Author: Marcel LaFlamme, Open Research Manager, PLOS When authors submit a Lab Protocol to PLOS ONE, they prepare a short manuscript that…
IsoBank – Stable Isotope Research + Open Data
The use of stable isotopes (the non-radioactive form of an element) has become increasingly prevalent in a wide variety of scientific research fields. The fact that many elements have stable isotopes, which exhibit unique properties, allows for their distribution and ratios in natural environments to be measured. These data can be used to shed insight on the history, fate and transport of elements in water, soil and even archeological specimens. Our curated collection of research using stable isotopes highlights the diversity of fields that utilize these invaluable measurements.
To meet the needs of this growing research community, and to facilitate accessibility and data sharing, the US National Science Foundation has funded the IsoBank project – a common repository for stable isotope data.
Here, we chat with some of the IsoBank organizers about the importance of the project, and how they use stable isotopes in their own research.
Jonathan Pauli is an Associate Professor in the Department of Forest and Wildlife Ecology at University of Wisconsin-Madison. His research explores the response of mammal populations and communities to human disturbance, particularly as it relates to developing effective conservation strategies. He works in diverse ecosystems and employs a variety of techniques, from traditional ones like live capture, radiotelemetry and observation to more advanced ones involving molecular markers, stable isotopes and population modeling to answer questions relating to mammalian ecology and conservation.
Gabriel Bowen is a Professor of Geology and Geophysics and member of the Global Change and Sustainability Center at the University of Utah, where he leads the Spatio-temporal Isotope Analytics Lab (SPATIAL) and serves as co-director of the SIRFER stable isotope facility. His research focuses on the use of spatial and temporally resolved geochemical data to study Earth system processes ranging from coupled carbon and water cycle change in geologic history to the movements of modern and near-modern humans. In addition to fundamental research, he has been active in developing cyberinformatics tools and training programs supporting the use of large-scale environmental geochemistry data across a broad range of scientific disciplines, including the waterisotopes.org and IsoMAP.org web sites and the Inter-University Training for Continental-scale Ecology training program.
Brian Hayden is an Assistant Professor in Food Web Ecology at the University of New Brunswick, Canada, where he leads the Stable Isotopes in Nature Laboratory. His research focuses on the trophic responses to environmental change, predominantly in aquatic systems — he considers himself extremely fortunate to collaborate with researchers around the globe addressing these issues.
Seth Newsome is an animal ecology and eco-physiologist whose research blends biochemical, morphometric, and phylogenetic analyses to provide a holistic understanding of the role of energy transport in the assembly and maintenance of biological communities. He is the Associate Director of the University of New Mexico (UNM) Center for Stable Isotopes and an Associate Professor in the UNM Biology Department. Besides science and fixing mass spectrometers, he enjoys mountain biking, rafting, and fly fishing.
Oliver Shipley is an applied ecologist at the University of New Mexico, with training in a suite of laboratory and field techniques. He is broadly interested in food-web dynamics and animal ecophysiology and employs a suite of chemical tracer and biotelemetry approaches to investigate these processes with a strong focus on marine ecosystems. His research can be defined by three interconnected themes 1) defining the drivers and food web implications of ecological niche variation at various levels of biological organization, 2) applying ecophysiological principles to predict the timing of important biological events, 3) investigating the fitness consequences of niche variation for food web and broader ecosystem dynamics.
Research using stable isotopes spans a wide array of fields, from the geosciences to ecology to archeology – has organizing the IsoBank group highlighted the different forms that isotopic research can take? Have there been any challenges in communication with scientists of such varied backgrounds?
BH: This is one of the main challenges we faced when developing IsoBank. Isotopes have huge a diversity of applications and researchers working in environmental, ecological, and archaeological isotope systems have developed metadata relevant to their specific discipline. Our goal was to build a single large database capable to serving all of these disciplines, which meant we needed to somehow combine all of the distinct metadata into a single framework. This can be challenging within a field; for example, most of my research involves freshwater fish but much the information I use to describe a datapoint, (e.g., habitat, organism size, tissue type) may or may not be relevant to ecologists studying birds, insects or plants. Working across disciplines exacerbates things considerably. For example, ‘date’ means very different things to ecologists, archaeologists, and paleoecologists, despite us all using the same techniques. We tried to address this by developing core metadata terms which are common to all disciplines and therefore required in order for a datapont to be uploaded to IsoBank, and discipline specific optional metadata terms which can be selected by the user.
