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

Posted on January 27, 2022 by Natasha McDonald

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.**

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 CO₂concentrations. 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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IsoBank – Stable Isotope Research + Open Data

Posted on August 17, 2021 by Natasha McDonald

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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Introducing the Microbial Ecology of Changing Environments Collection

Posted on September 22, 2020 by Jamie Males

We are very pleased to be launching our Microbial Ecology in Changing Environments Collection, the product of a call for papers convened by PLOS ONE and our Guest Editors, Melissa Cregger and Stephanie Kivlin. The research in the Collection crosses disciplinary boundaries and represents a wide range of geographies, providing a snapshot of the diversity of research in contemporary microbial ecology. More articles will be added in due course, so please check back for updates!

Several articles highlighted in the Collection address the structure and dynamics of microbial communities in marine or aquatic environments. Three North American studies feature in the initial set of articles. Working in the Southern Californian Bight, Larkin and colleagues explored the effect of El Niño events on cyanobacterial populations [1]. Meanwhile, Vogel and colleagues found evidence for environmental and host-specific influences on microbial community structure on seagrass off the coast of Florida [2]. Finally, using a wetland mesocosm in Connecticut, Donato and co-workers performed an integrative study of microbial and plant responses to simulated chemical pollution [3].

The impact of natural disturbance on microbial communities was another theme that emerged in submissions to the Collection. In this first batch of articles, this is represented by the work of Eaton and colleagues, who examined how a major hurricane affected soil microbes in primary forests in Costa Rica [4].

The microbial ecology of manmade environments also features in the Collection. Maguvu and co-workers analysed the microbiome and physicochemical properties of drinking water production plants in South Africa, identifying significant variation in microbial community structure between facilities [5].

Last but not least, the Collection includes new research on the relationships between microbial communities living in dynamic environments within host organisms. Working in the UK, Garber and colleagues examined the effect of abrupt dietary changes in ponies on gut microbiota, with important implications for animal management [6].

The research in the Collection provides valuable insights into the mechanisms and consequences of microbial interactions with dynamic environments, and highlights the broad range of systems in which scientists are actively engaged in elucidating these phenomena.

References

Larkin AA, Moreno AR, Fagan AJ, Fowlds A, Ruiz A, Martiny AC (2020) Persistent El Niño driven shifts in marine cyanobacteria populations. PLoS ONE 15(9): e0238405. https://doi.org/10.1371/journal.pone.0238405
Vogel MA, Mason OU, Miller TE (2020) Host and environmental determinants of microbial community structure in the marine phyllosphere. PLoS ONE 15(7): e0235441. https://doi.org/10.1371/journal.pone.0235441
Donato M, Johnson O, Steven B, Lawrence BA (2020) Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses. PLoS ONE 15(7): e0235225. https://doi.org/10.1371/journal.pone.0235225
Eaton WD, McGee KM, Alderfer K, Jimenez AR, Hajibabaei M (2020) Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica. PLoS ONE 15(7): e0231187. https://doi.org/10.1371/journal.pone.0231187
Maguvu TE, Bezuidenhout CC, Kritzinger R, Tsholo K, Plaatjie M, Molale-Tom LG, et al. (2020) Combining physicochemical properties and microbiome data to evaluate the water quality of South African drinking water production plants. PLoS ONE 15(8): e0237335. https://doi.org/10.1371/journal.pone.0237335
Garber A, Hastie P, McGuinness D, Malarange P, Murray J-A (2020) Abrupt dietary changes between grass and hay alter faecal microbiota of ponies. PLoS ONE 15(8): e0237869. https://doi.org/10.1371/journal.pone.0237869

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Taking a walk on the wild side: An interview with the Guest Editors of our Rewilding & Restoration Call for Papers

Posted on August 28, 2020 by Jamie Males

PLOS ONE has an open Call for Papers on Rewilding & Restoration, with selected submissions to be featured in an upcoming Collection. We hope to feature a diverse range of multidisciplinary and interdiscipinary research, and are especially keen to encourage studies from ecoregions and voices that are underrepresented in the restoration literature.

