Hydrogen isotopes in individual amino acids reflect differentiated pools of hydrogen from food and water in Escherichia coli

Biosynthetic and catabolic pathways control amino acid δ2H values in aerobic heterotrophs

The hydrogen isotope ratios (δ2HAA values) of amino acids in all organisms are substantially fractionated relative to growth water. In addition, they exhibit large variations within microbial biomass, animals, and human tissues, hinting at rich biochemical information encoded in such signals. In lipids, such δ2H variations are thought to primarily reflect NADPH metabolism. Analogous biochemical controls for amino acids remain largely unknown, but must be elucidated to inform the interpretation of these measurements. Here, we measured the δ2H values of amino acids from five aerobic, heterotrophic microbes grown on different carbon substrates, as well as five Escherichia coli mutant organisms with perturbed NADPH metabolisms. We observed similar δ2HAA patterns across all organisms and growth conditions, which-consistent with previous hypotheses-suggests a first-order control by biosynthetic pathways. Moreover, δ2HAA values varied systematically with the catabolic pathways activated for substrate degradation, with variations explainable by the isotopic compositions of important cellular metabolites, including pyruvate and NADPH, during growth on each substrate. As such, amino acid δ2H values may be useful for interrogating organismal physiology and metabolism in the environment, provided we can further elucidate the mechanisms underpinning these signals.

Examination of amino acid hydrogen isotope measurements of scalp hair for region-of-origin studies

RATIONALE

Hydrogen isotope (δ2 H) analysis of keratinaceous bulk tissues has been used in forensic science to reconstruct an individual's travel history or determine their region-of-origin. Here, we use a compound-specific approach to examine patterns of individual amino acid δ2 H values in relation to those of local tap water, bulk scalp hair tissues, and region-of-origin.

METHODS

We measured δ2 H values of amino acids in anonymously collected scalp hair (n = 67) and tap water from 28 locations in the United States. Samples were hydrolyzed into their constituent amino acids, derivatized alongside in-house reference materials, and analyzed in triplicate using a GC-C-IRMS system.

RESULTS

Non-essential amino acid (AANESS ) δ2 H values and their corresponding tap water samples varied systematically across continental regions. Hydrogen isotope values of alanine, glutamic acid, and glycine were significantly correlated with tap water and an estimated 42%-51% of the hydrogen atoms in these AANESS were derived from tap water. We used linear discriminate analysis (LDA) to explore regional patterns in scalp hair bulk tissue and amino acid δ2 H values. For the model that included AANESS data, 87% of the variance was explained by the first linear discriminant axis (LD1), and was driven by bulk hair tissue, alanine, and proline. This model had an overall 72% successful reclassification with samples from the south and northwest regions reclassifying correctly 92% and 78% of the time, respectively. For the model that included AAESS data, LD1 explained 81% of the variation and was driven bulk hair, threonine, valine, phenylalanine, and isoleucine. The overall reclassification rate for the model that included AAESS was 70%.

CONCLUSIONS

Our findings suggest that δ2 H analyses of AANESS and AAESS could help improve geolocation models for human and wildlife forensics by simultaneously providing information about both dietary and tap water inputs of hydrogen to tissue synthesis.

Stable isotope analysis in food web research: Systematic review and a vision for the future for the Baltic Sea macro-region

Food web research provides essential insights into ecosystem functioning, but practical applications in ecosystem-based management are hampered by a current lack of knowledge synthesis. To address this gap, we provide the first systematic review of ecological studies applying stable isotope analysis, a pivotal method in food web research, in the heavily anthropogenically impacted Baltic Sea macro-region. We identified a thriving research field, with 164 publications advancing a broad range of fundamental and applied research topics, but also found structural shortcomings limiting ecosystem-level understanding. We argue that enhanced collaboration and integration, including the systematic submission of Baltic Sea primary datasets to stable isotope databases, would help to overcome many of the current shortcomings, unify the scattered knowledge base, and promote future food web research and science-based resource management. The effort undertaken here demonstrates the value of macro-regional synthesis, in enhancing access to existing data and supporting strategic planning of research agendas.