JP: Indeed, one of the greatest assets of IsoBank is also one of its greatest challenges. Because isotopes span so many different disciplines – e.g., environmental, geological, archaeological, biomedical, ecological, physiological – there are a variety of discipline-specific metadata that are needed. To accommodate these different needs, we have convened a number of working group meetings to bring together experts within these disciplines to identify what metadata are necessary, and fold them into a single and operational framework. I’ve been impressed, though, that our discussions with scientists with such varied interests and backgrounds have been able to effectively communicate what is needed. I’d even offer that these discussions with other people, employing isotopes for different questions, has been a highlight of this project for me personally and has expanded my thinking and generated new ideas of application to my own work.
Tell us about how you use stable isotopes in your own research.
BH: I think I am drawn to isotopes because of the diversity of the applications of the techniques, it’s such a useful tool the only limit is our imagination. I am an aquatic ecologist at heart – my research focuses on understanding how aquatic ecosystems, especially food webs, respond to environmental change. Initially I used isotopes to improve our understanding of the trophic ecology of specific species, but over time this has changed to a community level perspective.
GB: Isotopes are incredibly powerful tracers of the flow of matter (including organisms!) through the environment. Many of the applications in my research group leverage this potential in one way or another. We use isotopes in water to understand hydrological connectivity – how rain falling in different seasons or weather systems contributes to water resources or plant water uptake and transpriation. We use isotope values of solutes to better understand biogeochemical cycles – sources of carbon stored in soils or how mineral weathering in different systems contributes to global geochemical cycling. We use isotope values measured in human and animal tissues to map the movement of individuals – migration pathways, sources of potentially poached game, or the childhood residence location of the victims of violent crime.
SN: As an animal ecologist and eco-physiologist, I’m interested in tracing the flow of energy within and among organisms, which is governed by species interactions and food web structure. To do so, I meld isotopic, morphometric, and phylogenetic analyses to provide a holistic understanding of the role of energy transport in the assembly and maintenance of ecological communities. I use lab-based feeding experiments in which the stable isotope composition and concentrations of dietary macromolecules are varied to understand how animals process dietary macromolecules to build and maintain tissues. I use this information to quantify niche breadth from individual to community-levels to better understand the energetic basis of community assembly and structure. Finally, I adopt a broad temporal perspective by comparing species interactions in modern versus ancient ecosystems, providing the full range of behavioral and ecological flexibility important for designing effective management strategies and assessing a species sensitivity to environmental change.
JP: I am a community ecologist and conservation biologist, and am interested in the biotic interplay between organisms that ultimately shape community structure and dynamics, and how we can predict these interactions into the future and within emerging novel environments. To that end, I use isotopes to understand animal foraging and trophic identities and combine these data with fieldwork studying animal behavior, movement and space use as well as species distributions and abundances. After developing a better understanding of contemporary community structure and interactions, I use this information to explore past communities and project what future communities will look like and how they will behave.
You recently organized the IsoEcol workshop to provide researchers in the Ecology community with training on sharing their data through IsoBank. How has IsoBank allowed for better collaboration in the ecological sciences community? Are there any particular themes or questions that have arisen?
OS: We were extremely excited to host the first IsoBank workshop for the broader research community at this years IsoEcol – this was held in an online format through Zoom. The workshop provided participants with a brief history of IsoBank’s development but focused heavily on the metadata structure and data ingest process. Since the workshop we have received many new modern and historical datasets across terrestrial, freshwater and marine systems. As we continue to ingest a growing number of datasets, the collaborative potential of IsoBank becomes increasingly realized. This moves us closer to exciting questions that can be addressed using the big-data model IsoBank will soon support. At the last IsoBank workshop we identified several potential research priorities that can be addressed in the coming years, these include but are by no means limited to 1) the development of novel isoscapes (spatial interpolations of stable isotope data) and 2) broadscale patterns in animal trophic interactions and broader food-web dynamics.
Oliver, for Early Career Researchers, being part of a robust and supportive research community can be instrumental to growth as a scientist and to career success. How has your involvement in the IsoBank project led to opportunities that you may not have otherwise had?
