High-resolution food webs based on nitrogen isotopic composition of amino acids

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.

Integrated approach for the isotope trophic position of black-tailed gull (Larus crassirostris) eggs over a decade: Combining stable isotopes of amino acids and fatty acids composition

Recently, compound-specific isotope analysis (CSIA) using the amino acid nitrogen stable isotope ratio (δ15NAAs) has been widely used for accurate estimation of trophic position (TP). In addition, a quantitative fatty acid signature analysis (QFASA) offers insights into diet sources. In this study, we used these techniques to estimate the TP for seabirds that rely on diverse food sources across multiple ecosystems. This allows for the proper combination of factors used in TP calculation which are different for each ecosystem. The approach involved the application of a multi-mixing trophic discrimination factor (TDF) and mixing β which is a Δδ15N between trophic and source amino acid of primary producer. Since the black-tailed gulls (BTGs) are income-breeding seabirds, which rely on energy sources obtained around their breeding sites, they and their eggs could be useful bioindicators for environmental monitoring. However, the ecological properties of BTGs such as habitats, diets, and TP are not well known due to their large migration range for wintering or breeding and their feeding habits on both aquatic and terrestrial prey. In this study, the eggs were used for estimating TP and for predicting TP of mother birds to overcome difficulties such as capturing birds and collecting non-invasive tissue samples. Eggs, sampled over a decade from three Korean islands, showed spatial differences in diet origin. Considering both the food chain and physiology of BTG, the TP of eggs was estimated to be 3.3-4.0. Notably, the TP was significantly higher at site H (3.8 ± 0.1) than at site B (3.5 ± 0.2), which indicated a higher contribution of marine diet as confirmed by QFASA. Using a reproductive shift of δ15NAAs, the TP of the mother birds was predicted to be 3.6-4.3, positioning them as the top predator in the food web. The advanced integration of multiple approaches provides valuable insights into bird ecology.

A female woolly mammoth's lifetime movements end in an ancient Alaskan hunter-gatherer camp

Woolly mammoths in mainland Alaska overlapped with the region's first people for at least a millennium. However, it is unclear how mammoths used the space shared with people. Here, we use detailed isotopic analyses of a female mammoth tusk found in a 14,000-year-old archaeological site to show that she moved ~1000 kilometers from northwestern Canada to inhabit an area with the highest density of early archaeological sites in interior Alaska until her death. DNA from the tusk and other local contemporaneous archaeological mammoth remains revealed that multiple mammoth herds congregated in this region. Early Alaskans seem to have structured their settlements partly based on mammoth prevalence and made use of mammoths for raw materials and likely food.

Compound-specific stable nitrogen isotope analysis of amino acids shows that bulk methods provide higher estimates of mercury biomagnification in the Gulf of St. Lawrence

Compound-specific stable isotope analysis of amino acids (CSIA-AA) provides a method to estimate baseline δ15N values of food chains, allowing less biased estimates of trophic positions for organisms. Greater accuracy in trophic positions can improve estimates of contaminant biomagnification. We calculated trophic positions with various CSIA-AA equations for four species of fish and northern gannets (Morus bassanus) from the Gulf of St. Lawrence. We examined the effect of CSIA-AA-derived trophic positions on mercury biomagnification metrics (trophic magnification factors (TMF) and biomagnification factors) and compared these with trophic position estimates and metrics obtained from traditional bulk stable isotope analysis. The TMFs for the CSIA-AA equations ranged from 10 to 19, and bulk stable isotope analysis produced TMFs of 43, one of the highest TMFs recorded yet in the literature. Biomagnification factors between prey and northern gannets ranged from 20 to 42 using dietary observations and stable isotope mixing models. Our study demonstrates that discrepancies in biomagnification assessed using different approaches may go undetected when using a single approach.

Trophodynamics of halogenated organic pollutants (HOPs) in aquatic food webs

Halogenated organic pollutants (HOPs) represent hazardous and persistent compounds characterized by their capacity to accumulate within organisms and endure in the environment. These substances are frequently transmitted through aquatic food webs, engendering potential hazards to ecosystems and human well-being. The trophodynamics of HOPs in aquatic food webs has garnered worldwide attention within the scientific community. Despite comprehensive research endeavors, the prevailing trajectory of HOPs, whether inclined toward biomagnification or biodilution within global aquatic food webs, remains unresolved. Furthermore, while numerous studies have probed the variables influencing the trophic magnification factor (TMF), the paramount determinant remains elusive. Collating a compendium of pertinent literature encompassing TMFs from the Web of Science between 1994 and 2023, our analysis underscores the disparities in attention accorded to legacy HOPs compared to emerging counterparts. A discernible pattern of biomagnification characterizes the behavior of HOPs within aquatic food webs. Geographically, the northern hemisphere, including Asia, Europe, and North America, has demonstrated greater biomagnification than its southern hemisphere counterparts. Utilizing a boosted regression tree (BRT) approach, we reveal that the food web length and type emerge as pivotal determinants influencing TMFs. This review provides a valuable basis for gauging ecological and health risks, thereby facilitating the formulation of robust standards for managing aquatic environments.

Trophic Transfer of Halogenated Organic Pollutants in a Wetland Food Web: Insights from Compound-Specific Nitrogen Isotope of Amino Acids and Food Source Analysis

A trophic position (TP) model (TPmix model) that simultaneously considered trophic discrimination factor and βGlu/Phe variations was developed in this study and was first applied to investigate the trophic transfer of halogenated organic pollutants (HOPs) in wetland food webs. The TPmix model characterized the structure of the wetland food web more accurately and significantly improved the reliability of TMF compared to the TPbulk, TPAAs, and TPsimmr models, which were calculated based on the methods of stable nitrogen isotope analysis of bulk, traditional AAs-N-CSIA, and weighted βGlu/Phe, respectively. Food source analysis revealed three interlocking food webs (kingfisher, crab, and frogs) in this wetland. The highest HOP biomagnification capacities (TMFmix) were found in the kingfisher food web (0.24-82.0), followed by the frog (0.08-34.0) and crab (0.56-11.7) food webs. The parabolic trends of TMFmix across combinations of log KOW in the frog food web were distinct from those of aquatic food webs (kingfisher and crab), which may be related to differences in food web composition and HOP bioaccumulation behaviors between aquatic and terrestrial organisms. This study provides a new tool to accurately study the trophic transfer of contaminants in wetlands and terrestrial food webs with diverse species and complex feeding relationships.

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.

