot of mostly eutrophic lakes (median total phosphorus [TP] = 0.06 and total nitrogen [TN] = 0.7 mg L−1), and its subsets (2 depth types and 3 climatic zones), show that light climate and stratification strength were the most significant explanatory variables for chlorophyll a(Chl a) variance. TN was a significant predictor for phytoplankton biomass for shallow and continental lakes, while TP never appeared as an explanatory variable, suggesting that under high TP, light, which partially controls stratification strength, becomes limiting for phytoplankton development. Mediterranean lakes were the warmest yet most weakly stratified and had significantly less Chl athan Boreal lakes, where the temperature anomaly from the long‐term average, during a summer heatwave was the highest (+4°C) and showed a significant, exponential relationship with stratification strength. This European survey represents a summer snapshot of phytoplankton biomass and its drivers, and lends support that light and stratification metrics, which are both affected by climate change, are better predictors for phytoplankton biomass in nutrient‐rich lakes than nutrient concentrations and surface temperature.

The concentration of dissolved oxygen in aquatic systems helps to regulate biodiversity1,2, nutrient biogeochemistry3, greenhouse gas emissions4, and the quality of drinking water5. The long-term declines in dissolved oxygen concentrations in coastal and ocean waters have been linked to climate warming and human activity6,7, but little is known about the changes in dissolved oxygen concentrations in lakes. Although the solubility of dissolved oxygen decreases with increasing water temperatures, long-term lake trajectories are difficult to predict. Oxygen losses in warming lakes may be amplified by enhanced decomposition and stronger thermal stratification8,9or oxygen may increase as a result of enhanced primary production10. Here we analyse a combined total of 45,148 dissolved oxygen and temperature profiles and calculate trends for 393 temperate lakes that span 1941 to 2017. We find that a decline in dissolved oxygen is widespread in surface and deep-water habitats. The decline in surface waters is primarily associated with reduced solubility under warmer water temperatures, although dissolved oxygen in surface waters increased in a subset of highly productive warming lakes, probably owing to increasing production of phytoplankton. By contrast, the decline in deep waters is associated with stronger thermal stratification and loss of water clarity, but not with changes in gas solubility. Our results suggest that climate change and declining water clarity have altered the physical and chemical environment of lakes. Declines in dissolved oxygen in freshwater are 2.75 to 9.3 times greater than observed in the world’s oceans6,7and could threaten essential lake ecosystem services2,3,5,11.

Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magnacarcasses and 13C-labelled maize leaves (Zea mays)were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). 13C stable-isotope measurements of CO2analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C–N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.

The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.

The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.

Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magnacarcasses and 13C-labelled maize leaves (Zea mays)were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). 13C stable-isotope measurements of CO2analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C–N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.

The intensity and frequency of storms are projected to increase in many regions of the world because of climate change. Storms can alter environmental conditions in many ecosystems. In lakes and reservoirs, storms can reduce epilimnetic temperatures from wind‐induced mixing with colder hypolimnetic waters, direct precipitation to the lake's surface, and watershed runoff. We analyzed 18 long‐term and high‐frequency lake datasets from 11 countries to assess the magnitude of wind‐ vs. rainstorm‐induced changes in epilimnetic temperature. We found small day‐to‐day epilimnetic temperature decreases in response to strong wind and heavy rain during stratified conditions. Day‐to‐day epilimnetic temperature decreased, on average, by 0.28°C during the strongest windstorms (storm mean daily wind speed among lakes: 6.7 ± 2.7 m s−1, 1 SD) and by 0.15°C after the heaviest rainstorms (storm mean daily rainfall: 21.3 ± 9.0 mm). The largest decreases in epilimnetic temperature were observed ≥2 d after sustained strong wind or heavy rain (top 5thpercentile of wind and rain events for each lake) in shallow and medium‐depth lakes. The smallest decreases occurred in deep lakes. Epilimnetic temperature change from windstorms, but not rainstorms, was negatively correlated with maximum lake depth. However, even the largest storm‐induced mean epilimnetic temperature decreases were typically <2°C. Day‐to‐day temperature change, in the absence of storms, often exceeded storm‐induced temperature changes. Because storm‐induced temperature changes to lake surface waters were minimal, changes in other limnological variables (e.g., nutrient concentrations or light) from storms may have larger impacts on biological communities than temperature changes.

