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Death is a common outcome of infection, but most disease models do not track hosts after death. Instead, these hosts disappear into a void. This assumption lacks critical realism, because dead hosts can alter host–pathogen dynamics. Here, we develop a theoretical framework of carbon-based models combining disease and ecosystem perspectives to investigate the consequences of feedbacks between living and dead hosts on disease dynamics and carbon cycling. Because autotrophs (i.e. plants and phytoplankton) are critical regulators of carbon cycling, we developed general model structures and parameter combinations to broadly reflect disease of autotrophic hosts across ecosystems. Analytical model solutions highlight the importance of disease–ecosystem coupling. For example, decomposition rates of dead hosts mediate pathogen spread, and carbon flux between live and dead biomass pools are sensitive to pathogen effects on host growth and death rates. Variation in dynamics arising from biologically realistic parameter combinations largely fell along a single gradient from slow to fast carbon turnover rates, and models predicted higher disease impacts in fast turnover systems (e.g. lakes and oceans) than slow turnover systems (e.g. boreal forests). Our results demonstrate that a unified framework, including the effects of pathogens on carbon cycling, provides novel hypotheses and insights at the nexus of disease and ecosystem ecology.

Greenhouse gas (GHG) emissions from small inland waters are disproportionately large. Climate warming is expected to favor dominance of algae and free-floating plants at the expense of submerged plants. Through different routes these functional plant types may have far-reaching impacts on freshwater GHG emissions in future warmer waters, which are yet unknown. We conducted a 1,000 L mesocosm experiment testing the effects of plant type and warming on GHG emissions from temperate inland waters dominated by either algae, free-floating or submerged plants in controls and warmed (+4 °C) treatments for one year each. Our results show that the effect of experimental warming on GHG fluxes differs between dominance of different functional plant types, mainly by modulating methane ebullition, an often-dominant GHG emission pathway. Specifically, we demonstrate that the response to experimental warming was strongest for free-floating and lowest for submerged plant-dominated systems. Importantly, our results suggest that anticipated shifts in plant type from submerged plants to a dominance of algae or free-floating plants with warming may increase total GHG emissions from shallow waters. This, together with a warming-induced emission response, represents a so far overlooked positive climate feedback. Management strategies aimed at favouring submerged plant dominance may thus substantially mitigate GHG emissions.

The physiological performance of organisms depends on their environmental context, resulting in performance-response curves along environmental gradients. Parasite performance-response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we 1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and 2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesise knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host-parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance-response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions. This article is protected by copyright. All rights reserved.

The microbial food-loop is critical to energy flow in aquatic food webs. We tested the hypothesis that species composition and relative abundance in a microbial community would be modified by the development of toxic algal blooms either by enhanced carbon production or toxicity. This study tracked the response of the microbial community with respect to composition and relative abundance during a 7-day algal bloom event in the Three Gorges Reservoir in May 2018. Chlorophyll a biomass, microscopic identification and cell counting of algae and algal abundance (ind. L−1) and carbon, nutrient concentrations (total phosphorus and nitrogen, dissolved total phosphorus and nitrogen), and DNA high throughput sequencing were measured daily. Algal density (1.2 × 109 ind. L−1) and Chlorophyll a (219 μg L−1) peaked on May 20th–21st, when the phytoplankton community was dominated by Chlorella spp. and Microcystis spp. The concentrations of both dissolved total nitrogen and phosphorus declined during the bloom period. Based on DNA high throughput sequencing data, the relative abundance of eukaryotic phytoplankton, microzooplankton (20–200 μm), mesozooplankton (>200 μm), and fungal communities varied day by day while the prokaryotic community revealed a more consistent structure. Enhanced carbon production during the bloom was closely associated with increased heterotrophic microbial composition in both the prokaryotic and eukaryotic communities. A storm event, however, that caused surface cooling and deep mixing of the water column greatly modified the composition and relative abundance of species in the microbial loop. The high temporal variability and dynamics observed in this study suggest that many factors, and not just algal blooms, were interacting to determine the composition and relative abundance of species of the microbial loop.