Metal bioaccumulation and transfer in benthic species based on isotopic signatures of individual amino acids in South China Sea cold seep environments

Cold seeps are deep-sea 'oases' with dense and dominant coexisting populations of large mussels and tubeworms under extreme environments. Under such natural source of high metal concentrations, the present study investigated the metal bioaccumulation and transfer with trophic positions in six benthic species by the isotopic δ¹⁵N and δ¹³C signatures in the active Haima cold seep, South China Sea. Comparing the isotopic signatures of bulk-tissue and amino acids by compound-specific isotopic analysis (CSIA-AA), we found that the bulk trophic (TP_B) values in the benthos except mussels were significantly higher than those of CSIA-based TP_Glu-Phe values. The estimated CSIA-based TP_Glu-Phe values showed a relatively compressed food chain with much changeable and unique amino acid isotopic heterogeneity, followed slim tubeworms (1.20)<mussels (1.38)<clams (1.52)<brittle stars (1.82)<giant tubeworms (2.16)<shrimps (2.31). All species accumulated relatively high concentrations of Fe, Zn, Cu, and Cr, especially for Zn in clams. Pearson correlation analysis showed that most metals had no significant relationship between their bioaccumulation and trophic positions, whereas Hg showed a significantly positive bioaccumulation through trophic transfer in such a compressed food chain. Water exposure was a major metal source rather than bacterial assimilation for most metals in the cold seep higher consumers. Hyperaccumulation of specific metals in some tissues of different benthos indicated different metal overflows in the Haima cold seep (As and Ni for tubeworms, Zn and Cd for clam gills, Ag and Cu for mussel gills). This study demonstrated high metal adaptations in different species and stable isotopic characteristics of amino acid metabolism in a natural high metal source of an active deep-sea cold seep, which is important for deep-sea development and environmental protection.

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.

Trophodynamics and health risk assessment of toxic trace metals in the food web of a plateau freshwater lake

The trophodynamics of toxic trace metals is significant for assessing the threat of toxic trace metals to the aquatic ecosystem and human safety. However, due to the difficulty of accurately calculating the trophic positions of freshwater aquatic organisms in the food web, the comprehensive process of trophodynamics of toxic trace metals in freshwater ecosystems was still rarely known. By integrating the compound-specific nitrogen stable isotopic analysis of amino acids (CSIA-AAs) and the Bayesian stable isotope mixing model (SIMM) as a novel approach, the present study investigated the trophodynamics of five toxic trace metals (Zn, As, Cr, Cu, and Hg) in the food web of the YangZong Lake, a plateau freshwater lake that was once heavily polluted by arsenic in Yunnan Province, China. The results revealed that Hg tended to be efficiently biomagnified in the food web with a trophic magnification factor of 1.75; As, Cr, and Cu were biodiluted significantly, while Zn showed no biomagnification or biodilution trends. The dietary health risk assessment indicated the potential health risk of toxic trace metals for the local residents of long-term fish consumption. The present work highlights the accuracy and reliability of the novel CSIA-AAS+SIMM approach in the calculation of the trophic positions of freshwater organisms.

Isotopic Niche Analysis of Long-Finned Pilot Whales (Globicephala melas edwardii) in Aotearoa New Zealand Waters

Simple Summary

Isotopic niche analyses can elucidate a species’ foraging ecology. Using isotopic values of δ¹³C, δ¹⁵N and δ³⁴S, the isotopic niche of long-finned pilot whales (Globicephala melas edwardii) in Aotearoa New Zealand was investigated for animals that stranded in six different events across two locations between 2009 and 2017. Generalised additive models revealed that stranding event was a stronger predictor for δ¹³C and δ¹⁵N values than body length, sex, or reproductive status, indicating that spatiotemporal differences explained isotopic variation of G. m. edwardii in New Zealand waters better than ontogenetic factors.

Abstract

The quantification of a species’ trophic niche is important to understand the species ecology and its interactions with the ecosystem it resides in. Despite the high frequency of long-finned pilot whale (Globicephala melas edwardii) strandings on the Aotearoa New Zealand coast, their trophic niche remains poorly understood. To assess the isotopic niche of G. m. edwardii within New Zealand, ontogenetic (sex, total body length, age, maturity status, reproductive group) and spatiotemporal (stranding location, stranding event, and stranding year) variation were investigated. Stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N) were examined from skin samples of 125 G. m. edwardii (67 females and 58 males) collected at mass-stranding events at Onetahua Farewell Spit in 2009 (n = 20), 2011 (n = 20), 2014 (n = 27) and 2017 (n = 20) and at Rakiura Stewart Island in 2010 (n = 19) and 2011 (n = 19). Variations in δ³⁴S values were examined for a subset of 36 individuals. General additive models revealed that stranding event was the strongest predictor for δ¹³C and δ¹⁵N values, whilst sex was the strongest predictor of δ³⁴S isotopic values. Although similar within years, δ¹³C values were lower in 2014 and 2017 compared to all other years. Furthermore, δ¹⁵N values were higher within Farewell Spit 2017 compared to any other stranding event. This suggests that the individuals stranded in Farewell Spit in 2017 may have been feeding at a higher trophic level, or that the nitrogen baseline may have been higher in 2017 than in other years. Spatiotemporal differences explained isotopic variation of G. m. edwardii in New Zealand waters better than ontogenetic factors.

Empirical food webs of 12 tropical reservoirs in Singapore

Background

Food webs summarise trophic interactions of the biotic components within an ecosystem, which can influence nutrient dynamics and energy flows, ultimately affecting ecosystem functions and services. Food webs represent the hypothesised trophic links between predators and prey and can be presented as empirical food webs, in which the relative strength/importance of the respective links are quantified. Some common methods used in food web research include gut content analysis (GCA) and stable isotope analysis (SIA). We combine both methods to construct empirical food web models as a basis for monitoring and studying ecosystem-level outcomes of natural (e.g. species turnover in fish assemblage) and intentional environmental change (e.g. biomanipulation).

New information

We present 12 food webs from tropical reservoir communities in Singapore and summarise the topology of each with widely-used network indices (e.g. connectance, link density). Each reservoir was surveyed over 4-6 sampling occasions, during which, representative animal groups (i.e. fish species and taxonomic/functional groups of zooplankton and benthic macroinvertebrates) and all likely sources of primary production (i.e. macrophytes, periphyton, phytoplankton and riparian terrestrial plants) were collected. We analysed gut content in fishes and bulk isotope (d¹³C and d¹⁵N) profiles of all animals (i.e. fishes and invertebrates) and plants collected. Both sets of information were used to estimate the relative strength of trophic relationships using Bayesian mixing models. We document our protocol here, alongside a script in the R programming language for executing data management/analyses/visualisation procedures used in our study. These data can be used to glean insights into trends in inter- and intra-specific or guild interactions in analogous freshwater lake habitats.

Compound specific isotope evidence points to use of freshwater resources as weaning food in Middle Neolithic Paris Basin

Objectives

Methods

Results

Conclusions

Typical scaled food web structure and total mercury enrichment characteristics in Xingkai Lake, China

Different from the widely used constant discrimination factor Δ¹⁵N = 3.4‰ between two adjacent trophic positions (TPs), a scaled Δ¹⁵N framework for evaluating the TP of species was developed in 2014, that is, the Δ¹⁵N between two adjacent TPs decreases as the TP increases which is considered to be in closer conformity to the trophic cascade in the natural food web. In this study, we compared the two TP calculation methods and then reconsidered the evaluation of the trophic magnification factors (TMFs). Our results show that the TP_scaled value is higher and the TMFs value is lower under the scaled Δ¹⁵N framework, indicating that the TMFs value under the constant Δ¹⁵N framework is often overestimated. We further constructed a diet proportion food web model, which shows that species with lower TP has higher contribution rate as food sources. In Xingkai Lake, the enrichment process of mercury in the food web is not strictly consistent with the diet proportion of the food web. Based on the diet proportion food web model and the mercury enrichment model, it can be found that the White shrimp (Exopalaemon modestus) is not only an important food source, but also the main source of mercury transmission in the food web. Overall, our findings have quantified the food web construction and thus facilitated a better understanding of the interaction between the diet proportion and the bio-concentration in the food web.