We asked three of the Guest Editors- Karen Holl, Benis Egoh, and Chris Sandom- to share their thoughts on the past, present, and future of research in rewilding and ecological restoration.

Why is rewilding and restoration an important area of research? How is it relevant to contemporary society and the challenges we face?

KH: Over the past few years there have been a growing number of commitments at the global, national and regional scale to restore ecosystems to conserve biodiversity, sequester carbon, improve water quality and supply, and provide goods and services to people. For example, the United Nations has declared 2021-2030 the Decade on Ecosystem Restoration and the Bonn Challenge aims to get countries to commit to restore 350 million hectares of forest (an area roughly the size of India) by 2030. So there is a dramatic need for ecological and social studies of how to successfully scale up restoration to the large areas proposed.

BE: Restoration is important because it is the only means through which we can recover nature that has been lost. However, it is important that we understand what, how and where we want to restore. One of the biggest challenges is how to measures restoration success. In my opinion, many times we set out to restore with an objective in mind without thinking of the trade-offs and how to measure our success.

CS: We are about to enter the UN’s Decade on Ecosystem Restoration (2021-2030). It has been declared to ‘massively scale up the restoration of degraded and destroyed ecosystems’ to help ‘fight the climate crisis and enhance food security, water supply and biodiversity’. It is an exciting prospect! But, there is a danger this decade will be squandered if restoration practice is not combined with effective rewilding and restoration research. We need this science to improve our understanding of how to increase the probability of rewilding and restoration success across different ecosystems and circumstances. If we can do the science right, we will make restoration more effective and efficient, meaning limited resources can be put to the greatest use in our efforts to meet the big sustainability challenges.

How does your own research fit into this theme?

KH: For the past 25 years, I have studied how to restore forests, primarily in Latin America, and a range of ecosystems in California and worked with practitioners on how to implement the results of this work. I hope that the papers in this Collection will provide additional insights and case studies that complement my recent Primer of Ecological Restoration book and that I can use in teaching.

BE: In my research, I investigate the trade-offs and benefits from restoration and how we can plan to minimise these trade-offs- where should we be restoring to get the biggest benefits while minimizing cost?

CS: My research is focused on rewilding, in particular, trophic rewilding. I want to understand how reintroducing large mammals can help ecosystems restore and maintain themselves. I typically look at how carnivores influence herbivores, herbivores influence vegetation structure, and how this effects ecosystem functioning and the delivery of ecosystem services like mitigating climate change. I do my best to cover multiple spatial and temporal scales, covering local field projects, such as the Knepp rewilding project, to global macroecological research and looking at snapshot comparisons in the present to palaeoecology that spans millennia.

What trends or exciting advances have you seen in your field recently?

KH: There is increasing recognition of the importance of socioeconomic considerations. The scale of studies is also slowly increasing, which is important. There is increasing recognition that we are restoring in a time of rapid global change and that our restoration approaches need to reflect this reality.

BE: The most exciting advances to me is the research around financing restoration and how a variety of sectors including insurance companies are coming on board to fund restoration measures. Beneficiaries of restoration projects are starting to understand the benefit they get from nature through research on ecosystem services. Also, our research on planning restoration to achieve multiple benefits moves away from traditional ad-hoc restoration. However, implementation of restoration plans is still very low because restoration is mostly opportunistic.

CS: Two papers I’ve really enjoyed this year are “The megabiota are disproportionately important for biosphere functioning” by Brian Enquist and colleagues and “Trophic rewilding revives biotic resistance to shrub invasion” (paywall) by Jennifer Guyton and colleagues. The first provides a theoretical underpinning for the importance of ‘megabiota’ – the largest plants and animals – for driving biosphere scale processes like ecosystem total biomass, resource flows and fertility using metabolic scaling theory. The second reports that in Gorongosa National Park, Mozambique, a decade of large ungulate population recovery has reversed the expansion of an invasive woody species, which had established after the megafauna had been massively reduced in the preceding decades. I think these papers offer important advances in the theory and empirical evidence supporting trophic rewilding.

