Compound-specific stable isotope analysis of amino acids in pelagic shark vertebrae reveals baseline, trophic, and physiological effects on bulk protein isotope records

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Magozzi, S., Thorrold, S. R., Houghton, L., Bendall, V. A., Hetherington, S., Mucientes, G., Natanson, L. J., Queiroz, N., Santos, M. N., & Trueman, C. N. Compound-specific stable isotope analysis of amino acids in pelagic shark vertebrae reveals baseline, trophic, and physiological effects on bulk protein isotope records. Frontiers in Marine Science, 8, (2021): 673016, https://doi.org/10.3389/fmars.2021.673016.Variations in stable carbon and nitrogen isotope compositions in incremental tissues of pelagic sharks can be used to infer aspects of their spatial and trophic ecology across life-histories. Interpretations from bulk tissue isotopic compositions are complicated, however, because multiple processes influence these values, including variations in primary producer isotope ratios and consumer diets and physiological processing of metabolites. Here we challenge inferences about shark tropho-spatial ecology drawn from bulk tissue isotope data using data for amino acids. Stable isotope compositions of individual amino acids can partition the isotopic variance in bulk tissue into components associated with primary production on the one hand, and diet and physiology on the other. The carbon framework of essential amino acids (EAAs) can be synthesised de novo only by plants, fungi and bacteria and must be acquired by consumers through the diet. Consequently, the carbon isotopic composition of EAAs in consumers reflects that of primary producers in the location of feeding, whereas that of non-essential amino acids (non-EAAs) is additionally influenced by trophic fractionation and isotope dynamics of metabolic processing. We determined isotope chronologies from vertebrae of individual blue sharks and porbeagles from the North Atlantic. We measured carbon and nitrogen isotope compositions in bulk collagen and carbon isotope compositions of amino acids. Despite variability among individuals, common ontogenetic patterns in bulk isotope compositions were seen in both species. However, while life-history movement inferences from bulk analyses for blue sharks were supported by carbon isotope data from essential amino acids, inferences for porbeagles were not, implying that the observed trends in bulk protein isotope compositions in porbeagles have a trophic or physiological explanation, or are suprious effects. We explored variations in carbon isotope compositions of non-essential amino acids, searching for systematic variations that might imply ontogenetic changes in physiological processing, but patterns were highly variable and did not explain variance in bulk protein δ13C values. Isotopic effects associated with metabolite processing may overwhelm spatial influences that are weak or inconsistently developed in bulk tissue isotope values, but interpreting mechanisms underpinning isotopic variation in patterns in non-essential amino acids remains challenging.The internship of SM at the Woods Hole Oceanographic Institution was funded by the School of Ocean and Earth Science at University of Southampton. Stable isotope analyses were paid by CT and ST research budgets and SM Ph.D. and placement funding

A global perspective on the trophic geography of sharks

Carbon isotopic analysis reveals global biogeographic traits in shark trophic interactions, and sheds light on the diverse foraging behaviour of sharks

Combining Models of Environment, Behavior, and Physiology to Predict Tissue Hydrogen and Oxygen Isotope Variance Among Individual Terrestrial Animals

