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Freshwater ecosystems and their biodiversity are presently seriously threatened by global development and population growth, leading to increases in nutrient inputs and intensification of eutrophication-induced problems in receiving fresh waters, particularly in lakes. Climate change constitutes another threat exacerbating the symptoms of eutrophication and species migration and loss. Unequivocal evidence of climate change impacts is still highly fragmented despite the intensive research, in part due to the variety and uncertainty of climate models and underlying emission scenarios but also due to the different approaches applied to study its effects. We first describe the strengths and weaknesses of the multi-faceted approaches that are presently available for elucidating the effects of climate change in lakes, including space-for-time substitution, time series, experiments, palaeoecology and modelling. Reviewing combined results from studies based on the various approaches, we describe the likely effects of climate changes on biological communities, trophic dynamics and the ecological state of lakes. We further discuss potential mitigation and adaptation measures to counteract the effects of climate change on lakes and, finally, we highlight some of the future challenges that we face to improve our capacity for successful prediction.

Food availability is the primary limitation for terrestrial Arctic predators, many of which rely on rodents that fluctuate in abundance over a 3-5-year period. During rodent scarcity, predators such as Arctic foxes (Vulpes lagopus) consume alternative prey, such as migratory birds, which are plentiful during summer. In most of the Arctic these birds return south by August, but in northern Manitoba, near the southern edge of the Arctic fox distribution, large numbers of lesser snow geese (Chen caerulescens caerulescens) and Canada geese (Branta canadensis interior) persist into October. This extended availability of geese late into fall may reduce the dependence of Arctic foxes on rodents. We used stable isotope and faecal analyses to reconstruct the Arctic fox fall and winter diet and related the most probable contributions of lemmings, goose eggs and juvenile geese with changes in prey availability and fox reproduction. Geese were a potentially important component of the fall diet for Arctic foxes, especially in years with high goose productivity, but rodents were the main component of the diet in late winter, even though rodents were scarce each summer (2010-2013). Furthermore, rodent density had a greater influence on Arctic fox reproduction, which was correlated with the subsequent winter harvest, than any other variable examined. Although geese were important fall prey for Arctic foxes at the southern edge of their distribution, they did not buffer declines in availability of rodents, which were the primary prey in April when food availability is critical for Arctic fox reproduction.

Soil bacteria and fungi mediate terrestrial biogeochemical cycling, but we know relatively little about how trophic interactions influence their community composition, diversity, and function. Specifically, it is unclear how consumer populations affect the activity of microbial taxa they consume, and therefore the interaction of those taxa with other members of the microbial community. Due to its extreme diversity, studying trophic dynamics in soil is a complex feat. Seeking to address these challenges, we performed a microcosm-based consumer manipulation experiment to determine the impact of a common fungal-feeding nematode (Aphelenchus avenae) on soil microbial community composition, diversity, and activity (e.g., C cycling parameters). Fungivory decreased fungal and bacterial α-diversity and stimulated C and N cycling, possibly via cascading impacts of fungivory on bacterial communities. Our results present experimental evidence that soil trophic dynamics are intimately linked with microbial diversity and function, factors that are key in understanding global patterns in biogeochemical cycling.

Intraguild predation (IGP), that is, feeding interaction between two consumers that share the same resource species, is commonly observed in natural food webs. IGP expands vertical niche space and slows down energy flows from lower to higher trophic levels, which potentially affects the diversity and dynamics of food webs. Here, we use food-web models to investigate the effects of IGP on species diversity and ecosystem functioning. We first simulate a five-species food-web module with different strengths of IGP at the herbivore and/or carnivore level. Results show that as the strength of IGP within a trophic level increases, the biomass of its resource level increases because of predation release; this increased biomass in turn alters the energy fluxes and biomass of other trophic levels. These results are then extended by subsequent simulations of more diverse food webs. As the strength of IGP increases, simulated food webs maintain (1) higher species diversity at different trophic levels, (2) higher total biomasses at different trophic levels, and (3) larger energy fluxes across trophic levels. Our results challenge the intuitive hypothesis that food-web structure should maximize the efficiency of energy transfer across trophic levels; instead, they suggest that the assembly of food webs should be governed by a balance between efficiency (of energy transfer) and persistence (i.e., the maintenance of species and biomasses). Our simulations also show that the relationship between biodiversity and ecosystem functioning (e.g., total biomass or primary production) is much stronger in the presence of IGP, reconciling the contrast from recent studies based on food-chain and food-web models. Our findings shed new light on the functional role of IGP and contribute to resolving the debate on structure, diversity and functioning in complex food webs.