How does interdisciplinarity contribute to progress in this area of research?

KH: Restoration ecology is an inherently interdisciplinary field. Even if we knew everything about the science of the physical and ecological processes needed to restore ecosystems, which we don’t, success of ecological restoration projects depends critically on engaging stakeholders throughout the process, from planning to implementation to maintenance and monitoring. We need good examples of projects that have succeeded in addressing legal, economic, and social considerations to result in ecological restoration projects that last beyond the first few years.

BE: Successful restoration requires information on land suitability from soil scientists, cost of restoration from an economic perspective, type of species and habitat requirement from ecologists, consideration of the social aspect and careful planning to maximize benefits. Interdisciplinarity is therefore at the center of research in restoration.

CS: Interdisciplinary research is absolutely essential in rewilding and restoration. While the practices of rewilding and restoration seem to be focused on ecology, the factors governing success or failure are typically more about people. As a result, we need social scientists, psychologists, economists, researchers across the humanities as well as practitioners and indigenous and local knowledge to develop and implement innovative rewilding and restoration science.

What advice would you give to a student keen to work in this area of research?

KH: I tell my students to get training in both the natural and social sciences. It is important thing to get hands on experience working on restoration projects to understand the constraints and opportunities of on-the-ground projects and to collaborate with practitioners on designing research questions that are both scientifically rigorous and will help improve restoration efforts.

BE: This is an exciting area of research with a variety of directions that can be pursued.

CS: Think big and get creative. Rewilding and restoration are systems science. They are all about understanding how all the parts of nature, including people, fit together and function. You need to think about the system as a whole, and how whatever it is you are researching fits into that bigger picture. You need to address the question: what are the potential cascading effects of any particular rewilding or restoration action? Because nature is a complex system it is dynamic and chaotic, so you need to be comfortable with uncertainty and work in probabilities. Also, we still have a lot to learn so get creative and embrace diversity in thinking and practice. It is an exciting and challenging field to work in, it makes it very rewarding!

The post Taking a walk on the wild side: An interview with the Guest Editors of our Rewilding & Restoration Call for Papers appeared first on EveryONE.

Introducing the Biodiversity Conservation Collection

Posted on May 7, 2020 by Miquel Vall-llosera Camps

It is with great pleasure that we announce the launch of our Biodiversity Conservation Collection. This Collection showcases research on a broad range of conservation science related topics, including anthropogenic impacts on biodiversity, such

Introducing the Biodiversity Conservation Collection

Posted on May 7, 2020 by Miquel Vall-llosera Camps

It is with great pleasure that we announce the launch of our Biodiversity Conservation Collection. This Collection showcases research on a broad range of conservation science related topics, including anthropogenic impacts on biodiversity, such as habitat degradation, the spread of invasive species and global warming; conservation of key ecosystem services, such as carbon sequestration and pest regulation; and new management strategies to prevent further biodiversity loss.

We are extremely grateful to our team of Guest Editors, Steve Beissinger (University of California, Berkeley), Thomas Couvreur (Pontificia Universidad Catolica del Ecuador), Carlos Duarte (KAUST), Claudia Mettke-Hoffmann (Liverpool John Moores University) and Stuart Pimm (Duke University), for evaluating all submitted research and selecting articles for inclusion in the Collection. We also want to express our thanks to the PLOS ONE Academic Editors involved in the handling of submissions, to the reviewers, and to all the authors who submitted their research to this Call for Papers.

Habitat loss

Eight of the studies published in the initial Collection release focus on habitat destruction in a wide range of regions, ecosystems and species. In the North Pacific Ocean, Edwards et al. investigated the ecological consequences of marine deforestation caused by shifting trophic interactions in the Aleutian Archipelago. They show that the rapid decline of sea otter populations, caused by increased predation pressure from killer whales, led to high sea urchin densities causing widespread deforestation of the kelp forests and general loss of biodiversity and ecosystem function. In the mainland USA, Bradshaw et al. evaluated whether wetland management practices for waterfowl were also beneficial to other wetland-dependent species such as bitterns, grebes and crakes. Habitats for marsh bird species have more than halved in the last 50 years due to wetland loss and degradation; their results highlight the importance of maintaining wetland hydrologic and vegetation complexity for the conservation of breeding marsh birds.