Chemoautotrophy, symbiosis and sedimented diatoms support high biomass of benthic molluscs in the Namibian shelf

The molluscs Lucinoma capensis, Lembulus bicuspidatus and Nassarius vinctus are highly abundant in Namibian oxygen minimum zone sediments. To understand which nutritional strategies allow them to reach such impressive abundances in this extreme habitat we investigated their trophic diversity, including a chemosymbiosis in L. capensis, focussing on nitrogen biochemical pathways of the symbionts. We combined results of bulk nitrogen and carbon (δ¹³C and δ¹⁵N) and of compound-specific isotope analyses of amino acid nitrogen (AAs—δ¹⁵N_Phe and δ¹⁵N_Glu), with 16S rRNA gene sequencing of L. capensis tissues and also with exploratory results of ammonium, nitrate and nitrite turnover. The trophic position (TP) of the bivalve L. capensis is placed between autotrophy and mixotrophy, consistent with its proposed symbiosis with sulfur-oxidizing Candidatus Thiodiazotropha sp. symbionts. The symbionts are here revealed to perform nitrate reduction and ammonium uptake, with clear indications of ammonium host-symbionts recycling, but surprisingly unable to fix nitrogen. The TP of the bivalve L. bicuspidatus is placed in between mixotrophy and herbivory. The TP of the gastropod N. vinctus reflected omnivory. Multiple lines of evidences in combination with current ecosystem knowledge point to sedimented diatoms as important components of L. bicuspidatus and N. vinctus’ diet, likely supplemented at times with chemoautotrophic bacteria. This study highlights the importance of benthic-pelagic coupling that fosters the dietary base for macrozoobenthos in the OMZ. It further unveils that, in contrast to all shallow water lucinid symbionts, deeper water lucinid symbionts rely on ammonium assimilation rather than dinitrogen fixation to obtain nitrogen for growth.

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.

Apex Predator Nematodes and Meso-Predator Bacteria Consume Their Basal Insect Prey through Discrete Stages of Chemical Transformations

Microbial symbiosis drives physiological processes of higher-order systems, including the acquisition and consumption of nutrients that support symbiotic partner reproduction. Metabolic analytics provide new avenues to examine how chemical ecology, or the conversion of existing biomass to new forms, changes over a symbiotic life cycle. We applied these approaches to the nematode Steinernema carpocapsae, its mutualist bacterium, Xenorhabdus nematophila, and the insects they infect. The nematode-bacterium pair infects, kills, and reproduces in an insect until nutrients are depleted. To understand the conversion of insect biomass over time into either nematode or bacterium biomass, we integrated information from trophic, metabolomic, and gene regulation analyses. Trophic analysis established bacteria as meso-predators and primary insect consumers. Nematodes hold a trophic position of 4.6, indicative of an apex predator, consuming bacteria and likely other nematodes. Metabolic changes associated with Galleria mellonella insect bioconversion were assessed using multivariate statistical analyses of metabolomics data sets derived from sampling over an infection time course. Statistically significant, discrete phases were detected, indicating the insect chemical environment changes reproducibly during bioconversion. A novel hierarchical clustering method was designed to probe molecular abundance fluctuation patterns over time, revealing distinct metabolite clusters that exhibit similar abundance shifts across the time course. Composite data suggest bacterial tryptophan and nematode kynurenine pathways are coordinated for reciprocal exchange of tryptophan and NAD⁺ and for synthesis of intermediates that can have complex effects on bacterial phenotypes and nematode behaviors. Our analysis of pathways and metabolites reveals the chemistry underlying the recycling of organic material during carnivory. IMPORTANCE The processes by which organic life is consumed and reborn in a complex ecosystem were investigated through a multiomics approach applied to the tripartite Xenorhabdus bacterium-Steinernema nematode-Galleria insect symbiosis. Trophic analyses demonstrate the primary consumers of the insect are the bacteria, and the nematode in turn consumes the bacteria. This suggests the Steinernema-Xenorhabdus mutualism is a form of agriculture in which the nematode cultivates the bacterial food sources by inoculating them into insect hosts. Metabolomics analysis revealed a shift in biological material throughout progression of the life cycle: active infection, insect death, and conversion of cadaver tissues into bacterial biomass and nematode tissue. We show that each phase of the life cycle is metabolically distinct, with significant differences including those in the tricarboxylic acid cycle and amino acid pathways. Our findings demonstrate that symbiotic life cycles can be defined by reproducible stage-specific chemical signatures, enhancing our broad understanding of metabolic processes that underpin a three-way symbiosis.

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.

Extreme bill dimorphism leads to different but overlapping isotopic niches and similar trophic positions in sexes of the charismatic extinct huia

The New Zealand huia (Heteralocha acutirostris) had the most extreme bill sexual dimorphism among modern birds. Given the quick extinction of the species, the cause of the dimorphism could only be hypothesised to reflect different trophic niches and reduce male/female competition. We tested that hypothesis by combining museum specimens, geometric morphometrics, and isotopic analyses. We used geometric morphometrics to describe bill shape; measured bulk (δ¹⁵N_bulk) and (δ¹³C_bulk) values from feather as proxies of the birds’ foraging habitat and diet; and compared compound-specific stable isotopes analyses (CSIA) of nitrogen in amino acids (δ¹⁵N_AA) in male–female pairs to estimate their trophic position. Sexes had significantly different, but overlapping feather δ¹⁵N_bulk and δ¹³C_bulk values, but δ¹⁵N_AA indicated identical trophic positions and δ¹⁵N_bulk was not related to bill shape. Trophic position was less variable among females, consistent with a specialised foraging behaviour and, thus, supporting a partial male/female foraging segregation.