The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labelling for NMR spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy can be used to determine the structure, dynamics and interactions of proteins. However, protein NMR requires stable isotope labelling for signal detection. The cells used for the production of recombinant proteins must therefore be grown in medium containing isotopically labelled substrates. Stable isotope labelling is well established in Escherichia coli, but bacteria are only suitable for the production of simple proteins without post-translational modifications. More complex proteins require eukaryotic production hosts, but their growth can be impaired by labelled media, thus reducing product yields and increasing costs. To address this limitation, we used media supplemented with isotope-labelled substrates to cultivate the tobacco-derived cell line BY-2, which was then cast into plant cell packs (PCPs) for the transient expression of a labelled version of the model protein GB1. Mass spectrometry confirmed the feasibility of isotope labelling with ¹⁵ N and ² H using this approach. The resulting NMR spectrum featured a signal dispersion comparable to recombinant GB1 produced in E. coli. PCPs therefore offer a rapid and cost-efficient alternative for the production of isotope-labelled proteins for NMR analysis, especially suitable for complex proteins that cannot be produced in microbial systems.

Correlation and Influence of Seasonal Variation of Diet with Gut Microbiota Diversity and Metabolism Profile of Chipmunk

Tamias Sibiricus is the only member of the genus Tamias, a significant and vigorous seed distributor and vital food for their predators. No information is known about the strict diet, gut microbiota structure, and metabolism profile of chipmunks and how they diversify seasonally. The above factors, as well as flexibility toward seasonal shifts, are critical in defining its growth rates, health, survivorship, and population stability. This study explored the diet, gut microbiota composition, and chipmunk metabolism. Additionally, the influence of different seasons was also investigated by using next-generation sequencing. Results revealed that seasons strongly affected a diet: streptophyte accounted for 37% in spring, which was lower than in summer (34.3%) and autumn (31.4%). Further, Ascomycota was observed at 43.8% in spring, which reduced to 36.6% in summer and the lowest (31.3%) in autumn. Whereas, nematodes showed maximum abundance from spring (15.8%) to summer (20.6%) and autumn (24.1%). These results signify the insectivorous nature of the chipmunk in summer and autumn. While herbivorous and fungivorous nature in spring. The DNA analysis revealed that chipmunk mainly feeds on fungi, including Aspergillus and Penicillium genus. Similar to diet composition, the microbiome also exhibited highly significant dissimilarity (p < 0.001, R = 0.235) between spring/autumn and spring/summer seasons. Proteobacteria (35.45%), Firmicutes (26.7%), and Bacteroidetes (23.59%) were shown to be the better discriminators as they contributed the most to causing differences between seasons. Moreover, PICRUSt showed that the assimilation of nutrients were also varied seasonally. The abundance of carbohydrates, lipids, nucleotides, xenobiotics, energy, terpenoids, and polyketides metabolism was higher in spring than in other seasons. Our study illustrates that seasonal reconstruction in the chipmunk diet has a significant role in shaping temporal variations in gut microbial community structure and metabolism profile.

Central Metabolism and Growth Rate Impacts on Hydrogen and Carbon Isotope Fractionation During Amino Acid Synthesis in E. coli

Compound specific stable isotope analysis (CSIA) of amino acids from bacterial biomass is a newly emerging powerful tool for exploring central carbon metabolism pathways and fluxes. By comparing isotopic values and fractionations relative to water and growth substrate, the impact of variable flow path for metabolites through different central metabolic pathways, perturbations of these paths, and their resultant consequences on intracellular pools and resultant biomass may be elucidated. Here, we explore the effects that central carbon metabolism and growth rate can have on stable hydrogen (δ2H) and carbon (δ13C) compound specific isotopic values of amino acids, and whether diagnostic isotopic fingerprints are revealed by these paired analyses. We measured δ2H and δ13C in amino acids in the wild type Escherichia coli (MG1655) across a range of growth rates in chemostat cultures to address the unknown isotopic consequences as metabolic fluxes are shuffled between catabolic and anabolic metabolisms. Additionally, two E. coli knockout mutants, one with deficiency in glycolysis -pgi (LC1888) and another inhibiting the oxidative pentose phosphate pathway (OPPP) -zwf (LC1889), were grown on glucose and used as a comparison against the wild type E. coli (MG1655) to address the isotopic changes of amino acids produced in these perturbed metabolic pathways. Amino acid δ2H values, which collectively vary in composition by more than 400‰, are altered along with δ13C values demonstrating fundamental shifts in central metabolic pathways and/or fluxes. Within our linear discriminant analysis with a simple model organism to examine potential amino acid fingerprinting, our knockout strains and variable growth rate samples plot across a wider array of organism classification than merely within the boundaries of other bacterial data.

