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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.

Land-water transition areas play a significant role in the functioning of aquatic ecosystems. However, anthropogenic pressures are posing severe threats on land-water transition areas, which leads to degradation of the ecological integrity of many lakes worldwide. Enhancing habitat complexity and heterogeneity by restoring land-water transition areas in lake systems is deemed a suitable method to restore lakes bottom-up by stimulating lower trophic levels. Stimulating productivity of lower trophic levels (phytoplankton, zooplankton) generates important food sources for declining higher trophic levels (fish, birds). Here, we study ecosystem restoration project Marker Wadden in Lake Markermeer, The Netherlands. This project involved the construction of a 700-ha archipelago of five islands in a degrading shallow lake, aiming to create additional sheltered land-water transition areas to stimulate food web development from its base by improving phytoplankton quantity and quality. We found that phytoplankton quantity (chlorophyll-a concentration) and quality (inversed carbon:nutrient ratio) in the shallow waters inside the Marker Wadden archipelago were significantly improved, likely due to higher nutrient availabilities, while light availability remained sufficient, compared to the surrounding lake. Higher phytoplankton quantity and quality was positively correlated with zooplankton biomass, which was higher inside the archipelago than in the surrounding lake due to improved trophic transfer efficiency between phytoplankton and zooplankton. We conclude that creating new land-water transition areas can be used to increase light and nutrient availabilities and thereby enhancing primary productivity, which in turn can stimulate higher trophic levels in degrading aquatic ecosystems.

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.

Hellweger et al . (Reports, 27 May 2022, pp. 1001) predict that phosphorus limitation will increase concentrations of cyanobacterial toxins in lakes. However, several molecular, physiological, and ecological mechanisms assumed in their models are poorly supported or contradicted by other studies. We conclude that their take-home message that phosphorus load reduction will make Lake Erie more toxic is seriously flawed.

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.

Primary consumers in aquatic ecosystems are frequently limited by the quality of their food, often expressed as phytoplankton elemental and biochemical composition. Effects of these food quality indicators vary across studies, and the relative importance of elemental (nitrogen and phosphorus) versus biochemical (fatty acid and sterol) limitation in aquatic food webs has been debated. Here we present results of a meta-analysis using >100 experimental studies, which confirms that limitation by N, P, essential fatty acids, and sterols all have significant negative effects on zooplankton performance. However, effects varied by grazer response (growth versus reproduction), specific manipulation, and across taxa. P limitation had greater effects on zooplankton growth than fatty acids, but P and fatty acid limitation had equal effects on reproduction. Furthermore, we show that nutrient co-limitation in zooplankton occurs, that indirect effects induced by P limitation exceed direct effects of mineral P limitation, that effects of nutrient amendments using laboratory phytoplankton isolates exceed those using natural field communities, and that algal physiology mediates zooplankton responses to nutrient limitation. Our meta-analysis reconciles contrasting views about the role of various food quality indicators, and their interactions, for zooplankton performance, and provides a mechanistic understanding of how environmental change affects trophic transfer.

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.

Shallow lakes can shift between stable states as a result of anthropogenic or natural drivers. Four common stable states differ in dominant groups of primary producers: submerged, floating, or emergent macrophytes or phytoplankton. Shifts in primary producer dominance affect key supporting, provisioning, regulating, and cultural ecosystem services supplied by lakes. However, links between states and services are often neglected or unknown in lake management, resulting in conflicts and additional costs. Here, we identify major shallow lake ecosystem services and their links to Sustainable Development Goals (SDGs), compare service provisioning among the four ecosystem states and discuss potential trade-offs. We identified 39 ecosystem services potentially provided by shallow lakes. Submerged macrophytes facilitate most of the supporting (86%) and cultural (63%) services, emergent macrophytes facilitate most regulating services (60%), and both emergent and floating macrophytes facilitate most provisioning services (63%). Phytoplankton dominance supports fewer ecosystem services, and contributes most to provisioning services (42%). The shallow lake ecosystem services we identified could be linked to 10 different SDGs, notably zero hunger (SDG 2), clean water and sanitation (SDG 6), sustainable cities and communities (SDG 11), and climate action (SDG13). We highlighted several trade-offs (1) among ecosystem services, (2) within ecosystem services, and (3) between ecosystem services across ecosystems. These trade-offs can have significant ecological and economic consequences that may be prevented by early identification in water quality management. In conclusion, common stable states in shallow lakes provide a different and diverse set of ecosystem services with numerous links to the majority of SDGs. Conserving and restoring ecosystem states should account for potential trade-offs between ecosystem services and preserving the natural value of shallow lakes.

