Author Archives: Natasha McDonald

An Interview with Biogeochemist Alex Cory

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Alex Cory is a final-year PhD student in the department of Earth, Ocean, and Atmospheric Science at Florida State University. She received her B.A. in geology (and music) at Lawrence University before pursuing a post-bachelors Research Associateship at Pacific Northwest National Laboratory (PNNL). Before entering grad school, she took a one-year break to travel around Southeast Asia. While in Indonesia, she witnessed some of the destructive impacts that agriculture was having on the natural landscape. The beautiful, diverse forests of Indonesia were being ripped up and replaced with rows of palm trees. The locals hated it. She would later come to learn that these alterations cause devastating effects on the climate because peatlands scrub C out of the atmosphere (and palm plantations do not). Now, as a PhD student, her job is to understand what drives the changes in peatland-climate interactions.

In this interview, we chat with Alex about her recent publication in PLOS ONE, life as an early career researcher, and the important role that peatlands play in sequestering CO2.

Your recent paper focuses on the biogeochemical components and processes involved in peatlands. Can you explain the role of peatlands in global climate change and why these carbon sinks (reservoirs that store carbon) are so critical? How much carbon do these bogs sequester?

AC: As carbon sinks, peatlands have a critical influence on the climate. Their ability to scrub carbon dioxide from the atmosphere has facilitated the formation of mind-boggling amounts of organic carbon (60% – 134% of the current atmospheric carbon pool!). Throughout most of the Holocene, this C sink function enabled peatlands to effectively cool the planet. Unfortunately, this cooling effect has lessened over the last ~150 years due to a combination of rising decomposition rates and, in some regions, increasing production of methane (which is a far more potent greenhouse gas than carbon dioxide). This phenomenon can be attributed to rising temperatures and permafrost thaw (among other factors). Determining the extent of this change (and future change) is a top priority to peatland researchers like myself.

You have mentioned that in your travels you’ve witnessed the impact of deforestation on local communities. Do you think that industry-related climate change disproportionately affects certain regions and communities more than others?

AC: Absolutely. Communities with less money/fewer resources are typically the last to receive aid after extreme weather events (such as hurricanes), which are expected to increase in frequency as a result of climate change. Poorer communities also tend to have higher rates of chronic obstructive pulmonary disease (COPD), which can be exacerbated by heat waves. Combined with the dearth of healthcare among these communities, these effects can be devastating. These are just a few examples of the inequities at play.

You’re investigating a number of really important questions regarding Earth’s carbon stores, but the day to day experimentation involves a lot of tedious processing. Did you expect so much of your PhD to entail sampling and filtering?

AC: I spent two years as a research associate before entering graduate school, wherein most of my day-to-day work involved weighing out samples on the microgram scale. (I listened to an impressive number of audiobooks during this time.) Because of this experience, the tedious aspects of lab-work did not come as a surprise to me. While they certainly do tend to lose their charm over time, I definitely find myself missing the lab more and more now that I am spending most of my time at a computer! I would advise anyone in the early stages of their career to embrace the hands-on nature of their work.

Alex in the lab in the early days of the COVID-19 pandemic. Image courtesy of Alex Cory.

Your latest work found that soluble phenolic compounds may be a crucial reason that peat bogs are so recalcitrant (unchanging). Can you tell us a bit more about these important findings?

AC: While the ability for soluble phenolics to inhibit enzyme activity is well established, the importance of phenolics in regulating carbon mineralization in peatlands has been heavily contested. For example, some studies demonstrated that removal of phenolics resulted in significantly elevated rates of enzyme hydrolysis (which is the first stage of peat decomposition). Others, on the other hand, found no significant relationship between phenolic content and rates of hydrolysis.

In our study, we found evidence that the regulatory impact of soluble phenolics varies significantly between bogs and fens (which are two types of peatland habitats). Bogs have a topic of interest for decades due to their extraordinary recalcitrance—which becomes evident when you take a look at the perfectly preserved facial features of humans bodies that were buried in the bog subsurface thousands of years ago. This recalcitrance, combined with the generally high (relative to other peatland habitats) CO2/CH4 production ratios significantly lowers the global warming potential of bogs relative to fens.

In our study, we determined that soluble phenolics could contribute to bogs’ recalcitrance and relatively high CO2/CH4 ratios—at least at our study site (Stordalen Mire, Sweden).

Our evidence for this claim was threefold. First, we noted higher soluble phenolic content in the bog. Second, we found that removal of soluble phenolics results in a far more significant uptick in bog carbon mineralization rates. Third—we noted that while the impact of soluble phenolic content on methane production was negligible in the fen, it was significant in the bog.

A typical sample incubation. Image courtesy of Alex Cory.

You have mentioned that you are part of a research institute called EMERGE. Can you tell us more about that?

AC: EMERGE (“EMergent Ecosystem Response to ChanGE”) is an NSF-funded research institute that works to understand (and predict) how ecosystems will respond to change. This is a tall order given the complexity of such interactions. To effectively carry it out, EMERGE brings in a diverse group of scientists, with expertise in 15 different subdisciplines (including, but not limited to biogeochemistry, ecology, remote sensing, modeling, and genetics). We all work on our ability to (1) communicate outside our areas of expertise and (2) function as effective team members.

One of the coolest aspects of EMERGE (in my opinion) is that we all get to learn about current research on team science (the study of teams). Through EMERGE workshops/meetings, I’ve learned that trust is a cornerstone to team success. I’ve had the opportunity to participate in a number of activities aimed at building that trust. These experiences, combined with the supportive culture within EMERGE, have helped me to speak up more at meetings and enjoy my work that much more.

We have to ask! In addition to your undergraduate and PhD studies in the Geosciences, you have a degree in Music. Can you tell us more about that? Do you see any parallels between music and science?

AC: What I love most about music and science is that they both offer the opportunity to explore one’s curiosity. For me, this always comes back to the mysteries of nature. The more analytical approach that I employ during scientific exploration is nicely complemented by the world-building narrative that I get to create when writing songs. Engaging in both strengthens my drive to understand (and even help protect) natural habitats.

Here is an example of one of my favorite nature-based songs: “Trees are like icebergs, they sit on a mirror, reflecting the secrets beneath the veneer..”

As you may know, PLOS is a huge proponent of Open Science – including Open Access publications, open peer review, open data/code sharing, etc. How do you think Open Science plays a role in Earth Sciences and Climate research?

AC: The aims of climate research—to predict future change and discern viable methods to prepare for that change—can only be effectively approached if the community of climate researchers are able to stay up to date on one another’s research. Open Science does just that! It prevents redundant research (which wastes valuable time and resources) AND offers new questions/ideas for the research community. For these reasons, I am a HUGE proponent of open science. Thank you PLOS One for being a part of that movement!