Recent discovery of methane (CH4) production in oxic waters challenges the conventional understanding of strict anoxic requirement for biological CH4production. High‐resolution field measurements in Lake Stechlin, as well as incubation experiments, suggested that oxic‐water CH4production occurred throughout much of the water column and was associated with phytoplankton especially diatoms, cyanobacteria, green algae, and cryptophytes. In situ concentrations and δ13C values of CH4in oxic water were negatively correlated with soluble reactive phosphorus concentrations. Using 13C‐labeling techniques, we showed that bicarbonate was converted to CH4, and the production exceeded oxidation at day, but was comparable at night. These experimental data, along with complementary field observations, indicate a clear link between photosynthesis and the CH4production‐consumption balance in phosphorus‐limited epilimnic waters. Comparison between surface CH4emission data and experimental CH4production rates suggested that the oxic CH4source significantly contributed to surface emission in Lake Stechlin. These findings call for re‐examination of the aquatic CH4cycle and climate predictions.

The discovery of methane (CH4) accumulation in oxic marine and limnic waters has redefined the role of aquatic environments in the regional CH4cycle. Although CH4accumulation in oxic surface waters became apparent in recent years, the sources are still subject to controversial discussions. We present high-resolution in situ measurements of CH4concentration and its stable isotope composition in a stratified mesotrophic lake. We show that CH4accumulation in surface waters originates from a highly dynamic interplay between (oxic) CH4production and emission to the atmosphere. Laboratory incubations of different phytoplankton types and application of stable isotope techniques provide a first unambiguous evidence that major phytoplankton classes in Lake Stechlin per se produce CH4under oxic conditions. Combined field and lab results show that the photoautotroph community is an important driver for CH4production and its highly dynamic accumulation in oxic surface waters.

Trichodesmiumis an important dinitrogen (N2)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmiumcolonies with their diverse epibionts support various nitrogen (N) transformations beyond N2fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmiumcolonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmiumcolonies. Colonies were net-autotrophic, with carbon and N2fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60–200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmiumcolonies.

Trichodesmiumis an important dinitrogen (N2)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmiumcolonies with their diverse epibionts support various nitrogen (N) transformations beyond N2fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmiumcolonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmiumcolonies. Colonies were net-autotrophic, with carbon and N2fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60–200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmiumcolonies.

Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense and a general challenge is to understand how metabolism and interactions of single organisms shape microbial community dynamics and ecosystem‐scale biogeochemical transformations. Metagenomic approaches have developed rapidly, and proven to be powerful in linking microbial community dynamics to biogeochemical processes. In this review, we provide an overview of metagenomic approaches, followed by a discussion on some recent insights they have provided, including those in this special issue. These include the discovery of new taxa and metabolisms in aquatic microbiomes, insights into community assembly and functional ecology as well as evolutionary processes shaping microbial genomes and microbiomes, and the influence of human activities on aquatic microbiomes. Given that metagenomics can now be considered a mature technology where data generation and descriptive analyses are relatively routine and informative, we then discuss metagenomic‐enabled research avenues to further link microbial dynamics to biogeochemical processes. These include the integration of metagenomics into well‐designed ecological experiments, the use of metagenomics to inform and validate metabolic and biogeochemical models, and the pressing need for ecologically relevant model organisms and simple microbial systems to better interpret the taxonomic and functional information integrated in metagenomes. These research avenues will contribute to a more mechanistic and predictive understanding of links between microbial dynamics and biogeochemical cycles. Owing to rapid climate change and human impacts on aquatic ecosystems, the urgency of such an understanding has never been greater.

Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosaduring blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystisinteractome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosais cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystisand the microbiome bacteria shared many genes, whole‐community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystisblooms, thereby providing initial support for the hypothesized Microcystisinteractome.