Combining isotopic analysis of bulk-skin and individual amino acids to investigate the trophic position and foraging areas of multiple cetacean species in the western South Atlantic

We investigated the trophic structure and habitat use of ten cetacean species occurring in the oceanic waters of the western South Atlantic using naturally-occurring stable isotopes. We analysed δ¹⁵N in individual amino acids (AA) to estimate cetacean trophic position (TP) and to evaluate the spatial differences in baseline δ¹⁵N (source AAs). We adjusted cetacean bulk-skin δ¹³C and δ¹⁵N for the effect of trophic level using their estimated TPs, obtaining δ¹³C_Adjusted and δ¹⁵N_Adjusted, respectively. These values were applied to estimate the overlap in the niche areas of cetacean baseline sources. Our analyses showed spatial segregation between Steno bredanensis and the remaining odontocetes, and the high δ¹⁵N in this species reflects its occurrence in neritic waters of the southern region. The highest TPs were observed in Physeter macrocephalus, Stenella attenuata and Globicephala melas, while the lowest TPs were reported for S. longirostris, S. clymene and Orcinus orca. Overall, source AA-δ¹⁵N showed similar patterns as those of baseline-δ¹⁵N (zooplankton) and were higher in species sampled in the southernmost region of the study area (e.g., Delphinus delphis). Isotopic niche areas estimated using δ¹³C_Adjusted and δ¹⁵N_Adjusted suggested high overlap in foraging area between S. frontalis and Tursiops truncatus, with the latter occupying a higher TP. Our analyses of δ¹⁵N in AAs provide a unique insight into the trophic ecology, forage areas and spatial segregation in resource use among these cetacean populations. Additionally, our work provides AA-δ¹⁵N baseline for future studies on the trophic ecology and habitat use of marine organisms in the western South Atlantic.

Dietary protein content and digestibility influences discrimination of amino acid nitrogen isotope values in a terrestrial omnivorous mammal

RATIONALE

Ecologists increasingly determine the δ¹⁵ N values of amino acids (AA) in animal tissue; "source" AA typically exhibit minor variation between diet and consumer, while "trophic" AA have increased δ¹⁵ N values in consumers. Thus, trophic-source δ¹⁵ N offsets (i.e., Δ¹⁵ N_T-S ) reflect trophic position in a food web. However, even minor variations in δ¹⁵ N_{source AA} values may influence the magnitude of offset that represents a trophic step, known as the trophic discrimination factor (i.e., TDF_T-S ). Diet digestibility and protein content can influence the δ¹⁵ N values of bulk animal tissue, but the effects of these factors on AA Δ¹⁵ N_T-S and TDF_T-S in mammals are unknown.

METHODS

We fed captive mice (Mus musculus) either (A) a low-fat, high-fiber diet with low, intermediate, or high protein; or (B) a high-fat, low-fiber diet with low or intermediate protein. Mouse muscle and dietary protein were analyzed for bulk tissue δ¹⁵ N using elemental analyzer-isotope ratio mass spectrometry (EA-IRMS), and were also hydrolyzed into free AA that were analyzed for δ¹⁵ N using gas chromatography-combustion-IRMS.

RESULTS

As dietary protein increased, Δ¹⁵ N_{Consumer-Diet} slightly declined for bulk muscle tissue in both experiments; increased for AA in the low-fat, high-fiber diet (A); and remained the same or decreased for AA in the high-fat, low-fiber diet (B). The effects of dietary protein on Δ¹⁵ N_T-S and on TDF_T-S varied by AA but were consistent between variables.

CONCLUSIONS

Diets were less digestible and included more protein in Experiment A than in Experiment B. As a result, the mice in Experiment A probably oxidized more AA, resulting in greater Δ¹⁵ N_{Consumer-Diet} values. However, the similar responses of Δ¹⁵ N_T-S and of TDF_T-S to diet variation suggest that if diet samples are available, Δ¹⁵ N_T-S accurately tracks trophic position. If diet samples are not available, the patterns presented here provide a basis to interpret Δ¹⁵ N_T-S values. The trophic-source offset of Pro-Lys did not vary across diets, and therefore may be more reliable for omnivores than other offsets (e.g., Glu-Phe).

Proteomic profile of bone "collagen" extracted for stable isotopes: Implications for bulk and single amino acid analyses

RATIONALE

Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed.

METHODS

Protein samples that had been previously analyzed for stable isotopes, including those with marginal and poor sample quality, were characterized by liquid chromatography/mass spectrometry using an LTQ Orbitrap Velos mass spectrometer after separation on a Dionex Ultimate 3000 LC system. Data were analyzed using MetaMorpheus and custom R scripts.

RESULTS

We found a variety of proteins in addition to collagen, although collagen I was found in the majority of the samples (most samples >80%). We also found a positive correlation between total deamidation and wt% N, suggesting that deamidation may impact the overall nitrogen signal in bulk analyses. The amino acid profiles of samples, including those of marginal or poor stable isotope quality, reflect the expected collagen I percentages, allowing their use in single amino acid stable isotope analyses.

CONCLUSIONS

All the samples regardless of quality were found to have high concentrations of collagen I, making interpretations of dietary routing based on collagen I reasonably valid. The amino acid profiles on the marginal and poor samples reflect an expected collagen I profile and allow these samples to be recovered for single amino acid analyses.

Beyond bulk δ15N: Combining a suite of stable isotopic measures improves the resolution of the food webs mediating contaminant signals across space, time and communities

Top predators are used as indicators of contaminant trends across space and time. However, signals are integrated over complex food webs, and variation in diet may confound such signals. Trophic position, assessed by bulk δ¹⁵N, is widely used to infer the variation in diet relevant to contamination, yet a single variable cannot completely describe complex food webs. Thus, we examined relationships across three aquatic systems varying from a single species to a small food web using bulk values from four isotopes and 21 amino acid-specific values. Because variation in baseline ('source') δ¹⁵N can confound estimates of trophic position , we calculated trophic position from the difference between δ¹⁵N_trophic (δ¹⁵N for amino acids that change with trophic position) and δ¹⁵N_source (δ¹⁵N for amino acids that do not change with trophic position). Across all three systems, variation in δ¹⁵N_source explained over half of the variation in bulk δ¹⁵N, and stable isotope values that reflected the base of the food web (δ¹³C, δ¹⁸O, δ³⁴S) predicted contaminants as well or better than δ¹⁵N-which was supported by a meta-analysis of other studies. In ospreys feeding in lakes, variation in δ¹⁵N_source across space created a spurious relationship between ΣDDT and apparent trophic position, and masked a relationship between ΣPCB and trophic position. In a seabird guild, changes in diet over time obscured temporal variation in contaminants over five decades. In Arctic fish and invertebrates, more accurate trophic magnification factors were calculated using δ¹⁵N_{trophic-source}. Thus, (1) using δ¹⁵N_{trophic-source}, instead of bulk δ¹⁵N, avoided incorrect conclusions and improved accuracy of trophic magnification factors necessary to assess risk to top predators; and (2) diet assessed with multiple spatial isotopes, rather than δ¹⁵N alone, was essential to understand patterns in contaminants across space, time and biological communities. Trophic position was most important for lipophilic 'legacy' contaminants (ΣDDT, ΣPCB) and habitat was most important for other contaminants (ΣPBDE, ΣPFAS, mercury). We argue that the use of amino acid-specific analysis of δ¹⁵N alongside 'non-trophic' isotopes should be a core feature of any study that examines the influence of trophic position on chemical pollution, as required for a chemical to be added to international conventions such as the Stockholm Convention.