Despite the ubiquity of pathogens in ecological systems, their roles in influencing ecosystem services are often overlooked. Pathogens that infect primary producers (i.e., plants, algae, cyanobacteria) can have particularly strong effects because autotrophs are responsible for a wide range of provisioning, regulating, and cultural services. We review the roles of pathogens in mediating ecosystem services provided by autotrophs and outline scenarios in which infection may lead to unexpected outcomes in response to global change. Our synthesis highlights a deficit of information on this topic, and we outline a vision for future research that includes integrative theory and cross-system empirical studies. Ultimately, knowledge about the mediating roles of pathogens on ecosystem services should inform environmental policy and practice.

Wind-induced sediment resuspension in shallow lakes may enhance nutrient availability while reducing light availability for phytoplankton growth, thereby affecting the entire food-web. Lake restoration projects that reduce wind-induced resuspension are expected to enhance trophic transfer efficiencies, thereby improving food-web structure and functioning. Yet, reduced resuspension may also lead to lower nutrient concentrations in the water column, promote benthic algae development, reduce phytoplankton biomass production and thereby reduce secondary production by zooplankton. Lake Markermeer is a shallow delta lake in The Netherlands subject to wind-induced sediment resuspension. Restoration project Marker Wadden consists of newly built islands aiming to reduce sediment resuspension and promote higher trophic levels. Here, we tested the effects of reduced sediment resuspension on phytoplankton biomass build-up, benthic algae development, and zooplankton abundances at different temperatures in a 14-day indoor microcosm experiment. We used Marker Wadden sediment with three resuspension intensities combined with three temperatures, to also test effects of higher temperatures in shallow sheltered waters. Reduced sediment resuspension decreased nutrient concentrations and phytoplankton biomass build-up, while increasing light availability and enhancing benthic algae biomass development. Reduced sediment resuspension furthermore increased zooplankton biomass. Enhanced sediment resuspension and higher temperatures synergistically interacted, maintaining a high level of inorganic suspended solids. Our experimental results are in line with long-term seasonal observations from Lake Markermeer. Our findings demonstrate that for shallow lakes suffering from wind effects, measures such as Marker Wadden aimed at reducing sediment resuspension can be effective in restoring secondary production and supporting higher trophic levels.

Phytoplankton photosynthesis strongly relies on the operation of carbon‐concentrating mechanisms (CCMs) to accumulate CO2 around their carboxylating enzyme ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO). Earlier evolved phytoplankton groups were shown to exhibit higher CCM activities to compensate for their RuBisCO with low CO2 specificities. Here, we tested whether earlier evolved phytoplankton groups also exhibit a higher CCM plasticity. To this end, we collected data from literature and applied a Bayesian linear meta‐analytic model. Our results show that with elevated pCO2, photosynthetic CO2 affinities decreased strongest and most consistent for the earlier evolved groups, i.e., cyanobacteria and dinoflagellates, while CO2‐dependent changes in affinities for haptophytes and diatoms were smaller and less consistent. In addition, responses of maximum photosynthetic rates toward elevated pCO2 were generally small and inconsistent across species. Our results demonstrate that phytoplankton groups with an earlier origin possess a high CCM plasticity, whereas more recently evolved groups do not, which likely results from evolved differences in the CO2 specificity of RuBisCO.