In Brazil, three independent studies provide evidence of the impacts of habitat fragmentation in the Amazon rain forest, where biodiversity has rapidly declined in recent decades. Palmeirim et al. quantified the effect of deforestation on small mammals and found that forest dwelling species are being replaced by open-habitat species as the deforestation frontier expands. Teixeira-Santos et al. studied four endangered emblematic large terrestrial mammals and showed that the survival ability was different for each species and that some species can adapt to tolerate anthropogenically altered habitats. Paschoalini et al. studied the effects of habitat fragmentation on the Araguaian river dolphin, whose populations have been dramatically reduced due to dam construction. This research provides potential practical applications to help species management and conservation in the region, as occupation and development of the Amazon is currently being encouraged in Brazil.

When the habitat is fragmented, isolated populations lose genetic diversity, leaving them more vulnerable to changing environmental conditions and with a higher risk of extinction. In the Midwestern USA, Douglas et al. examined the genetic population structure of three upland game birds inhabiting the declining American prairie grasslands, including the endangered Greater Prairie Chicken, and found that their populations are experiencing a genetic bottleneck. They advocate for a multi-species approach as a more effective management strategy for endangered upland game birds and for making more land available to prairie species. In the United Kingdom, Ball et al. conducted a study on the conservation genetic state of adder populations and found that the species’ polyandrous breeding system is, for the moment, protecting it against inbreeding. However, this might become a problem in the future as loss of connectivity prevents movement of individuals between patches of suitable habitat. Dondina et al. studied the suitability of ecological corridors to connect two isolated wolf populations through the degraded lowlands of Northern Italy and showed the importance of keeping natural areas, such as rivers, for maintaining habitat connectivity for the conservation of endangered species in a fragmented landscape.

Climate change

Three studies among the first batch of articles published in this Collection address the impacts of climate change on biodiversity and potential mitigation strategies. Carbon sequestration has been suggested as a potential approach to mitigating the effects of greenhouse gas emissions responsible for global warming. In Spain, Morant et al. investigated the relationships between wetlands’ ecological characteristics, conservation measures and carbon emissions in the Ebro Delta wetlands. Wetlands are an important ecosystem service acting as natural carbon sinks but are under threat due to habitat destruction.

Large-scale empirical studies of the existing and projected impacts of climate change on wildlife are vital to scientifically-informed conservation management strategies aimed at minimizing and mitigating these impacts. In Southern California, Fogarty et al. used a large bird abundance dataset to investigate whether annual variation in seasonal temperature and precipitation was associated with relative abundances of breeding bird species. They found that species in arid areas may be negatively affected by increased temperature and aridity, but species from cooler areas may respond positively to those fluctuations in climate. Carbon pricing policies can also have unintended consequences for biodiversity through changing land management. Hashida et al. modelled forest habitat changes in response to forest landowner decision-making under multiple carbon pricing scenarios in Western USA. Their results predict a major shift from coniferous forest to hardwoods which could result in a dramatic loss of biodiversity in the region.

Invasive species

Three studies published in the Collection showcase research on species invasions. International trade is a major pathway of introduction of invasive species. Lucardi et al. conducted a comprehensive survey of the plant community at the largest container terminal in the USA . Their research identified the presence of a high number of invasive plant species in the port, providing important evidence that shipping ports are crucial sources of emergent plant invasions but are largely under-researched. Invasive species can have complex ecological impacts on the regions of invasion. Besterman et al. studied the ecological impacts of the establishment of one of the most invasive macroalgae on habitat selection and foraging behaviour of shorebirds in the mid-Atlantic region of the USA and found that generalist species preferred invaded habitats while specialist shorebirds preferred uninvaded mudflats. Invasive species also cause major economic losses in the regions of invasion. One of the most successful methods for sustainable management of invasive species is using their own natural enemies against them. In Morocco, Qessaoui et al. discovered the insecticidal activity of native rhizobacteria present in the soil against an important pest of tomato crops and suggested that using biological control agents would reduce the amount of synthetic chemical pesticides being used to control plant pests.