Citation: Cory AB, Chanton JP, Spencer RGM, Ogles OC, Rich VI, McCalley CK, et al. (2022) Quantifying the inhibitory impact of soluble phenolics on anaerobic carbon mineralization in a thawing permafrost peatland. PLoS ONE 17(2): e0252743. https://doi.org/10.1371/journal.pone.0252743

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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An Interview with Palaeoclimate Modeler, Hu Yang

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Here, we chat with Dr. Hu Yang about his recent publication in PLOS ONE and his predictions of the future of the Greenland Ice Sheet – the second largest body of ice on Earth, which has the potential to dramatically raise global sea level.


Dr Hu Yang is a research scientist in the Paleoclimate Dynamics group at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research. His research interests include climate dynamics, sea-level change and paleoclimate change. To gather his results, he is particularly focused on combining observations with numerical model simulations. Dr Yang’s studies, including the discovery of a poleward shift in major ocean currents, the interpretation of tropical expansion and reconstruction of the Greenland ice sheet evolution have gained widespread attention and recognition.

Your recent paper published in PLOS ONE focuses on the Greenland Ice Sheet (GrIS) – can you tell us a bit about the ice sheet, how it is changing and what this means for global climate change? 

HY: The GrIS holds a huge amount of ice which has the potential to raise sea level by 7.3 m if it completely melts away. Understanding the GrIS’s response to climate change, therefore, is critically important for us to understand how future sea level will rise. In our study, we revisited the past evolution of the GrIS using numerical model simulations and compared it with geological reconstruction. The results show that the ice volume response of the GrIS (the amplitude of the melting and sea level rise) strongly delayed climate change, which is on the order of thousands of years. That means if we warm our planet within 100 years, the sea level rise within our generation will be minor. However, the rising sea level can last for quite a long period of time, with a much larger amplitude.

Could you explain, how does the response of the Greenland ice volume delay climate change?

HY: The Greenland ice sheet has been standing there for at least 3 million years. The mass balance of the ice sheet is determined by the surface mass gain (snowfall) and mass loss (melting and ice discharge) at its margin. Ice melt usually only takes place at the margins of the ice sheet during a few months in summer. The inner portion or the summit of the ice sheet almost never melts, because of high elevation and cold temperature. When climate warms, it removes the ice from the margin, then more ice will flow down to the margin and begin to melt. This process takes time – not a few decades, but hundreds or even thousands of years. According to the latest IPCC report, in the worst warming scenario, sea level rise within this century will be around 1-2 meters. But geological evidence suggests that the Greenland and Antarctic Ice Sheets will both be melted away if that kind of worst warming stabilized. So, there is a delay for the melt of the ice sheet and sea level rise.

How does an understanding of past climates help us to better understand future changes to the Earth’s environment? 

HY: As a human-being, most of us believe what we see within our lifetime, which is usually less than 100 years. But, 100 years relative to Earth’s history is only equivalent to a minute of time in a person’s life. If we only check one minute’s behavior of a person, we will not be able to get a comprehensive understanding of his personality. For the same reason, an understanding of past climates informs us about the current status, and how it could evolve under the forcing of rapidly rising greenhouse gases.

In the case of the Greenland ice sheet, the past ice evolution tells us that the GrIS is currently at its biggest size within at least the past 7000 years. It will shrink in response to the committed warming. And this shrinking could continue for a long period of time, even if the warming stabilized at the current level.

We have recently seen examples where the unprecedented rate of change to a number of environments has in turn made it more difficult to study those environments – for example, ice breaking off of the Thwaites glacier in the Antarctic is preventing research ships from accessing it. Do you foresee similar challenges in studying the GrIS, as it continues to melt? 

HY: The Antarctic ice sheet is different from the GrIS. The Antarctic ice mostly terminates into the ocean, but most of the margins of the GrIS stop on land. So, I don’t see similar challenges. But unlike the Antarctic ice sheet, which has almost no surface melt, the surface melt of the Greenland ice sheet may produce large river discharge, which may cause problems, perhaps.

Your study utilized openly available models and data to simulate changes to the ice sheet – do you think that Open Data and code/model sharing is important for our improved understanding of global environmental change? 

HY: Definitely, open sharing of data, models and research outputs, accelerate the advance of science.  I can hardly imagine how scientists did research one century ago. I hope in the future, all the journals could make their publications open access, like PLOS ONE, to promote the transformation of knowledge.

Dr Yang holds ocean sediment, from which researchers can extract information about past climates.

Given new and unpredicted changes that have arisen on the GrIS – for example, last year, rain fell on the ice sheet for the first time that we know of – how will existing models account for this? Or do we need ever-changing models? 

HY: There is no best model, but always a better model. Model developing takes decades. Development of climate models started more than half a century ago, and are still developing with higher resolution and new physical parameterizations. Ice sheet modelling is relatively new compared to climate modelling. A lot of processes have not been taken into account, such as rain and the meltwater pool. However, the current ice sheet model can already simulate the general geometry and ice velocity resembling observations. And with more and more processes included in the system, we could expect to have more and more accurate results.  

Have you had an opportunity to do fieldwork on the Ice Sheet yourself? 

HY: Unfortunately, not yet. This seems odd for a scientist doing ice sheet research without ever doing fieldwork on it. But today, scientific research is so specialized. For example, in our team, we have colleagues who have a background in geology. We also have experts on climate dynamics and ice sheet dynamics and computer science. Cooperation between multidisciplinary fields will fill the knowledge gaps and make research easier.

What do you find to be the most challenging aspect of being an Early Career Researcher? 

HY: Currently, I find the most challenging aspect is to find a good balance between funding and doing research. The best science is not planned, it needs time not only for developing the idea, but also for publishing. The newest idea usually takes more time to get published. But, a common working contract for an Early Career Researcher usually lasts for only 2-3 years. When I got my Greenland paper published, the project that supported this study had already been expired for two years already.

Reference: Yang H, Krebs-Kanzow U, Kleiner T, Sidorenko D, Rodehacke CB, Shi X, et al. (2022) Impact of paleoclimate on present and future evolution of the Greenland Ice Sheet. PLoS ONE 17(1): e0259816. https://doi.org/10.1371/journal.pone.0259816

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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Physical Oceanography – a chat with the Guest Editors of our upcoming collection

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PLOS ONE has an open Call for Papers on Physical Oceanography, for which selected publications will be showcased in a special collection. This call for papers aims to highlight the breadth of physical oceanography research across a wide range of regions and disciplines. We welcome submissions including those that feature multidisciplinary research and encourage studies that utilize Open Science resources, such as data and code repositories.

The upcoming collection will be curated by three accomplished researchers in the field, all of whom additionally serve as Editorial Board Members for PLOS: Dr. Maite deCastro (University of Vigo, Spain); Dr. Isabel Iglesias Fernandez (CIIMAR, University of Porto, Portugal); and Dr. Vanesa Magar (CICESE, Mexico).