Methylmercury biomagnification in aquatic food webs of Poyang Lake, China: Insights from amino acid signatures

As the dominant mercury species in fish, methylmercury (MeHg) biomagnifies during its trophic transfer through aquatic food webs. MeHg is known to bind to cysteine, forming the complex of MeHg-cysteine. However, relationship between MeHg and cysteine in large-scale food webs has not been explored and contrasted with MeHg biomagnification models. Here, we quantified the compound-specific nitrogen isotopic analysis of amino acids (CSIA-AA), MeHg, and amino acid composition in aquatic organisms of Poyang Lake, the largest freshwater lake in China. The trophic positions (TP_AA) of organisms ranged from 1.0 ± 0.1-3.7 ± 0.2 based on CSIA-AA approach. The trophic magnification factor (TMF) of MeHg, derived from the regression slope of Log-transformed MeHg in organisms upon their TP_AA for the entire food web was 9.5 ± 0.5. Significantly positive regression between MeHg and cysteine (R² = 0.64, p < 0.01) was documented, suggesting MeHg-cysteine complex may potentially play a critical role in the bioaccumulation of MeHg. Furthermore, TMFs of MeHg calculated with and without cysteine normalization compared well (7.7-8.7) when excluding primary producers. Our results implied that MeHg may biomagnify as the complex of MeHg-cysteine and contribute to our understanding of MeHg trophic transfer at the molecular level.

Discovery of a colossal slickhead (Alepocephaliformes: Alepocephalidae): an active-swimming top predator in the deep waters of Suruga Bay, Japan

A novel species of the family Alepocephalidae (slickheads), Narcetes shonanmaruae, is described based on four specimens collected at depths greater than 2171 m in Suruga Bay, Japan. Compared to other alepocephalids, this species is colossal (reaching ca. 140 cm in total length and 25 kg in body weight) and possesses a unique combination of morphological characters comprising anal fin entirely behind the dorsal fin, multiserial teeth on jaws, more scale rows than congeners, precaudal vertebrae less than 30, seven branchiostegal rays, two epurals, and head smaller than those of relatives. Mitogenomic analyses also support the novelty of this large deep-sea slickhead. Although most slickheads are benthopelagic or mesopelagic feeders of gelatinous zooplankton, behavioural observations and dietary analyses indicate that the new species is piscivorous. In addition, a stable nitrogen isotope analysis of specific amino acids showed that N. shonanmaruae occupies one of the highest trophic positions reported from marine environments to date. Video footage recorded using a baited camera deployed at a depth of 2572 m in Suruga Bay revealed the active swimming behaviour of this slickhead. The scavenging ability and broad gape of N. shonanmaruae might be correlated with its colossal body size and relatively high trophic position.

Fluid-preserved fishes are one solution for assessing historical change in fish trophic level

There are few resources available for assessing historical change in fish trophic dynamics, but specimens held in natural history collections could serve as this resource. In contemporary trophic ecology studies, trophic and source information can be obtained from compound-specific stable isotope analysis of amino acids of nitrogen (CSIA-AA-N).We subjected whole Sebastes ruberrimus and Clupea pallasii to formalin fixation and 70% ethanol preservation. We extracted tissue samples from each fish pre-fixation, after each chemical change, and then in doubling time for 32-64 days once placed in the final preservative. All samples were subjected to CSIA-AA-N, and their glutamic acid and phenylalanine profiles and associated trophic position were examined for differences over time by species.Glutamic acid and phenylalanine values were inconsistent in direction and magnitude, particularly during formalin fixation, but stabilized similarly (in 70% ethanol) among conspecifics. In some cases, the amino acid values of our final samples were significantly different than our initial pre-preservation samples. Nonetheless, significant differences in glutamic acid, phenylalanine, and estimated trophic position were not detected among samples that were in 70% ethanol for >24 hr.Our results suggest that the relative trophic position of fluid-preserved specimens can be estimated using CSIA-AA-N, and CSIA-AA-N estimates for fluid-preserved specimens should only be reported as relative differences. Timelines of trophic position change can be developed by comparing specimens collected at different points in time, revealing trophic information of the past and cryptic ecosystem responses.

Nitrogen isotope composition of amino acids reveals trophic partitioning in two sympatric amphipods

According to ecological theory, two species cannot occupy the same niche. Using nitrogen isotope analyses (δ¹⁵N) of amino acids, we tested the extent to which two sympatric deposit‐feeding amphipods, Monoporeia affinis and Pontoporeia femorata, partition their trophic resources. We found that trophic position (TP) and resynthesis index (∑V; a proxy for degradation status of ingested material prior to assimilation by the consumer) differ between species. The surface‐feeding M. affinis had higher TP and intermediate ∑V, both pointing to a large contribution of metazoans in its diet. P. femorata, which feeds in the subsurface layers, had lower TP and a bimodal distribution of the ∑V values, supporting previous experimental evidence of a larger feeding niche. We also evaluated whether TP and ∑V values have consequences for amphipod fecundity and embryo viability and found that embryo viability in M. affinis was negatively linked to TP. Our results indicate that the amino acid‐δ¹⁵N data paired with information about reproductive status are useful for detecting differences in the trophic ecology of sympatric amphipods.

Forest conversion to oil palm compresses food chain length in tropical streams

In Southeast Asia, biodiversity-rich forests are being extensively logged and converted to oil palm monocultures. Although the impacts of these changes on biodiversity are largely well documented, we know addition to samples we collected in 201 little about how these large-scale impacts affect freshwater trophic ecology. We used stable isotope analyses (SIA) to determine the impacts of land-use changes on the relative contribution of allochthonous and autochthonous basal resources in 19 stream food webs. We also applied compound-specific SIA and bulk-SIA to determine the trophic position of fish apex predators and meso-predators (invertivores and omnivores). There was no difference in the contribution of autochthonous resources in either consumer group (70-82%) among streams with different land-use type. There was no change in trophic position for meso-predators, but trophic position decreased significantly for apex predators in oil palm plantation streams compared to forest streams. This change in maximum food chain length was due to turnover in identity of the apex predator among land-use types. Disruption of aquatic trophic ecology, through reduction in food chain length and shift in basal resources, may cause significant changes in biodiversity as well as ecosystem functions and services. Understanding this change can help develop more focused priorities for mediating the negative impacts of human activities on freshwater ecosystems.

How isotopic signatures relate to meat consumption in wild chimpanzees: A critical reference study from Taï National Park, Côte d'Ivoire

The roots of human hunting and meat eating lie deep in our evolutionary past shared with chimpanzees (Pan troglodytes). From the few habituated wild populations, we know that there is considerable variation in the extent to which chimpanzees consume meat. Expanding our knowledge of meat eating frequencies to more, yet unhabituated, populations requires noninvasive, indirect quantitative techniques. We here evaluate the use of stable isotopes to reconstruct meat-eating behavior in wild chimpanzees. We present hair isotope data (n = 260) of two western chimpanzee (P. troglodytes verus) groups from Taï forest (Côte d'Ivoire) and relate them to directly observed amounts of meat consumed, sex/female reproductive state, and group, while controlling for differences between individuals, seasons, and observation efforts. Succeeding seven months of hunting observations, we collected hair of 25 individuals for sequential analysis of δ¹⁵N and δ¹³C. Hunting success in the 7-month study period varied between the groups, with 25 successful hunts in the East group and only 8 in the North group. However, our models only found a direct relationship between amounts of meat consumed and variation within individual hair δ¹⁵N values in the East group, but not in the North group and not when comparing between individuals or groups. Although on average East group individuals consumed more than double the amount of meat than North group individuals, their δ¹⁵N values were significantly lower, suggesting that differences in microhabitat are substantial between group territories. The effect of sex/female reproductive state was significant in δ¹⁵N and δ¹³C, suggesting it related to access to food or feeding preferences. We conclude that several factors additional to diet are influencing and thus obscuring the isotope ratios in wild chimpanzee hair, particularly when comparing between sexes and social groups.