Conservation strategies

Finally three papers report methodological advances in conservation of endangered species. Endangered species are usually difficult to study because their population densities are low which hampers conservation efforts. Here, Nagarajan et al. report successful results of a non-invasive method for monitoring a wood-boring beetle species threatened by habitat loss in California. Current monitoring efforts require extensive field work looking for this rare species. In this study, the authors collected faecal samples from exit holes on trees and applied genetic barcoding techniques to identify the makers of the holes.

Large terrestrial carnivores are often keystone species in the ecosystems but have historically been persecuted and their populations are in decline globally. In the USA, sport hunting is used as a tool for managing puma populations. Laundré et al. investigated the effectiveness of this strategy for reducing conflict with humans, livestock and game species. Their results indicate that there is little evidence that puma control reduces conflict, and remark the need to reassess traditional predator control practices.

Management of captive populations is crucial for conservation of endangered species whose wild populations are at high risk of extinction. Fazio et al. studied the stress physiology of the fishing cat, a threatened wild cat from Southeast Asia, that is notoriously difficult to breed in captivity. Their study suggests that management actions such as transfers between facilities increases levels of stress while reduced animal-keeper interaction and social housing could lower stress levels and increase breeding success. This study might provide insights to better manage translocations of captive individuals of easily stressed species.

At the time of launch, there are 17 research articles featured in the Collection but more papers will be added as they are published over the coming weeks – so do check back for updates!

About the Guest Editors:

Steve Beissinger

Steve Beissinger is Professor of Ecology & Conservation Biology at the University of California, Berkeley, where he held the A. Starker Leopold Chair in Wildlife Biology (2003-13), is a research associate of the Museum of Vertebrate Zoology, and is the co-Director of the Berkeley Institute for Parks, People and Biodiversity. Professor Beissinger’s current research centers on wildlife responses to global change and species’ extinctions – with recent fieldwork carried out in protected areas and working landscapes in California and Latin America. He directs the Grinnell Resurvey Project – a 15 year effort to revisit locations throughout California first surveyed by Joseph Grinnell in the early 1900’s in order to quantify the impacts of a century of climate and land-use change on the birds and mammals of California. Steve’s studies of parrotlets in Venezuela extend more than 30 years. Integrative studies of secretive, threatened rails in California provide a model for understanding coupled natural and human systems. He has authored over 200 scientific publications and is senior editor of three books. He served on the editorial boards of Ecology Letters, Ecology, Conservation Biology, Studies in Avian Biology, and Climate Change Responses. Steve is a Fellow of the American Association for the Advancement of Science, the Ecological Society of America (ESA), the Wissenschaftskolleg zu Berlin, and the American Ornithological Society, which awarded him the William Brewster Memorial Award in 2010 for his research on Western Hemisphere birds.

Thomas Couvreur

Thomas L.P. Couvreur is a senior researcher at the French National Institute for Sustainable Development, and is currently based at the “Pontificia Universidad Catolica del Ecuador”, in Quito Ecuador. He received his PhD in tropical biodiversity from the Wageningen University in the Netherlands, and worked as post doc at the Osnabruck University in Germany and The New York Botanical Garden in the USA. His main interest lies in understanding the evolution, resilience and diversity of tropical biodiversity, and rain forests in particular, one of the most complex and diverse ecosystems on the planet. He undertakes research in taxonomy, conservation, molecular phylogenetics and phylogeography of tropical plants. His research mainly focuses on tropical Africa and South America. He is chair of the IUCN Species Survival Commission for palms since 2018.

