There's no harm in having too much: A comprehensive toolbox of methods in trophic ecology

Unexpected trophic diversity in the endemic fish Orestias chungarensis in a high-altitude freshwater ecosystem, Lake Chungará (4520 m), northern Chile

Orestias chungarensis Vila & Pinto, 1986 is a small-bodied (max fork length = 120 mm) cyprinodontiform fish with a very restricted global distribution. The species is limited to a single, small (283 km2), high-altitude (4520 m) catchment located in the Altiplano of northern Chile. Until the late 20th century, O. chungarensis was the only fish species inhabiting both Lake Chungará and its main afferent river, the River Chungará. The introduction of rainbow trout [Oncorhynchus mykiss (Walbaum, 1792)] at this time raised concerns for the long-term conservation of Orestias. By 2017, O. chungarensis were no longer present in the River Chungará but remain relatively numerous in Lake Chungará. Although O. chungarensis are of elevated conservation concern, little is known regarding their ecology, and the few studies conducted have relied on individuals captured from shallow littoral habitats. Here, we captured O. chungarensis from different lake habitats and analysed multi-tissue stable isotopes (δ13C, δ15N, δ34S) and stomach contents to characterise their trophic ecology. We also used geometric morphometrics to analyse any putative habitat-associated variation in body shape. O. chungarensis showed very wide variation in their stable isotope values (range: δ13C = -15.1 to -8.0‰; δ15N = 8.9-14.1‰; δ34S = -10.5-1.7‰). A k-means cluster analysis indicated that individuals could be best classified into two groups in stable isotope space. A discriminant function analysis supported the separation of the sampled population into two groups (jack-knifed classification success = 98%). Individuals belonging to either a putative littoral group (13C-enriched, 15N-depleted and 34S-depleted) or a group associated with pelagic-derived materials (13C-depleted, 15N-enriched, 34S-enriched), which likely fed offshore or in deeper waters. Stomach contents results showed that O. chungarensis from the two putative groups had consumed similar prey prior to capture, feeding mainly on benthic macroinvertebrates (amphipods, chironomid larvae and pupae and gastropods). Mixing models analysis showed a broadly similar diet between groups, but the scale of contribution to the assimilated diet differed between groups. Comparisons of stable isotope niche size and overlap showed limited niche overlap, providing more evidence for differential foraging patterns. The dichotomy between the results from stable isotope and stomach content analysis suggests that O. chungarensis individuals forage on taxonomically similar diets, but their prey are fuelled from materials derived from different lake habitats (littoral and open-water). Given the remarkable plasticity found in the genus, our results could reflect the existence of a previously unrecognised ecotype.

Role of trophic interactions in transfer and cascading impacts of plant protection products on biodiversity: a literature review

Plant protection products (PPPs) have historically been one of the classes of chemical compounds at the frontline of raising scientific and public awareness of the global nature of environmental pollution and the role of trophic interactions in shaping the impacts of chemicals on ecosystems. Despite increasingly strong regulatory measures since the 1970s designed to avoid unintentional effects of PPPs, their use is now recognised as a driver of biodiversity erosion. The French Ministries for the Environment, Agriculture and Research commissioned a collective scientific assessment to synthesise the current science and knowledge on the impacts of PPPs on biodiversity and ecosystem services. Here we report a literature review of the state of knowledge on the propagation of PPP residues and the effects of PPPs in food webs, including biopesticides, with a focus on current-use PPPs. Currently used PPPs may be stronger drivers of the current biodiversity loss than the banned compounds no longer in use, and there have been far fewer reviews on current-use PPPs than legacy PPPs. We first provide a detailed overview of the transfer and propagation of effects of PPPs through trophic interactions in both terrestrial and aquatic ecosystems. We then review cross-ecosystem trophic paths of PPP propagation, and provide insight on the role of trophic interactions in the impacts of PPPs on ecological functions. We conclude with a summary of the available knowledge and the perspectives for tackling the main gaps, and address areas that warrant further research and pathways to advancing environmental risk assessment.