Variations in stable hydrogen and oxygen isotope ratios in terrestrial animal tissues are used to reconstruct origin and movement. An underlying assumption of these applications is that tissues grown at the same site share a similar isotopic signal, representative of the location of their origin. However, large variations in tissue isotopic compositions often exist even among conspecific individuals within local populations, which complicates origin and migration inferences. Field-data and correlation analyses have provided hints about the underlying mechanisms of within-site among-individual isotopic variance, but a theory explaining the causes and magnitude of such variance has not been established. Here we develop a mechanistic modeling framework that provides explicit predictions of the magnitude, patterns, and drivers of isotopic variation among individuals living in a common but environmentally heterogeneous habitat. The model toolbox includes isoscape models of environmental isotopic variability, an agent-based model of behavior and movement, and a physiology-biochemistry model of isotopic incorporation into tissues. We compare model predictions against observed variation in hatch-year individuals of the songbird Spotted Towhee (Pipilo maculatus) in Red Butte Canyon, Utah, and evaluate the ability of the model to reproduce this variation under different sets of assumptions. Only models that account for environmental isotopic variability predict a similar magnitude of isotopic variation as observed. Within the modeling framework, behavioral rules and properties govern how animals nesting in different locations acquire resources from different habitats, and birds nesting in or near riparian habitat preferentially access isotopically lighter resources than those associated with the meadow and slope habitats, which results in more negative body water and tissue isotope values. Riparian nesters also have faster body water turnover and acquire more water from drinking (vs. from food), which exerts a secondary influence on their isotope ratios. Thus, the model predicts that local among-individual isotopic variance is linked first to isotopic heterogeneity in the local habitat, and second to how animals sample this habitat during foraging. Model predictions provide insight into the fundamental mechanisms of small-scale isotopic variance and can be used to predict the utility of isotope-based methods for specific groups or environments in ecological and forensic research.</jats:p

A global perspective on the trophic geography of sharks

Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30° and 50° of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches.This research was conducted as part of C.S.B.’s Ph.D dissertation, which was funded by the University of Southampton and NERC (NE/L50161X/1), and through a NERC Grant-in-Kind from the Life Sciences Mass Spectrometry Facility (LSMSF; EK267-03/16). We thank A. Bates, D. Sims, F. Neat, R. McGill and J. Newton for their analytical contributions and comments on the manuscripts.Peer reviewe

CONSERVATION PHYSIOLOGY: TOWARDS AN INTEGRATIVE COMPARATIVE FRAMEWORK FOR PREDICTING SPECIES’ RELATIVE VULNERABILITY TO GLOBAL WARMING

Conservation physiology offers powerful approaches to develop mechanistic explanations of shifts in species’ biogeography putatively attributed to Global Warming. Nevertheless, a comparative framework that integrates the multiple physiological traits underlying species’ thermal biology is to date still lacking. Here I demonstrate the fundamental importance of integrating metabolic performance, thermal tolerance and plasticity to provide more accurate predictions on species’ relative vulnerability to Global Warming. Six Caridean species occurring in a common garden were selected as model and acclimated to four temperature treatments: 10, 15, 20 and 25 °C. The effect temperature on their metabolic rates and thermal tolerance limits was tested, and plasticity for these physiological abilities was calculated according to a Reaction Norm approach. Metabolic rate increased exponentially with increasing temperature in all the species examined (except in Pandalus montagui). Nevertheless, species living in thermally unstable environments (Palaemon elegans and Palaemonetes varians) showed higher temperature dependence of metabolism than their subtidal counterparts (Crangon crangon and Palaemon serratus), thereby appearing to be at greater risk from sub-lethal effects of Global Warming. By contrast, the hypothesis of an evolutionary/functional trade-off between thermal tolerance and its plasticity suggests that both the most heat-tolerant species (P. elegans, P. varians and C. crangon) and the most plastic species (P. serratus) are likely to be in danger from acute lethal effects of Global Warming. Both P. montagui and Palaemon macrodactylus are exceptions, appearing to be the most and the least vulnerable species to Global Warming respectively

Reconstructing ontogenetic movements in pelagic sharks coupling ocean models and stable isotope data in incrementally grown tissues