Ecological studies have rarely been performed at the community level across a large biogeographic region. Sponges are now the primary habitat-forming organisms on Caribbean coral reefs. Recent species-level investigations have demonstrated that predatory fishes (angelfishes and some parrotfishes) differentially graze sponges that lack chemical defenses, while co-occurring, palatable species heal, grow, reproduce, or recruit at faster rates than defended species. Our prediction, based on resource allocation theory, was that predator removal would result in a greater proportion of palatable species in the sponge community on overfished reefs. We tested this prediction by performing surveys of sponge and fish community composition on reefs having different levels of fishing intensity across the Caribbean. A total of 109 sponge species was recorded from 69 sites, with the 10 most common species comprising 51.0% of sponge cover (3.6—7.7% per species). Nonmetric multidimensional scaling indicated that the species composition of sponge communities depended more on the abundance of sponge-eating fishes than geographic location. Across all sites, multiple-regression analyses revealed that spongivore abundance explained 32.8% of the variation in the proportion of palatable sponges, but when data were limited to geographically adjacent locations with strongly contrasting levels of fishing pressure (Cayman Islands and Jamaica; Curaçao, Bonaire, and Martinique), the adjusted R2 values were much higher (76.5% and 94.6%, respectively). Overfishing of Caribbean coral reefs, particularly by fish trapping, removes sponge predators and is likely to result in greater competition for space between faster-growing palatable sponges and endangered reef-building corals.

We present a framework to explain how prey stress responses to predation can resolve context dependency in ecosystem properties and functions such as food chain length, secondary production, elemental stoichiometry, and cycling. We first describe the major nonspecific physiological stress mechanisms and their ecologically relevant consequences. We next synthesize the evidence for prey physiological responses to predation risk and demonstrate that they are similar across taxa and fit well within the general stress paradigm. We then illustrate the utility of our idea by applying our understanding of the ecological consequences of stress to explain how herbivore‐prey physiological antipredator responses affect ecosystem dynamics. We hypothesize that stressed herbivores should forage on plant species with higher digestible carbohydrates than should unstressed herbivores to meet heightened energy demands. Increased consumption of carbohydrate‐rich plants should reduce their relative abundance in the community, hence altering the quantity and quality of plant litter entering the detrital pool. We further hypothesize that stress should change the elemental composition and energy content of prey excreta, egesta, and carcasses that enter the detrital pool. Finally, prey stress should lower energy and nutrient conversion efficiency and hence the transfer of materials and energy up the food chain, which should, in turn, weaken the association between ecosystem productivity and food chain length.

This study examines the feeding ecology and trophic dynamics of the critically endangered large yellow croaker ( Larimichthys crocea ) in the differing habitats of Hong Kong and Taiwan using 18S gut content metabarcoding and stable isotope analysis. As a top predator, the large yellow croaker plays a crucial role in regulating fish populations and maintaining balance in the marine ecosystem. We found isotopic niche differences between juveniles and adults, with juveniles consuming more planktonic prey and adults more benthic species. In the more disrupted waters of Hong Kong, disrupted ontogenetic trophic transitions were observed, as adults exhibited unexpectedly low stable nitrogen isotope values, indicating prolonged consumption of prey at low trophic levels. In contrast, the relatively less impacted waters of Taiwan showed normal ontogenetic trophic transition. These findings highlight the impact of habitat degradation on large yellow croaker and underscore the urgent need for conservation measures, including stricter fishing regulations and habitat protection, to preserve this essential species and its ecological role.

Metabolism provides a basis for using first principles of physics, chemistry, and biology to link the biology of individual organisms to the ecology of populations, communities, and ecosystems. Metabolic rate, the rate at which organisms take up, transform, and expend energy and materials, is the most fundamental biological rate. We have developed a quantitative theory for how metabolic rate varies with body size and temperature. Metabolic theory predicts how metabolic rate, by setting the rates of resource uptake from the environment and resource allocation to survival, growth, and reproduction, controls ecological processes at all levels of organization from individuals to the biosphere. Examples include: (1) life history attributes, including development rate, mortality rate, age at maturity, life span, and population growth rate; (2) population interactions, including carrying capacity, rates of competition and predation, and patterns of species diversity; and (3) ecosystem processes, including rates of biomass production and respiration and patterns of trophic dynamics. Data compiled from the ecological literature strongly support the theoretical predictions. Eventually, metabolic theory may provide a conceptual foundation for much of ecology, just as genetic theory provides a foundation for much of evolutionary biology.