OS: As a postdoctoral research fellow, it has been an extremely rewarding experience serving as the project manager for IsoBank. One of the primary reasons I was excited to work on IsoBank, were the potential collaborative and networking opportunities facilitated by the projects diverse userbase. Since I began working with the IsoBank team, and extended userbase I have formed new collaborations with researchers across the US and Europe. For example, working closely with Drs Seth Newsome (University of New Mexico, USA) and Bailey McMeans (University of Toronto Mississauga, CA) we are using stable isotopes of individual amino acids to understand how energy flow mediates the nutritional condition in lake trout. Further, in collaboration with PhD student Lucien Besnard (University of Western Brittany, France) we are building mercury stable isotope clocks to quantifying the age at which scalloped hammerhead sharks migrate from inshore nurseries to offshore foraging grounds. These exciting opportunities have been possible through working with IsoBanks advisory committee and the repositories diverse userbase.
Gabe, you were one of the first people to use the term “isoscape”, which has since become a hallmark of numerous scientific studies. What is an isoscape, and how do they feature in your research?
GB: Isoscapes are quantitative models representing spatiotemporal isotopic variation in any natural or anthropogenic system…they are isotopic maps. And I think they embody the biggest reason we need IsoBank. Isoscapes are useful because almost any isotopic measurement needs to be interpreted in the context of reference data. We can use isotope values of animal tissues to understand the individual’s diet, but only if we know the isotope values of the foods it might eat. We can use isotope values of groundwater to assess where and when recharge occurred, but only if we know the isotopic compositions of those potential sources. Isoscapes are generated by combining isotopic datasets with statistical or process models to predict the values we would expect for sources at different locations and times, and we can make isoscapes for different substrates. Whether they are used to support the development of isoscapes, or more directly as reference data for a local study, access to the vast wealth of isotopic data that our different communities have produced is a critical limitation for most isotopic studies.
In some environments, stable isotope ratios alone do not provide sufficiently detailed information. What combination of techniques or analytical methods do you use to yield more conclusive results and to elucidate unseen patterns or trends?
BH: As isotope ecologists, we are often drawn to using techniques which have worked well for us in the past, but it’s always important to remember that isotope analysis is just another tool in our kit. In my work, I typically use isotopes to understand trophic interactions. They can fill in a lot of the gaps other methods of diet analysis leave open, but they still just provide one piece of the puzzle. Isotopes are a really nice way of getting a broad idea of what a specific consumer is doing or what sources of primary production are most important to a food web, but for questions which require more detailed answer, such as whether consumers are feeding on specific species of prey, isotopes may be limited. We typically use isotopes in combination with diet analyses, fatty acid analysis or even mercury analysis to get a more complete understanding of the community we are interested in. Sometimes the best insights come when different techniques give contrasting results, that can really help us to understand the complexity of the ecological systems we are studying.
SN: Stable isotope analysis has become a standard tool in animal ecology because it can provide time-integrated measures of diet composition, albeit at a limited taxonomic resolution. As such, a new frontier is combining isotope analysis with proxies that can identify the taxonomic composition of animal diets, such as fecal DNA metabarcoding. The advantage of combining these two dietary proxies is that their respective strengths complement the weaknesses of the other. Specifically, fecal metabarcoding provides high-resolution taxonomic information for recently consumed (~24 hours) resources, but estimating the proportional consumption and assimilation of individual resources is confounded by assumptions about the relative digestibility of different foods. In contrast, isotope analysis provides a time-integrated measure of resource assimilation with low taxonomic resolution often only capable of discriminating between plant functional groups (e.g., C3 or C4) and providing an estimate of relative trophic level for consumers. Such multi-proxy metrics will transform how animal ecologists use diet composition data to understand foraging strategies, species interactions, and food web structure.
PLOS is dedicated to Open Science, which expands upon the notion of Open Access to include concepts such as Open Data. Do you envision IsoBank changing data sharing and transparency amongst the stable isotopes community? – And what impact will this have on scientific research?
BH: This was one of the driving force behind our desire to develop IsoBank. Jon Pauli, Seth Newsome, and another colleague, Dr. Shawn Stefan, wrote an opinion article in Bioscience in 2014 highlighting how isotope ecology was at a similar position to molecular ecology when GenBank was developed. We had all seen how crucial GenBank had become to molecular ecology by facilitating new science from old data and felt that IsoBank could have a similar effect on the ecological, geological, and anthropological sciences. So much of our work is still being done in relative isolation, the knowledge gained from our research is available through our papers; but unless the data are readily available in a usable and publicly accessible format, they will end up being stored in a hard drive on someone’s computer. This limits our ability to do large scale metanalysis or continental-global scale spatial studies using isotopes. Our hope is that IsoBank will allow us to generate new insights by combining many small datasets.