Urbanization-induced simplification of isotopic space in birds from a big Neotropical city

Among the many changes associated with the urbanization process, changes in resource availability can directly impact local wildlife populations. Urban areas suppress native vegetation and convert natural environments into impervious surfaces, modifying the composition and quantity of available food resources. Understanding the food requirements of species is crucial, mainly because it is one of the main elements that characterize their ecological niche and structure local communities. Our aim in this study was to assess the impact of urbanization intensity on the isotopic niche space of birds commonly found in urban areas of Brasília, the capital of Brazil, a big city in central Brazil with approximately 3 million inhabitants. By analyzing the δ13C and δ15N isotopic metrics of feathers from bird species found along a gradient of urbanization intensity, we evidenced a simplification but not a displacement of the bird assembly isotopic space due to urban intensification. Bird assemblage access similar food resources in the higher urban intensification areas, although less diversified than in lower urban intensification areas. In most cases, the response to urban intensification is more specific than convergent among guild members. The studied species maintain themselves in highly intensified urban areas by restricting, changing, and expanding their access to resources. The trophic dimension is one of the key components of the species' ecological niche, and understanding the urban intensification impacts on this dimension is essential for maintaining biodiversity and ecosystem services in cities.

A Strong Link Between Oceanographic Conditions and Zooplankton δ13C and δ15N Values in the San Jorge Gulf, Argentina

Maps of (baseline) δ13C and δ15N values of primary producers or consumers near the base of food webs provide crucial information for interpreting patterns in the isotopic composition of consumers that occupy higher trophic levels. In marine systems, understanding how oceanographic variables influence these values enables the creation of dynamic isoscapes across time and space, providing insights into how ecosystems function. The San Jorge Gulf (SJG) in the southwest Atlantic Ocean (45° S-47° S) is an area of particular importance, as it is located on one of the most productive continental shelves in the world, supporting large fisheries and marine mammal and seabird populations. We reconstructed spatial variation in zooplankton δ13C and δ15N values across SJG and investigated their relationship with physical and chemical oceanographic conditions. During cruises in the austral spring of 2016 and 2017, we collected medium-sized copepods whose isotopic composition integrate short-term (days to weeks) variation in oceanographic conditions recorded by phytoplankton at the base of the food web. We also collected data on water column depth, surface and bottom temperatures, water column stability, and macronutrient (nitrate, phosphate, and silicic acid) concentrations. The results revealed significant variation in both δ13C and δ15N values of up to 7-8‱ over a relatively small spatial scale (200-300 km). Copepod δ13C values were lower at the center of the SJG, showing an inverse correlation with water column stability, surface nitrate concentration, and water column depth. δ15N values showed a strong and negative relationship with surface nitrate concentration and water column stability, increasing from south to north in the SJG. δ15N values also showed a positive relationship with surface silicic acid concentration. These spatial patterns in nutrient dynamics and copepod carbon and nitrogen isotope values are interpreted in the context of the dominant northward current and temporal development of the frontal systems in the SJG.

DNA metabarcoding reveals the dietary profiles of a benthic marine crustacean, Nephrops norvegicus

Norwegian lobster, Nephrops norvegicus, are a generalist scavenger and predator capable of short foraging excursions but can also suspension feed. Existing knowledge about their diet relies on a combination of methods including morphology-based stomach content analysis and stable isotopes, which often lack the resolution to distinguish prey items to species level particularly in species that thoroughly masticate their prey. DNA metabarcoding overcomes many of the challenges associated with traditional methods and it is an attractive approach to study the dietary profiles of animals. Here, we present the diet of the commercially valuable Nephrops norvegicus using DNA metabarcoding of gut contents. Despite difficulties associated with host amplification, our cytochrome oxidase I (COI) molecular assay successfully achieves higher resolution information than traditional approaches. We detected taxa that were likely consumed during different feeding strategies. Dinoflagellata, Chlorophyta and Bacillariophyta accounted for almost 50% of the prey items consumed, and are associated with suspension feeding, while fish with high fisheries discard rates were detected which are linked to active foraging. In addition, we were able to characterise biodiversity patterns by considering Nephrops as natural samplers, as well as detecting parasitic dinoflagellates (e.g., Hematodinium sp.), which are known to influence burrow related behaviour in infected individuals in over 50% of the samples. The metabarcoding data presented here greatly enhances a better understanding of a species' ecological role and could be applied as a routine procedure in future studies for proper consideration in the management and decision-making of fisheries.