Here, we chat with Profs. deCastro and Iglesias to learn more about their research, their thoughts on the future of Physical Oceanography and how advances in this field can provide a better understanding of future environmental change.

Tell us about your research.

MdC: My research is clearly aligned with Climate and Renewable Energy, especially on the impact of climate change on marine ecosystems and on wind and wave renewable energy resources. It is also aligned with Food, Bioeconomy, Natural Resources, and Environment, especially in the relationship between climate and species of commercial value.

II: I’d like to say that my research interests are multidisciplinary but always with something in common, and this nexus is physical oceanography. My main research topic is related with estuarine hydrodynamics. I work with numerical models, which are versatile tools that help to unravel the hydrodynamic patterns in these complex areas. Once these models are implemented for a specific region, they can be used for multiple purposes such as representation of sediment, contaminant and marine litter transportation patterns, forecasting the effects of extreme events, anthropic activities or climate change conditions, or even calculating the potential of hydrokinetic energy production. These are some works that I have performed in collaboration with several colleagues and in the scope of national and international research projects.

At the same time, I am also interested in coastal and oceanic dynamics. I have conducted research that related long-term variability sea level anomalies in the North Atlantic with teleconnection patterns; I supervised a study related with wave forecast, and I am collaborating in the generation of a tool to forecast the dispersion patterns of sediment plumes generated by potential deep-sea mining activities in the Atlantic region.

What new finding or growing research topic in the field of physical oceanography are you currently excited about?

MdC: I am very enthusiastic about the research I have carried out in recent years, as it has allowed us to delve into the effect of climate change on historical trends in coastal upwelling, sea surface temperature, and mixed layer, among others, and to analyze its biological impact on species such as sea bream, tuna, and algae. We have also analyzed the future projections of these variables under different climate change scenarios and their possible impacts on bivalves such as mussels, different clam species, and cockles in the Galician estuaries. This approach will allow us to know both the evolution of these ecosystems in the future and to determine what measures will be necessary to mitigate the effect of climate change in order to make these ecosystems more resilient.

II: Ecoengineering. In recent decades, the focus of coastal and estuarine engineering research has shifted from technical approaches towards the integrated combination of technical, ecological, and nature-orientated solutions to reduce environmental impacts. Practical ecoengineering solutions for estuarine regions should be based on numerical modelling tools, which can provide the necessary knowledge of the relevant hydrodynamic processes and an understanding of natural processes, hydrodynamic–ecological interactions, and the impacts of structures on the environment.

At the same time, deep-sea mining is a hot topic. In recent years, deep-sea mining has become an attractive and economically viable solution to provide metals and minerals for the worldwide industry. Although promising, a large proportion of these resources are located in the vicinity of still poorly studied and understood sensitive ecosystems. The generated sediment laden plumes and the trace elements released to the water column that are associated with the extraction procedures can change the biogeochemical equilibrium of the surrounding area. This can alter deep-sea life-support services, damaging the local ecosystems with potential impacts that can persist through decades. Reliable ocean numerical models reproducing the dynamics of deep-sea areas can help to mapping the potential scale of deep-sea mining effects, being one of the key technological advances needed to implement risk assessment and better anticipate possible impacts.

For each of you, your research features an exploration of the effects of wind and the role it plays in ocean and climatological processes. Can you discuss the close link between atmospheric and ocean sciences?

MdC: A part of my most recent research is closely related to the development of renewable energies as an alternative to burning fossil fuels in the fight against climate change. Specifically, my research analyzes future offshore wind and wave energy resources under different climate change scenarios. This research field is an example of the close link between atmospheric and ocean sciences.

II: The atmosphere and the ocean are two different parts of the same system, jointly with the lithosphere, the biosphere and the cryosphere. The atmosphere and the ocean are in contact, constantly exchange mass, momentum and energy between them. The wind is one clear example of this link between the atmosphere and the ocean, generating waves and currents and affecting the sea surface temperature. But there are many others: evaporation, precipitation, heating, cooling, … And these links are the bases of short- (meteorological) and long-term (climatological) processes as winter rainfall, hurricanes or ENSO events, among others.

Many physical oceanographers spend a lot of their time working at a computer – do you ever get to do field work or research cruises?

MdC: At the beginning of my research career, I carried out several oceanographic campaigns in the Galician estuaries to take field measurements that would allow us to characterize their hydrodynamics. These campaigns were carried out jointly with chemists and biologists who analyzed other aspects of the estuaries.

II: Yes! I was in field work in the middle of January and I am expecting to have more campaigns in March and June of this year. Most of the time I am in front of a computer, but numerical models need real data to be calibrated and validated. For that we must go out into the field and measure the physical variables that we need. And although sometimes it hard to start the campaigns at six in the morning, the truth is that it is a breath of fresh air.

There is an undeniable link between anthropogenic pressures on the global environment and changes that we are seeing in marine systems. Can you discuss how you have observed this in your own research and the implications your findings have for the future?

MdC: The enormous increase in global energy consumption, together with the need to avoid the burning of fossil fuels to mitigate climate change, has led the scientific community to make the development of alternative energy sources, such as renewable energies, a priority objective. This has motivated a part of my most recent research where the offshore wind and wave energy resource is analyzed both now and in the near future under different climate change scenarios that take into account different concentrations of greenhouse gas emissions, socioeconomic measures, and land uses. This renewable energy resource analysis is complemented, in some locations, with an economic viability analysis.

II: It is clear that something is happening. Now the effects of the anthropogenic pressures on the global environment are visible. In the Iberian Peninsula we are facing one of the most severe droughts in the last decades. But other recent signals are the floods in western Germany in July 2021, the record-breaking high temperature in Moscow during July 2021, the snowfall in Madrid in January 2021, heavy cyclones and dust storms, or a heavier-than-normal wildfire season. So it is not just something that scientists are saying. It is something that the non-scientific population can see now. And, as the United Nations Secretary General Antonio Guterres has warned, the world is reaching a “point of no return”.

The complex estuarine systems can be considered as one of the most sensitive areas to environmental stressors due to the strong coupling between physics, sediments, chemistry and biology. In this sense, the effects of the climate change conditions in estuaries can be diverse based on changes in river flow, in extreme events frequency, and in water temperature and water level, affecting the circulation, salinity distribution, suspended sediments, dissolved oxygen and biogeochemistry. I used numerical models to forecast the effect of sea level rise inside the estuarine regions. It was demonstrated that the sea level rise can cause more severe floods in some estuaries. However, what should be taken into account is that the sea level rise inside the estuaries will produce a change in the circulation patterns and in the water masses configuration. This will undoubtedly affect the ecological and socio-economic aspects, due to the great value of the estuarine ecosystem services.

Historically, women have had to push for equality, respect and recognition in the field of physics. Do you think that the field is changing to become more inclusive, and what do you think research advisors, university leaders and funding agencies can do to better support women in physical oceanography?