Carlos Duarte

Professor Carlos M. Duarte (Ph.D. McGill University, 1987) is the Tarek Ahmed Juffali Research Chair in Red Sea Ecology at the King Abdullah University of Science and Technology (KAUST), in Saudi Arabia. Before this he was Research Professor with the Spanish National Research Council (CSIC) and Director of the Oceans Institute at The University of Western Australia.
Duarte’s research focuses on understanding the effects of global change in aquatic ecosystems, both marine and freshwater. He has conducted research across all continents and oceans, spanning most of the marine ecosystem types, from inland to near-shore and the deep sea and from microbes to whales. Professor Duarte led the Malaspina 2010 Expedition that sailed the world’s oceans to examine the impacts of global change on ocean ecosystems and explore their biodiversity. Professor Duarte served as President of the American Society of Limnology and Oceanography between 2007 and 2010. In 2009, was appointed member of the Scientific Council of the European Research Council (ERC), the highest-level scientific committee at the European Level, where he served until 2013. He has published more than 700 scientific papers and has been ranked within the top 1% Highly-Cited Scientist by Thompson Reuters in all three assessments of this rank, including the 2018 assessment released by Clarivate Analytics.

Claudia Mettke-Hofmann

Dr Claudia Mettke-Hofmann is Reader in Animal Behaviour at Liverpool John Moores University, UK, and Subject Leader of the Animal Behaviour team. She received her externally conducted PhD from Free University of Berlin, Germany, and subsequently worked as a postdoc at the Max-Planck Institute for Ornithology in Radolfzell and Andechs, Germany, in collaboration with the Konrad Lorenz Institute for Comparative Behaviour, Vienna, Austria, before moving to the Smithsonian Migratory Bird Center, Washington DC, USA. She is now based at Liverpool John Moores University. Her research area is cognitive ecology, mainly in birds, with strong links to conservation aspects and animal welfare. She investigates how animals collect and store environmental information in relation to their ecology on the species level but also on the individual level (personality). A focus is how animals respond to environmental change, particularly in species that differ in their movement patterns such as being resident, migratory or nomadic. Differences in cognitive abilities in these groups help explain and predict population developments in our rapidly changing environments. More recently, her research has focussed on individual differences in cognition in colour-polymorphic species highlighting exciting differences in responses to environmental change between colour morphs. Claudia has been a PLOS ONE Section Editor since 2014.

Stuart Pimm

Stuart Pimm is the Doris Duke Chair of Conservation Ecology at the Nicholas School of the Environment at Duke University. He is a world leader in the study of present day extinctions and what we can do to prevent them. Pimm received his BSc degree from Oxford University in 1971 and his Ph.D from New Mexico State University in 1974. Pimm is the author of over 300 scientific papers and four books. Pimm directs SavingSpecies, a 501c3 non-profit that uses funds for carbon emissions offsets to fund local conservation groups to restore degraded lands in areas of exceptional tropical biodiversity. His international honours include the Tyler Prize for Environmental Achievement (2010), the Dr. A.H. Heineken Prize for Environmental Sciences from the Royal Netherlands Academy of Arts and Sciences (2006).

The post Introducing the Biodiversity Conservation Collection appeared first on EveryONE.

Maximizing the rigor and reproducibility of citizen science in ecological research

Posted on March 18, 2020 by Jamie Males

PLOS ONE is organizing a Twitter chat on citizen science methodologies on 2nd April- see details below Citizen science (CS) encompasses a broad range of research methodologies that involve public participation for data collection, transcription

Maximizing the rigor and reproducibility of citizen science in ecological research

Posted on March 18, 2020 by Jamie Males

PLOS ONE is organizing a Twitter chat on citizen science methodologies on 2^nd April- see details below

