Tracing carbon sources through aquatic and terrestrial food webs using amino acid stable isotope fingerprinting

Lipid extraction alters amino acid composition and bulk, but not amino acid, carbon and nitrogen isotope values

RATIONALE

Concerns exist over observed shifts in value and variance of nitrogen isotopes following physicochemical extraction of lipids from organic matter. The mechanisms behind these apparent changes in bulk tissue δ15N values are not fully understood yet have major implications for analytical costs and integrity of data interpretations.

METHODS

Changes in proximate analysis, amino acid composition, C:N ratios, bulk tissue and amino acid δ13C and δ15N values, and resulting isotope-based food web metrics were compared between lipid-intact and lipid-extracted muscle tissue of fishes spanning <1% to >20% muscle fat content to identify mechanisms of nitrogen isotope fractionation associated with physicochemical lipid extraction.

RESULTS

Bulk δ13C and δ15N values increased and %N, C:N ratios and crude protein content decreased following lipid extraction. Resulting bulk isotope niche spacing and overlap varied significantly between lipid-intact and lipid-extracted tissues. While amino acid composition significantly changed during lipid extraction, particularly for lipid-associated amino acids (e.g., Glu, Lys, Ser), individual amino acid δ13C and δ15N values, and their associated compound-specific isotope analysis of amino acids (CSIA-AA)-based food web metrics, did not.

CONCLUSIONS

Physicochemical lipid extraction caused significant tissue composition changes (e.g., leaching of amino acids and 15N-deplete nitrogenous waste) that affected δ13C and δ15N values and tissue %C and %N beyond simply removing lipids. However, lipid extraction did not alter individual amino acid δ13C or δ15N values or their associated CSIA-AA-based food web metrics.

Deep antiquity of seagrasses supporting European eel fisheries in the western Baltic

Protecting ocean habitats is critical for international efforts to mitigate climate impacts and ensure food security, but the ecological data upon which policy makers base conservation and restoration targets often reflect ecosystems that have already been deeply impacted by anthropogenic change. The archaeological record is a biomolecular archive offering a temporal scope that cannot be gathered from historical records or contemporary fieldwork. Insights from biogeochemical and osteometric analyses of fish bones, combined with context from contemporary field studies, show how prehistoric fisheries in the western Baltic relied on seagrass meadows. European eels (Anguilla anguilla) harvested by Mesolithic and Neolithic peoples over millennia showed a strong fidelity for eelgrass foraging habitats, an ecological relationship that remains largely overlooked today, demonstrating the value of protecting these habitats. These data open new windows onto ecosystem- and species-level behaviours, highlighting the need for wider incorporation of archaeological data in strategies for protecting our oceans.

Dietary plasticity and broad North Atlantic origins inferred from bulk and amino acid-specific δ15N and δ13C favour killer whale range expansions into Arctic waters

Killer whales (Orcinus orca) occur seasonally in the eastern Canadian Arctic (ECA), where their range expansion associated with declining sea ice have raised questions about the impacts of increasing killer whale predation pressure on Arctic-endemic prey. We assessed diet and distribution of ECA killer whales using bulk and compound-specific stable isotope analysis (CSIA) of amino acids (AA) of 54 skin biopsies collected from 2009 to 2020 around Baffin Island, Canada. Bulk ECA killer whale skin δ15N and δ13C values did not overlap with potential Arctic prey after adjustment for trophic discrimination, and instead reflected foraging history in the North Atlantic prior to their arrival in the ECA. Adjusted killer whale stable isotope (SI) values primarily overlapped with several species of North Atlantic baleen whales or tuna. Amino acid (AA)-specific δ15N values indicated the ECA killer whales fed primarily on marine mammals, having similar glutamic acid δ15N-phenylalanine δ15N (δ15NGlx-Phe) and threonine δ15N (δ15NThr) as mammal-eating killer whales from the eastern North Pacific (ENP) that served as a comparative framework. However, one ECA whale grouped with the fish-eating ENP ecotype based δ15NThr. Distinctive essential AA δ13C of ECA killer whale groups, along with bulk SI similarity to killer whales from different regions of the North Atlantic, indicates different populations converge in Arctic waters from a broad source area. Generalist diet and long-distance dispersal capacity favour range expansions, and integration of these insights will be critical for assessing ecological impacts of increasing killer whale predation pressure on Arctic-endemic species.

Individual diet variability shapes the architecture of Antarctic benthic food webs

Antarctic biodiversity is affected by seasonal sea-ice dynamics driving basal resource availability. To (1) determine the role of intraspecific dietary variability in structuring benthic food webs sustaining Antarctic biodiversity, and (2) understand how food webs and the position of topologically central species vary with sea-ice cover, single benthic individuals' diets were studied by isotopic analysis before sea-ice breakup and afterwards. Isotopic trophospecies (or Isotopic Trophic Units) were investigated and food webs reconstructed using Bayesian Mixing Models. As nodes, these webs used either ITUs regardless of their taxonomic membership (ITU-webs) or ITUs assigned to species (population-webs). Both were compared to taxonomic-webs based on taxa and their mean isotopic values. Higher resource availability after sea-ice breakup led to simpler community structure, with lower connectance and linkage density. Intra-population diet variability and compartmentalisation were crucial in determining community structure, showing population-webs to be more complex, stable and robust to biodiversity loss than taxonomic-webs. The core web, representing the minimal community 'skeleton' that expands opportunistically while maintaining web stability with changing resource availability, was also identified. Central nodes included the sea-urchin Sterechinus neumayeri and the bivalve Adamussium colbecki, whose diet is described in unprecedented detail. The core web, compartmentalisation and topologically central nodes represent crucial factors underlying Antarctica's rich benthic food web persistence.

Comparing trophic position estimates using bulk and compound specific stable isotope analyses: applying new approaches to mackerel icefish Champsocephalus gunnari

Quantifying the tropic position (TP) of an animal species is key to understanding its ecosystem function. While both bulk and compound-specific analyses of stable isotopes are widely used for this purpose, few studies have assessed the consistency between and within such approaches. Champsocephalus gunnari is a specialist teleost that predates almost exclusively on Antarctic krill Euphausia superba. This well-known and nearly constant trophic relationship makes C. gunnari particularly suitable for assessing consistency between TP methods under field conditions. In the present work, we produced and compared TP estimates for C. gunnari and its main prey using a standard bulk and two amino acid-specific stable isotope approaches (CSI-AA). One based on the difference between glutamate and phenylalanine (TPGlx-Phe), and the other on the proline-phenylalanine difference (TPPro-Phe). To do that, samples from C. gunnari, E. superba and four other pelagic invertebrate and fish species, all potential prey for C.gunnari, were collected off the South Orkney Islands between January and March 2019, analyzed using standard isotopic ratio mass spectrometry methods and interpreted following a Bayesian approach. Median estimates (CI95%) for C. gunnari were similar between TPbulk (3.6; CI95%: 3.0-4.8) and TPGlx-Phe(3.4; CI95%:3.2-3.6), and lower for TPPro-Phe (3.1; CI95%:3.0-3.3). TP differences between C. gunnari and E. superba were 1.4, 1.1 and 1.2, all compatible with expectations from the monospecific diet of this predator (ΔTP=1). While these results suggest greater accuracy for Glx-Phe and Pro-Phe, differences observed between both CSI-AA approaches suggests these methods may require further validation before becoming a standard tool for trophic ecology.