MdC: Personally, I have always felt treated exactly the same as any other colleague throughout my scientific career, both in my closest circle and at an institutional level. I think I’ve had the same opportunities and help. I think that in this sense the field of physics, or at least this is my personal perception, is a privileged field. Despite this, I consider that there are still few women in this field compared to men and any activity aimed at making women feel more attracted to the field of physics is necessary.

II: I must say that I never need to fight more than a “man” to achieve the same respect and recognition for my work neither in my research group, nor in my research institute, country or even internationally. I had the same opportunities as anyone being men or woman. And curiously, we are more women in my research group, which develop research topics that were traditionally associated with “man”, like physics, engineering, mathematics, algorithms, numerical modelling, computational sciences, etc. I know that I am lucky, because other women before me pushed hard for equality and recognition and there are other women in different areas that still need to push to gain respect and visibility.

The term Open Science has been used to highlight the fact that transparency in scientific research goes beyond just Open Access publications. In the field of physical oceanography how do you think that making code and data publicly available can benefit researchers and policy makers?

MdC: In general terms, for the sake of transparency and the progress of the investigation, I consider it important to be able to have all the necessary material (code, data) so that any researcher can reproduce the results of another.  We will move faster and save resources if the data generated by other entities are public and if we all have access to each other’s progress instead of repeating what other researchers have already done. All this, of course, is within a framework of respect for the work of each one.

II: In my opinion, the science needs to be open. We are paying science with public funds, and it is not ethical to keep our research only for us on a long term basis. Of course, there must be some nuances regarding data for articles or patents. But I think that, at the end, the generated research should be public available. And it is not only the Open Access publications, which guarantee the transparency and the replicability of the research methodology, but also the numerical codes, the tools and the data generated in the scope of public funded research projects. Only in this way will we manage to advance faster in science, sharing our knowledge with other researchers and supporting the policy makers with proper tools to ensure the safety of populations and the sustainability of ecosystems and services.

About the Guest Editors


Isabel Iglesias holds a PhD in Climatic Sciences: Meteorology, Physical Oceanography and Climatic Change by the University of Vigo (2010). Since 2011 Isabel is working as an Assistant Researcher at the Interdisciplinary Centre for Marine and Environmental Research (CIIMAR) of the University of Porto, Portugal. Her main research topics are related with physical oceanography, atmosphere-ocean interaction, transport (sediments and marine litter), extreme events and climate change. Particularly she has experience in analysing the hydrodynamic behaviour of the water masses and in applying numerical models at oceanic, including surface and deep-sea areas, coastal and estuarine regions. Other areas of expertise include the performance and analysis of physical data obtained in sampling campaigns and the evaluation and analysis of remote sensing data for numerical modelling calibration/validation.


Maite deCastro is a Professor of Applied Physics at the University of Vigo. She obtained her PhD in Physics from the University of Santiago de Compostela (1998). The main focus of her research deals with (a) the study of hydrodynamics, waves and transport phenomena in shallow waters by means of in situ field data and numerical simulations; (b) the analysis of the variability (inter-annual and inter-decadal) of coastal and oceanic sea surface temperature (SST) using numerical and satellite data; (c) the analysis of the water masses around the Iberian Peninsula using salinity and temperature data obtained from the SODA base or ARGO buoys; (d) The effects of meteorological forcing on the ocean using satellite data or reanalysis such as: wind data, Ekman transport, sea level pressure (SLP), SST, teleconnection indices (NAO, EA, EA-WR, SCA, POL…); (e) The analysis of the plume development of rivers using radiance data from the Oceancolor MODIS base. (f) the influence of climate change on oceanographic variables, both present and in the future and, (h) the analysis of present and future wind, solar and wave resources for renewable energy production.


Vanesa Magar holds a BSc in Physics from UNAM, and a master’s in advanced studies in Mathematics and a PhD in Applied Mathematics from the University of Cambridge, UK. She has been working in coastal and physical oceanography since 2002, and in renewable energy research and development since 2008. She joined the Physical Oceanography Department of CICESE as a senior researcher in 2014, where she co-leads the GEMlab (Geophysical and Environmental Modelling Lab) with Dr Markus Gross. Her research interests include wind energy, marine renewable energy, coastal hydrodynamics, and sustainable development issues in relation to renewable energy project development. She is member of the Energy Group of the Institute of Physics (IOP), UK, and a fellow and chartered mathematician from the IMA. She served in the Mexican Geophysical Union director’s board (as Secretary General, Vice President, and President) from 2016 to 2021. Currently, she is part of the Executive Committee of the National Strategic Programme (PRONACE) in Energy and Climate Change of CONACYT (2018- ).

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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An Interview with Dr. Travis Courtney – Marine Chemist and PLOS Author

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Here, we chat with Dr. Travis Courtney about his newest publication in PLOS ONE, his exciting research on coral reefs, and his thoughts on equity and openness in science.

Dr. Courtney at Red Rock Canyon National Recreation Area. Photo by Lark Starkey.

Travis Courtney (he/him/his) grew up in the coastal city of Wilmington, North Carolina, USA where he gained an intense appreciation for coastal ecosystems. He completed his BS in Geological and Environmental Sciences at the University of North Carolina at Chapel Hill while conducting research on the effects of ocean warming and acidification on a tropical sea urchin. Courtney later attended Scripps Institution of Oceanography for his PhD and postdoctoral research on quantifying the rates and drivers of coral and coral reef calcification. He is currently an assistant professor of marine chemistry in the Department of Marine Sciences at the University of Puerto Rico Mayagüez.

PLOS: You currently head the Biogeochemistry and Ecology Research Group (BERG) at the University of Puerto Rico Mayagüez. Tell us all about your research.

My previous research has largely focused on understanding the drivers of the growth and maintenance of coral reef structures under environmental change. While I plan to continue this research here in Puerto Rico, the BERG lab is also looking to broaden our research goals to include research themes that will be most beneficial to Puerto Rico through conversations with local governmental and non-profit agencies. Climate change, coral diseases, land-use change, fishing practices, and degrading water quality are all potentially important research themes impacting the health and functioning of coastal marine ecosystems here in Puerto Rico. By understanding how these driving forces are influencing coastal ecosystems, we can also work with local agencies and community groups to develop and implement evidence-based conservation, restoration, and remediation efforts.

Travis Courtney setting up a photo quadrat as part of coral reef benthic survey work with Heather Page in Kāne’ohe Bay, Hawai’i. Photo by Andreas Andersson.
Travis Courtney setting up a photo quadrat as part of coral reef benthic survey work with Heather Page in Kāne’ohe Bay, Hawai’i. Photo by Andreas Andersson.

PLOS: Your research has ranged from fieldwork-centric studies (in Bermuda, Belize, etc.) to more data and/or mesocosm-based approaches. Tell us why both types of approaches are needed to create a comprehensive understanding of environmental impacts on coral reefs?