Previous reports suggest planktonic and under-ice winter microbial communities in Lake Erie are dominated by diatoms. Here, we report the assembled metatranscriptomes of 79 Lake Erie surface water microbial communities spanning both the winter (28 samples) and spring (51 samples) months over spatial, temporal, and climatic gradients in 2019 through 2020.

Datasets and R scripts for the COVID anthropause case study sites for the publication entitled "Lessons learned from the COVID-19 anthropause in the Netherlands on urban aquatic ecosystem services provisioning and management" When using the .csv files for Figure 2B (bathing waters, file: Zwemmen buiten) and Figure 2C (national parks; files: De Alde Feanen, De Biesbosch, De Groote Peel, Dwingelderveld, Lauwersmeer and Weerribben-Wieden), make sure the dates are in the following format: dd-mm-yyyy When running the Figure 2C codes (in R script "COVID_GoogleTrends_Script"), set the working directory to a folder containing only the national parks .csv files.

An overlooked effect of ecosystem eutrophication is the potential to alter disease dynamics in primary producers, inducing disease‐mediated feedbacks that alter net primary productivity and elemental recycling. Models in disease ecology rarely track organisms past death, yet death from infection can alter important ecosystem processes including elemental recycling rates and nutrient supply to living hosts. In contrast, models in ecosystem ecology rarely track disease dynamics, yet elemental nutrient pools (e.g. nitrogen, phosphorus) can regulate important disease processes including pathogen reproduction and transmission. Thus, both disease and ecosystem ecology stand to grow as fields by exploring questions that arise at their intersection. However, we currently lack a framework explicitly linking these disciplines. We developed a stoichiometric model using elemental currencies to track primary producer biomass (carbon) in vegetation and soil pools, and to track prevalence and the basic reproduction number (R0) of a directly transmitted pathogen. This model, parameterised for a deciduous forest, demonstrates that anthropogenic nutrient supply can interact with disease to qualitatively alter both ecosystem and disease dynamics. Using this element‐focused approach, we identify knowledge gaps and generate predictions about the impact of anthropogenic nutrient supply rates on infectious disease and feedbacks to ecosystem carbon and nutrient cycling.

Autotrophs play an essential role in the cycling of carbon and nutrients, yet disease-ecosystem relationships are often overlooked in these dynamics. Importantly, the availability of elemental nutrients like nitrogen and phosphorus impacts infectious disease in autotrophs, and disease can induce reciprocal effects on ecosystem nutrient dynamics. Relationships linking infectious disease with ecosystem nutrient dynamics are bidirectional, though the interdependence of these processes has received little attention. We introduce disease-mediated nutrient dynamics (DND) as a framework to describe the multiple, concurrent pathways linking elemental cycles with infectious disease. We illustrate the impact of disease–ecosystem feedback loops on both disease and ecosystem nutrient dynamics using a simple mathematical model, combining approaches from classical ecological (logistic and Droop growth) and epidemiological (susceptible and infected compartments) theory. Our model incorporates the effects of nutrient availability on the growth rates of susceptible and infected autotroph hosts and tracks the return of nutrients to the environment following host death. While focused on autotroph hosts here, the DND framework is generalizable to higher trophic levels. Our results illustrate the surprisingly complex dynamics of host populations, infection patterns, and ecosystem nutrient cycling that can arise from even a relatively simple feedback between disease and nutrients. Feedback loops in disease-mediated nutrient dynamics arise via effects of infection and nutrient supply on host stoichiometry and population size. Our model illustrates how host growth rate, defense, and tissue chemistry can impact the dynamics of disease–ecosystem relationships. We use the model to motivate a review of empirical examples from autotroph–pathogen systems in aquatic and terrestrial environments, demonstrating the key role of nutrient–disease and disease–nutrient relationships in real systems. By assessing existing evidence and uncovering data gaps and apparent mismatches between model predictions and the dynamics of empirical systems, we highlight priorities for future research intended to narrow the persistent disciplinary gap between disease and ecosystem ecology. Future empirical and theoretical work explicitly examining the dynamic linkages between disease and ecosystem ecology will inform fundamental understanding for each discipline and will better position the field of ecology to predict the dynamics of disease and elemental cycles in the context of global change.