There is now increasing evidence for the importance of microbial regulation of biogeochemical cycling in streams. Resource availability shapes microbial community structure, but less is known about how landscape‐mediated availability of nutrients and carbon can control microbial functions in streams. Using comparative metagenomics, we examined the relationship between microbial functional genes and composition of dissolved organic matter (DOM), nutrients, and suspended microbial communities in 11 streams, divided into three groups based on the predominant land cover category (agriculture, forested, or wetland). Using weighted gene co‐occurrence network analysis, we identified clusters of functions related to DOM composition, agricultural land use, and/or wetland and forest land cover. Wetland‐dominated streams were characterized by functions related to nitrogen metabolism and processing of aromatic carbon compounds, with strong positive correlations with dissolved organic carbon concentration and DOM aromaticity. Forested streams were characterized by metabolic functions related to monomer uptake and carbohydrates, such as mannose and fructose metabolism. In agricultural streams, microbial functions were correlated with more labile, protein‐like DOM, PO4, and NO3, likely reflecting functional adaptation to labile DOM and higher nutrient concentrations. Distinct changes in the functional composition and loss of functional diversity of microorganisms became evident when comparing natural to agricultural catchments. Although all streams showed signs of functional redundancy, loss of species richness per function in agricultural catchments suggests that microbial functions in natural catchments may be more resilient to disturbance. Our results provide new insight into microbial community functions involved in nutrient and carbon biogeochemical cycles and their dependence on specific environmental settings.

Studies on the ecological role of fungi and, to a lesser extent, oomycetes, are receiving increasing attention, mainly due to their participation in the cycling of organic matter in aquatic ecosystems. To unravel their importance in humification processes, we isolated several strains of fungi and oomycetes from Anzali lagoon, Iran. We then performed taxonomic characterization by morphological and molecular methods, analyzed the ability to degrade several polymeric substrates, performed metabolic fingerprinting with Ecoplates, and determined the degradation of humic substances (HS) using liquid chromatography‐organic carbon detection. Our analyses highlighted the capacity of aquatic fungi to better degrade a plethora of organic molecules, including complex polymers. Specifically, we were able to demonstrate not only the utilization of these complex polymers, but also the role of fungi in the production of HS. In contrast, oomycetes, despite some morphological and physiological similarities with aquatic fungi, exhibited a propensity toward opportunism, quickly benefitting from the availability of small organic molecules, while exhibiting sensitivity toward more complex polymers. Despite their contrasting roles, our study highlights the importance of both oomycetes and fungi in aquatic organic matter transformation and cycling with potential implications for the global carbon cycle.

Mixotrophy is increasingly recognized as an important trophic pathway among phytoplankton, yet its underlying drivers remain largely unknown and unexplored. Here, we present a study utilizing 69 lake samplings in boreal Quebec, Canada, identifying variables driving the success of phytoplankton that have a capacity for mixotrophy and pointing to the underlying mechanisms. We found that the success of mixotrophs (% of total biomass) was positively influenced by both colored dissolved organic matter (cDOM) and dissolved CO2concentration but limited by the abundance of crustacean zooplankton. The effect of cDOM manifested as a consequence of limited autotrophic phytoplankton biomass in lakes with reduced light penetration. We observed a nonlinear (u‐shaped) relation between CO2and mixotrophs, with biomass favored at both low and high CO2concentrations. A reduced fitness of mixotrophs at near‐atmospheric CO2concentrations is likely owing to the costs of rapidly switching between or maintaining multiple trophic strategies. The abundance of zooplankton had a negative effect on mixotroph biomass but a positive effect on autotrophic phytoplankton. We also found that while the community composition of potentially mixotrophic phytoplankton was to some degree likely influenced by zooplankton biomass, composition was unaffected by the CO2and cDOM gradients. Overall, this study highlights mixotrophy in boreal lake systems as a strategy of persistence, with the maintenance of a moderate but constant presence across a changing gradient of light and trophic conditions. The results of our study support the hypothesis that phytoplankton with a capacity for mixotrophy provide a superior and stable stoichiometric food source for zooplankton, implicating mixotrophs as a vital component of boreal lake food webs.

Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

The vertical distribution of chlorophyll in stratified lakes and reservoirs frequently exhibits a maximum peak deep in the water column, referred to as the deep chlorophyll maximum (DCM). DCMs are ecologically important hot spots of primary production and nutrient cycling, and their location can determine vertical habitat gradients for primary consumers. Consequently, the drivers of DCM structure regulate many characteristics of aquatic food webs and biogeochemistry. Previous studies have identified light and thermal stratification as important drivers of summer DCM depth, but their relative importance across a broad range of lakes is not well resolved. We analyzed profiles of chlorophyll fluorescence, temperature, and light during summer stratification from 100 lakes in the Global Lake Ecological Observatory Network (GLEON) and quantified two characteristics of DCM structure: depth and thickness. While DCMs do form in oligotrophic lakes, we found that they can also form in eutrophic to dystrophic lakes. Using a random forest algorithm, we assessed the relative importance of variables associated with light attenuation vs. thermal stratification for predicting DCM structure in lakes that spanned broad gradients of morphometry and transparency. Our analyses revealed that light attenuation was a more important predictor of DCM depth than thermal stratification and that DCMs deepen with increasing lake clarity. DCM thickness was best predicted by lake size with larger lakes having thicker DCMs. Additionally, our analysis demonstrates that the relative importance of light and thermal stratification on DCM structure is not uniform across a diversity of lake types.

The ecological relevance of fungi in freshwater ecosystems is becoming increasingly evident, particularly in processing the extensive amounts of polymeric organic carbon such as cellulose, chitin, and humic substances (HS). We isolated several fungal strains from oligo‐mesotrophic Lake Stechlin, Brandenburg, Germany, and analyzed their ability to degrade polymeric‐like substrates. Using liquid chromatography‐organic carbon detection, we determined the byproducts of HS transformation by the freshwater fungus Cladosporiumsp. KR14. We demonstrate the ability of this fungus to degrade and simultaneously synthesize HS, and that transformation processes were intensified when iron, as indicator of the occurrence of Fenton reactions, was present in the medium. Furthermore, we showed that structural complexity of the HS produced changed with the availability of other polymeric substances in the medium. Our study highlights the contribution of freshwater Ascomycetes to the transformation of complex organic compounds. As such, it has important implications for understanding the ecological contribution of fungi to aquatic food webs and related biogeochemical cycles.

Many lakes exhibit seasonal stratification, during which they develop strong thermal and chemical gradients. An expansion of depth‐integrated monitoring programs has provided insight into the importance of organic carbon processing that occurs below the upper mixed layer. However, the chemical and physical drivers of metabolism and metabolic coupling remain unresolved, especially in the metalimnion. In this depth zone, sharp gradients in key resources such as light and temperature co‐occur with dynamic physical conditions that influence metabolic processes directly and simultaneously hamper the accurate tracing of biological activity. We evaluated the drivers of metalimnetic metabolism and its associated uncertainty across 10 stratified lakes in Europe and North America. We hypothesized that the metalimnion would contribute highly to whole‐lake functioning in clear oligotrophic lakes, and that metabolic rates would be highly variable in unstable polymictic lakes. Depth‐integrated rates of gross primary production (GPP) and ecosystem respiration (ER) were modelled from diel dissolved oxygen curves using a Bayesian approach. Metabolic estimates were more uncertain below the epilimnion, but uncertainty was not consistently related to lake morphology or mixing regime. Metalimnetic rates exhibited high day‐to‐day variability in all trophic states, with the metalimnetic contribution to daily whole‐lake GPP and ER ranging from 0% to 87% and < 1% to 92%, respectively. Nonetheless, the metalimnion of low‐nutrient lakes contributed strongly to whole‐lake metabolism on average, driven by a collinear combination of highlight, low surface‐water phosphorous concentration and high metalimnetic volume. Consequently, a single‐sensor approach does not necessarily reflect whole‐ecosystem carbon dynamics in stratified lakes.