Trophic response to ecological conditions of habitats: Evidence from trophic variability of freshwater fish

To adapt to ecological and environmental conditions, species can change their ecological niche (e.g., interactions among species) and function (e.g., prey-predation, diet competition, and habitat segregation) at the species and guild levels. Stable isotope analysis of bulk carbon and nitrogen of organisms has conventionally been used to evaluate such adaptabilities in the scenopoetic and bionomic views as the isotopic niche width.Compound-specific stable isotope analysis (CSIA) of nitrogen within amino acids provides trophic information without any disruption of scenopoetic views in the isotope ratios, unlike conventional bulk isotope analysis provides both information and therefore frequently hinders its usefulness for trophic information.We performed CSIA of amino acids to understand the trophic variability of the pike gudgeon Pseudogobio esocinus and largemouth bass Micropterus salmoides as representative specialist and generalist fish species, respectively, from 16 ecologically variable habitats in the four major rivers of Korea.There was little variation (1σ) in the trophic position (TP) among habitats for P. esocinus (± 0.2); however, there was considerably large variation for M. salmoides (± 0.6). The TP of M. salmoides was negatively correlated with the benthic invertebrate indices of the habitats, whereas the TP of P. esocinus showed no significant correlation with any indices. Thus, these two representative fish species have different trophic responses to ecological conditions, which is related to known differences in the trophic niche between specialists (i.e., small niche width) and generalists (i.e., large niche width).Over the past four decades, the conventional bulk isotope analysis has not been capable of deconvoluting "scenopoetic" and "bionomic" information. However, in the present study, we demonstrated that the CSIA of amino acids could isolate trophic niches from the traditional ecological niche composed of trophic and habitat information and evaluated how biological and ecological indices influence the trophic response of specialists and generalists.

Reductions in the dietary niche of southern sea otters (Enhydra lutris nereis) from the Holocene to the Anthropocene

The sea otter (Enhydra lutris) is a marine mammal hunted to near extinction during the 1800s. Despite their well-known modern importance as a keystone species, we know little about historical sea otter ecology. Here, we characterize the ecological niche of ancient southern sea otters (E. lutris nereis) using δ13C analysis and δ15N analysis of bones recovered from archaeological sites spanning ~7,000 to 350 years before present (N = 112 individuals) at five regions along the coast of California. These data are compared with previously published data on modern animals (N = 165) and potential modern prey items. In addition, we analyze the δ15N of individual amino acids for 23 individuals to test for differences in sea otter trophic ecology through time. After correcting for tissue-specific and temporal isotopic effects, we employ nonparametric statistics and Bayesian niche models to quantify differences among ancient and modern animals. We find ancient otters occupied a larger isotopic niche than nearly all modern localities; likely reflecting broader habitat and prey use in prefur trade populations. In addition, ancient sea otters at the most southerly sites occupied an isotopic niche that was more than twice as large as ancient otters from northerly regions. This likely reflects greater invertebrate prey diversity in southern California relative to northern California. Thus, we suggest the potential dietary niche of sea otters in southern California could be larger than in central and northern California. At two sites, Año Nuevo and Monterey Bay, ancient otters had significantly higher δ15N values than modern populations. Amino acid δ15N data indicated this resulted from shifting baseline isotope values, rather than a change in sea otter trophic ecology. Our results help in better understanding the contemporary ecological role of sea otters and exemplify the strength of combing zooarchaeological and biological information to provide baseline data for conservation efforts.

Methylmercury exposure in wildlife: A review of the ecological and physiological processes affecting contaminant concentrations and their interpretation

Exposure to methylmercury (MeHg) can result in detrimental health effects in wildlife. With advances in ecological indicators and analytical techniques for measurement of MeHg in a variety of tissues, numerous processes have been identified that can influence MeHg concentrations in wildlife. This review presents a synthesis of theoretical principals and applied information for measuring MeHg exposure and interpreting MeHg concentrations in wildlife. Mercury concentrations in wildlife are the net result of ecological processes influencing dietary exposure combined with physiological processes that regulate assimilation, transformation, and elimination. Therefore, consideration of both physiological and ecological processes should be integrated when formulating biomonitoring strategies. Ecological indicators, particularly stable isotopes of carbon, nitrogen, and sulfur, compound-specific stable isotopes, and fatty acids, can be effective tools to evaluate dietary MeHg exposure. Animal species differ in their physiological capacity for MeHg elimination, and animal tissues can be inert or physiologically active, act as sites of storage, transformation, or excretion of MeHg, and vary in the timing of MeHg exposure they represent. Biological influences such as age, sex, maternal transfer, and growth or fasting are also relevant for interpretation of tissue MeHg concentrations. Wildlife tissues that represent current or near-term bioaccumulation and in which MeHg is the predominant mercury species (such as blood and eggs) are most effective for biomonitoring ecosystems and understanding landscape drivers of MeHg exposure. Further research is suggested to critically evaluate the use of keratinized external tissues to measure MeHg bioaccumulation, particularly for less-well studied wildlife such as reptiles and terrestrial mammals. Suggested methods are provided to effectively use wildlife for quantifying patterns and drivers of MeHg bioaccumulation over time and space, as well as for assessing the potential risk and toxicological effects of MeHg on wildlife.

Amino acid δ15N underestimation of cetacean trophic positions highlights limited understanding of isotopic fractionation in higher marine consumers

Compound-specific stable isotope analysis (CSIA) of amino acids (AAs) has been rapidly incorporated in ecological studies to resolve consumer trophic position (TP). Differential 15N fractionation of "trophic" AAs, which undergo trophic 15N enrichment, and "source" AAs, which undergo minimal trophic 15N enrichment and serve as a proxy for primary producer δ15N values, allows for internal calibration of TP. Recent studies, however, have shown the difference between source and trophic AA δ15N values in higher marine consumers is less than predicted from empirical studies of invertebrates and fish. To evaluate CSIA-AA for estimating TP of cetaceans, we compared source and trophic AA δ15N values of multiple tissues (skin, baleen, and dentine collagen) from five species representing a range of TPs: bowhead whales, beluga whales, short-beaked common dolphins, sperm whales, and fish-eating (FE) and marine mammal-eating (MME) killer whale ecotypes. TP estimates (TPCSIA) using several empirically derived equations and trophic discrimination factors (TDFs) were 1-2.5 trophic steps lower than stomach content-derived estimates (TPSC) for all species. Although TPCSIA estimates using dual TDF equations were in better agreement with TPSC estimates, our data do not support the application of universal or currently available dual TDFs to estimate cetacean TPs. Discrepancies were not simply due to inaccurate TDFs, however, because the difference between consumer glutamic acid/glutamine (Glx) and phenylalanine (Phe) δ15N values (δ15NGlx-Phe) did not follow expected TP order. In contrast to pioneering studies on invertebrates and fish, our data suggest trophic 15N enrichment of Phe is not negligible and should be examined among the potential mechanisms driving "compressed" and variable δ15NGlx-Phe values at high TPs. We emphasize the need for controlled diet studies to understand mechanisms driving AA-specific isotopic fractionation before widespread application of CSIA-AA in ecological studies of cetaceans and other marine consumers.