Simultaneous, High-Precision Measurements of δ2H and δ13C in Nanomole Quantities of Acetate Using Electrospray Ionization-Quadrupole-Orbitrap Mass Spectrometry

Stable hydrogen isotope compositions (²H/¹H ratios) have been an invaluable tool for studying biogeochemical processes in nature, but the diversity of molecular targets amenable to such analysis is limited. Here, we demonstrate a new technique for measuring δ²H of biomolecules via Orbitrap mass spectrometry (MS) using acetate as a model analyte. Acetate was chosen as a target molecule because its production and consumption are central to microbial carbon cycling, yet the mechanisms behind acetate turnover remain poorly understood. δ²H of acetate could provide a useful constraint on these processes; however, it remains uncharacterized in nature due to analytical challenges. Electrospray ionization (ESI)-Orbitrap MS circumvents these challenges and delivers methyl-specific H-isotope compositions of acetate with nanomole sensitivity, enough to enable analyses of environmental samples. This approach quantifies the methyl-specific δ²H and molecular-average δ¹³C of acetate simultaneously while achieving <3 and <0.5‰ uncertainty, respectively. Using optimized ionization and Orbitrap parameters, this level of precision is obtained within 15 min using only 15 nmol of acetate. As a demonstration of our analytical approach, we cultured three acetogenic bacteria and found a large ²H-fractionation between acetate and water (>310‰ depletion) associated with the Wood-Ljungdahl pathway, while fermentation expressed a muted (∼80‰) fractionation. With its high precision and sensitivity, Orbitrap MS is a promising tool for investigating these signals in nature after offline purification. Furthermore, the ESI-Orbitrap method presented here could be applied to other molecules amenable to ESI, including central metabolites and sugars, greatly expanding the molecular targets used in hydrogen isotope biogeochemistry.

Physiology Drives Reworking of Amino Acid δ2H and δ13C in Butterfly Tissues

Studies of animal movement and migration over large geospatial scales have long relied on natural continental-scale hydrogen isotope (δ2H) gradients in precipitation, yet the physiological processes that govern incorporation of δ2H from precipitation into plant and then herbivore tissues remain poorly understood, especially at the molecular level. Establishing a biochemical framework for the propagation of δ2H through food webs would enable us to resolve more complicated regional-scale animal movements and potentially unlock new applications for δ2H data in animal ecology and eco-physiology. Amino acid δ2H analysis offers a promising new avenue by which to establish this framework. We report bulk tissue δ2H, δ13C, and δ15N data as well as amino acid δ2H and δ13C data from three Pipevine swallowtail (Battus philenor) tissues—caterpillars, butterfly bodies, and wings—as well as their obligate plant source: pipevine leaves (Aristolochia macrophylla). Insects are often dominant herbivores in terrestrial food webs and a major food source for many higher-level consumers, so it is particularly important to understand the mechanisms that influence insect tissue δ2H values. Our data reveal extensive δ2H variation within and among individuals of a relatively simple plant-herbivore system that cannot be explained by temporal or geospatial gradients of precipitation δ2H or dietary differences. Variations in essential amino acid δ2H and δ13C indicate that B. philenor acquire these compounds from an additional source that is isotopically distinct from pipevine leaves, potentially gut microbes. We also found multiple isotopic carryover effects associated with metamorphosis. This study emphasizes the strong influence of physiology on consumer-diet δ2H discrimination in a local population of pipevines and swallowtails and provides a template that can be broadly applied to Lepidoptera—the second most diverse insect order—and other holometabolous insects. Understanding these physiological mechanisms is critical to interpreting the large degree of δ2H variation in consumer tissues often observed at a single collection site, which has implications for using δ2H isoscapes to study animal movement. Further investigation into amino acid δ2H holds promise to elucidate how subsets of amino acids may be best utilized to address specific ecological and physiological questions for which bulk tissue δ2H is insufficient.

Compound-specific stable hydrogen isotope (δ2 H) analyses of fatty acids: A new method and perspectives for trophic and movement ecology

RATIONALE

Compound-specific stable isotope analysis (CSIA) is a powerful tool for a better understanding of trophic transfer of dietary molecules in and across ecosystems. Hydrogen isotope values (δ² H) in consumer tissues have potential to more clearly distinguish dietary sources than ¹³ C or ¹⁵ N values within and among habitats, but have not been used at the fatty acid level for ecological purposes.