Comparison of δ13C and δ15N of ecologically relevant amino acids among beluga whale tissues

Ecological applications of compound-specific stable isotope analysis (CSIA) of amino acids (AAs) include 1) tracking carbon pathways in food webs using essential AA (AAESS) δ13C values, and 2) estimating consumer trophic position (TP) by comparing relative differences of 'trophic' and 'source' AA δ15N values. Despite the significance of these applications, few studies have examined AA-specific SI patterns among tissues with different AA compositions and metabolism/turnover rates, which could cause differential drawdown of body AA pools and impart tissue-specific isotopic fractionation. To address this knowledge gap, especially in the absence of controlled diet studies examining this issue in captive marine mammals, we used a paired-sample design to compare δ13C and δ15N values of 11 AAs in commonly sampled tissues (skin, muscle, and dentine) from wild beluga whales (Delphinapterus leucas). δ13C of two AAs, glutamic acid/glutamine (Glx, a non-essential AA) and, notably, threonine (an essential AA), differed between skin and muscle. Furthermore, δ15N of three AAs (alanine, glycine, and proline) differed significantly among the three tissues, with glycine δ15N differences of approximately 10 ‰ among tissues supporting recent findings it is unsuitable as a source AA. Significant δ15N differences in AAs such as proline, a trophic AA used as an alternative to Glx in TP estimation, highlight tissue selection as a potential source of error in ecological applications of CSIA-AA. Amino acids that differed among tissues play key roles in metabolic pathways (e.g., ketogenic and gluconeogenic AAs), pointing to potential physiological applications of CSIA-AA in studies of free-ranging animals. These findings underscore the complexity of isotopic dynamics within tissues and emphasize the need for a nuanced approach when applying CSIA-AA in ecological research.

Enhanced gut microbiome supplementation of essential amino acids in Diploptera punctata fed low-protein plant-based diet

Introduction

Building on our previous work, we investigate how dietary shifts affect gut microbial essential amino acid (EAA) provisioning in the lactating cockroach Diploptera punctata.

Method

To that end, we fed cockroaches three distinct diets: a plant-only Gari diet composed of starchy and granulated root tuber Yucca (Manihot esculenta), a dog food diet (DF), and a cellulose-amended dog food (CADF) diet. We anticipated that the high carbohydrate, low protein Gari would highlight increased microbial EAA supplementation to the host.

Results

By day 28, we observed distinct profiles of 14 bacterial families in the insect gut microbiomes of the three dietary groups. CADF-fed insects predominantly harbored cellulolytic and nitrogen-fixing bacteria families Streptococcaceae and Xanthomonadaceae. In contrast, Gari-fed insects were enriched in anaerobic lignocellulolytic bacteria families Paludibacteraceae and Dysgonomonadaceae, while DF-fed insects had a prevalence of proteolytic anaerobes Williamwhitmaniaceae and sulfate-reducing bacteria Desulfovibrionaceae. Furthermore, we confirmed significantly higher EAA supplementation in Gari-fed insects than in non-Gari-fed insects based on δ13C-EAA offsets between insect and their diets. The δ13C-EAA offsets between DF and CADF were nearly indistinguishable, highlighting the relevance of using the plant-based Gari in this experiment to unequivocally demonstrate this function in this insect. These results were underscored by lower standard metabolic rate (SMR) relative to the DF insect in Gari-fed (intermediate SMR and dietary quality) and CADF (least SMR and dietary quality) insects.

Discussion

The influence of diet on EAA provisioning and SMR responses in insects underscores the need for further exploration into the role of gut microbial functions in modulating metabolic responses.

Compound-specific stable isotopes of amino acids reveal influences of trophic level and primary production sources on mercury concentrations in fishes from the Aleutian Islands, Alaska

Total mercury concentrations ([THg]) exceed thresholds of concern in some Steller sea lion (Eumetopias jubatus) tissues from certain portions of the Aleutian Islands, Alaska. We applied compound-specific stable isotope analyses of both carbon and nitrogen in amino acids from fish muscle tissue to quantify the proportional contributions of primary production sources and trophic positions of eight prey species (n = 474 total) that are part of Steller sea lion diets. Previous THg analyses of fish muscle, coupled with monomethylmercury analyses of a subset of samples, substantiated previous findings that fishes from the west of Amchitka Pass, a discrete oceanographic boundary of the Aleutian Archipelago, have higher muscle Hg concentrations relative to fishes from the east. The δ13C values of essential amino acids (EAAs) in fish muscle demonstrated that although most fishes obtained their EAAs primarily from algae, some species varied in the extent to which they relied on this EAA source. The δ15N values of phenylalanine (0.9 to 7.8 ‰), an indicator of the isotopic baseline of a food web, varied widely within and among fish species. Trophic position estimates, accounting for this baseline variation, were higher from the west relative to the east of the pass for some fish species. Trophic magnification slopes using baseline-corrected trophic position estimates indicated similar rates of Hg biomagnification to the east and west of Amchitka Pass. Multiple linear regression models revealed that trophic position was the most important driver of fish muscle [THg] with less variation explained by other parameters. Thus, higher trophic positions but not the rate of Hg biomagnification to the west of Amchitka Pass may play a role in the regional differences in both fish and Steller sea lion [THg]. Although, differences in Hg contamination and uptake at the base of the east and west food webs could not be excluded.

Tissue-specific carbon isotope patterns of amino acids in southern sea otters

The measurement of stable isotope values of individual compounds, such as amino acids (AAs), has become a powerful tool in animal ecology and ecophysiology. As with any emerging technique, questions remain regarding the capabilities and limitations of this approach, including how metabolism and tissue synthesis impact the isotopic values of individual AAs and subsequent multivariate patterns. We measured carbon isotope (δ13C) values of essential (AAESS) and nonessential (AANESS) AAs in bone collagen, whisker, muscle, and liver from ten southern sea otters (Enhydra lutris nereis) that stranded in Monterey Bay, California. Sea otters in this population exhibit high degrees of individual dietary specialization, making this an excellent dataset to explore differences in AA δ13C values among tissues in a wild population. We found the δ13C values of the AANESS glutamic acid, proline, serine, and glycine and the AAESS threonine differed significantly among tissues, indicating possible isotopic discrimination during tissue synthesis. Threonine δ13C values were higher in liver relative to bone collagen and muscle, which may indicate catabolism of threonine for gluconeogenesis, an interpretation further supported by correlations between the δ13C values of threonine and its gluconeogenic products glycine and serine in liver. This intraindividual isotopic variation yielded different ecological interpretations among tissues; for 6/10 of the sea otter individuals analyzed, at least one tissue indicated reliance on a different primary producer source than the other tissues. Our results highlight the importance of gluconeogenesis in a carnivorous marine mammal and indicate that metabolic processes influence AAESS and AANESS δ13C values and multivariate AA δ13C patterns.

Stable isotopes and a changing world

The measurement of naturally occurring stable isotope ratios of the light elements (C, N, H, O, S) in animal tissues and associated organic and inorganic fractions of associated environments holds immense potential as a means of addressing effects of global change on animals. This paper provides a brief review of studies that have used the isotope approach to evaluate changes in diet, isotopic niche, contaminant burden, reproductive and nutritional investment, invasive species and shifts in migration origin or destination with clear links to evaluating effects of global change. This field has now reached a level of maturity that is impressive but generally underappreciated and involves technical as well as statistical advances and access to freely available R-based packages. There is a need for animal ecologists and conservationists to design tissue collection networks that will best answer current and anticipated questions related to the global change and the biodiversity crisis. These developments will move the field of stable isotope ecology toward a more hypothesis driven discipline related to rapidly changing global events.

Application of a porous graphitic carbon column to carbon and nitrogen isotope analysis of underivatized individual amino acids using high-performance liquid chromatography coupled with elemental analyzer/isotope ratio mass spectrometry

RATIONALE

Isolation of underivatized amino acids (AAs) using high-performance liquid chromatography (HPLC) is becoming a popular method for carbon (δ13 C) and nitrogen isotope (δ15 N) analyses of AAs because of the high analytical precision and for performing dual-isotope analysis. However, some AAs in natural samples, especially small, hydrophilic AAs, are not suitably separated using reversed-phase columns (e.g., C18) and ion-exchange columns (e.g., Primesep A).

METHODS

We developed a new method for HPLC using a porous graphitic carbon column for the separation of nine hydrophilic AAs. After purification, δ13 C and δ15 N values of AAs were determined using elemental analyzer/isotope ratio mass spectrometry (EA/IRMS). We demonstrated the application of this method by determining δ13 C and δ15 N values of individual hydrophilic AAs in a biological sample, the muscle of blue mackerel (Scomber australasicus).

RESULTS

Chromatographically, the baseline separation of hydrophilic AAs was achieved in both the standard mixture and the biological sample. We confirmed that δ13 C and δ15 N values of AA standards remained unchanged during the whole experimental procedure. The δ13 C values of AAs in mackerel muscle are also in good agreement with the values obtained using another verified method for δ13 C analysis.