There’s always a trade-off between working in the field vs working in controlled laboratory settings such as mesocosms. On one hand, field-based studies allow us to directly quantify how coral reefs are changing but attributing these changes to individual environmental drivers can be difficult. There are often so many co-varying environmental factors impacting reefs, which makes it challenging to determine the direct and indirect effects of any single variable in the field. On the other hand, mesocosm-based studies allow us to precisely test how selected environmental variables influence coral reefs while keeping all other variables constant. However, controlling for so many variables means that these types of mesocosm studies may not necessarily mimic the true responses of coral reefs occurring in the field. By combining the data and insights gained from these field and mesocosm-based approaches, we can test hypotheses in a controlled setting (mesocosms) and see if those hypotheses are supported in the real world (fieldwork) to increase our understanding for how environmental change impacts coral reef systems.

PLOS: As many researchers know, community-wide adherence to protocols and standards can be critical for temporal research and the intercomparison of results. This is especially true for ocean and atmospheric measurements, where the lack of a uniform approach can impede the identification of long-term trends. In your recent paper, published in PLOS ONE, you discuss the implications of total alkalinity data with respect to salinity. You simulated the potential uncertainties associated with salinity normalization of coral reef total alkalinity data and propose a series of recommendations to reduce these uncertainties in future studies. What was your motivation for pursuing this research, and how do you think it will influence the research community’s approaches to salinity normalization of total alkalinity data on coral reefs?

The original motivation for this study was to develop user friendly tools to rapidly assess coral reef calcification tipping points under climate change as part of a project funded by NOAA’s Ocean Acidification Program. For example, our first ecology-based tool estimates coral reef calcification from coral reef images in CoralNet. When developing the chemistry-based tool, we found a lack of clear guidelines in the literature describing the various assumptions and resulting uncertainties associated with normalizing coral reef total alkalinity data to a common reference salinity. Salinity normalization is an important step that is used to isolate the effects of coral reef calcification on total alkalinity from other processes such as freshwater dilution, evaporation, and mixing. Repeated measurements of coral reef calcification through time are one tool we have as researchers to quantify the impacts of environmental change on the growth of coral reefs so increasing the precision of these measurements is important for detecting any changes in coral reef calcification through time.

The primary goal of this study was to test how the salinity normalization process potentially influences measurements of coral reef calcification derived from seawater total alkalinity data. I hope that by providing a discussion of the uncertainties associated with salinity normalized total alkalinity data and suggestions to reduce these uncertainties, this study will increase our capacity as a research community to reliably detect any potential changes in coral reef calcification under ongoing environmental change.

PLOS: There is a close link between coral reef research and a better understanding of global climate change – how have your findings on reefs contributed to our knowledge of Earth’s rapidly changing climate?

Coral reefs are often called the canaries in the coal mine, owing to the widespread observed declines in global coral cover associated with climate change and other local factors. They can provide unique insights into our knowledge of Earth’s changing climate by quantifying the impacts of climate change on present-day coral reefs as well as historical coral reefs preserved in the geologic record. Additionally, geochemical analysis of calcium carbonate from reef environments can generate useful reconstructions of historical climate change.

For example, my first experiment as an undergraduate researcher cultured sea urchins under various ocean warming and acidification conditions. We quantified changes in growth rates to see how ocean warming and acidification might influence the growth of sea urchins under climate change. Additionally, we quantified how sea urchin skeletal geochemistry was influenced by ocean warming and ocean acidification. This allowed us to develop proxies that could be used to estimate historical seawater temperatures and carbonate chemistry from the skeletal geochemistry of sea urchin spines preserved in the rock record. I’m currently involved in a range of other projects quantifying the impacts of climate change on coral reef calcification and reconstructing historical seawater temperatures from coral skeletons. I hope these ongoing projects will continue to increase our collective understanding for how the Earth’s climate has changed and how these changes influence coral reef structures and the ecosystem services they provide to humanity.

Dr. Courtney setting up instruments to record seawater parameters at the Hawai’i Institute of Marine Biology. Photo by Andreas Andersson.

PLOS: Some people have expressed the belief that the ocean will simply uptake and offset increased carbon emissions, providing a natural solution to the problem of elevated atmospheric CO2 concentrations. Some have even posited that the dissolution of corals and other calcium-rich organisms could create a negative feedback loop, increasing ocean pH and offsetting ocean acidification. Can you discuss the limitations to these theories and why we cannot rely on the ocean to sequester CO2 without making changes to emissions?

While there are a range of feedback mechanisms in the Earth’s climate system that can mitigate climate change, there are also feedback mechanisms capable of accelerating climate change. In the context of global climate change, the current input of CO2 to the atmosphere is more rapid than the rates of CO2 uptake by these naturally occurring CO2 uptake mechanisms. As a result, atmospheric and oceanic CO2 concentrations are currently increasing, and we are experiencing unprecedented ocean warming, acidification, and deoxygenation in response to greenhouse gas emissions. Current estimates suggest we’ve lost approximately 50% of global coral cover in recent decades, and widespread coral bleaching events are expected to continue to intensify in the coming decades and drive further declines in coral reefs. While researchers continue to explore various natural and artificial climate regulatory mechanisms further, the best way to mitigate climate change, and the negative impacts for coral reefs and people around the world, is to reduce emissions of CO2 to the atmosphere as soon as possible. Project Drawdown has many resources for further details on addressing the global climate crisis.

Dr. Courtney sampling a coral core in Bermuda. Photo by Andreas Andersson.

PLOS: The BERG lab’s website has a section titled “We believe” which outlines your support of equity and inclusivity in science (and other realms). Can you talk here in a bit more depth about your views on equity in science and research and how your lab supports efforts to promote this?

I witnessed the “leaky pipeline” throughout my studies with decreasingly diverse classrooms and academic environments as I progressed from high school to undergraduate, graduate, and postgraduate work. How can we, as a research community, promote the importance of diversity for improving success of ecological communities and fail to do the same to promote success within our own research communities? I believe we must do better to promote a more just, equitable, diverse, and inclusive research community.

Maintaining a commitment to these principles of inclusion and equity is an important part of developing a supportive lab environment that actively promotes the success of students to the next stage of their careers. I’m also working on developing relationships with local governmental and non-governmental organizations to identify research needs where our work in the BERG lab can be most beneficial to the coastal ecosystems and people of Puerto Rico. Outside of the lab, I teach a class on ethics that focuses on principles of justice, equity, diversity, and inclusion, where we discuss some of latest scientific literature on these issues within academic science and debate how we can work to improve academic culture.

PLOS: As you may know, PLOS is dedicated to advancing not just Open Access, but Open Science, which includes transparency and equitable access to data, code, protocols, preprints, etc. What are your thoughts on Open Science and how does this ethos fit in with your research?