Since the industrial revolution 30% of the anthropogenic CO2 is absorbed by oceans, resulting in ocean acidification, which is a threat to calcifying algae. As a result, there has been profound interest in the study of calcifying algae, because of their important role in the global carbon cycle. The species studied, coccolithophore Emiliania huxleyi, is considered to be globally the single most dominant calcifying algae, which creates a unique exoskeleton from inorganic calcium carbonate platelets. The PIC (particulate inorganic carbon): POC (particulate organic carbon) ratio describes the relative amount of inorganic carbon in the algae and is a critical parameter in the ocean carbon cycle. In this research we explore the use of microfluidic single-cell impedance spectroscopy in the field of calcifying algae. Microfluidic impedance spectroscopy enables us to characterize single-cell electrical properties in a non-invasive and label-free way. We use the ratio of the impedance at high frequency vs. low frequency, known as opacity, to discriminate between calcified coccolithophores and coccolithophores with a calcite exoskeleton dissolved by acidification (decalcified). We have demonstrated that using opacity we can discriminate between calcified and decalcified coccolithophores with an accuracy of 94.1%. We have observed a correlation between the measured opacity and the cell height in the channel, which is supported by FEM simulations. The difference in cell density between calcified and decalcified cells can explain the difference in cell height and therefore the measured opacity.

Trait-based approaches provide a mechanistic framework crossing scales from cellular traits to community dynamics, while ecological stoichiometry applies first principles to understand how the balance of energy and elements shape ecological interactions. However, few studies have explicitly linked both frameworks. In this study, we tested the stoichiometric regulation of a number of carbon (C) based (e.g., extracellular polysaccharides and colony formation) and nitrogen (N) containing traits (i.e., chlorophyll a, phycocyanin, and gas vesicle content) in cyanobacteria in laboratory experiments and in the field. We exposed the cosmopolitan colony forming freshwater cyanobacterium Microcystis sp. in batch experiments to light, N and phosphorus (P) limitation, and enhanced CO2 levels, and assessed the regulation of these traits. Cyanobacterial traits followed stoichiometrically predictable patterns, where N containing traits increased with cellular N content, and decreased with increasing C : N ratios. C-based traits increased with cellular C content and C : N ratios under nutrient, particularly N, limitation. The pattern of colony formation was confirmed with field data from Lake Taihu (China), showing an increase in colony size when N was limiting and N : P ratios were low. These findings demonstrate how an explicit coupling of trait-based approaches to ecological stoichiometry can support our mechanistic understanding of responses of cyanobacteria toward shifts in resource availability.

Dissolved oceanic CO

Evidence for global environmental and climate change-related loss of biodiversity is accumulating. Understanding the causes of species community change is thus essential for effective management and conservation policies. Nonetheless, disentangling the relative influence of the individual or multiple drivers determining the species communities is challenging, as ecosystems are simultaneously affected by variable drivers acting on different spatial and temporal scales. To this end, paleolimnological data may provide critical information on long-term community changes, species dominance shifts, and their underlying drivers. Natural forced changes in the aquatic environments can be used to study the response of biota to repeated fluctuations in essential key variables. In this study, we investigated the planktonic diatom communities in a continuous, 1.36 Ma sedimentary succession from ancient Lake Ohrid (North Macedonia/Albania). This is the oldest, continuously existing freshwater lake in Europe, acknowledged as a site of exceptional biodiversity and endemic species richness. An extended biogeochemical dataset from the DEEP site sedimentary record and previously-published variables representing global climate variability was used to: i) quantify the relative influence of individual environmental variables in governing species communities, and ii) disentangle the contribution of basin-scale environmental processes and global-scale climate variability in driving community patterns over time. The results show that the structure of planktonic communities was primarily determined by the basin-scale environment, particularly, nutrient availability, water temperature and water column mixing, but also local tectonic processes, since lake ontogeny. However, since the onset of the penultimate glacial period 0.185 Ma ago, global-scale climate variability became the principal drivers of the diatom community structure. Our proxy time-series illustrates how various factors at different spatial scales may determine the freshwater planktonic communities over geological time-scales. Extended periods of stable communities can be terminated by changes in climate, environmental conditions and/or lake ontogeny, leading to species extinctions and community turnovers. Thereby lake ecosystem structure and functioning are affected and effective management and conservation policies are required to minimize additional anthropogenic change-related loss of biodiversity.