Ecological interactions in the marine pelagic environment are difficult to study, mostly because the open-ocean is vast and largely inaccessible. Migration is a common ecological trait in pelagic settings, with large impacts on community structure and dynamics, and ecosystem functioning. However, migratory predators are rapidly declining worldwide, with unclear ecological consequences.Pelagic sharks have declined regionally by &gt; 90% in the past 15 years, largely as a result of overfishing and by-catch. Shark vulnerability to fishery capture depends on individual movements, and on the presence of movement traits across individuals, populations or species, which may implyshared vulnerability. Yet, the movements of pelagic sharks and other migratory oceanic animals are difficult to monitor or reconstruct.Natural-abundance stable isotopes allow retrospective movement reconstruction, by relating the isotopic composition of animal tissues to geographically indexed measurements or predictions of isotopic ratios at the base of the food web (isoscapes). Where incrementally grown, metabolically inert tissues are available, movements can be reconstructed throughout life. However, the application of stable isotopes in bulk tissues to study migration is complicated by mixed baseline and trophic effects and, in pelagic settings, by large uncertainties in the spatio-temporal distributions of isotopic baselines.In this study, I explored how the ontogenetic movements of two pelagic shark model species, the blue (Prionace glauca) and porbeagle (Lamna nasus) sharks, could be reconstructed using modelled global ocean carbon isoscapes, and carbon and nitrogen isotopes in bulk cartilage collagen and single amino acids from vertebrae.To provide a possible solution for poor sampling of isotopic baselines, I developed a process-based, mechanistic carbon isotope model, predicting the likely spatio-temporal distributions of the carbon isotopic composition of phytoplankton across the global ocean.To provide information on pelagic shark life-history traits, I recovered individual-level life history carbon and nitrogen isotope records for bulk cartilage collagen from vertebrae of sharks caught across the North Atlantic. I also recovered comparable carbon isotope records for single amino acids,producing the first compound-specific isotopic dataset of within-individual ontogenetic variance in sharks. Consistent ontogenetic isotope patterns across individuals of each species revealed species level life-history traits. Whilst the interpretation of traits for bulk collagen using modelled isoscapeswas ultimately limited from confounding influences from trophic level change, that of traits for essential amino acids conclusively demonstrated ontogenetic and transgenerational movement traits.During juvenile growth, blue sharks increasingly utilised foraging grounds with more positive carbon isotopic baselines, whereas porbeagles made increasing use of isotopically more negative grounds. Blue shark pupping and maternal foraging occurred in isotopically distinct grounds, with the possibility of natal homing by adult individuals. Pregnant female porbeagles, by contrast,migrated to isotopically distinct foraging grounds prior to giving birth.Isotope-derived information on ontogenetic movements complements tag-derived information over a snap-shot of the entire life of individuals, but explicit isoscape-based geo-location is limited by large uncertainties in isoscape models, and trophic influences on bulk tissue isotopiccompositions

Sensitivity of δ¹³C values of seabird tissues to combined spatial, temporal and ecological drivers: a simulation approach

Biologging technologies have revolutionised our understanding of the foraging ecology and life history traits of marine predators, allowing for high resolution information about location, and in some cases, foraging behaviour of wild animals. At the same time, stable isotope ecologists have independently developed methods to infer location and foraging ecology (trophic geography). To date, relatively few studies have combined these two approaches, despite the potential wealth of complementary information. In marine systems, spatial and trophic information are coded in the isotopic composition of carbon and nitrogen in animal tissues, but interpretation of isotope values is limited by both the lack of reference maps (isoscapes) needed to relate the isotopic composition of an animal's tissues to a location, and the relatively large number of variables that could influence tissue isotope compositions. Simulation modelling can help to interpret measured tissue isotope compositions of migratory animals in the context of spatio-temporally dynamic isotopic baselines. Here, we couple individual-based movement models with global marine isotope models to explore the sensitivity of tissue δ13C values to a range of extrinsic (environmental) and intrinsic (behavioural, physiological) drivers. We use in-silico experiments to simulate isotopic compositions expected for birds exhibiting different movement and foraging behaviours and compare these simulated data to isotopic data recovered from biologger-equipped female northern giant petrels Macronectes halli incubating eggs on sub-Antarctic Marion Island. Our simulations suggest that in the studied system, time is a strong driver of isotopic variance. Accordingly, this implies that caution should be used when comparing δ13C values of marine predators’ tissues between seasons and years. We show how an in-silico experimental approach can be used to explore the sensitivity of animal tissue isotopic compositions to complex and often interacting drivers. Appreciation of the principle drivers behind isotopic variance specific to a given animal and geographic context can enhance inferences of geolocation as well as foraging behaviour, and can be applied to any mobile predator. Models can be relativey simple or complex and multi-layered depending on the level of ecological realism required. Future investigations can use other isoscapes, including terrestrial isoscapes and more complex or different movement models.</p