CONCLUSIONS

The good separation performance of hydrophilic AAs and the reliability of δ13 C and δ15 N analyses of individual AAs using the porous graphite column offer a significant advantage over conventional settings. We suggest that, in the future, the HPLC × EA/IRMS method can be used for reliable δ13 C and δ15 N analyses of AAs in natural samples.

Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics

Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended use and interpretation of specimens and archived databases. In this article, we explore the potential for transformative research in ecology integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like genomic DNA, SIA provides a common currency interpreted in the context of biogeochemical principles. Integration of SIA data across collections allows for evaluation of long-term ecological change at local to continental scales. Challenges including the analysis of sparse samples, a lack of information about baseline isotopic composition, and the effects of preservation remain, but none of these challenges is insurmountable. The proposed research framework interfaces with existing databases and observatories to provide benchmarks for retrospective studies and ecological forecasting. Collections and SIA add historical context to fundamental questions in freshwater ecological research, reference points for ecosystem monitoring, and a means of quantitative assessment for ecosystem restoration.

Reconstructing herbivore diets: a multivariate statistical approach to interpreting amino acid nitrogen isotope values

Recent studies have demonstrated that there exists significant variability in amino acid (AA) δ¹⁵N values of terrestrial plants, discriminating among plant types (i.e., legume seeds, grasses, tree leaves) as well as tissues of the same plant. For the first time, we investigate the potential of the spacing between the δ¹⁵N values of different AAs to differentiate between plant types and thus elucidate their relative importance in herbivore diet. Using principal component analysis, we show that it is possible to distinguish among five plant categories-cereal grains, rachis, legume seeds, herbaceous plants, and woody plants-whose consumption has different implications for understanding herbivore ecology and management practices. Furthermore, we were able to correctly classify the herbaceous plant diet of modern cattle using AA δ¹⁵N values of their tooth dentine adjusted for trophic enrichment. The AA δ¹⁵N patterns of wild and domestic herbivores from archaeological sites seem to be consistent with diets comprised predominantly of herbaceous plants, but there is variation in AA δ¹⁵N values among individuals that may reflect differing inputs of other plant types. The variation in AA δ¹⁵N values does not necessarily reflect the variation in herbivore bulk collagen δ¹³C and δ¹⁵N values, indicating that AA δ¹⁵N values have the potential to provide additional insights into plant dietary sources compared to bulk tissue isotope values alone. Future work should focus on defining trophic enrichment factors for a wider range of terrestrial herbivores and expanding libraries of primary producer AA δ¹⁵N values.

Dietary plasticity linked to divergent growth trajectories in a critically endangered sea turtle

Foraging habitat selection and diet quality are key factors that influence individual fitness and meta-population dynamics through effects on demographic rates. There is growing evidence that sea turtles exhibit regional differences in somatic growth linked to alternative dispersal patterns during the oceanic life stage. Yet, the role of habitat quality and diet in shaping somatic growth rates is poorly understood. Here, we evaluate whether diet variation is linked to regional growth variation in hawksbill sea turtles (Eretmochelys imbricata), which grow significantly slower in Texas, United States versus Florida, United States, through novel integrations of skeletal growth, gastrointestinal content (GI), and bulk tissue and amino acid (AA)-specific stable nitrogen (δ15N) and carbon (δ13C) isotope analyses. We also used AA δ15N ΣV values (heterotrophic bacterial re-synthesis index) and δ13C essential AA (δ13CEAA) fingerprinting to test assumptions about the energy sources fueling hawksbill food webs regionally. GI content analyses, framed within a global synthesis of hawksbill dietary plasticity, revealed that relatively fast-growing hawksbills stranded in Florida conformed with assumptions of extensive spongivory for this species. In contrast, relatively slow-growing hawksbills stranded in Texas consumed considerable amounts of non-sponge invertebrate prey and appear to forage higher in the food web as indicated by isotopic niche metrics and higher AA δ15N-based trophic position estimates internally indexed to baseline nitrogen isotope variation. However, regional differences in estimated trophic position may also be driven by unique isotope dynamics of sponge food webs. AA δ15N ΣV values and δ13CEAA fingerprinting indicated minimal bacterial re-synthesis of organic matter (ΣV &lt; 2) and that eukaryotic microalgae were the primary energy source supporting hawksbill food webs. These findings run contrary to assumptions that hawksbill diets predominantly comprise high microbial abundance sponges expected to primarily derive energy from bacterial symbionts. Our findings suggest alternative foraging patterns could underlie regional variation in hawksbill growth rates, as divergence from typical sponge prey might correspond with increased energy expenditure and reduced foraging success or diet quality. As a result, differential dispersal patterns may infer substantial individual and population fitness costs and represent a previously unrecognized challenge to the persistence and recovery of this critically endangered species.

Stable isotope analyses of amino acids reveal the importance of aquatic resources to Mediterranean coastal hunter-gatherers

Determining the degree to which humans relied on coastal resources in the past is key for understanding long-term social and economic development, as well as for assessing human health and anthropogenic impacts on the environment. Prehistoric hunter-gatherers are often assumed to have heavily exploited aquatic resources, especially those living in regions of high marine productivity. For the Mediterranean, this view has been challenged, partly by the application of stable isotope analysis of skeletal remains which has shown more varied coastal hunter-gatherer diets than in other regions, perhaps due to its lower productivity. By undertaking a more specific analysis of amino acids from bone collagen of 11 individuals from one of the oldest and best-known Mesolithic cemeteries in the Mediterranean, at El Collado, Valencia, we show that high levels of aquatic protein consumption were achieved. By measuring both carbon and nitrogen in amino acids, we conclude that some of the El Collado humans relied heavily on local lagoonal fish and possibly shellfish, rather than open marine species. By contrast to previous suggestions, this study demonstrates that the north-western coast of the Mediterranean basin could support maritime-oriented economies during the Early Holocene.

The coupling of green and brown food webs regulates trophic position in a montane mammal guild

Food web ecology has revolutionized our understanding of ecological processes, but the drivers of food web properties like trophic position (TP) and food chain length are notoriously enigmatic. In terrestrial ecosystems, above- and belowground systems were historically compartmentalized into "green" and "brown" food webs, but the coupling of these systems by animal consumers is increasingly recognized, with potential consequences for trophic structure. We used stable isotope analysis (δ¹³ C, δ¹⁵ N) of individual amino acids to trace the flow of essential biomolecules and jointly measure multichannel feeding, food web coupling, and TP in a guild of small mammals. We then tested the hypothesis that brown energy fluxes to aboveground consumers increase terrestrial food chain length via cryptic trophic transfers during microbial decomposition. We found that the average small mammal consumer acquired nearly 70% of their essential amino acids (69.0% ± 7.6%) from brown food webs, leading to significant increases in TP across species and functional groups. Fungi were the primary conduit of brown energy to aboveground consumers, providing nearly half the amino acid budget for small mammals on average (44.3% ± 12.0%). These findings illustrate the tightly coupled nature of green and brown food webs and show that microbially mediated energy flow ultimately regulates food web structure in aboveground consumers. Consequently, we propose that the integration of green and brown energy channels is a cryptic driver of food chain length in terrestrial ecosystems.

A new technique to study nutrient flow in host-parasite systems by carbon stable isotope analysis of amino acids and glucose

Stable isotope analysis of individual compounds is emerging as a powerful tool to study nutrient origin and conversion in host-parasite systems. We measured the carbon isotope composition of amino acids and glucose in the cestode Schistocephalus solidus and in liver and muscle tissues of its second intermediate host, the three-spined stickleback (Gasterosteus aculeatus), over the course of 90 days in a controlled infection experiment. Similar linear regressions of δ¹³C values over time and low trophic fractionation of essential amino acids indicate that the parasite assimilates nutrients from sources closely connected to the liver metabolism of its host. Biosynthesis of glucose in the parasite might occur from the glucogenic precursors alanine, asparagine and glutamine and with an isotope fractionation of - 2 to - 3 ‰ from enzymatic reactions, while trophic fractionation of glycine, serine and threonine could be interpreted as extensive nutrient conversion to fuel parasitic growth through one-carbon metabolism. Trophic fractionation of amino acids between sticklebacks and their diets was slightly increased in infected compared to uninfected individuals, which could be caused by increased (immune-) metabolic activities due to parasitic infection. Our results show that compound-specific stable isotope analysis has unique opportunities to study host and parasite physiology.