Physiological acclimation to elevated CO2 will intensify cyanobacterial blooms in lakes., Although phenotypic plasticity is a widespread phenomenon, its implications for species responses to climate change are not well understood. For example, toxic cyanobacteria can form dense surface blooms threatening water quality in many eutrophic lakes, yet a theoretical framework to predict how phenotypic plasticity affects bloom development at elevated pCO2 is still lacking. We measured phenotypic plasticity of the carbon fixation rates of the common bloom-forming cyanobacterium Microcystis. Our results revealed a 1.8- to 5-fold increase in the maximum CO2 uptake rate of Microcystis at elevated pCO2, which exceeds CO2 responses reported for other phytoplankton species. The observed plasticity was incorporated into a mathematical model to predict dynamic changes in cyanobacterial abundance. The model was successfully validated by laboratory experiments and predicts that acclimation to high pCO2 will intensify Microcystis blooms in eutrophic lakes. These results indicate that this harmful cyanobacterium is likely to benefit strongly from rising atmospheric pCO2.

Enrichment of the oceans with CO2 may be beneficial for some marine phytoplankton, including harmful algae. Numerous laboratory experiments provided valuable insights into the effects of elevated pCO(2) on the growth and physiology of harmful algal species, including the production of phycotoxins. Experiments close to natural conditions are the next step to improve predictions, as they consider the complex interplay between biotic and abiotic factors that can confound the direct effects of ocean acidification. We therefore investigated the effect of ocean acidification on the occurrence and abundance of phycotoxins in bulk plankton samples during a long-term mesocosm experiment in the Gullmar Fjord, Sweden, an area frequently experiencing harmful algal blooms. During the experimental period, a total of seven phycotoxin-producing harmful algal genera were identified in the fjord, and in accordance, six toxin classes were detected. However, within the mesocosms, only domoic acid and the corresponding producer Pseudo-nitzschia spp. was observed. Despite high variation within treatments, significantly higher particulate domoic acid contents were measured in the mesocosms with elevated pCO(2). Higher particulate domoic acid contents were additionally associated with macronutrient limitation. The risks associated with potentially higher phycotoxin levels in the future ocean warrants attention and should be considered in prospective monitoring strategies for coastal marine waters.

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.

Biological Stoichiometry is an ecological framework connecting the balance of elements to the functioning of organisms. Here, we applied this framework to study the relationships between carbon:nitrogen:phosphorus (C:N:P) ratios and synthesis of industrial high value biochemicals in the highly oleaginous alga Tetradesmus bernardii. We expected an increase in protein content with increasing cellular N content and decreasing C:N stoichiometry, and an increase in lipid content with increasing C:N and C:P stoichiometry. We tested these hypotheses by exposing T. bernardii to N and P limitation at a range of N:P supply ratios in chemostats set at low and high dilution rates. Following expectations, the cellular protein content increased with the N content, and decreased with cellular C:N ratios across all treatments. Carbohydrates and lipids largely followed the relative availability of C and increased under both N and P limitation, with higher C:N and C:P ratios. Specifically, lipid content increased by 100–125% upon N and P limitation, with a shift towards more neutral lipids at the cost of glycolipids and phospholipids. Generally, we observed a re-allocation of cellular C from protein to carbohydrates upon modest N limitation, and towards lipids under P and severe N limitation. Our results demonstrate stoichiometrically predictable patterns of industrially valuable compounds in an oleaginous microalga.