Describing the mechanisms that drive variation in species interaction strengths is central to understanding, predicting, and managing community dynamics. Multiple factors have been linked to trophic interaction strength variation, including species densities, species traits, and abiotic factors. Yet most empirical tests of the relative roles of multiple mechanisms that drive variation have been limited to simplified experiments that may diverge from the dynamics of natural food webs. Here, we used a field-based observational approach to quantify the roles of prey density, predator density, predator-prey body-mass ratios, prey identity, and abiotic factors in driving variation in feeding rates of reticulate sculpin (Cottus perplexus). We combined data on over 6,000 predator-prey observations with prey identification time functions to estimate 289 prey-specific feeding rates at nine stream sites in Oregon. Feeding rates on 57 prey types showed an approximately log-normal distribution, with few strong and many weak interactions. Model selection indicated that prey density, followed by prey identity, were the two most important predictors of prey-specific sculpin feeding rates. Feeding rates showed a positive relationship with prey taxon densities that was inconsistent with predator saturation predicted by current functional response models. Feeding rates also exhibited four orders-of-magnitude in variation across prey taxonomic orders, with the lowest feeding rates observed on prey with significant anti-predator defenses. Body-mass ratios were the third most important predictor variable, showing a hump-shaped relationship with the highest feeding rates at intermediate ratios. Sculpin density was negatively correlated with feeding rates, consistent with the presence of intraspecific predator interference. Our results highlight how multiple co-occurring drivers shape trophic interactions in nature and underscore ways in which simplified experiments or reliance on scaling laws alone may lead to biased inferences about the structure and dynamics of species-rich food webs.

Food web studies rely heavily on the use of traditional gut content analysis or the fairly popular stable isotope analysis rather than fatty acid analysis (FAA) despite its straightforward process, and ability to identify and characterize more diverse trophic pathways. In this study, we employed fatty acid (FA) biomarkers as a preliminary attempt to trace and characterize trophic pathways in food webs of four tropical lakes of volcanic origin in Luzon Island, Philippines - three clustered maar lakes (Yambo, Pandin and Calibato) and a large caldera lake (Taal). These lakes have a long history of human disturbance but limited ecological data. Knowledge of basal food sources and existing trophic dynamics of organisms are generally non-existent. Particulate organic matter (POM), zooplankton, and fish species were collected in August 2019 from the study lakes as representative of three trophic guilds. Non-metric multidimensional scaling (NMDS) and principal component analysis (PCA) were conducted to analyse FA profiles and characterize trophic relationships between representative organisms. For the POM, within lakes comparison of taxon-specific FA profiles showed a significant difference between the surface and near bottom depths, with the former dominated by photoautorophs and the latter by chemotrophs, suggesting the ability of FAA to effectively delineate between micro-organisms. Between lakes comparison also showed significant difference between the caldera and maar lakes, with the latter containing higher composition of bacterial FA, reminiscent of the considerably smaller lakes’ response to the impact of unmitigated organic loadings from anthropogenic activities. Taken together with the primary consumers’ FA profiles, analysis confirmed the ability of FAA to discriminate between FA profile sources. PCA explained >70% of the variance in the FA compositions for three trophic guilds in the two deepest lakes, which delineated both zooplankton and fish species food selectivity in each lake, alluding to FAA’s capacity to characterize dietary reliance of various species in an environment with numerous food sources. Although certain limitations were encountered, such as the specificity of the sampling depths for POM, and the small sample size of the representative species of the third trophic level, this study demonstrated the effectiveness of FAA as a powerful ecological tool for disentangling intricate lake food webs comprising various food sources. Overall, this study provided baseline information on basal food sources and trophic pathways of representative organisms from four tropical lakes. Taken together, FAA studies have wide application in understanding food webs, including anthropogenically-threatened lake ecosystems.