Using MixSIAR to quantify mixed contributions of primary producers from amino acid δ15N of marine consumers

Estimations of the trophic position and the food web nitrogen baseline from compound-specific isotope analysis of individual amino acids (CSIA-AA) are challenged when the diet of consumer organisms relies on different proportions of vascular and non-vascular primary producers. Here we propose a method to infer such proportions using mixing models and the δ¹⁵N CSIA-AA values from marine herbivores. Combining published and new data, we first characterized CSIA-AA values in phytoplankton, macroalgae and vascular plants, and determined their characteristic β values (i.e. the isotopic difference between trophic and source AA). Then, we applied MixSIAR Bayesian isotope mixing models to investigate the transfer of these isotopic signals to marine herbivores (molluscs, green turtles, zooplankton and fish), and their utility to quantify autotrophic sources. We demonstrated that primary producer groups have distinct δ¹⁵N_AA fingerprints that can be tracked into their primary consumers, thus offering a rapid solution to quantify resource utilization and estimate β_mix values in mixed-sourced environments.

Multiple trophic pathways support fish on floodplains of California's Central Valley

We used compound-specific isotope analysis of carbon isotopes in amino acids (AAs) to determine the biosynthetic source of AAs in fish from major tributaries to California's Sacramento-San Joaquin river delta (i.e., the Sacramento, Cosumnes and Mokelumne rivers). Using samples collected in winter and spring between 2016 and 2019, we confirmed that algae are a critical component of floodplain food webs in California's Central Valley. Results from bulk stable isotope analysis of carbon and nitrogen in producers and consumers were adequate to characterize a general trophic structure and identify potential upstream and downstream migration into our study site by American shad Alosa sapidissima and rainbow trout Oncorhynchus mykiss, respectively. However, owing to overlap and variability in source isotope compositions, our bulk data were unsuitable for conventional bulk isotope mixing models. Our results from compound-specific carbon isotope analysis of AAs clearly indicate that algae are important sources of organic matter to fish of conservation concern, such as Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. However, algae were not the exclusive source of energy to metazoan food webs. We also revealed that other sources of AAs, such as bacteria, fungi and higher plants, contributed to fish as well. While consistent with the well-supported notion that algae are critical to aquatic food webs, our results highlight the possibility that detrital subsidies might intermittently support metazoan food webs.

Spatial Dynamics and Fine-Scale Vertical Behaviour of Immature Eastern Australasian White Sharks (Carcharodon carcharias)

Knowledge of the 3-dimensional space use of large marine predators is central to our understanding of ecosystem dynamics and for the development of management recommendations. Horizontal movements of white sharks, Carcharodon carcharias, in eastern Australian and New Zealand waters have been relatively well studied, yet vertical habitat use is less well understood. We dual-tagged 27 immature white sharks with Pop-Up Satellite Archival Transmitting (PSAT) and acoustic tags in New South Wales coastal shelf waters. In addition, 19 of these individuals were also fitted with Smart Position or Temperature Transmitting (SPOT) tags. PSATs of 12 sharks provided useable data; four tags were recovered, providing highly detailed archival data recorded at 3-s intervals. Horizontal movements ranged from southern Queensland to southern Tasmania and New Zealand. Sharks made extensive use of the water column (0-632 m) and experienced a broad range of temperatures (7.8-28.9 °C). Archival records revealed pronounced diel-patterns in distinct fine-scale oscillatory behaviour, with sharks occupying relatively constant depths during the day and exhibiting pronounced yo-yo diving behaviour (vertical zig-zag swimming through the water column) during the night. Our findings provide valuable new insights into the 3-dimensional space use of Eastern Australasian (EA) white sharks and contribute to the growing body on the general ecology of immature white sharks.

Intercontinental analysis of temperate steppe stream food webs reveals consistent autochthonous support of fishes

Quantifying the trophic basis of production for freshwater metazoa at broad spatial scales is key to understanding ecosystem function and has been a research priority for decades. However, previous lotic food web studies have been limited by geographic coverage or methodological constraints. We used compound-specific stable carbon isotope analysis of amino acids (AAs) to estimate basal resource contributions to fish consumers in streams spanning grassland, montane and semi-arid ecoregions of the temperate steppe biome on two continents. Across a range of stream sizes and light regimes, we found consistent trophic importance of aquatic resources. Essential AAs of heterotrophic microbial origin generally provided secondary support for fishes, while terrestrial carbon did not seem to provide significant, direct support. These findings provide strong evidence for the dominant contribution of carbon to higher-order consumers by aquatic autochthonous resources (primarily) and heterotrophic microbial communities (secondarily) in temperate steppe streams.

Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism

RATIONALE

Position-specific ¹³ C/¹² C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids.

METHODS

Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The ¹³ C/¹² C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ¹³ C values relative to a working standard.

RESULTS

This methodology constrains position-specific δ¹³ C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ¹³ C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7-5‰ for each carbon position. Position-specific δ¹³ C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO₂ , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline.

CONCLUSIONS

This study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

Insights into amino acid fractionation and incorporation by compound-specific carbon isotope analysis of three-spined sticklebacks

Interpretation of stable isotope data is of upmost importance in ecology to build sound models for the study of animal diets, migration patterns and physiology. However, our understanding of stable isotope fractionation and incorporation into consumer tissues is still limited. We therefore measured the δ¹³C values of individual amino acids over time from muscle and liver tissue of three-spined sticklebacks (Gasterosteus aculeatus) on a high protein diet. The δ¹³C values of amino acids in the liver quickly responded to small shifts of under ± 2.0‰ in dietary stable isotope compositions on 30-day intervals. We found on average no trophic fractionation in pooled essential (muscle, liver) and non-essential (muscle) amino acids. Negative Δδ¹³C values of − 0.7 ± 1.3‰ were observed for pooled non-essential (liver) amino acids and might indicate biosynthesis from small amounts of dietary lipids. Trophic fractionation of individual amino acids is reported and discussed, including unusual Δδ¹³C values of over + 4.9 ± 1.4‰ for histidine. Arginine and lysine showed the lowest trophic fractionation on individual sampling days and might be useful proxies for dietary sources on short time scales. We suggest further investigations using isotopically enriched materials to facilitate the correct interpretation of ecological field data.

Amino acid nitrogen and carbon isotope data: Potential and implications for ecological studies

Explaining food web dynamics, stability, and functioning depend substantially on understanding of feeding relations within a community. Bulk stable isotope ratios (SIRs) in natural abundance are well-established tools to express direct and indirect feeding relations as continuous variables across time and space. Along with bulk SIRs, the SIRs of individual amino acids (AAs) are now emerging as a promising and complementary method to characterize the flow and transformation of resources across a diversity of organisms, from microbial domains to macroscopic consumers. This significant AA-SIR capacity is based on empirical evidence that a consumer's SIR, specific to an individual AA, reflects its diet SIR coupled with a certain degree of isotopic differences between the consumer and its diet. However, many empirical ecologists are still unfamiliar with the scope of applicability and the interpretative power of AA-SIR. To fill these knowledge gaps, we here describe a comprehensive approach to both carbon and nitrogen AA-SIR assessment focusing on two key topics: pattern in AA-isotope composition across spatial and temporal scales, and a certain variability of AA-specific isotope differences between the diet and the consumer. On this basis we review the versatile applicability of AA-SIR to improve our understanding of physiological processes as well as food web functioning, allowing us to reconstruct dominant basal dietary sources and trace their trophic transfers at the specimen and community levels. Given the insightful and opportunities of AA-SIR, we suggest future applications for the dual use of carbon and nitrogen AA-SIR to study more realistic food web structures and robust consumer niches, which are often very difficult to explain in nature.