Global concern about human impact on biological diversity has triggered an intense research agenda on drivers and consequences of biodiversity change in parallel with international policy seeking to conserve biodiversity and associated ecosystem functions. Quantifying the trends in biodiversity is far from trivial, however, as recently documented by meta-analyses, which report little if any net change in local species richness through time.Here, we summarise several limitations of species richness as a metric of biodiversity change and show that the expectation of directional species richness trends under changing conditions is invalid. Instead, we illustrate how a set of species turnover indices provide more information content regarding temporal trends in biodiversity, as they reflect how dominance and identity shift in communities over time.We apply these metrics to three monitoring datasets representing different ecosystem types. In all datasets, nearly complete species turnover occurred, but this was disconnected from any species richness trends. Instead, turnover was strongly influenced by changes in species presence (identities) and dominance (abundances). We further show that these metrics can detect phases of strong compositional shifts in monitoring data and thus identify a different aspect of biodiversity change decoupled from species richness.Synthesis and applications: Temporal trends in species richness are insufficient to capture key changes in biodiversity in changing environments. In fact, reductions in environmental quality can lead to transient increases in species richness if immigration or extinction has different temporal dynamics. Thus, biodiversity monitoring programmes need to go beyond analyses of trends in richness in favour of more meaningful assessments of biodiversity change.Synthesis and applications:Temporal trends in species richness are insufficient to capture key changes in biodiversity in changing environments. In fact, reductions in environmental quality can lead to transient increases in species richness if immigration or extinction has different temporal dynamics. Thus, biodiversity monitoring programmes need to go beyond analyses of trends in richness in favour of more meaningful assessments of biodiversity change.

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.

Elevated pCO2 and warming may promote algal growth and toxin production, and thereby possibly support the proliferation and toxicity of harmful algal blooms (HABs). Here, we tested whether empirical data support this hypothesis using a meta‐analytic approach and investigated the responses of growth rate and toxin content or toxicity of numerous marine and estuarine HAB species to elevated pCO2 and warming. Most of the available data on HAB responses towards the two tested climate change variables concern dinoflagellates, as many members of this phytoplankton group are known to cause HAB outbreaks. Toxin content and toxicity did not reveal a consistent response towards both tested climate change variables, while growth rate increased consistently with elevated pCO2. Warming also led to higher growth rates, but only for species isolated at higher latitudes. The observed gradient in temperature growth responses shows the potential for enhanced development of HABs at higher latitudes. Increases in growth rates with more CO2 may present an additional competitive advantage for HAB species, particularly as CO2 was not shown to enhance growth rate of other non‐HAB phytoplankton species. However, this may also be related to the difference in representation of dinoflagellate and diatom species in the respective HAB and non‐HAB phytoplankton groups. Since the proliferation of HAB species may strongly depend on their growth rates, our results warn for a greater potential of dinoflagellate HAB development in future coastal waters, particularly in temperate regions., Elevated pCO2 and warming may promote algal growth and toxin production, and thereby possibly support the proliferation and toxicity of HABs. Using a meta‐analytic approach we found that elevated pCO2 increased growth rates of dinoflagellate HAB species, while this was not the case for non‐HAB phytoplankton species. Warming also led to higher growth rates, but mainly for species isolated at higher latitudes. These results warn for a greater potential of dinoflagellate HAB development in future coastal waters, particularly in temperate regions.

Global change involves shifts in multiple environmental factors that act in concert to shape ecological systems in ways that depend on local biotic and abiotic conditions. Little is known about the effects of combined global change stressors on phytoplankton communities, and particularly how these are mediated by distinct community properties such as productivity, grazing pressure and size distribution. Here, we tested for the effects of warming and eutrophication on phytoplankton net growth rate and C:N:P stoichiometry in two phytoplankton cell size fractions (30 µm) in the presence and absence of grazing in microcosm experiments. Because effects may also depend on lake productivity, we used phytoplankton communities from three Dutch lakes spanning a trophic gradient. We measured the response of each community to multifactorial combinations of temperature, nutrient, and grazing treatments and found that nutrients elevated net growth rates and reduced carbon:nutrient ratios of all three phytoplankton communities. Warming effects on growth and stoichiometry depended on nutrient supply and lake productivity, with enhanced growth in the most productive community dominated by cyanobacteria, and strongest stoichiometric responses in the most oligotrophic community at ambient nutrient levels. Grazing effects were also most evident in the most oligotrophic community, with reduced net growth rates and phytoplankton C:P stoichiometry that suggests consumer‐driven nutrient recycling. Our experiments indicate that stoichiometric responses to warming and interactions with nutrient addition and grazing are not universal but depend on lake productivity and cell size distribution., We measured the response of three phytoplankton communities to multifactorial combinations of temperature, nutrient and grazing treatments. Nutrients elevated net growth rates and reduced carbon:nutrient and nitrogen:phosphorus ratios of all communities. Warming effects on growth and stoichiometry depended on lake productivity: warming enhanced growth in the most productive community and caused strongest stoichiometric responses in the least productive community. Grazing reduced C:P and N:P ratios in the least productive community, suggesting consumer‐driven nutrient recycling. Our experiments indicate that stoichiometric responses to warming, and interactions with nutrient supply and grazing, depend on lake productivity and cell size distribution.