METHODS

Here we demonstrate a new online high-capacity gas chromatography-isotope ratio mass spectrometry technique (² H-CSIA) that offers accurate and reproducible determination of δ² H values for a range of fatty acids from organisms of aquatic food webs.

RESULTS

We show that lipid extracts obtained from aquatic sources, such as biofilms, leaves, invertebrates, or fish muscle tissue, have distinctive δ² H values that can be used to assess sources and trophic interactions, as well as dietary allocation and origin of fatty acids within consumer tissue.

CONCLUSIONS

The new ² H-CSIA method can be applied to evaluate sources and trophic dynamics of fatty acids in organisms ranging from food web ecology to migratory connectivity.

Hydrogen isotope assimilation and discrimination in green turtles

Although hydrogen isotopes (δ2H) are commonly used as tracers of animal movement, minimal research has investigated the use of δ2H as a proxy to quantify resource and habitat use. While carbon and nitrogen are ultimately derived from a single source (food), the proportion of hydrogen in consumer tissues originates from two distinct sources: body water and food. Before hydrogen isotopes can be effectively used as a resource and habitat tracer, we need estimates of (net) discrimination factors (Δ2HNet) that account for the physiologically mediated differences in the δ2H values of animal tissues relative to that of the food and water sources they use to synthesize tissues. Here, we estimated Δ2HNet in captive green turtles (Chelonia mydas) by measuring the δ2H values of tissues (epidermis and blood components) and dietary macromolecules collected in two controlled feeding experiments. Tissue δ2H and Δ2HNet values varied systematically among tissues, with epidermis having higher δ2H and Δ2HNet values than blood components, which mirrors patterns between keratinaceous tissues (feathers, hair) and blood in birds and mammals. Serum/plasma of adult female green turtles had significantly lower δ2H values compared with juveniles, likely due to increased lipid mobilization associated with reproduction. This is the first study to quantify Δ2HNet values in a marine ectotherm, and we anticipate that our results will further refine the use of δ2H analysis to better understand animal resource and habitat use in marine ecosystems, especially coastal areas fueled by a combination of marine (e.g. micro/macroalgae and seagrass) and terrestrial (e.g. mangroves) primary production.

Analysis of amino acids, hydroxy acids, and amines in CR chondrites

The abundances, relative distributions, and enantiomeric and isotopic compositions of amines, amino acids, and hydroxy acids in Miller Range (MIL) 090001 and MIL 090657 meteorites were determined. Chiral distributions and isotopic compositions confirmed that most of the compounds detected were indigenous to the meteorites and not the result of terrestrial contamination. Combined with data in the literature, suites of these compounds have now been analyzed in a set of six CR chondrites, spanning aqueous alteration types 2.0-2.8. Amino acid abundances ranged from 17 to 3300 nmol g^-1 across the six CRs; hydroxy acid abundances ranged from 180 to 1800 nmol g^-1; and amine abundances ranged from 40 to 2100 nmol g^-1. For amino acids and amines, the weakly altered chondrites contained the highest abundances, whereas hydroxy acids were most abundant in the more altered CR2.0 chondrite. Because water contents in the meteorites are orders of magnitude greater than soluble organics, synthesis of hydroxy acids, which requires water, may be less affected by aqueous alteration than amines and amino acids that require nitrogen-bearing precursors. Two chiral amino acids that were plausibly extraterrestrial in origin were present with slight enantiomeric excesses: L-isovaline (~10% excess) and D-β-amino-n-butyric acid (~9% excess); further studies are needed to verify that the chiral excess in the latter compound is truly extraterrestrial in origin. The isotopic compositions of compounds reported here did not reveal definitive links between the different compound classes such as common synthetic precursors, but will provide a framework for further future in-depth analyses.

Compound-specific δ2H analysis highlights the relationship between direct assimilation and de novo synthesis of amino acids from food and water in a terrestrial mammalian omnivore