Bottom-Up Control of the Groundwater Microbial Food-Web in an Alpine Aquifer

Groundwater ecosystems are typically poor in organic carbon and productivity sustaining a low standing stock of microbial biomass. In consequence, microbial food webs in oligotrophic groundwater are hypothesized to be bottom-up controlled. To date, quantitative information on groundwater microbial communities, food web interactions, and carbon flow is relatively lacking in comparison to that of surface waters. Studying a shallow, porous alpine aquifer we collected data on the numbers of prokaryotes, virus-like particles and heterotrophic nanoflagellates (HNFs), the concentration of dissolved (DOC) and assimilable organic carbon (AOC), bacterial carbon production (BCP), and physical-chemical conditions for a 1 year hydrological cycle. The potential effects of protozoan grazing and viral lysis onto the prokaryotic biomass was tested. Flow of organic carbon through the microbial food web was estimated based on data from the literature. The abundance of prokaryotes in groundwater was low with 6.1 ± 6.9 × 104 cells mL–1, seasonally influenced by the hydrological dynamics, with higher densities coinciding with a lower groundwater table. Overall, the variability in cell numbers was moderate, and so it was for HNFs (179 ± 103 HNFs mL–1) and virus-like particles (9.6 ± 5.7 × 105 VLPs mL–1). The virus to prokaryotes and prokaryote to HNF ratios ranged between 2–230 and 33–2,084, respectively. We found no evidence for a viral control of prokaryotic biomass, and the biomass of HNFs being bottom-up controlled. First estimations point at carbon use efficiencies of 0.2–4.2% with prokaryotic production, and carbon consumed and recycled by HNFs and phages to be of minor importance. This first groundwater microbial food web analysis strongly hints at a bottom-up control on productivity and standing stock in oligotrophic groundwater ecosystems. However, direct measurement of protozoan grazing and phage mediated lysis rates of prokaryotic cells are urgently needed to deepen our mechanistic understanding. The effect of microbial diversity on the population dynamics still needs to be addressed.

The impact of mobile demersal fishing on carbon storage in seabed sediments

Subtidal marine sediments are one of the planet's primary carbon stores and strongly influence the oceanic sink for atmospheric CO₂ . By far the most widespread human activity occurring on the seabed is bottom trawling/dredging for fish and shellfish. A global first-order estimate suggested mobile demersal fishing activities may cause 0.16-0.4 Gt of organic carbon (OC) to be remineralized annually from seabed sediment carbon stores (Sala et al., 2021). There are, however, many uncertainties in this calculation. Here, we discuss the potential drivers of change in seabed sediment OC stores due to mobile demersal fishing activities and conduct a literature review, synthesizing studies where this interaction has been directly investigated. Under certain environmental settings, we hypothesize that mobile demersal fishing would reduce OC in seabed stores due to lower production of flora and fauna, the loss of fine flocculent material, increased sediment resuspension, mixing and transport and increased oxygen exposure. Reductions would be offset to varying extents by reduced faunal bioturbation and community respiration, increased off-shelf transport and increases in primary production from the resuspension of nutrients. Studies which directly investigated the impact of demersal fishing on OC stocks had mixed results. A finding of no significant effect was reported in 61% of 49 investigations; 29% reported lower OC due to fishing activities, with 10% reporting higher OC. In relation to remineralization rates within the seabed, four investigations reported that demersal fishing activities decreased remineralization, with three reporting higher remineralization rates. Patterns in the environmental and experimental characteristics between different outcomes were largely indistinct. More evidence is urgently needed to accurately quantify the impact of anthropogenic physical disturbance on seabed carbon in different environmental settings and to incorporate full evidence-based carbon considerations into global seabed management.

Substrate Composition Influences Amino Acid Carbon Isotope Profiles of Fungi: Implications for Tracing Fungal Contributions to Food Webs

Fungi link detrital resources and metazoan consumers through their role as decomposers. However, fungal contributions to metazoans may be misestimated in amino acid isotope studies because fungi are capable of both synthesizing amino acids (AAs) de novo and absorbing AAs from their environment. While fungi cultured in AA-free media have been used to represent fungi in studies of natural environments, fungi likely gain energetic benefits by taking up substrate AAs directly in situ. Consequently, fungi cultured on AA-free media may not be representative of the true variability of natural fungal δ¹³ C_AA profiles. Therefore, the objective of this experiment was to determine the effect of substrate AA availability on yeast δ¹³ C_AA profiles. We found that yeasts cultured in media of relatively higher AA content had different δ¹³ C_AA profiles than fungi grown in AA-free media, in part because yeasts utilized two essential AAs (Leu and Val) directly from media substrates when available in sufficient amounts. Furthermore, these differences among yeast δ¹³ C_AA profiles remained after normalization of δ¹³ C_AA values. We recommend further characterization of the variation in fungal δ¹³ C_AA profiles and the incorporation of this potential variability into interpretations of basal resource use by metazoans. This article is protected by copyright. All rights reserved.

Environmental fate and trophic transfer of synthetic musk compounds and siloxanes in Geum River, Korea: Compound-specific nitrogen isotope analysis of amino acids for accurate trophic position estimation

Despite the extensive usage of synthetic musk compounds (SMCs) and siloxanes in various personal care products (PCPs), trophic magnification of such chemicals in aquatic environments remains unexplored. In June and September 2020, eleven SMCs and nineteen siloxanes were measured in water, sediments, and biota. Samples were collected from two sites where levels were expected to be influenced by the distance from the wastewater treatment plant (WWTP) in the Geum River, Republic of Korea, were expected. High concentrations of SMCs and siloxanes entered through WWTP were measured in water, sediment, and biota at the both sites and both seasons. The δ¹⁵N of amino acids provided a high-resolution food web and accurate trophic position (TP), which is an important factor for determining the trophic magnification factor (TMF). Among 24 TMFs, 19 of them were <1, ranging 0.7-0.8 for 1,3,4,6,7,8‑hexahydro‑4,6,6,7,8,8‑hexamethyl‑cyclopenta‑γ‑2‑benzopyran (HHCB), 0.6-0.8 for 6-Acetyl-1,1,2,4,4,7-hexamethyltetralin (AHTN), 0.7-0.8 for 4-tert-Butyl-3,5-dinitro-2,6-dimethylacetophenone (MK), 0.7-0.9 for octamethylcyclotetrasiloxane (D4), 0.1-0.4 for decamethylcyclopentasiloxane (D5), and 0.04-0.8 for dodecamethylcyclohexasiloxane (D6), and the remaining ones including HHCB, AHTN, MK, and D4 showed values close to 1 or slightly higher (TMF range: 1.0-2.3) indicating no or a little trophic magnification. The TMFs of these compounds were constant across sites and seasons. The TMF values of PCPs might be affected by species specificity and food web structure rather than by chemical properties such as log K_ow, which describes a wide range of TMF values in various environments. This study presents valuable implications for assessing risk and managing environmental fate and trophic transfer of SMCs and siloxanes in freshwater environments.

OUP accepted manuscript

Stable isotope analysis of teeth and bones is regularly applied by archeologists and paleoanthropologists seeking to reconstruct diets, ecologies, and environments of past hominin populations. Moving beyond the now prevalent study of stable isotope ratios from bulk materials, researchers are increasingly turning to stable isotope ratios of individual amino acids to obtain more detailed and robust insights into trophic level and resource use. In the present article, we provide a guide on how to best use amino acid stable isotope ratios to determine hominin dietary behaviors and ecologies, past and present. We highlight existing uncertainties of interpretation and the methodological developments required to ensure good practice. In doing so, we hope to make this promising approach more broadly accessible to researchers at a variety of career stages and from a variety of methodological and academic backgrounds who seek to delve into new depths in the study of dietary composition.