Microalga Dunaliella salina is known for its carotenogenesis. At the same time, it can also produce high-quality protein. The optimal conditions for D. salina to co-produce intracellular pools of both compounds, however, are yet unknown. This study investigated a two-phase cultivation strategy to optimize combined high-quality protein and carotenoid production of D. salina. In phase-one, a gradient of nitrogen concentrations was tested. In phase-two, effects of nitrogen pulse and high illumination were tested. Results reveal optimized protein quantity, quality (expressed as essential amino acid index EAAI) and carotenoids content in a two-phase cultivation, where short nitrogen starvation in phase-one was followed by high illumination during phase-two. Adopting this strategy, productivities of protein, EAA and carotenoids reached 22, 7 and 3 mg/L/d, respectively, with an EAAI of 1.1. The quality of this biomass surpasses FAO/WHO standard for human nutrition, and the observed level of β-carotene presents high antioxidant pro-vitamin A activity.

Alexandrium ostenfeldii is an emerging harmful algal bloom species forming a global threat to coastal marine ecosystems, with consequences for fisheries and shellfish production. The Oosterschelde estuary is a shallow, macrotidal and mesotrophic estuary in the southwest of The Netherlands with large stocks of mussels, oysters, and cockles. These shellfish stocks were threatened by a recent A. ostenfeldii bloom in the Ouwerkerkse Kreek, which is a brackish water creek discharging water into the Oosterschelde. Little is yet known about the characteristics of the A. ostenfeldii population in this creek. We therefore isolated 20 clones during an A. ostenfeldii bloom in 2013, and characterized these clones on their growth and toxin profile in their exponential growth phase. The cyclic imines were identified by comparison of A. ostenfeldii extracts with the retention time and CID spectra of standard solutions, or with published CID spectra. We furthermore assessed the allelochemical potency and phylogeny of a selection of 10–12 clones. Morphology and molecular phylogeny showed that all clones belong to Group 1 of A. ostenfeldii. All clones showed comparable growth rates of on average 0.22 ± 0.03 d−1. During exponential growth, they all produced a unique combination of paralytic shellfish poisoning toxins, spirolides and gymnodimines, of which particularly the latter showed a high intra-specific variability, with a 25-fold difference between clones with the lowest and highest cell quota. Furthermore, the selected 12 clones showed high allelopathic potencies with EC50 values based on lysis assays against the cryptophyte Rhodomonas salina between 212 and 525 A. ostenfeldii cells mL−1. Lytic activities were lower for cell extracts, indicating an important extracellular role of these compounds. A high intra-specific variability may add to the success of genotypically diverse A. ostenfeldii blooms, and make populations resilient to changes in environmental and climatic conditions.

Predicting the effects of multiple global change stressors on microbial communities remains a challenge because of the complex interactions among those factors. Here, we explore the combined effects of major global change stressors on nutrient acquisition traits in marine phytoplankton. Nutrient limitation constrains phytoplankton production in large parts of the present-day oceans, and is expected to increase owing to climate change, potentially favouring small phytoplankton that are better adapted to oligotrophic conditions. However, other stressors, such as elevated p CO 2 , rising temperatures and higher light levels, may reduce general metabolic and photosynthetic costs, allowing the reallocation of energy to the acquisition of increasingly limiting nutrients. We propose that this energy reallocation in response to major global change stressors may be more effective in large-celled phytoplankton species and, thus, could indirectly benefit large-more than small-celled phytoplankton, offsetting, at least partially, competitive disadvantages of large cells in a future ocean. Thus, considering the size-dependent responses to multiple stressors may provide a more nuanced understanding of how different microbial groups would fare in the future climate and what effects that would have on ecosystem functioning. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

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.