I believe science should be freely accessible to everyone. Especially since so much research currently remains behind internet paywalls, I think we as a scientific community really need to ask ourselves who this paywalled research benefits and explore Open Science options to share the knowledge and resources we produce. Much of this science is also funded by taxpayer dollars, so I believe publicly funded researchers owe it to those taxpayers to make our research outputs accessible to the people who paid for it. Moreover, the data and code we produce for any given publication or project can often be incredibly useful to other scientific research projects and monitoring efforts for community, non-profit, and governmental organizations so having that data openly available can help to accelerate new discoveries and improve policies. Open science also increases transparency and trust in the scientific process by making everything freely available for review to ensure that any conclusions in the published papers are adequately supported by the data and analyses. Overall, I think that the increased accessibility provided by the Open Science movement has been an incredible step forward in the scientific process and making science more accessible, and I look forward to continuing to educate myself and the students here at UPRM on the latest Open Science best practices.

Citation: Courtney TA, Cyronak T, Griffin AJ, Andersson AJ (2021) Implications of salinity normalization of seawater total alkalinity in coral reef metabolism studies. PLoS ONE 16(12): e0261210. https://doi.org/10.1371/journal.pone.0261210

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Meet PLOS ONE’s new Biogeochemistry Section Editor, Professor Lee Cooper

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Join us as we chat with our Editorial Board member and new Biogeochemistry Section Editor Dr. Lee Cooper. Here, he discusses his research in marine biogeochemistry, long-running field campaigns to the Arctic and his view on the importance of Open Science.


Lee Cooper is a Professor at the Chesapeake Biological Laboratory, a part of the University of Maryland Center for Environmental Sciences. His work in the Arctic is centered around understanding how the ecosystem and biogeochemical cycles are responding to climate changes such as the disappearance of seasonal sea ice, with approaches that include the use of stable isotope and other biogeochemical tracers.

Biogeochemistry spans a wide range of scientific disciplines – from soil science to oceanography to atmospheric science. Has serving on the PLOS ONE Editorial Board given you an opportunity to learn more about research outside of your own specific field?

LC: Oh, absolutely. Although as a biogeochemist, I work across many fields, I teach a stable isotope applications course for the University of Maryland, and one thing that is always a constant is how fast the field is changing, and how many new applications are published each year. Working with manuscripts that are applying modern biogeochemical tools can be very challenging because you have to know enough about the disciplinary topic, whether it is food web biomagnification or paleoclimate, or atmospheric chemistry, or whatever, that I think that the maxim that learning never ends really applies to handling manuscripts for PLOS.

What has been your favorite part of serving on the PLOS ONE Editorial Board?

LC:  One of the challenges of course is finding good reviewers who want to contribute to open access scientific publishing, and it is a common complaint among editors about how many potential reviewers will turn you down. I can appreciate that everyone’s time is limited, but on the other hand, if you publish in the peer-reviewed literature, you shouldn’t just have a reflex to turn down review requests because multiple people have taken turns reviewing and improving your manuscripts. But I like turning that whole problem around by searching out people who are underrepresented in the reviewer pool. Maybe they are from countries outside western Europe and North America, or they are early career researchers who names are not well-recognized yet. Identifying those individuals and learning about their research and how they might be in a position to contribute is a very satisfying part of being on the editorial board.

Tell us about your research interests. How does biogeochemistry play a role in your own work?

LC: I work in the Arctic, which of course is undergoing a lot of changes due to climate shifts and so we are seeing a lot of surprising things, fish not seen before coming north, sea ice disappearing and biogeochemical shifts in nutrient cycles too. My specialty is stable isotopes, but I also had the chance while working at Oak Ridge National Laboratory in the 1990’s to contribute to the use of natural and anthropogenic radionuclides in understanding cycling of materials in the marine environment. Stable isotopes are a tool, and often need to be combined with other analyses in order to make sense of the biogeochemical processes at work. So, when we go to sea, I am also involved in collecting water samples for chlorophyll and nutrient measurements, and have interests in dissolved organic materials and the links to water masses in the Arctic and beyond. Oceanography is in the end a rather multidisciplinary research endeavor, so when you mix in biogeochemistry with oceanography, you have to know a bit about most everything.

PLOS recently published a curated collection of stable isotope research. Can you describe how you use stable isotopes in your own work? What new information about spatial and temporal changes can these measurements reveal?

LC: This is a fascinating collection of papers and shows the breadth of research published in PLOS. These are also very state of the art papers, and I highly recommend this special collection for anyone wanting to get up to speed on what is happening in stable isotope methodologies and applications. Clumped isotope analysis for example is a new branch of stable isotope geochemistry that is looking at minor heavy isotope distributions—whether they are random or not, and it turns out that diagnostic interpretations that can arise from non-random distributions are helping to fill in uncertainties in paleoclimate and atmospheric processes. I use stable isotopes in varied ways, including looking at biogeochemical cycles of carbon and nitrogen in sediments in the Arctic and understanding how oceanographic processes influence them. Another theme is to use the oxygen isotope composition of surface sea water to understand how melting sea is influencing ecosystems in the Arctic. Sea ice is isotopically distinct from rain and snow that we normally think of as freshwater, but melting sea ice is also primarily freshwater, so the oxygen isotope composition of that melted sea ice can be distinguished easily in Arctic marine systems.

For you, scientific research has been a family affair. You work closely with your wife, Professor Jacqueline Grebmeier and last year your daughter joined both of you on a research cruise to the Arctic. Do you think that long field campaigns in remote locations are easier when the whole family can be together?

LC: Well, the pandemic has been a challenge for everyone, particularly for anyone doing field research because of the requirements for quarantining ahead of time and making sure no one was bringing the virus aboard a shipboard platform. So, costs in funds and time have gone up significantly and we would see less of our family if we weren’t working together. I know with all the disruptions to field research schedules, that the long absences from families have been hard all around. It also helps even in “normal” times when we get back to them, that researcher couples or families who share complementary research interests and who find ways to work together on projects can accomplish a lot. It won’t work for every case and for everyone in this situation, but I feel that when we merge individual goals and take the “me” out of what we do, it seems like we can get more done and use more tools to arrive at more synergistic results.

You began your career as a researcher in Southern California – how did you transition to research in the Arctic?

LC: I grew up in a well-known southern California beach community and was always interested in plants, whether on land in the dry local chaparral, or in the ocean, but I settled on studying seagrasses, which I like to say are the whales of the plant kingdom, as they evolved on land in the pond weed family and went back to the ocean with an odd set of vascular plant characteristics, pollen, seeds, flowers relative to marine algae. Seagrasses have odd carbon isotope compositions, which probably has to do with their evolution on land and submerged photosynthesis, but I got interested in the ecophysiology that is behind the stable isotope ratios in the 1980’s when I was a graduate student, first at the University of Washington, and then at the University of Alaska Fairbanks. Some of the same seagrass species that grow in southern California also grow in Alaska, so to me, it seemed natural to take advantage of that biological connection between Santa Monica Bay, and Izembek Lagoon on the Alaska Peninsula where my advisor, Peter McRoy had worked for many years. Of course, there isn’t chaparral in Fairbanks, but moving south to north, Sitka Spruce grows from northern California to Kodiak, and there are hints of dry chaparral on Vancouver Island with the beautiful madrone trees there, so for me it was an easy transition, and Arctic research has been central to my work ever since. I came back to UCLA for a postdoc with a great advisor, Michael DeNiro, and he helped fill in a lot of knowledge about stable isotope applications, so I feel a tremendous debt for his mentorship.

