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

Abstract

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.

Trophic plasticity in a common reef‐building coral: Insights from δ13C analysis of essential amino acids

“…Therefore, it is possible that carbon sharing does not strongly affect δ 13 C values of AA ESS synthesized by the endosymbionts in P. meandrina . The same may not be true for AA NESS as these are typically subjected to larger isotopic fractionations during de novo synthesis by basal sources or consumers themselves (Whiteman et al, ), but this has yet to be investigated within a mutualistic symbiosis. We also do not know the exact time period reflected in our samples, as turnover rates for AA ESS have not been established for mixotrophic corals.…”

“…Most animals cannot synthesize AA ESS de novo and must acquire them directly from diet, which results in little to no carbon isotopic fractionation across trophic levels (Hare, Fogel, Stafford, Mitchell, & Hoering, ; Jim, Jones, Ambrose, & Evershed, ; McMahon, Fogel, Elsdon, & Thorrold, ). Thus, AA ESS δ 13 C analysis can trace the relative contribution of basal sources of production to consumers at different trophic levels (Howland et al, ; Whiteman, Elliott Smith, Besser, & Newsome, ). Perhaps most importantly, taxa that can synthesize AA ESS de novo can use different biochemical pathways to do so, resulting in unique patterns among AA ESS δ 13 C values, or ‘fingerprints’ sensu Larsen, Taylor, Leigh, and O'Brien () that are characteristic of each taxon (e.g.…”

Quantifying terrestrial carbon in freshwater food webs using amino acid isotope analysis: Case study with an endemic cavefish

“…Vertical dashed lines represent mean β 3 values estimated from Bayesian logistic regression of observed data leucine-normalized to the mean (δ 13 C fingerprints), are generalizable tracers of allochthonous carbon in aquatic food webs across trophic levels. This addresses one of the major gaps in our understanding of CSIA (Whiteman, Elliot Smith, Besser, & Newsome, 2019), at least when used to answer broad ecological questions.…”

Compound‐specific isotope analysis of amino acids as a new tool to uncover trophic chains in soil food webs

“…However, in the latter studies, 13 C offsets among multiple eAAs between consumers and their food resources varied among different consumer–resource relationships, indicating that there is a need for controlled feeding experiments on a wider range of taxa, specifically testing persistence of eAA fingerprints from dietary protein into consumer tissue (Whiteman et al. ). In particular, diet‐to‐consumer 13 C offsets in eAAs of important soil animal taxa such as arachnids, including spiders and mites with differing types of excretion and feeding mode, have not been tested yet.…”

“…Due to cryptic lifestyles and variable microbial contributions to the diet, fingerprinting can be most useful for soil-living species; it has been used already to differentiate food sources of earthworms and enchytraeids (Larsen et al 2016a, Potapov et al 2019a) and to uncover eAA supplementation from gut microbes to consumers (Ayayee et al 2016, Larsen et al 2016b). However, in the latter studies, 13 C offsets among multiple eAAs between consumers and their food resources varied among different consumer-resource relationships, indicating that there is a need for controlled feeding experiments on a wider range of taxa, specifically testing persistence of eAA fingerprints from dietary protein into consumer tissue (Whiteman et al 2019). In particular, diet-to-consumer 13 C offsets in eAAs of important soil animal taxa such as arachnids, including spiders and mites with differing types of excretion and feeding mode, have not been tested yet.…”