Multiple stable isotopes (C, N & S) provide evidence for fin whale (Balaenoptera physalus) trophic ecology and movements in the Humboldt Current System of northern Chile

Reflecting the intense coastal upwelling and high primary productivity characteristic of the Humboldt Current System (HCS), the northern coast of Chile supports a diverse and productive community of marine consumers, including worldwide important pelagic fisheries resources. Although marine mammals are relatively understudied in the region, recent studies have demonstrated that fin whale (Balaenoptera physalus) is the most frequently encountered whale species, and forages in these waters year-round. However, a current lack of information limits our understanding of whether fin whales actively feed and/or remain resident in these waters or whether whales are observed feeding as they migrate along this part of the Pacific. Here, we use stable isotope ratios of carbon, nitrogen and sulphur of fin whale skin samples collected in early summer 2020 (n = 18) and in late winter 2021 (n = 22) to examine evidence of temporal isotopic shifts that could provide information on potential migratory movements and to estimate likely consumption patterns of putative prey (i.e. zooplankton, krill, pelagic fishes and Pleuroncodes sp.). We also analysed prey items in fin whale faecal plumes (n = 8) collected during the study period. Stable isotope data showed significant differences in the isotopic values of fin whales from summer and winter. On average, summer individuals were depleted in 15N and 34S relative to those sampled during winter. Whales sampled in summer showed greater isotopic variance than winter individuals, with several showing values that were atypical for consumers from the HCS. During winter, fin whales showed far less inter-individual variation in stable isotope values, and all individuals had values indicative of prey consumption in the region. Analysis of both stable isotopes and faeces indicated that fin whales sighted off the Mejillones Peninsula fed primarily on krill (SIA median contribution = 32%; IRI = 65%) and, to a lesser extent, zooplankton (SIA zooplankton = 29%; IRI copepod = 33%). These are the first isotopic-based data regarding the trophic ecology of fin whales in the north of Chile. They provide evidence that fin whales are seasonally resident in the area, including individuals with values that likely originated outside the study area. The information presented here serves as a baseline for future work. It highlights that many aspects of the ecology of fin whales in the Humboldt Current and wider SE Pacific still need to be clarified.

Multidimensional trace metals and nutritional niche differ between sexually immature and mature common dolphins (Delphinus delphis)

There is a need to understand the links between metals and nutrition for apex marine predators, which may be subject to different ecotoxicological effects at different life stages. We combined stomach content analyses (SCA), prey composition analysis (PCA), the Multidimensional Niche Framework (MNNF) with Bayesian multivariate ellipses, trace metal analysis and nicheROVER to investigate nutrition and trace metals across sex, age, and sexual maturity status in common dolphins (Delphinus delphis) from New Zealand. A broader prey composition niche breadth (SEAc) was estimated for immature compared to mature conspecifics, showing a higher degree of prey and nutrient generalism driven by protein (P) intake. Cd and Zn niche similarities suggests these metals were incorporated through similar prey in both immature and mature dolphins, whereas Hg and Se niche divergence indicates uptake occurred via different prey. Our multidisciplinary assessment demonstrated how nutrients and metal interactions differ in common dolphins depending upon sexual maturity. This approach has relevance when considering how marine pollution, environmental fluctuations and climate change may affect nutritional and trace metal interactions during different reproductive stages within marine predators.

Stoichiometric stability of aquatic organisms increases with trophic level under warming and eutrophication