You are one of the Principal Investigators of the NOAA/NSF funded Distributed Biological Observatory, a long-running Arctic time series. Can you talk about some of the unique challenges of operating a time series? Especially one that involves researchers from numerous backgrounds and institutes?

LC: We started out with interesting scientific problems about how and why the shallow continental shelf of the northern Bering Sea and the Chukchi Sea is so productive but over time that morphed into studies of how the system was changing in response to climate change. So, like most people with time-series studies, I don’t think we envisioned a 30+ year time-series of biological and biogeochemical data when we started, but that is what we have ended up with through cooperation internationally with others working in the Bering Strait region. We can do more if we work with others and it has been to great satisfaction over the years to see what new insights arise from multiple, leveraged efforts we would never have accomplished just by ourselves.

In addition to open access research, people are now interested in ‘open data’. What do you think the benefits of open data are – and how does open data feature in your own research?

LC: One of the challenges is just getting the data out there for people to use and to make sure all the corrections are made and there is also a lot of work in fielding questions from people who send you emails.  So, I don’t think we have incorporated all the costs in open data access, especially for biological and biogeochemical data. Taxonomy changes, as does precision as instrumentation improves, and data entry errors all come back to bite, so to speak. But I absolutely support making data available at the earliest practical opportunity. This is now formally required in our US National Science Foundation grants, and beyond that it is the right thing to do so that we make the best use of data collected to help society in general or to understand and mitigate climate change in our case in the Arctic.

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An Interview with PLOS ONE Editorial Board Member, Professor Tara Mastren

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As we launch our curated collection of Radiochemistry research we chat with Dr. Tara Mastren about her work in nuclear medicine, life as an Early Career Researcher, and Open Science.


Dr. Tara Mastren is an Assistant Professor in the Nuclear Engineering Program at the University of Utah. She obtained her PhD in Nuclear and Radiochemistry at Washington University in St. Louis in December 2014. She then worked in the Radiology Department at the University of Texas Southwestern Medical School as a postdoctoral researcher. In May 2016 she joined Los Alamos National Laboratory, for her second postdoc, in their Isotope Production Program. Dr. Mastren’s interests are focused on the production and use of radionuclides for the targeted treatment of cancer and other diseases.

Radioisotopes are utilized in a vast array of research fields. Do you think the breadth of the applications affects advances/progress in analytical techniques using these elements? Is there opportunity for interdisciplinarity amongst the various radiochemistry-related fields? 

TM: Yes, I believe as the field of radiochemistry and its techniques become more well known more researchers will see the advantage of using radionuclides in their research. There is a lot of opportunity for interdisciplinary research amongst the various radiochemistry-related fields. For instance, radiochemical separations overlap a multitude of fields including medicine, forensics, and fuel reprocessing.

How did you become interested in nuclear and radiochemistry?  

TM: Like many I was not exposed to nuclear and radiochemistry in high school or during my undergraduate study. When I attended graduate school, my original plan was to study biochemistry.  One day, however, I attended a professor’s lecture on nuclear reactions in stars and I was intrigued. I went to speak to him about research and he discussed with me a possible opportunity to apply nuclear research to medicine and I got excited about it. I have been a radiochemist ever since.

For many researchers, the use of radionuclides, especially alpha-emitters, demands a high level of meticulous care. Does your field require this level of fastidiousness and what if any precautions do you take in working with these materials? 

TM: Yes, working with radioactivity is a huge responsibility. We undergo lots of training to work with these materials plus have the appropriate radiation detection and dosimetry in place to make sure we are working safely. Work with radionuclides is highly regulated, requires a lot of training, internal safety audits and regulation at the state and/or national level. 

Your own research focuses largely on the new and emerging field of Targeted Alpha Therapy. Can you explain what this is, how it utilizes radionuclides, and what potential it has as an effective cancer treatment? 

TM: Targeted alpha therapy (TAT) has been of interest to nuclear medicine for decades; however, its popularity has grown significantly in recent years as a methodology of interest for cancer therapy. In TAT a highly energized alpha particle emitted during decay is used to induce cell death in cancer cells. An alpha particle is a fully ionized helium atom that is emitted from the nucleus during decay. These alpha particles travel ~10 cell lengths; depositing their energy and destroying the cells throughout their path. The alpha emitting radionuclide can be attached to a biological molecule that acts as a mailman delivering the radioactivity directly to the cancer sites, which maximizes the dose to cancer cells while minimizing the impact to healthy tissues. TAT has shown great promise in cancer therapy – in a study by Kratochwil and colleagues in the Journal of Nuclear Medicine1 patients with stage 4 prostate cancer have gone into remission after several treatments with TAT. These results have caused a lot of excitement in the field and jumpstarted additional research for the use of TAT in other cancer types.

Can you tell us about any new and exciting projects you’re working on? What do you foresee as the next step in your research journey? 

TM: I am working on projects that involve using nanoparticles for the advancement of TAT. One project is aimed at containing the daughter radionuclides at the cancer site to increase cancer cell killing effectiveness. Several of the alpha emitting radionuclides of interest to nuclear medicine have a cascade of alpha emissions. Each alpha emission results in the formation of a new “daughter” radionuclide. As alpha decay is high in energy, the daughter recoils, traveling ~100nm. This can cause the daughter to be released from the cancer site, increasing the dose to healthy tissues. Encompassing the radionuclides in a nanoparticle can help to mitigate this issue. We have successfully made nanoparticles containing alpha emitting radionuclides, and our next step will be to study them in vitro for their stability and cancer killing abilities.

What are the biggest challenges you currently face as an Early Career Researcher? 

TM: One of my biggest challenges as an Early Career Researcher is learning time and management skills. We aren’t really taught to manage people during our education and becoming an Assistant Professor one of the biggest parts of your job is managing graduate students and postdocs. Additionally, you wear many hats; instructing classes, mentoring students on research, writing grants, creating and using budgets, internal and external service, and making sure all research is conducted safely. It’s a big job that no one prepared you for, but it is also so very rewarding when you observe the progress that is being made as you watch your students evolve into independent scientists.

What are your thoughts on Open Science, and in what ways has your research community embraced this philosophy? (e.g., publishing in open access journals, making data available in public repositories, etc.). 