Biosynthesis and Isotopic Routing of Dietary Protein by Sea Cucumber Apostichopus japonicus (Selenka): Evidence from Compound-Specific Carbon Stable Isotope Analysis

Compound-specific stable isotope analysis of individual amino acids (AAs) has been widely used in studies on food webs, resource tracing, and biochemical cycling. In the present study, juvenile sea cucumbers Apostichopus japonicus were fed the microalga Cylindrotheca fusiformis (CF) or Sargassum thunbergii (ST) during a 130-day experiment. The δ¹³C values of individual AAs in the experimental diet and body wall of sea cucumbers were determined to calculate the variability in carbon isotopic fractionation (Δ¹³C) and elucidate the isotopic routing of essential AAs and biosynthesis of nonessential AAs. The results showed that the sea cucumbers fed with diet CF had higher specific growth and ingestion rates but relatively lower feed conversion efficiency compared to those fed with diet ST. The experimental diets were generally less abundant in nonessential AAs (i.e., glycine, serine, aspartic acid, and arginine) but more abundant in essential AAs (i.e., isoleucine, leucine, lysine, phenylalanine, and histidine) than body walls. The fluctuations in the δ¹³C values of total AAs analyzed were 19.8 ± 4.6‰ for diets and 21.3 ± 2.7‰ for body walls. Serine and threonine were ¹³C-enriched AAs, while leucine and phenylalanine were ¹³C-depleted AAs. The diet ST treatment exhibited more positive Δ¹³C values of nonessential AAs (e.g., glycine, alanine, aspartic acid, and proline) compared to diet CF. There were significant negative relationships between Δ¹³C values and differences in nonessential AA percent abundance between the experimental diets and body walls of sea cucumber (for diet CF: y = -0.79 - 0.56x, r² = 0.47; diet ST: y = 0.75 - 0.29x, r² = 0.51), which implied the flexibility in the routing of various dietary macronutrients (protein, lipids, and carbohydrates) by sea cucumber. This study can greatly provide a new understanding of nutrient utilization and metabolism routing during juvenile sea cucumber culturing.

New geochemical tools for investigating resource and energy functions at deep-sea cold seeps using amino acid δ15 N in chemosymbiotic mussels (Bathymodiolus childressi)

In order to reconstruct the ecosystem structure of chemosynthetic environments in the fossil record, geochemical proxies must be developed. Here, we present a suite of novel compound-specific isotope parameters for tracing chemosynthetic production with a focus on understanding nitrogen dynamics in deep-sea cold seep environments. We examined the chemosymbiotic bivalve Bathymodiolus childressi from three geographically distinct seep sites on the NE Atlantic Margin and compared isotope data to non-chemosynthetic littoral mussels to test whether water depth, seep activity, and/or mussel bed size are linked to differences in chemosynthetic production. The bulk isotope analysis of carbon (δ¹³ C) and nitrogen (δ¹⁵ N), and δ¹⁵ N values of individual amino acids (δ¹⁵ N_AA ) in both gill and muscle tissues, as well as δ¹⁵ N_AA- derived parameters including trophic level (TL), baseline δ¹⁵ N value (δ¹⁵ N_Phe ), and a microbial resynthesis index (ΣV), were used to investigate specific geochemical signatures of chemosynthesis. Our results show that δ¹⁵ N_AA values provide a number of new proxies for relative reliance on chemosynthesis, including TL, ∑V, and both δ¹⁵ N values and molar percentages (Gly/Glu mol% index) of specific AA. Together, these parameters suggested that relative chemoautotrophy is linked to both degree of venting from seeps and mussel bed size. Finally, we tested a Bayesian mixing model using diagnostic AA δ¹⁵ N values, showing that percent contribution of chemoautotrophic versus heterotrophic production to seep mussel nutrition can be directly estimated from δ¹⁵ N_AA values. Our results demonstrate that δ¹⁵ N_AA analysis can provide a new set of geochemical tools to better understand mixotrophic ecosystem function and energetics, and suggest extension to the study of ancient chemosynthetic environments in the fossil record.

Experimentally derived trophic enrichment and discrimination factors for Chinook salmon, Oncorhynchus tshawytscha

RATIONALE

Stable isotope analysis (SIA) can provide important insights into food web structure and is a widely used tool in ecological conservation and management. It has recently been augmented by compound-specific stable isotope analysis of amino acids (CSIA-AA), an innovation that can provide greater precision when analyzing trophic level and food web connectivity. The utility of SIA rests on confidence in its constituent parameters such as the trophic enrichment factor (TEF). There is increasing emphasis on the need to experimentally derive species and tissue specific TEFs for studies utilizing SIA. Chinook salmon, Oncorhynchus tshawytscha, is a species with high potential for study using SIA due to the difficulty in observing its ecology during its marine phase and the significance of the conservation consequences of recent population declines.

METHODS

Bulk and amino acid-specific TEFs were determined for juvenile and adult Chinook salmon fed specific diets. Three controlled feeding studies were performed: adult salmon were fed a biofeed, juvenile salmon were fed a biofeed, and juvenile salmon were fed krill. Bulk and compound-specific stable isotope data were collected from diet samples and from salmon muscle tissue after a minimum of 8 weeks of controlled feeding. Bulk isotope signatures were measured using EA-IRMS and CSIA-AA signatures using GC/C-IRMS, allowing the TEFs to be calculated.

RESULTS

The bulk isotope TEFs were higher than those predicted for similar marine organisms and averaged 3.5‰ for ∆¹⁵ N and 1.3‰ for ∆¹³ C. The TEFs derived for nitrogen isotopes of amino acids were in line with expectations for this approach: the mean value for ∆¹⁵ N_Glu  - ∆¹⁵ N_Phe was 7.06‰ and, using a multi-AA approach, the value for ∆¹⁵ N_Trophic  - ∆¹⁵ N_Source was 6.67‰. For carbon isotopes of amino acids, the derived TEFs of Iso, Leu and Phe were near 0‰, as was that of Met, supporting their use of as source amino acids in future CSIA studies.

CONCLUSIONS

This study presents Chinook salmon-specific TEFs for bulk and amino acid SIA. It supports the application of future research applying SIA to the study of Chinook salmon and validates previous research on species-specific TEFs.

Stable isotope signatures in historic harbor seal bone link food web-assimilated carbon and nitrogen resources to a century of environmental change

Anthropogenic climate change will impact nutrient cycles, primary production, and ecosystem structure in the world's oceans, although considerable uncertainty exists regarding the magnitude and spatial variability of these changes. Understanding how regional-scale ocean conditions control nutrient availability and ultimately nutrient assimilation into food webs will inform how marine resources will change in response to climate. To evaluate how ocean conditions influence the assimilation of nitrogen and carbon into coastal marine food webs, we applied a novel dimension reduction analysis to a century of newly acquired molecular isotope data derived from historic harbor seal bone specimens. By measuring bulk δ¹³ C and δ¹⁵ N values of source amino acids of these top predators from 1928 to 2014, we derive indices of primary production and nitrogen resources that are assimilated into food webs. We determined coastal food webs responded to climate regimes, coastal upwelling, and freshwater discharge, yet the strength of responses to individual drivers varied across the northeast Pacific. Indices of primary production and nitrogen availability in the Gulf of Alaska were dependent on regional climate indices (i.e., North Pacific Gyre Oscillation) and upwelling. In contrast, the coastal Washington and Salish Sea food webs were associated with local indices of freshwater discharge. For some regions (eastern Bering Sea, northern Gulf of Alaska) food web-assimilated production was coupled with nitrogen sources; however, other regions demonstrated no production-nitrogen coupling (Salish Sea). Temporal patterns of environmental indices and isotopic data from Washington state varied about the long-term mean with no directional trend. Data from the Gulf of Alaska, however, showed below average harbor seal δ¹³ C values and above average ocean conditions since 1975, indicating a change in primary production in recent decades. Altogether, these findings demonstrate stable isotope data can provide useful indices of nitrogen resources and phytoplankton dynamics specific to what is assimilated by food webs.