The balance of stoichiometric traits of organisms is crucial for nutrient cycling and energy flow in ecosystems. However, the impacts of different drivers on stoichiometric (carbon, C; nitrogen, N; and phosphorus, P) variations of organisms have not been well addressed. In order to understand how stoichiometric traits vary across trophic levels under different environmental stressors, we performed a mesocosm experiment to explore the impacts of warming (including +3 °C consistent warming above ambient and heat waves ranging from 0 to 6 °C), eutrophication, herbicide and their interactions on stoichiometric traits of organisms at different trophic levels, which was quantified by stable nitrogen isotopes. Results showed that herbicide treatment had no significant impacts on all stochiometric traits, while warming and eutrophication significantly affected the stoichiometric traits of organisms at lower trophic levels. Eutrophication increased nutrient contents and decreased C: nutrient ratios in primary producers, while the response of N:P ratios depended on the taxonomic group. The contribution of temperature treatments to stoichiometric variation was less than that of eutrophication. Heat waves counteracted the impacts of eutrophication, which was different from the effects of continuous warming, indicating that eutrophication impacts on organism stoichiometric traits depended on climate scenarios. Compared to environmental drivers, taxonomic group was the dominant driver that determined the variations of stoichiometric traits. Furthermore, the stoichiometric stability of organisms was strongly positively correlated with their trophic levels. Our results demonstrate that warming and eutrophication might substantially alter the stoichiometric traits of lower trophic levels, thus impairing the nutrient transfer to higher trophic level, which might further change the structure of food webs and functions of the ecosystems.

Salt to conserve: a review on the ecology and preservation of hypersaline ecosystems

When it comes to the investigation of key ecosystems in the world, we often omit salt from the ecological recipe. In fact, despite occupying almost half of the volume of inland waters and providing crucial services to humanity and nature, inland saline ecosystems are often overlooked in discussions regarding the preservation of global aquatic resources of our planet. As a result, our knowledge of the biological and geochemical dynamics shaping these environments remains incomplete and we are hesitant in framing effective protective strategies against the increasing natural and anthropogenic threats faced by such habitats. Hypersaline lakes, water bodies where the concentration of salt exceeds 35 g/l, occur mainly in arid and semiarid areas resulting from hydrological imbalances triggering the accumulation of salts over time. Often considered the 'exotic siblings' within the family of inland waters, these ecosystems host some of the most extremophile communities worldwide and provide essential habitats for waterbirds and many other organisms in already water-stressed regions. These systems are often highlighted as natural laboratories, ideal for addressing central ecological questions due to their relatively low complexity and simple food web structures. However, recent studies on the biogeochemical mechanisms framing hypersaline communities have challenged this archetype, arguing that newly discovered highly diverse communities are characterised by specific trophic interactions shaped by high levels of specialisation. The main goal of this review is to explore our current understanding of the ecological dynamics of hypersaline ecosystems by addressing four main research questions: (i) why are hypersaline lakes unique from a biological and geochemical perspective; (ii) which biota inhabit these ecosystems and how have they adapted to the high salt conditions; (iii) how do we protect biodiversity from increasing natural and anthropogenic threats; and (iv) which scientific tools will help us preserve hypersaline ecosystems in the future? First, we focus on the ecological characterisation of hypersaline ecosystems, illustrate hydrogeochemical dynamics regulating such environments, and outline key ecoregions supporting hypersaline systems across the globe. Second, we depict the diversity and functional aspects of key taxa found in hypersaline lakes, from microorganisms to plants, invertebrates, waterbirds and upper trophic levels. Next, we describe ecosystem services and discuss possible conservation guidelines. Finally, we outline how cutting-edge technologies can provide new insights into the study of hypersaline ecology. Overall, this review sheds further light onto these understudied ecosystems, largely unrecognised as important sources of unique biological and functional diversity. We provide perspectives for key future research avenues, and advocate that the conservation of hypersaline lakes should not be taken with 'a grain of salt'.

Stable isotopes of fatty acids: current and future perspectives for advancing trophic ecology

To understand consumer dietary requirements and resource use across ecosystems, researchers have employed a variety of methods, including bulk stable isotope and fatty acid composition analyses. Compound-specific stable isotope analysis (CSIA) of fatty acids combines both of these tools into an even more powerful method with the capacity to broaden our understanding of food web ecology and nutritional dynamics. Here, we provide an overview of the potential that CSIA studies hold and their constraints. We first review the use of fatty acid CSIA in ecology at the natural abundance level as well as enriched physiological tracers, and highlight the unique insights that CSIA of fatty acids can provide. Next, we evaluate methodological best practices when generating and interpreting CSIA data. We then introduce three cutting-edge methods: hydrogen CSIA of fatty acids, and fatty acid isotopomer and isotopologue analyses, which are not yet widely used in ecological studies, but hold the potential to address some of the limitations of current techniques. Finally, we address future priorities in the field of CSIA including: generating more data across a wider range of taxa; lowering costs and increasing laboratory availability; working across disciplinary and methodological boundaries; and combining approaches to answer macroevolutionary questions. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.