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.

Harmful cyanobacterial blooms are a major threat to water quality and human health. Adequate risk assessment is thus required, which relies strongly on comprehensive monitoring. Here, we tested novel multi-probe RNA chips developed in the European project, μAqua, to determine the abundance of harmful cyanobacterial species and expression of selected toxin genes in six Dutch lakes. All of the targeted cyanobacterial genera, except for Planktothrix, were detected using the microarray, with predominance of Dolichospermum and Microcystis signals, of which the former was found across all sites and detected by the probes for Anabaena where it was formerly placed. These were confirmed by microscopic cell counts at three sites, whereas at the other sites, microscopic cell counts were lower. Probe signals of Microcystis showed larger variation across sites but also matched microscopic counts for three sites. At the other sites, microscopic counts were distinctly higher. We detected anatoxin-a in the water at all sites, but unfortunately no genes for this toxin were on this generation of the toxin array. For microcystins, we found none or low concentrations in the water, despite high population densities of putative microcystin producers (i.e. Microcystis, Dolichospermum). The described method requires further testing with a wider range of cyanobacterial communities and toxin concentrations before implementation into routine cyanobacterial risk assessment. Yet, our results demonstrate a great potential for applying multi-probe RNA chips for species as well as toxins to eutrophic waters with high cyanobacterial densities as a routine monitoring tool and as a predictive tool for toxin potential.

Elevated pCO2 and warming are generally expected to influence cyanobacterial growth, and may promote the formation of blooms. Yet, both climate change factors may also influence cyanobacterial mortality by favoring pathogens, such as viruses, which will depend on the ability of the host to adapt. To test this hypothesis, we grew Plectonema boryanum IU597 under two temperature (25 and 29°C) and two pCO2 (400 and 800 μatm) conditions for 1 year, after which all treatments were re-exposed to control conditions for a period of 3 weeks. At several time points during the 1 year period, and upon re-exposure, we measured various infection characteristics of it associated cyanophage PP, including the burst size, latent period, lytic cycle and the efficiency of plaquing (EOP). As expected, elevated pCO2 promoted growth of P. boryanum equally over the 1 year period, but warming did not. Burst size increased in the warm treatment, but decreased in both the elevated pCO2 and combined treatment. The latent period and lytic cycle both became shorter in the elevated pCO2 and higher temperature treatment, and were further reduced by the combined effect of both factors. Efficiency of plaquing (EOP) decreased in the elevated pCO2 treatment, increased in the warm treatment, and increased even stronger in the combined treatment. These findings indicate that elevated pCO2 enhanced the effect of warming, thereby further promoting the virus infection rate. The re-exposure experiments demonstrate adaptation of the host leading to higher biomass build-up with elevated pCO2 over the experimental period, and lower performance upon re-exposure to control conditions. Similarly, virus burst size and EOP increased when given warm adapted host, but were lower as compared to the control when the host was re-exposed to control conditions. Our results demonstrate that adaptation but particularly physiological acclimation to climate change conditions favored viral infections, while limited host plasticity and slow adaptation after re-exposure to control conditions impeded host biomass build-up and viral infections.

The theories developed in ecological stoichiometry (ES) are fundamentally based on traits. Traits directly linked to cell/body stoichiometry, such as nutrient uptake and storage, as well as the associated trade-offs, have the potential to shape ecological interactions such as competition and predation within ecosystems. Further, traits that indirectly influence and are influenced by nutritional requirements, such as cell/body size and growth rate, are tightly linked to organismal stoichiometry. Despite their physiological and ecological relevance, traits are rarely explicitly integrated in the framework of ES and, currently, the major challenge is to more closely inter-connect ES with trait-based ecology (TBE). Here, we highlight four interconnected nutrient trait groups, i.e., acquisition, body stoichiometry, storage, and excretion, which alter interspecific competition in autotrophs and heterotrophs. We also identify key differences between producer-consumer interactions in aquatic and terrestrial ecosystems. For instance, our synthesis shows that, in contrast to aquatic ecosystems, traits directly influencing herbivore stoichiometry in forested ecosystems should play only a minor role in the cycling of nutrients. We furthermore describe how linking ES and TBE can help predict the ecosystem consequences of global change. The concepts we highlight here allow us to predict that increasing N:P ratios in ecosystems should shift trait dominances in communities toward species with higher optimal N:P ratios and higher P uptake affinity, while decreasing N retention and increasing P storage.