Isotopic and genetic methods reveal the role of the gut microbiome in mammalian host essential amino acid metabolism

Intestinal microbiota perform many functions for their host, but among the most important is their role in metabolism, especially the conversion of recalcitrant biomass that the host is unable to digest into bioavailable compounds. Most studies have focused on the assistance gut microbiota provide in the metabolism of carbohydrates, however, their role in host amino acid metabolism is poorly understood. We conducted an experiment on Mus musculus using 16S rRNA gene sequencing and carbon isotope analysis of essential amino acids (AA_ESS) to quantify the community composition of gut microbiota and the contribution of carbohydrate carbon used by the gut microbiome to synthesize AA_ESS that are assimilated by mice to build skeletal muscle tissue. The relative abundances of Firmicutes and Bacteroidetes inversely varied as a function of dietary macromolecular content, with Firmicutes dominating when mice were fed low-protein diets that contained the highest proportions of simple carbohydrates (sucrose). Mixing models estimated that the microbial contribution of AA_ESS to mouse muscle varied from less than 5% (threonine, lysine, and phenylalanine) to approximately 60% (valine) across diet treatments, with the Firmicute-dominated microbiome associated with the greatest contribution. Our results show that intestinal microbes can provide a significant source of the AA_ESS their host uses to synthesize structural tissues. The role that gut microbiota play in the amino acid metabolism of animals that consume protein-deficient diets is likely a significant but under-recognized aspect of foraging ecology and physiology.

Variability of trophic magnification factors as an effect of estimated trophic position: Application of compound-specific nitrogen isotope analysis of amino acids

The trophic magnification of persistent organic pollutants (POPs), which is the relationship between POP concentration and the trophic position (TPs) of an organism, is considered an important factor for prioritizing chemicals of concern in the environment. Organismal TPs are typically based on nitrogen isotope ratios of bulk tissue (δ¹⁵N_bulk). In this study, nitrogen isotope ratios of amino acids (δ¹⁵N_AAs), a more precise approach for TP estimation (TP_AAs), was applied and compared with estimations of TP based on δ¹⁵N_bulk (TP_bulk) in marine organisms living in Masan Bay, South Korea. Compound-specific isotope analysis of the amino acids (CSIA-AAs) in fish samples allows us to calculate robust TPs by correcting the variation in baseline isotope values with use of the δ¹⁵N_bulk technique. In a benthic food chain, this approach reveals more significant magnification trends for POPs [polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and organochlorine pesticides (OCPs)] than those revealed by analysis of the relationship between TP_bulk and POPs. The trophic magnification factors (TMF) associated with TP_AAs were significant for some POPs, especially pp'-DDD and chlordane. The results presented in this study suggest that TP calculations based on δ¹⁵N_AAs are an effective tool for characterizing trophic magnification trends related to the fates of various pollutants.

Elucidating stygofaunal trophic web interactions via isotopic ecology

Subterranean ecosystems host highly adapted aquatic invertebrate biota which play a key role in sustaining groundwater ecological functioning and hydrological dynamics. However, functional biodiversity studies in groundwater environments, the main source of unfrozen freshwater on Earth, are scarce, probably due to the cryptic nature of the systems. To address this, we investigate groundwater trophic ecology via stable isotope analysis, employing δ¹³C and δ¹⁵N in bulk tissues, and amino acids. Specimens were collected from a shallow calcrete aquifer in the arid Yilgarn region of Western Australia: a well-known hot-spot for stygofaunal biodiversity. Sampling campaigns were carried out during dry (low rainfall: LR) and the wet (high rainfall: HR) periods. δ¹³C values indicate that most of the stygofauna shifted towards more ¹³C-depleted carbon sources under HR, suggesting a preference for fresher organic matter. Conversion of δ¹⁵N values in glutamic acid and phenylalanine to a trophic index showed broadly stable trophic levels with organisms clustering as low-level secondary consumers. However, mixing models indicate that HR conditions trigger changes in dietary preferences, with increasing predation of amphipods by beetle larvae. Overall, stygofauna showed a tendency towards opportunistic and omnivorous habits—typical of an ecologically tolerant community—shaped by bottom-up controls linked with changes in carbon flows. This study provides baseline biochemical and ecological data for stygofaunal trophic interactions in calcretes. Further studies on the carbon inputs and taxa-specific physiology will help refine the interpretation of the energy flows shaping biodiversity in groundwaters. This will aid understanding of groundwater ecosystem functioning and allow modelling of the impact of future climate change factors such as aridification.

Metabolism and foraging strategies of mid-latitude mesozooplankton during cyanobacterial blooms as revealed by fatty acids, amino acids, and their stable carbon isotopes

Increasing sea surface temperatures (SST) and blooms of lipid-poor, filamentous cyanobacteria can change mesozooplankton metabolism and foraging strategies in marine systems. Lipid shortage and imbalanced diet may challenge the build-up of energy pools of lipids and proteins, and access to essential fatty acids (FAs) and amino acids (AAs) by copepods. The impact of cyanobacterial blooms on individual energy pools was assessed for key species temperate Temora longicornis and boreal Pseudo-/Paracalanus spp. that dominated field mesozooplankton communities isolated by seasonal stratification in the central Baltic Sea during the hot and the cold summer. We looked at (a) total lipid and protein levels, (b) FA trophic markers and AA composition, and (c) compound-specific stable carbon isotopes (δ13C) in bulk mesozooplankton and in a subset of parameters in particulate organic matter. Despite lipid-poor cyanobacterial blooms, the key species were largely able to cover both energy pools, yet a tendency of lipid reduction was observed in surface animals. Omni- and carnivory feeding modes, FA trophic makers, and δ13C patterns in essential compounds emphasized that cyanobacterial FAs and AAs have been incorporated into mesozooplankton mainly via feeding on mixo- and heterotrophic (dino-) flagellates and detrital complexes during summer. Foraging for essential highly unsaturated FAs from (dino-) flagellates may have caused night migration of Pseudo-/Paracalanus spp. from the deep subhalocline waters into the upper waters. Only in the hot summer (SST>19.0°C) was T. longicornis submerged in the colder subthermocline water (~4°C). Thus, the continuous warming trend and simultaneous feeding can eventually lead to competition on the preferred diet by key copepod species below the thermocline in stratified systems. A comparison of δ13C patterns of essential AAs in surface mesozooplankton across sub-basins of low and high cyanobacterial biomasses revealed the potential of δ13C-AA isoscapes for studies of commercial fish feeding trails across the Baltic Sea food webs.