Refining trophic dynamics through multi-factor Bayesian mixing models: A case study of subterranean beetles

Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ13C and δ15N) with radiocarbon data (Δ14C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ13C, δ15N, and Δ14C, multi-proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis, and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased-and species-specific-predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.

The potential of fatty acid isotopes to trace trophic transfer in aquatic food-webs

Compound-specific isotope analyses (CSIA) of fatty acids (FA) constitute a promising tool for tracing energy flows in food-webs. However, past applications of FA-specific carbon isotope analyses have been restricted to a relatively coarse food-source separation and mainly quantified dietary contributions from different habitats. Our aim was to evaluate the potential of FA-CSIA to provide high-resolution data on within-system energy flows using algae and zooplankton as model organisms. First, we investigated the power of FA-CSIA to distinguish among four different algae groups, namely cyanobacteria, chlorophytes, haptophytes and diatoms. We found substantial within-group variation but also demonstrated that δ¹³C of several FA (e.g. 18:3ω3 or 18:4ω3) differed among taxa, resulting in group-specific isotopic fingerprints. Second, we assessed changes in FA isotope ratios with trophic transfer. Isotope fractionation was highly variable in daphnids and rotifers exposed to different food sources. Only δ¹³C of nutritionally valuable poly-unsaturated FA remained relatively constant, highlighting their potential as dietary tracers. The variability in fractionation was partly driven by the identity of food sources. Such systematic effects likely reflect the impact of dietary quality on consumers' metabolism and suggest that FA isotopes could be useful nutritional indicators in the field. Overall, our results reveal that the variability of FA isotope ratios provides a substantial challenge, but that FA-CSIA nevertheless have several promising applications in food-web ecology. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.

Who is eating fructose within the Aedes albopictus gut microbiota?

The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito-borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies have emerged from the study of mosquito-associated microorganisms. Although the role of the microbiota in insect biology does not require further proof, much remains to be deciphered in mosquitoes, especially the contribution of the microbiota to host nutrient metabolism. Mosquitoes feed on plant nectar, composed of mostly fructose. We used stable isotope probing to identify bacteria and fungi assimilating fructose within the gut of Ae. albopictus. Mosquitoes were fed a ¹³ C-labelled fructose solution for 24 h. Differences in the active microbial community according to the sex of mosquitoes were highlighted. The bacterium Lelliottia and the fungi Cladosporium and Aspergillus dominated the active microbiota in males, whereas the bacterium Ampullimonas and the yeast Cyberlindnera were the most active in females. This study is the first to investigate trophic interactions between Ae. albopictus and its microbiota, thus underscoring the importance of the microbial component in nectar feeding in mosquitoes.

The Nutritional Ecology of Marine Apex Predators

Apex predators play pivotal roles in marine ecosystems, mediated principally through diet and nutrition. Yet, compared with terrestrial animals, the nutritional ecology of marine predators is poorly understood. One reason is that the field has adhered to an approach that evaluates diet principally in terms of energy gain. Studies in terrestrial systems, by contrast, increasingly adopt a multidimensional approach, the nutritional geometry framework, that distinguishes specific nutrients and calories. We provide evidence that a nutritional approach is likewise relevant to marine apex predators, then demonstrate how nutritional geometry can characterize the nutrient and energy content of marine prey. Next, we show how this framework can be used to reconceptualize ecological interactions via the ecological niche concept, and close with a consideration of its application to problems in marine predator research.

A nutritional perspective on plastic ingestion in wildlife

Although the perils of plastics to living organisms including humans have been neglected for decades, they have recently been recognized as a major environmental problem worldwide. Little progress has been made on understanding the factors that drive species' and populations' susceptibilities to the ingestion of plastic. Here, we propose using nutritional ecology as a multidisciplinary framework for bridging the gaps that link nutrition, behavior, plastics, physiology and ecology. We show that nutritional niches are tightly linked to plastic ingestion, illustrating the application of our framework in the context of nutritional niche theory, habitat-specific foraging from species to populations, and transfer patterns in food webs.