SUMMARY: As human mobility decreased in 2020, the interaction between humans and nature changed significantly. On one hand, water clarity improved in the Amsterdam canals because boat traffic was reduced. On the other hand increased use of fishing water and national parks formed potential threats to the aquatic ecosystems. It is important to use these experiences to foster a more eco-centric mindset, building up to handling handling climate change and future pandemics. ABSTRACT: The anomalous past two years of the COVID-19 pandemic have been a test of human response to global crisis management as typical human activities were significantly altered. The COVID-instigated anthropause has illustrated the influence that humans and the biosphere have on each other, especially given the variety of national mobility interventions that have been implemented globally. These local COVID-19-era restrictions influenced human-ecosystem interactions through changes in accessibility of water systems and changes in ecosystem service demand. Four urban aquatic case studies in the Netherlands demonstrated shifts in human demand during the anthropause. For instance, reduced boat traffic in Amsterdam canals led to improved water clarity. In comparison, ongoing service exploitation from increased recreational fishing, use of bathing waters and national parks visitation are heightening concerns about potential ecosystem degradation. We distilled management lessons from both the case studies as well as from recent literature pertaining to ecological intactness and social relevance. Equally important to the lessons themselves, however, is the pace at which informed management practices are established after the pandemic ends, particularly as many communities currently recognize the importance of aquatic ecosystems and are amenable to their protection.

Monitoring of cyanobacterial bloom biomass in large lakes at high resolution is made possible by remote sensing. However, monitoring cyanobacterial toxins is only feasible with grab samples, which, with only sporadic sampling, results in uncertainties in the spatial distribution of toxins. To address this issue, we conducted two intensive “HABs Grabs” of microcystin (MC)-producing Microcystis blooms in the western basin of Lake Erie. These were one-day sampling events during August of 2018 and 2019 in which 100 and 172 grab samples were collected, respectively, within a six-hour window covering up to 2,270 km2 and analyzed using consistent methods to estimate the total mass of MC. The samples were analyzed for 57 parameters, including toxins, nutrients, chlorophyll, and genomics. There were an estimated 11,513 kg and 30,691 kg of MCs in the western basin during the 2018 and 2019 HABs Grabs, respectively. The bloom boundary poses substantial issues for spatial assessments because MC concentration varied by nearly two orders of magnitude over very short distances. The MC to chlorophyll ratio (MC:chl) varied by a factor up to 5.3 throughout the basin, which creates challenges for using MC:chl to predict MC concentrations. Many of the biomass metrics strongly correlated (r > 0.70) with each other except chlorophyll fluorescence and phycocyanin concentration. While MC and chlorophyll correlated well with total phosphorus and nitrogen concentrations, MC:chl correlated with dissolved inorganic nitrogen. More frequent MC data collection can overcome these issues, and models need to account for the MC:chl spatial heterogeneity when forecasting MCs.

Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions. IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.

Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously., Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions. IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.

Fungal diseases threaten natural and man‐made ecosystems. Chytridiomycota (chytrids) infect a wide host range, including phytoplankton species that form the basis of aquatic food webs and produce roughly half of Earth's oxygen. However, blooms of large or toxic phytoplankton form trophic bottlenecks, as they are inedible to zooplankton. Chytrids infecting inedible phytoplankton provide a trophic link to zooplankton by producing edible zoospores of high nutritional quality. By grazing chytrid zoospores, zooplankton may induce a trophic cascade, as a decreased zoospore density will reduce new infections. Conversely, fewer infections will not produce enough zoospores to sustain long‐term zooplankton growth and reproduction. This intricate balance between zoospore density necessary for zooplankton energetic demands (growth/survival), and the loss in new infections (and thus new zoospores) because of grazing was tested empirically. To this end, we exposed a cyanobacterial host (Planktothrix rubescens) infected by a chytrid (Rizophydium megarrhizum) to a grazer density gradient (the rotifer Keratella cf. cochlearis). Rotifers survived and reproduced on a zoospore diet, but the Keratella population growth was limited by the amount of zoospores provided by chytrid infections, resulting in a situation where zooplankton survived but were restricted in their ability to control disease in the cyanobacterial host. We subsequently developed and parameterized a dynamical food‐chain model using an allometric relationship for clearance rate to assess theoretically the potential of different‐sized zooplankton groups to restrict disease in phytoplankton hosts. Our model suggests that smaller‐sized zooplankton may have a high potential to reduce chytrid infections on inedible phytoplankton. Together, our results point out the complexity of three‐way interactions between hosts, parasites, and grazers and highlight that trophic cascades are not always sustainable and may depend on the grazer's energetic demand.

Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature–ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 °C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6–20% per 1 °C increase), contributing to global warming., The impacts of climate change on natural methane (CH4) emissions via ebullition are unclear. Here, using published and experimental multi-seasonal CH4 ebullition data, the authors find a strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems globally.

Climate change is expected to favour infectious diseases across ecosystems worldwide. In freshwater and marine environments, parasites play a crucial role in controlling plankton population dynamics. Infection of phytoplankton populations will cause a transfer of carbon and nutrients into parasites, which may change the type of food available for higher trophic levels. Some phytoplankton species are inedible to zooplankton, and the termination of their population by parasites may liberate otherwise unavailable carbon and nutrients. Phytoplankton spring blooms often consist of large diatoms inedible for zooplankton, but the zoospores of their fungal parasites may serve as a food source for this higher trophic level. Here, we investigated the impact of warming on the fungal infection of a natural phytoplankton spring bloom and followed the response of a zooplankton community. Experiments were performed in ca. 1000 L indoor mesocosms exposed to a controlled seasonal temperature cycle and a warm (+4 °C) treatment in the period from March to June 2014. The spring bloom was dominated by the diatom Synedra. At the peak of infection over 40% of the Synedra population was infected by a fungal parasite (i.e. a chytrid) in both treatments. Warming did not affect the onset of the Synedra bloom, but accelerated its termination. Peak population density of Synedra tended to be lower in the warm treatments. Furthermore, Synedra carbon: phosphorus stoichiometry increased during the bloom, particularly in the control treatments. This indicates enhanced phosphorus limitation in the control treatments, which may have constrained chytrid development. Timing of the rotifer Keratella advanced in the warm treatments and closely followed chytrid infections. The chytrids' zoospores may thus have served as an alternative food source to Keratella. Our study thus emphasizes the importance of incorporating not only nutrient limitation and grazing, but also parasitism in understanding the response of plankton communities towards global warming.

During the end of spring and throughout summer, large‐sized phytoplankton taxa often proliferate and form dense blooms in freshwater ecosystems. In many cases, they are inedible to zooplankton and prevent efficient transfer of energy and elements to higher trophic levels. Such a constraint may be alleviated by fungal parasite infections on large‐sized phytoplankton taxa like diatoms and filamentous cyanobacteria, as infections may provide zooplankton with a complementary food source in the form of fungal zoospores. Zoospores have been shown to support somatic growth of large filter feeding zooplankton species. Here, we tested if selectively feeding zooplankton, more specifically rotifers, also can use fungal zoospores as a food source. Our results show that chytrid fungal parasites can indeed support population growth of rotifers (Keratella sp.). Specifically, in cultures of an inedible filamentous cyanobacterium (Planktothrix rubescens), Keratella populations rapidly declined, while in Planktothrix cultures infected with chytrids, Keratella population growth rate equaled the growth observed for populations fed with a more suitable green algal diet (Chlorella sorokiniana). Feeding of Keratella on zoospores was furthermore indicated by a reduced number of zoospores during the last sampling day. These findings not only imply that rotifers may survive on zoospores, but also that the zoospores can support high rotifer population growth rates. We thus show that fungal parasites of inedible cyanobacteria can facilitate grazers by providing them alternative food sources. Together, these results highlight the important role that parasites may play in the aquatic plankton food web.