Stable Isotope Ecology - A Rough Guide for Fishery Managers
Having reliable, accurate data is of fundamental importance when making good management decisions, and fishery manager’s ability to infer ecological processes from stable isotope data is only as strong as the underlying data. This can be challenging as stable isotope ecology is not comprehensively covered in most ecology undergraduate or graduate programs. Here, we provide this key information in a user-friendly format to guide you towards successfully implementing isotopes in your applied research.
Why are isotopes a useful tool to manage fish and the ecosystems which sustain them?
Fish diet and associated characterisations of food web structure can be derived from many different sources. In freshwater food webs, stomach content has traditionally been the most common approach to classifying fish diet but in the published literature stable isotope analysis is now equally prevalent. Stable isotope approaches have numerous advantages over stomach content or eDNA based analyses:
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Provide a time integrated characterisation of a fish’s diet over weeks and months
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Minimally invasive - scales, fin clips or mucus samples can be used without needing to sacrifice the fish,
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Cost effective due to time integrated values and reduced reliance on rare taxonomic identification skills
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Avoid bias towards hard bodied prey types - isotope ratios reflect what the fish assimilate
What to sample?
Unlike visual assessments of fish diet, stable isotope-based approaches require that the user establishes a thorough isotopic baseline from which to infer the diet of their target species. Stable isotope values alone are rarely sufficient to accurately estimate consumer diet. In isotope-based studies users use the relationship between the consumer and these baselines to infer consumer trophic ecology. Stable isotopes of carbon (δ13C) vary between distinct primary producers but are conserved in trophic relationships meaning that carbon can be used to estimate the primary producers at the base of the food chain which is supporting the consumer. In contrast, nitrogen isotope ratios (δ15N) increase at a fixed rate between predators and their prey allowing users to infer a consumer's trophic position. In combination, this allows users to infer what is fuelling a consumer and what trophic position they are sitting at in the food web. A thorough isotope food web study should include all components of the food web, though primary consumers can be used to infer values of primary producers.
Where to sample?
Adequate sampling of the food web baselines is key to a successfully implemented isotopic study. Users should focus on functional rather than taxonomic diversity, targeting all functional feeding groups within the potential prey community. In a stream or river systems this typically includes shredders which characterize the allochthonous contribution to a food web, grazers which characterise autochthonous production. Collectors and filterers may be used to assess the relative contribution of both trophic pathways to overall in-stream productivity. In lakes, zooplankton or filter feeding bivalves and littoral invertebrates or grazing gastropods can be used can be used to estimate baseline values of the pelagic and littoral food chains respectively. It is also worth noting that many lakes are characterised by strong depth related gradients in the δ13C and δ15N values of benthic invertebrates, so when possible, sampling should include sub littoral and profundal habitats. At a minimum, users should target 3-5 replicate samples of each functional feeding guild at each site before sampling fishes. When baseline sampling is impossible, baseline values may be estimated based on environmental conditions, though it is advisable to ground truth these measurements, especially when assessing a new site.
What tissue to sample?
The stable isotope ratios of a specific tissue reflect the consumer's diet during the period that tissue was grown. As soft tissues turn over at different rates, the period of time reflected by the isotope ratios differ between tissues. In fish, muscle, fins and whole blood typically reflect diet during the preceding 3-6 months whereas liver reflects diet during the preceding 3-4 weeks, and blood plasma reflects the previous 5-7 days. Fish scales are composed of keratin and are therefore biologically inert and don't change once formed. The whole body of invertebrates are routinely analysed, though care must be taken to remove any gastropod shells, as inorganic carbonate has a dramatically different isotope ratio that organic carbon. In most cases, a tissue sample of 1g wet mass will be sufficient, but more is always better!
When to sample?
As different tissues reflect time-integrated values over different time periods, stable isotope based approaches have potential to estimate both annual and interannual food webs of aquatic ecosystems. In most cases, users will sample towards the end of the main growing season, resulting in samples which integrate diet throughout the growing season.
Sample preparation
Collected samples need to be preserved prior to analysis. Samples can be dried (60C for 48 hrs), frozen (-20C) or stored in ethanol (70%) for indeterminate periods. Though preservation will affect tissue stable isotope ratios, these effects are not sufficient to alter ecological interpretations of the data. Care should be taken with lipid stored samples however as ethanol will cause 13C depleted lipid to leech from the sample leading to elevated δ13C values. If samples are stored in lipid, it is advisable to lipid treat all samples prior to analysis to avoid this potential bias.Preserved samples need to be further prepared for analysis by drying, homogenising and weighing a subsample for analysis. These services are provided by most analytical facilities but can also be conducted by users, though it is advised that users consult your analytical lab prior to submitting samples to ensure their sample processing meets the lab's requirements.
Data Analysis
A comprehensive suite of analytical tools have been developed to handle and analyse stable isotope datasets. These have predominantly been developed by academics and consequently operate through the R statistical language. Below we provide a brief description of the most commonly applied packages, though many others are available:​​​
What do my results mean?
Stable isotope-based assessments of consumer diet, niche width and food web structure are powerful tools but must be interpreted in the context of underlying assumptions and uncertainty. For example, estimates of trophic position are not derived based on the consumer's direct diet but rather an estimation of the number of trophic levels between a consumer and the baseline samples. Similarly, estimates of isotope niche reflect the isotopic variability within a population's prey, a trait which is not necessarily correlated with taxonomic diversity of the prey.
Isotopic pitfalls and how to avoid them
New users of stable isotope-based approaches may be overwhelmed by the abundance of information and how best to apply the technique. Recently developed large language models such as ChatGPT, GoogleONE etc, have been trained on academic literature including stable isotope studies and can be a useful resource, though with the usual constraints of these models should be acknowledged and users are advised to consult the primary literature before undertaking a new project. In addition, there are many online or in person courses available and multiple online resources on youtube, Physilia or directly at Atomic Ecology. Isotope researchers are ‘generally’ very nice people and are happy to talk about their science. If you have a question, reach out and get an answer before starting your project with a guess!
Atomic Ecology as your isotopic project partner
Working with Atomic Ecology makes me, Brian Hayden, a partner in your project. Driven by a passion to understand fisheries and the ecological mechanisms which govern them, I have spent my career working across many aspects of foundational and applied research,. With over 20 years’ experience applying stable isotope based techniques to this field I am here to help your research succeed, filling roles as an experienced advisor, data analysist or field technician depending on the needs of each project.
Food web study
A comprehensive food web study will include 50-100 samples encompassing 3-5 replicate samples of baseline invertebrates, and all target fishes within the community. At Atomic Ecology we will be happy to join you in the field, collecting and sorting material and providing training to field staff. We will identify an analytical lab best suited to your project based on location, costs and turn-around time. Once lab data become available, we will conduct all necessary analysis and provide a concise report describing the food web structure and resource pathways supporting your fishery. Costs vary with project requirements, but a full food web analysis will typically cost €4-8,000 + relevant taxes
Population study
Detailed assessments of a specific population are required to truly characterise within species trophic ecology, core niche and variability and to assess size related variation within a population. A population level study will involve sampling of 30 individuals of a given species, in addition to 10-20 baseline samples. Atomic Ecology is available as an experienced advisor or a ‘hands on’ field operative throughout this process. With data in hand, we will design a final report to address your key research questions.Costs vary with project requirements, but assuming €3-5,000 + relevant taxes per species is a good starting point for population level assessments.