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure

Changes in the complexity of planktonic food webs may be expected in future aquatic systems due to increases in sea surface temperature and an enhanced stratification of the water column. Under these conditions, the growth of unpalatable, filamentous, N₂ -fixing cyanobacterial blooms, and their effect on planktonic food webs will become increasingly important. The planktonic food web structure in aquatic ecosystems at times of filamentous cyanobacterial blooms is currently unresolved, with discordant lines of evidence suggesting that herbivores dominate the mesozooplankton or that mesozooplankton organisms are mainly carnivorous. Here, we use a set of proxies derived from amino acid nitrogen stable isotopes from two mesozooplankton size fractions to identify changes in the nitrogen source and the planktonic food web structure across different microplankton communities. A transition from herbivory to carnivory in mesozooplankton between more eutrophic, near-coastal sites and more oligotrophic, offshore sites was accompanied by an increasing diversity of microplankton communities with aging filamentous cyanobacterial blooms. Our analyses of 124 biotic and abiotic variables using multivariate statistics confirmed salinity as a major driver for the biomass distribution of non-N₂ -fixing microplankton species such as dinoflagellates. However, we provide strong evidence that stratification, N₂ fixation, and the stage of the cyanobacterial blooms regulated much of the microplankton diversity and the mean trophic position and size of the metabolic nitrogen pool in mesozooplankton. Our empirical, macroscale data set consistently unifies contrasting results of the dominant feeding mode in mesozooplankton during blooms of unpalatable, filamentous, N₂ -fixing cyanobacteria by identifying the at times important role of heterotrophic microbial food webs. Thus, carnivory, rather than herbivory, dominates in mesozooplankton during aging and decaying cyanobacterial blooms with hitherto uncharacterized consequences for the biogeochemical functions of mesozooplankton.

Exceptionally high δ15N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores

Identifying past hominin diets is a key to understanding adaptation and biological evolution. Bone collagen isotope studies have added much to the discussion of Neandertal subsistence strategies, providing direct measures of diet. Neandertals consistently show very elevated nitrogen isotope values. These values have been seen as the signature of a top-level carnivore diet, but this interpretation was recently challenged by a number of additional theories. We here apply compound-specific isotope analysis of carbon and nitrogen in bone collagen single amino acids of two Neandertals. These Neandertals had the highest nitrogen isotope ratios of bulk collagen measured so far, and our study confirms that these values can be most parsimoniously explained by a carnivorous diet.

Isotope and archeological analyses of Paleolithic food webs have suggested that Neandertal subsistence relied mainly on the consumption of large herbivores. This conclusion was primarily based on elevated nitrogen isotope ratios in Neandertal bone collagen and has been significantly debated. This discussion relies on the observation that similar high nitrogen isotopes values could also be the result of the consumption of mammoths, young animals, putrid meat, cooked food, freshwater fish, carnivores, or mushrooms. Recently, compound-specific C and N isotope analyses of bone collagen amino acids have been demonstrated to add significantly more information about trophic levels and aquatic food consumption. We undertook single amino acid C and N isotope analysis on two Neandertals, which were characterized by exceptionally high N isotope ratios in their bulk bone or tooth collagen. We report here both C and N isotope ratios on single amino acids of collagen samples for these two Neandertals and associated fauna. The samples come from two sites dating to the Middle to Upper Paleolithic transition period (Les Cottés and Grotte du Renne, France). Our results reinforce the interpretation of Neandertal dietary adaptations as successful top-level carnivores, even after the arrival of modern humans in Europe. They also demonstrate that high δ¹⁵N values of bone collagen can solely be explained by mammal meat consumption, as supported by archeological and zooarcheological evidence, without necessarily invoking explanations including the processing of food (cooking, fermenting), the consumption of mammoths or young mammals, or additional (freshwater fish, mushrooms) dietary protein sources.

Amino acid 15 N analysis reveals change in the importance of freshwater resources between the hunter-gatherer and farmer in the Neolithic upper Tigris

OBJECTIVE

The inhabitants of several sites in the Upper Tigris Valley, such as Hakemi Use, domesticated animals and cereals during the Pottery Neolithic period, while the inhabitants in this valley were hunter-gatherers in the Pre-Pottery Neolithic period, consuming freshwater and terrestrial food resources. However, there is considerable uncertainty surrounding whether or not changes in dietary food composition accompanied the shift in food production away from foraging. In order to reveal the impact of the development of agriculture on the human diet over the Pre-Pottery and Pottery Neolithic periods in this region, we analyzed the isotopic compositions of amino acids from the farmers at the Hakemi Use Pottery Neolithic site, and compared them with those from the Pre-Pottery hunter-gatherers in the close region.

MATERIALS AND METHODS

Herein, we report the nitrogen isotopic compositions of amino acids, as well as both carbon and nitrogen isotopic compositions of bulk collagen, from human and faunal remains collected from Hakemi Use.

RESULTS

Whereas freshwater resources were consumed by hunter-gatherers in this region during the Pre-Pottery period, the δ¹⁵ N values of glutamic acid (δ¹⁵ N_Glu ) and phenylalanine (δ¹⁵ N_Phe ) suggest that freshwater food resources were rarely consumed by inhabitants following the development of agriculture.

DISCUSSION

Despite living in similar settings by the Tigris as its inhabitants during the Pre-Pottery period, the farmers of the Pottery Neolithic period depended less on freshwater resources for their diets relative to the hunter-gatherers of the Pre-Pottery Neolithic period.

A Guide to Using Compound-Specific Stable Isotope Analysis to Study the Fates of Molecules in Organisms and Ecosystems

The measurement of stable isotopes in ‘bulk’ animal and plant tissues (e.g., muscle or leaf) has become an important tool for studies of functional diversity from organismal to continental scales. In consumers, isotope values reflect their diet, trophic position, physiological state, and geographic location. However, interpretation of bulk tissue isotope values can be confounded by variation in primary producer baseline values and by overlapping values among potential food items. To resolve these issues, biologists increasingly use compound-specific isotope analysis (CSIA), in which the isotope values of monomers that constitute a macromolecule (e.g., amino acids in protein) are measured. In this review, we provide the theoretical underpinnings for CSIA, summarize its methodology and recent applications, and identify future research directions. The key principle is that some monomers are reliably routed directly from the diet into animal tissue, whereas others are biochemically transformed during assimilation. As a result, CSIA of consumer tissue simultaneously provides information about an animal’s nutrient sources (e.g., food items or contributions from gut microbes) and its physiology (e.g., nitrogen excretion mode). In combination, these data clarify many of the confounding issues in bulk analysis and enable novel precision for tracing nutrient and energy flow within and among organisms and ecosystems.