Amino acid δ13C and δ15N analyses reveal distinct species-specific patterns of trophic plasticity in a marine symbiosis

Compound-specific isotope analyses (CSIA) and multivariate "isotope fingerprinting" track biosynthetic sources and reveal trophic interactions in food webs. However, CSIA have not been widely applied in the study of marine symbioses. Here, we exposed a reef coral (Montipora capitata) in symbiosis with Symbiodiniaceae algae to experimental treatments (autotrophy, mixotrophy, heterotrophy) to test for trophic shifts and amino acid (AA) sources using paired bulk (δ¹³C, δ¹⁵N) and AA-CSIA (δ¹³C_AA, δ¹⁵N_AA). Treatments did not influence carbon or nitrogen trophic proxies, thereby not supporting nutritional plasticity. Instead, hosts and symbionts consistently overlapped in essential- and nonessential-δ¹³C_AA (11 of 13 amino acids) and trophic- and source-δ¹⁵N_AA values (9 of 13 amino acids). Host and symbiont trophic-δ¹⁵N_AA values positively correlated with a plankton end-member, indicative of trophic connections and dietary sources for trophic-AA nitrogen. However, mass balance of AA-trophic positions (TP_Glx-Phe) revealed heterotrophic influences to be highly variable (1-41% heterotrophy). Linear discriminant analysis using M. capitata mean-normalized essential-δ¹³C_AA with previously published values (Pocillopora meandrina) showed similar nutrition isotope fingerprints (Symbiodiniaceae vs. plankton) but revealed species-specific trophic strategies. Montipora capitata and Symbiodiniaceae shared identical AA-fingerprints, whereas P. meandrina was assigned to either symbiont or plankton nutrition. Thus, M. capitata was 100% reliant on symbionts for essential-δ¹³C_AA and demonstrated autotrophic fidelity and contrasts with trophic plasticity reported in P. meandrina. While M. capitata AA may originate from host and/or symbiont biosynthesis, AA carbon is Symbiodiniaceae-derived. Together, AA-CSIA/isotope fingerprinting advances the study of coral trophic plasticity and are powerful tools in the study of marine symbioses.

Interactions at surface-subterranean ecotones: structure and function of food webs within spring orifices

Spring orifices are ecotones between surface and subterranean aquatic ecosystems. Invertebrates of different origins (e.g., surface, spring obligate, and subterranean) coexist in these spatially restricted environments, potentially competing for resources. However, processes that allow for population coexistence in these presumably low resource environments are not well understood. We examined invertebrate communities at two spring complexes in Texas, USA and assessed resource use and food web structure at spring orifices using stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N). Using bulk δ¹³C and δ¹⁵N of organisms and potential food sources, we elucidated dietary sources and found that invertebrate communities exhibited resource partitioning and contained two main food chains (periphyton versus terrestrial organic matter [OM]). In both spring complexes, several endemic spring orifice associated and subterranean taxa derived most of their diet from terrestrial OM. Analysis of compound-specific stable isotopes (i.e., δ¹³C of essential amino acids, EAAs) from two co-occurring elmid species indicated that the endemic spring orifice-associated species (Heterelmis comalensis) derived > 80% of its EAAs from bacteria, whereas the widespread surface species (Microcylloepus pusillus) derived its EAAs from a more equitable mix of bacteria, fungi, and algae. We additionally calculated niche overlap among of several taxonomically related groups (aquatic beetles and amphipods) that co-occur in spring ecotones and posterior probability estimates indicated little to no niche overlap among related species. Results indicate that invertebrates at subterranean-surface aquatic ecotones are partitioning food resources and highlight the importance of connections to riparian zones for persistence of several endemic invertebrates.

Nitrogen stable isotope turnover and discrimination in lizards

RATIONALE

Nitrogen stable isotope ratio (δ¹⁵ N) processes are not well described in reptiles, which limits reliable inference of trophic and nutrient dynamics. In this study we detailed δ¹⁵ N turnover and discrimination (Δ¹⁵ N) in diverse tissues of two lizard species, and compared these results with previously published carbon data (δ¹³ C) to inform estimates of reptilian foraging ecology and nutrient physiology.

METHODS

We quantified ¹⁵ N incorporation and discrimination dynamics over 360 days in blood fractions, skin, muscle, and liver of Sceloporus undulatus and Crotaphytus collaris that differed in body mass. Tissue samples were analyzed on a continuous flow isotope ratio mass spectrometer.

RESULTS

Δ¹⁵ N for plasma and red blood cells (RBCs) ranged between +2.7 and +3.5‰; however, skin, muscle, and liver did not equilibrate, hindering estimates for these somatic tissues. ¹⁵ N turnover in plasma and RBCs ranged from 20.7 ± 4 to 303 ± 166 days among both species. Comparison with previously published δ¹³ C results for these same samples showed that ¹⁵ N and ¹³ C incorporation patterns were uncoupled, especially during winter when hibernation physiology could have played a role.

CONCLUSIONS

Our results provide estimates of ¹⁵ N turnover rates and discrimination values that are essential to using and interpreting isotopes in studies of diet reconstruction, nutrient allocation, and trophic characterization in reptiles. These results also suggest that somatic tissues can be unreliable, while life history shifts in nutrient routing and metabolism potentially cause ¹⁵ N and ¹³ C dynamics to be decoupled.

The carbon isotope ratios of nonessential amino acids identify sugar-sweetened beverage (SSB) consumers in a 12-wk inpatient feeding study of 32 men with varying SSB and meat exposures

BACKGROUND

The carbon isotope ratios (CIRs) of individual amino acids (AAs) may provide more sensitive and specific biomarkers of sugar-sweetened beverages (SSBs) than total tissue CIR. Because CIRs turn over slowly, long-term controlled-feeding studies are needed in their evaluation.

OBJECTIVE

We assessed the responses of plasma and RBC CIRAA's to SSB and meat intake in a 12-wk inpatient feeding study.

METHODS

Thirty-two men (aged 46.2 ± 10.5 y) completed the feeding study at the National Institute of Diabetes and Digestive and Kidney Diseases in Phoenix, Arizona. The effects of SSB, meat, and fish intake on plasma and RBC CIRAA's were evaluated in a balanced factorial design with each dietary variable either present or absent in a common weight-maintaining, macronutrient-balanced diet. Fasting blood samples were collected biweekly from baseline. Dietary effects on the postfeeding CIR of 5 nonessential AAs (CIRNEAA's) and 4 essential AAs (CIREAA's) were analyzed using multivariable regression.

RESULTS

In plasma, 4 of 5 CIRNEAA's increased with SSB intake. Of these, the CIRAla was the most sensitive (β = 2.81, SE = 0.38) to SSB intake and was not affected by meat or fish intake. In RBCs, all 5 CIRNEAA's increased with SSBs but had smaller effect sizes than in plasma. All plasma CIREAA's increased with meat intake (but not SSB or fish intake), and the CIRLeu was the most sensitive (β = 1.26, SE = 0.23). CIRs of leucine and valine also increased with meat intake in RBCs. Estimates of turnover suggest that CIRAA's in plasma, but not RBCs, were in equilibrium with the diets by the end of the study.

CONCLUSIONS

The results of this study in men support CIRNEAA's as potential biomarkers of SSB intake and suggest CIREAA's as potential biomarkers of meat intake in US diets. This trial was registered at clinicaltrials.gov/ct2/show/NCT01237093 as NCT01237093.

Offshore pelagic subsidies dominate carbon inputs to coral reef predators

Coral reefs were traditionally perceived as productive hot spots in oligotrophic waters. While modern evidence indicates that many coral reef food webs are heavily subsidized by planktonic production, the pathways through which this occurs remain unresolved. We used the analytical power of carbon isotope analysis of essential amino acids to distinguish between alternative carbon pathways supporting four key reef predators across an oceanic atoll. This technique separates benthic versus planktonic inputs, further identifying two distinct planktonic pathways (nearshore reef-associated plankton and offshore pelagic plankton), and revealing that these reef predators are overwhelmingly sustained by offshore pelagic sources rather than by reef sources (including reef-associated plankton). Notably, pelagic reliance did not vary between species or reef habitats, emphasizing that allochthonous energetic subsidies may have system-wide importance. These results help explain how coral reefs maintain exceptional productivity in apparently nutrient-poor tropical settings, but also emphasize their susceptibility to future ocean productivity fluctuations.