Hydrogen isotope (δ²H) analysis has been routinely used as an ecological tracer for animal movement and migration, yet a biochemical understanding of how animals incorporate this element in the synthesis of tissues is poorly resolved. Here, we apply a new analytical tool, amino acid (AA) δ²H analysis, in a controlled setting to trace the influence of drinking water and dietary macromolecules on the hydrogen in muscle tissue. We varied the δ²H of drinking water and the proportions of dietary protein and carbohydrates with distinct hydrogen and carbon isotope compositions fed to house mice among nine treatments. Our results show that hydrogen in the non-essential (AA_NESS) and essential (AA_ESS) AAs of mouse muscle is not readily exchanged with body water, but rather patterns among these compounds can be described through consideration of the major biochemical pathway(s) used by organisms to synthesize or route them from available sources. Dietary carbohydrates contributed more hydrogen than drinking water to the synthesis of AA_NESS in muscle. While neither drinking water nor dietary carbohydrates directly contributed to muscle AA_ESS, we did find that a minor but measurable proportion (10-30%) of the AA_ESS in muscle was synthesized by the gut microbiome using hydrogen and carbon from dietary carbohydrates. δ²H patterns among individual AAs in mice muscle are similar to those we previously reported for bacteria, which provides additional support that this approach may allow for the simultaneous analysis of different AAs that are more influenced by drinking water (AA_NESS) versus dietary (AA_ESS) sources of hydrogen.

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

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

2H/1H variation in microbial lipids is controlled by NADPH metabolism

The hydrogen-isotopic compositions (2H/1H ratios) of lipids in microbial heterotrophs are known to vary enormously, by at least 40% (400‰) relative. This is particularly surprising, given that most C-bound H in their lipids appear to derive from the growth medium water, rather than from organic substrates, implying that the isotopic fractionation between lipids and water is itself highly variable. Changes in the lipid/water fractionation are also strongly correlated with the type of energy metabolism operating in the host. Because lipids are well preserved in the geologic record, there is thus significant potential for using lipid 2H/1H ratios to decipher the metabolism of uncultured microorganisms in both modern and ancient ecosystems. But despite over a decade of research, the precise mechanisms underlying this isotopic variability remain unclear. Differences in the kinetic isotope effects (KIEs) accompanying NADP+ reduction by dehydrogenases and transhydrogenases have been hypothesized as a plausible mechanism. However, this relationship has been difficult to prove because multiple oxidoreductases affect the NADPH pool simultaneously. Here, we cultured five diverse aerobic heterotrophs, plus five Escherichia coli mutants, and used metabolic flux analysis to show that 2H/1H fractionations are highly correlated with fluxes through NADP+-reducing and NADPH-balancing reactions. Mass-balance calculations indicate that the full range of 2H/1H variability in the investigated organisms can be quantitatively explained by varying fluxes, i.e., with constant KIEs for each involved oxidoreductase across all species. This proves that lipid 2H/1H ratios of heterotrophic microbes are quantitatively related to central metabolism and provides a foundation for interpreting 2H/1H ratios of environmental lipids and sedimentary hydrocarbons.

Stable isotopes of H, C and N in mice bone collagen as a reflection of isotopically controlled food and water intake. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2019;55:129-149. [PMID: 30793970 DOI: 10.1080/10256016.2019.1580279]

²H/¹H ratios in animal biomass reflect isotopic input from food and water. A 10-week controlled laboratory study raised 48 mice divided in two generations (8 mothers Mus musculus and their offspring). The mice were divided into four groups based on the combination of ²H, ¹³C, ¹⁵N-enriched and non-enriched food and water. Glycine, the most common amino acid in bone collagen, carried the ²H, ¹³C, ¹⁵N-isotopic spike in food. ANOVA data analysis indicated that hydrogen in food accounted for ∼81 % of the hydrogen isotope inventory in collagen whereas drinking water hydrogen contributed ∼17 %. Air humidity contributed an unspecified amount. Additionally, we monitored ¹³C and ¹⁵N-enrichment in bone collagen and found strong linear correlations with the ²H-enrichment. The experiments with food and water indicate two biosynthetic pathways, namely (i) de novo creation of non-essential amino acids using hydrogen from water, and (ii) the integration of essential and non-essential amino acids from food. The lower rate of isotope uptake in mothers' collagen relative to their offspring indicates incomplete bone collagen turnover after ten weeks. The variance of hydrogen stable isotope ratios within the same cohort may limit its usefulness as a single sample proxy for archaeological or palaeoenvironmental research.

Derivatization-free method for compound-specific isotope analysis of nonexchangeable hydrogen of 4-bromophenol

RATIONALE

Compound-specific isotope analysis (CSIA) is a valuable tool in environmental chemistry and in other fields of science. Currently, hydrogen CSIA of polar compounds containing exchangeable hydrogen is uncommon. To extend the scope of CSIA applications, we present an alternative method of analysis, bypassing the typical step of derivatization. The method is demonstrated for two environmental contaminants, 4-bromophenol (4BP) and 2,4,6-tribromophenol (TBP).