Optimizing stable isotope sampling design in terrestrial movement ecology research

The recognition of adequate sampling designs is an interdisciplinary topic that has gained popularity over the last decades. In ecology, many research questions involve sampling across extensive and complex environmental gradients. This is the case for stable isotope analyses, which are widely used to characterize large-scale movement patterns and dietary preferences of organisms across taxa. Because natural-abundance stable isotope variation in the environment is incorporated into inert animal tissues, such as feathers or hair, it is possible to draw inferences about the type of food and water resources that individuals consumed and the locations where tissues were synthesized. However, modern stable isotope research can benefit from the implementation of robust statistical analyses and well-designed sampling approaches to improve geographic assignment interpretation. We employed hydrogen stable isotope simulations to study inferences regarding the probability of origin of migratory individuals and reveal gaps in sampling efforts while highlighting uncertainties of assignment model extrapolations. We present an integrative approach that explores multiple sampling strategies across species with different geographic ranges to understand advantages and limitations of animal movement inferences based on stable isotope data. We show the characteristics of different sampling strategies through geographic and isotopic gradients and establish a set of diagnostic tools that uncover the attributes of these gradients and evaluate uncertainties of model results. Our analysis demonstrates that sampling regimes should be evaluated in relation to specific research questions and study constraints, and that adopting a single method across species ranges can lead to a costly but less effective sampling strategy

Baleen stable isotope data

This dataset contains d13C and d15N stable isotope data from northern hemisphere rorqual whale (Balaenoptera) baleen taken from our collections. This includes data from the baleen of the Hintze Hall blue whale. The data has been used in various research papers. Additional data allow the analyses in these papers to be carried out and mostly encompass environmental datasets or the outputs of various simulation models. **Note that if trying to link these data to analyses in GitHub, an update to this site has changed all &quot;.&quot; in column headers to &quot;_&quot;. These will need to be changed before the code will work. Apologies.**</span

Compound-specific stable isotope analysis of amino acids in pelagic shark vertebrae reveals baseline, trophic, and physiological effects on bulk protein isotope records

Variations in stable carbon and nitrogen isotope compositions in incremental tissues of pelagic sharks can be used to infer aspects of their spatial and trophic ecology across life-histories. Interpretations from bulk tissue isotopic compositions are complicated, however, because multiple processes influence these values, including variations in primary producer isotope ratios and consumer diets and physiological processing of metabolites. Here we challenge inferences about shark tropho-spatial ecology drawn from bulk tissue isotope data using data for amino acids. Stable isotope compositions of individual amino acids can partition the isotopic variance in bulk tissue into components associated with primary production on the one hand, and diet and physiology on the other. The carbon framework of essential amino acids (EAAs) can be synthesised de novo only by plants, fungi and bacteria and must be acquired by consumers through the diet. Consequently, the carbon isotopic composition of EAAs in consumers reflects that of primary producers in the location of feeding, whereas that of non-essential amino acids (non-EAAs) is additionally influenced by trophic fractionation and isotope dynamics of metabolic processing. We determined isotope chronologies from vertebrae of individual blue sharks and porbeagles from the North Atlantic. We measured carbon and nitrogen isotope compositions in bulk collagen and carbon isotope compositions of amino acids. Despite variability among individuals, common ontogenetic patterns in bulk isotope compositions were seen in both species. However, while life-history movement inferences from bulk analyses for blue sharks were supported by carbon isotope data from essential amino acids, inferences for porbeagles were not, implying that the observed trends in bulk protein isotope compositions in porbeagles have a trophic or physiological explanation, or are suprious effects. We explored variations in carbon isotope compositions of non-essential amino acids, searching for systematic variations that might imply ontogenetic changes in physiological processing, but patterns were highly variable and did not explain variance in bulk protein δ13C values. Isotopic effects associated with metabolite processing may overwhelm spatial influences that are weak or inconsistently developed in bulk tissue isotope values, but interpreting mechanisms underpinning isotopic variation in patterns in non-essential amino acids remains challenging