Fatty acid stable isotopes add clarity, but also complexity, to tracing energy pathways in aquatic food webs

Tracing the flow of dietary energy sources, especially in systems with a high degree of omnivory, is an ongoing challenge in ecology. In aquatic systems, one of the persistent challenges is in differentiating between autochthonous and allochthonous energy sources to top consumers. Bulk carbon stable isotope values of aquatic and terrestrial prey often overlap, making it difficult to delineate dietary energy pathways in food webs with high allochthonous prey subsidies, such as in many northern temperate waterbodies. We conducted a feeding experiment to explore how fatty acid stable isotopes may overcome the challenge of partitioning autochthonous and allochthonous energy pathways in aquatic consumers. We fed hatchery-reared Arctic Char (Salvelinus alpinus) diets of either benthic invertebrates, terrestrial earthworms, or a mixture of both. We then compared how the stable carbon isotopes of fatty acids (δ13CFA) distinguished between diet items and respective treatments in S. alpinus liver and muscle tissues, relative to bulk stable isotopes and fatty acid profiles. Although a high degree of variability of fatty acid stable carbon isotope values was present in all three measures, our results suggest that the ability of this method to overcome the challenges of bulk stable isotopes may be overstated. Finally, our study highlights the importance of further experimental investigation, and consideration of physiological and biochemical processes when employing this emerging method.

Validation of dried blood spot sampling for determining trophic positions of Arctic char using nitrogen stable isotope analyses of amino acids

RATIONALE

Dried blood spots (DBSs) are gaining popularity for biomarker analyses in ecological research due to their advantages for use in field-based research and in remote settings; however, many DBS biomarkers remain unvalidated. We validated the application of compound-specific stable nitrogen isotope analyses of amino acids (CSIA-AAs) to field-prepared DBSs for determining trophic positions of wild-caught Arctic char (Salvelinus alpinus).

METHODS

Whole blood and muscle from Arctic char were collected, and DBSs were created in the field. We measured the stable nitrogen isotope ratios (expressed as δ¹⁵ N values) of the amino acids glutamic acid (Glu) and phenylalanine (Phe) isolated from Arctic char samples using CSIA-AAs. We then compared amino acid δ¹⁵ N values from DBSs and the other sample types (whole blood and muscle) from the same specimens. We calculated and compared trophic position estimates generated from whole blood, DBSs, and muscle.

RESULTS

The δ¹⁵ N values of Glu and Phe, as well as trophic position estimates from DBSs, were highly correlated with δ¹⁵ N values and estimates from both whole blood and muscle. The DBS amino acid δ¹⁵ N values and trophic position estimates agreed well with those from whole blood. Although mean differences between amino acid δ¹⁵ N values from DBSs and muscle were noted, the offsets were small and resulted in a 0.2 mean difference between trophic position estimates for DBSs and muscle.

CONCLUSIONS

We demonstrate that the application of CSIA-AAs to field-prepared DBSs of Arctic char generates similar trophic position estimates to those from whole blood and muscle. We suggest that DBSs could be developed as a minimally invasive sampling technique to study feeding ecology of wild fish and perhaps other organisms of interest.

Primary role of increasing urea-N concentration in a novel Microcystis densa bloom: Evidence from ten years of field investigations and laboratory experiments

A novel Microcystis bloom caused by Microcystis densa has occurred in a typical subtropical reservoir every spring and summer since 2012, and it has caused several ecological and economic losses. To determine the environmental factors that influence the growth and physiological characteristics of M. densa, we investigated the variations in physicochemical factors and M. densa cell density from 2007 to 2017. The results showed that the urea-N concentration increased significantly (from 0.02 ± 0.00-0.20 ± 0.01 mg N l^-1), whereas other factors did not vary significantly. NO₃^--N and urea-N concentrations were higher than the NH₄⁺-N concentration during the M. densa bloom. The nitrogen composition changed, and urea-N and NO₃^--N became a major nitrogen sources in the reservoir. Water temperature and increased urea-N concentrations were the primary factors that influenced variations in M. densa cell density (45.5%, p < 0.05). Laboratory experiments demonstrated that M. densa cultured with urea-N exhibited a higher maximum cell density (9.8 ± 0.5 × 10⁸ cells l^-1), more cellular pigments for photosynthesis (chlorophyll a and phycocyanin) and photoprotection (carotenoid), and more proteins than those cultured with NH₄⁺-N and NO₃^--N. These results suggested that M. densa cultured with urea-N exhibited preferable growth and physiological conditions. Moreover, M. densa exhibited an increased maximum specific uptake rate (0.93 pg N cell^-1 h^-1) and reduced half-saturation constant (0.03 mg N l^-1) for urea-N compared with NH₄⁺-N and NO₃^--N, suggesting that M. densa preferred urea-N as its major nitrogen source. These results collectively indicated that the increasing urea-N concentration was beneficial for the growth and physiological conditions of M. densa. This study provided ten years of field data and detailed physiological information supporting the critical effect of urea-N on the growth of a novel bloom species M. densa. These findings helped to reveal the mechanism of M. densa bloom formation from the perspective of dissolved organic nitrogen.

Intraspecific variation and energy channel coupling within a Chilean kelp forest

The widespread importance of variable types of primary production, or energy channels, to consumer communities has become increasingly apparent. However, the mechanisms underlying this "multichannel" feeding remain poorly understood, especially for aquatic ecosystems that pose unique logistical constraints given the diversity of potential energy channels. Here, we use bulk tissue isotopic analysis along with carbon isotope (δ13 C) analysis of individual amino acids to characterize the relative contribution of pelagic and benthic energy sources to a kelp forest consumer community in northern Chile. We measured bulk tissue δ13 C and δ15 N for >120 samples; of these we analyzed δ13 C values of six essential amino acids (EAA) from nine primary producer groups (n = 41) and 11 representative nearshore consumer taxa (n = 56). Using EAA δ13 C data, we employed linear discriminant analysis (LDA) to assess how distinct EAA δ13 C values were between local pelagic (phytoplankton/particulate organic matter), and benthic (kelps, red algae, and green algae) endmembers. With this model, we were able to correctly classify nearly 90% of producer samples to their original groupings, a significant improvement on traditional bulk isotopic analysis. With this EAA isotopic library, we then generated probability distributions for the most important sources of production for each individual consumer and species using a bootstrap-resampling LDA approach. We found evidence for multichannel feeding within the community at the species level. Invertebrates tended to focus on either pelagic or benthic energy, deriving 13-67% of their EAA from pelagic sources. In contrast, mobile (fish) taxa at higher trophic levels used more equal proportions of each channel, ranging from 19% to 47% pelagically derived energy. Within a taxon, multichannel feeding was a result of specialization among individuals in energy channel usage, with 37 of 56 individual consumers estimated to derive >80% of their EAA from a single channel. Our study reveals how a cutting-edge isotopic technique can characterize the dynamics of energy flow in coastal food webs, a topic that has historically been difficult to address. More broadly, our work provides a mechanism as to how multichannel feeding may occur in nearshore communities, and we suggest this pattern be investigated in additional ecosystems.

Decadal shift in foraging strategy of a migratory southern ocean predator

Rapid anthropogenic environmental change is expected to impact a host of ecological parameters in Southern Ocean ecosystems. Of critical concern are the consequences of these changes on the range of species that show fidelity to migratory destinations, as philopatry is hypothesized to help or hinder adaptation to climate change depending on the circumstances. Many baleen whales show philopatry to feeding grounds and are also capital breeders that meet migratory and reproductive costs through seasonal energy intake. Southern right whales (Eubalaena australis, SRWs) are capital breeders that have a strong relationship between reproductive output and foraging success. The population dynamics of South Africa's population of SRWs are characterized by two distinct periods: the 1990s, a period of high calving rates; and the late 2010s, a period associated with lowered calving rates. Here we use analyses of stable carbon (δ13 C) and nitrogen (δ15 N) isotope values from SRW biopsy samples (n = 122) collected during these two distinct periods to investigate foraging ecology of the South African population of SRWs over a time period coincident with the demographic shift. We show that South African SRWs underwent a dramatic northward shift, and diversification, in foraging strategy from 1990s to 2010s. Bayesian mixing model results suggest that during the 1990s, South African SRWs foraged on prey isotopically similar to South Georgia/Islas Georgias del Sur krill. In contrast, in the 2010s, South African SRWs foraged on prey isotopically consistent with the waters of the Subtropical Convergence, Polar Front and Marion Island. We hypothesize that this shift represents a response to changes in preferred habitat or prey, for example, the decrease in abundance and southward range contraction of Antarctic krill. By linking reproductive decline to changing foraging strategies for the first time in SRWs, we show that altering foraging strategies may not be sufficient to adapt to a changing ocean.