TM: I think that Open Science is the future of publishing. It grants access to information to students and countries that otherwise would not have access. I believe that increasing access to science and research is important for the betterment of society. As a graduate student and post doc, my advisors embraced open access journals and several of my publications have been in these journals. I also see more and more of my colleagues publishing in these journals. I believe as these journals become more popular more scientists will feel comfortable publishing open access.

1Kratochwil et al., 225Ac-PSMA-617 for PSMA targeting alpha-radiation therapy of patients with metastatic castration-resistant prostate cancer, Journal of Nuclear Medicine, 2016.

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IsoBank – Stable Isotope Research + Open Data

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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.

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From Collecting Sediment Cores in Iceland to Mentoring Students: The Busy Life of an Early Career Researcher

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Have you ever wondered what life as an early career researcher entails?

From managing a lab group and mentoring PhD students, to applying for funding and leading intensive fieldwork campaigns, scientists in the early stages of their career do it all.

Here, we chat with Dr. Margit Simon from NORCE Climate and Bjerknes Centre for Climate Research and recent PLOS ONE author to find out more about her exciting work.

PLOS: Your recent work, published in PLOS ONE, investigated stable isotope data from a new marine core collected off of Iceland – how did using data with such a high temporal resolution (1-2 years) impact what we know about water mass changes?

MS: Marine sediment cores that have such high-resolution are still a quite rare finding globally. For that specific area, it was a new finding that the upper core section – the youngest sediment part – could resolve the historic time interval so well. Mostly, that is only possible with schlerochronological records, of which there are a few around Iceland actually. We found a good correspondence with the measured phosphate concentrations within the water column – a comparison only possible because we have such high temporal resolution. Stable carbon isotopes in planktonic foraminifera are influenced by a variety of factors and are normally not so easy to interpret. By constraining the influences on the carbon isotopes by comparing to modern measurements, we were able to detect an intermittent 30-year cycle over the entire time series length, that is likely reflecting the ocean response to atmospheric variability, presumably the East Atlantic Pattern. That was not known or found before in that area.

PLOS: Has your data highlighted changes in climate over the past 150 years? What impact have these changes had on ocean variability?

MS: What I was intrigued to see was the long-term trend in benthic δ18O, a proxy recording the water mass properties in the intermediate waters at that location. It suggests that Atlantic-derived waters are expanding their core within the water column, from the subsurface into deeper intermediate depths, towards the present day. That there is greater Atlantic-derived water mass influence in the surface waters offshore of NW Iceland over the past 150 years is well known by now. However, until now, we did not know that this process is also influencing the deeper realms in the water column contemporaneously. That was a new finding.

PLOS: What are some of the challenges of being an Early Career Researcher? Do you feel that these are mitigated by the specific opportunities for ECRs?

MS: Well, securing funding short-term and long-term for my position itself, but also for my research activities is challenging, as the field becomes more and more competitive. Basic research has to be very innovative and impactful to get funding these days. Hence, I am wondering how sustainable the system is over time. I would wish for some more basic funding security or baseline funding in the private research institute section in Norway.

Image credit: Margit Simon

PLOS: You’ve done fieldwork in a number of exciting locations – from Iceland all the way to Southern Africa. Do you have a favorite location? Were there any sampling campaigns that were particularly challenging?

MS: They were all very special and exciting. Despite the Greenland Ice sheet probably being the most ‘exotic’ one that I have been to, my favourite place remains Africa, or specifically South Africa. The most challenging sampling campaign was in Mozambique as part of a wider trip from Zambia to South Africa with the aim to collect modern day river sediments.

PLOS: Field work in many research areas has been delayed or postponed in 2020 due to the Covid-19 pandemic. Were your fieldwork plans affected? And if so, how did you regroup?

MS: I was part of a marine sediment coring campaign offshore South Africa in the beginning of 2020 and retrospectively, I am very happy that we managed to do everything as planned. How little did we know then what was coming! Parallelly on land in South Africa, my project partners did field work, field experiments and excavated archaeological sites that had to be stopped due to COVID-19. This affected me in the sense that I could not get the samples I had hoped for, and we will need to postpone that to approximately Nov/Dec. of this year (2021). It is obviously still unclear if then we can operate again with a kind of normalcy.

PLOS: Now that you have PhD students of your own, is there a particular strategy you take in mentoring them? How do you prepare them for to be Early Career Researchers themselves?

MS: Well, I don’t have a rocket science strategy in place, but I think it is important to be there for them for questions, reviewing and to bounce ideas. I think nothing is worse than when you don´t have someone that you can frequently go to and ventilate ideas and perhaps also frustration. I think when you are in your PhD yourself you might underestimate the value of someone actually taking the time to read your work and give thoughtful feedback back. I think further down the line of your career path that becomes rarer and you think back on those times where your supervisor always gave comments.

PLOS: The University of Bergen and NORCE are hubs of scientific research – how has being in such a diverse group of expertise helped your own work? Do you find yourself collaborating with people in different fields from your own?

MS: Definitely. Before moving to Norway and becoming a part of the Bjerknes Centre for Climate Research, I worked in smaller groups that are more specialised in one field. That is, of course for your own work, very beneficial. However, I recognised that the centre here and the diverse groups and topics really offer new opportunities to merge and reach out and broaden your topic. I have very much benefited and used that platform for my science ever since.

PLOS: What new projects do you have on the horizon?

MS: As much as I am fascinated by the ocean and reconstructing its past variability on various timescales, I am excited about my new project ideas that aim to reveal past climate information from land or specifically from South Africa itself. What is new is that I target specifically archaeological cave sites where we can extract environmental information from the same layer that the material culture information comes from. Key behavioural innovations emerged among Homo sapiens in South Africa around 120 ka ago and the drivers of this development remains debated. One hypothesis is centred around climate changes.

PLOS: As you know, PLOS ONE is an open access journal, and is devoted to promoting open science. We would be curious to know your thoughts and opinions on open access and/or open data and the importance of these concepts for researchers, particularly early career scientists.

MS: I think both are extremely important especially for ECRs, for different reasons.

It might be rather difficult if you are an “unknown scientist” to get access to data if that is not stored at an open access source. That might of course also cost you more time and delay the activity you are working on, while a more known scientist might have asked the same question and might have gotten the data already the next day. Especially currently, during COVID-19 times, universities are conducting more and more data synthesis projects as e.g., master’s projects for students since laboratories are closed. Hence, it is of vital importance to have access without barriers to this. I think data storage facilities like PANGEA are crucial and I think the movement in the community in the last years to use these platforms more and more is great and should be pursued. In this respect, I also appreciate and used recently myself the opportunity to publish data sets only in peer-reviewed journals. It ensures good quality control on the data published but does not force one to interpret the data. Still, one can gain credit for the work. Importantly, data such as this is also available to the community that otherwise might have been hidden in a drawer.

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