METHODS

Net isotope ratios obtained by CSIA combine the isotope composition of nonexchangeable, carbon-bound hydrogen and the exchangeable hydroxyl hydrogen. To constrain the isotope composition of the latter, an ethyl acetate solution of 4BP or TBP injected into the IRMS instrument was amended with excess water of known isotope composition. The results were calibrated using bracketing control samples analyzed in sequence with the unknown samples and the known isotope ratios of water present in ethyl acetate solution.

RESULTS

The analytical precision was comparable to the precision for halogenated compounds without exchangeable hydrogen, analyzed using similar instrumentation. The isotope ratios of the bromophenols correlated with the isotope composition of the water in the sample matrix, suggesting that the hydroxyl group of the target compound remained close to the equilibrium with the sample water during the passage through the instrument. Based on this relationship, the signatures of the nonexchangeable hydrogen were obtained using the isotope composition of sample water as the proxy for the isotope composition of the target compound hydroxyl group.

CONCLUSIONS

The developed method could be adopted to analysis of other low molecular weight compounds amenable to gas chromatography without the absolute need for derivatization. Currently, the method can be used for samples from laboratory experiments, with high concentrations of the target compound to provide mechanistic insight into the degradation mechanisms. Further work would be required to optimize the method to low concentration environmental samples.

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.

Compound-Specific Isotope Geochemistry in the Ocean

Compound-specific isotope analysis encompasses a variety of methods for examining the naturally occurring isotope ratios of individual organic molecules. In marine environments, these methods have revealed heterogeneous sources and alteration processes that underlie the more commonly measured isotope ratios of bulk materials, as well as revealing signatures of marine metabolisms that may otherwise be impossible to isolate. Recently, compound-specific isotopic techniques have improved the reconstruction of metazoan diets and revealed a new potential of metazoan biomass as an archive of paleoecological information. Despite six decades of practice and a diversity of applications, the use of compound-specific isotopic techniques remains uncommon in marine studies. This review examines broad theoretical motivations behind compound-specific isotopic approaches, some applications to studies of marine carbon cycling and trophic relationships, and methodological limitations. In coming years, improvements in analytical efficiency and molecular or intramolecular specificity may transform compound-specific isotope analysis into a tool that can be applied more broadly and help to build global oceanographic data sets.

Seasonal patterns in δ2 H values of multiple tissues from Andean birds provide insights into elevational migration

Elevational migration is a widespread phenomenon in tropical avifauna but it is difficult to identify using traditional approaches. Hydrogen isotope (δ² H) values of precipitation decrease with elevation so δ² H analysis of multiple bird tissues with different isotopic incorporation rates may be a reliable method for characterizing seasonal elevational migration. Here we compare δ² H values in metabolically inert (feathers and claws) and metabolically active (whole blood) tissues to examine whether an upslope migration occurs prior to the breeding season in the Yungas Manakin (Chiroxiphia boliviana). We compare results from C. boliviana with data from a known elevational migrant, the Streak-necked Flycatcher (Mionectes striaticollis). Opposite to our expectations, tissue δ² H values increased over time, largely reflecting seasonal patterns in precipitation δ² H rather than elevational effects; linear mixed-effects models with strongest support included ordinal date, tissue type, and elevation. This seasonal increase in precipitation δ² H is a general phenomenon in both tropical and temperate mountain ranges. We use these data to propose a hypothetical framework that predicts different patterns in tissue δ² H values collected in different seasons from residents and elevational migrants. This framework can serve as a reference for future studies that assess elevational migration in birds and other animals.

Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression

Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study, we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644^T, to investigate how these parameters were perturbed by changes in expression of the protein DsrC. DsrC is critical to the final metabolic step in sulfate reduction to sulfide. S and H isotopic fractionation imposed by the wild type was compared to three mutants. Discrimination against ³⁴S in sulfate, as calculated from the residual reactant, did not discernibly differ among all strains. However, a closed-system sulfur isotope distillation model, based on accumulated sulfide, produced inconsistent results in one mutant strain IPFG09. Lipids produced by IPFG09 were also slightly enriched in ²H. These results suggest that DsrC alone does not have a major impact on sulfate-S, though may influence sulfide-S and lipid-H isotopic compositions. While intriguing, a mechanistic explanation requires further study under continuous culture conditions.