Carbon isotope fractionation (εp) between the inorganic carbon source and organic matter has been proposed to be a function of pCO2. To understand the CO2-dependency of εp and species-specific differences therein, inorganic carbon fluxes in the four dinoflagellate species Alexandrium fundyense, Scrippsiella trochoidea, Gonyaulax spinifera and Protoceratium reticulatum have been measured by means of membrane-inlet mass spectrometry. In-vivo assays were carried out at different CO2 concentrations, representing a range of pCO2 from 180 to 1200 μatm. The relative bicarbonate contribution (i.e. the ratio of bicarbonate uptake to total inorganic carbon uptake) and leakage (i.e. the ratio of CO2 efflux to total inorganic carbon uptake) varied from 0.2 to 0.5 and 0.4 to 0.7, respectively, and differed significantly between species. These ratios were fed into a single-compartment model, and εp values were calculated and compared to carbon isotope fractionation measured under the same conditions. For all investigated species, modeled and measured εp values were comparable (A. fundyense, S. trochoidea, P. reticulatum) and/or showed similar trends with pCO2 (A. fundyense, G. spinifera, P. reticulatum). Offsets are attributed to biases in inorganic flux measurements, an overestimated fractionation factor for the CO2-fixing enzyme RubisCO, or the fact that intracellular inorganic carbon fluxes were not taken into account in the model. This study demonstrates that CO2-dependency in εp can largely be explained by the inorganic carbon fluxes of the individual dinoflagellates., Highlights • To understand 13C fractionation in dinoflagellates, inorganic carbon fluxes were measured by MIMS and used for modeling. • Changes in cellular carbon fluxes, i.e. HCO3− contribution and CO2 leakage were CO2-dependent. • These CO2-dependencies could largely explain the CO2-dependent fractionation patterns observed in the four tested species.

We studied the effect of ocean acidification (OA) on a coastal North Sea plankton community in a long-term mesocosm CO2-enrichment experiment (BIOACID II long-term mesocosm study). From March to July 2013, 10 mesocosms of 19 m length with a volume of 47.5 to 55.9 m3 were deployed in the Gullmar Fjord, Sweden. CO2 concentrations were enriched in five mesocosms to reach average CO2 partial pressures (pCO2) of 760 μatm. The remaining five mesocosms were used as control at ambient pCO2 of 380 μatm. Our paper is part of a PLOS collection on this long-term mesocosm experiment. Here, we here tested the effect of OA on total primary production (PPT) by performing 14C-based bottle incubations for 24 h. Furthermore, photoacclimation was assessed by conducting 14C-based photosynthesis-irradiance response (P/I) curves. Changes in chlorophyll a concentrations over time were reflected in the development of PPT, and showed higher phytoplankton biomass build-up under OA. We observed two subsequent phytoplankton blooms in all mesocosms, with peaks in PPT around day 33 and day 56. OA had no significant effect on PPT, except for a marginal increase during the second phytoplankton bloom when inorganic nutrients were already depleted. Maximum light use efficiencies and light saturation indices calculated from the P/I curves changed simultaneously in all mesocosms, and suggest that OA did not alter phytoplankton photoacclimation. Despite large variability in time-integrated productivity estimates among replicates, our overall results indicate that coastal phytoplankton communities can be affected by OA at certain times of the seasonal succession with potential consequences for ecosystem functioning.

An important requirement for continuous cultures is a homogeneous distribution of resources and microorganisms, often achieved by rigorous mixing. Many dinoflagellate species are known to be vulnerable to turbulence. Here, we present a newly developed continuous culture system based on gentle mixing in which the two dinoflagellate species Scrippsiella trochoidea and Alexandrium tamarense, with different turbulence sensitivities, grew well under steady state conditions. We also show that the continuous culture system can be applied at low nutrient conditions and low population densities.