Citizen science (CS) encompasses a broad range of research methodologies that involve public participation for data collection, transcription or analysis. Applications of CS have been found in many disciplines, but ecology has consistently been at the forefront. While some CS-based ecological monitoring schemes- such as the UK Butterfly Monitoring Scheme, established in 1976- have been running for decades, the popularity of CS has grown rapidly in more recent years. A wide range of projects based on CS methodologies are now being undertaken around the world, at local, national and international scales. The value of volunteer participation in activities ranging from transect-based species monitoring (Wepprich et al., 2019) and collection of biological specimens for lab-based analysis (Larson et al., 2020; Rasmussen et al., 2020) to crowdsourcing of creative thinking for study design (Can et al., 2017), has been repeatedly demonstrated. Studies have also highlighted the particular utility of CS methodologies in supporting long-term ecological monitoring in resource-limited contexts, including in economically developing countries (Gouraguine et al., 2019). Meanwhile, examples of the real-world impact of CS research are abundant, both in specific ecological interventions and the wider political discourse. For instance, the influential UK State of Nature 2019 report, likely to be a key source of evidence for future environmental legislation, cites the outcomes of a wealth of CS projects.

With the expansion of CS research, there is lively debate about how to maximise rigor and reproducibility in different types of CS methodologies. One of the crucial aspects of a successful CS study is an appropriately designed protocol, which features a realistic degree of complexity and accounts for the specific challenges of handling CS-derived data. An example of this is provided by a recent comprehensive report of the design, launch and assessment of the UK National Plant Monitoring Scheme (Pescott et al., 2019). Pre-testing of protocols prior to project launch can provide confidence in the robustness of the study design. When designing a CS study, it is also important to understand volunteer motivation and ensure that this is appropriately matched with the nature of the task to be performed (Lyons & Zhang, 2019). Some CS studies utilize narrower demographic groups to meet the required level of motivation and understanding, such as amateur naturalists (Hallmann et al., 2017) or students who are following a course in a related topic (Chiovitti et al., 2019). Depending on the type of study, researchers may also plan to support CS volunteers with training or technological aids, increasingly in the form of mobile apps (Ožana et al., 2019; Appenfeller et al., 2020).

A certain amount of error, either random or systematic, is likely to be introduced by the collection of data by CS volunteers, and study designs must account for this. The level of error can be reduced by allowing volunteers to provide clarifying metadata or to register uncertainty (Torre et al., 2019), or using incentives to reduce sampling bias (Callaghan et al., 2019), but researchers should also ensure that they have means to assess the accuracy of contributed data (Falk et al., 2019; Gibson et al., 2019). Much ecological research is based on large public databases of volunteer-contributed records of species distributions, phenological events and other observational data (e.g. Siljamo et al., 2020). There is an active discussion in the ecological research community about how to maximize the reliability and utility of such data (Ball-Damerow et al., 2019).

The particular considerations that have to be made in the design, execution and evaluation of CS studies has led to calls for dedicated standards and guidelines for CS research. Of course, any such tools must strike the balance between promoting appropriate levels of standardization and allowing the flexibility required for applications of CS methodologies across diverse settings and research questions. Whilst some progress has been made towards this goal, maintaining an open and constructive dialogue among CS practitioners and other stakeholders remains critical to ensure that researchers, volunteers and society are able to realize the full potential of CS.

To foster discussion of these important issues, PLOS ONE (@plosone) will be moderating a Twitter chat on citizen science methodologies on Thursday 2^nd April starting at 4pm BST (8am PDT, 11am EDT, 5pm CET). This is a chance for the CS community to share perspectives, experiences and suggestions for best practice. We’ll aim to cover the following questions (and more!):

How far can methods in CS projects be standardized?
What steps should be taken to maximize CS data quality?
Is there a need for clearer guidelines for the design and execution of CS studies?
How should credit for data collection be apportioned?

You can take part by using the hashtag #citscichat– we hope to see you there!

References

Appenfeller LR, Lloyd S, Szendrei Z (2020) Citizen science improves our understanding of the impact of soil management on wild pollinator abundance in agroecosystems. PLoS ONE 15(3): e0230007. https://doi.org/10.1371/journal.pone.0230007

Ball-Damerow JE, Brenskelle L, Barve N, Soltis PS, Sierwald P, Bieler R, et al. (2019) Research applications of primary biodiversity databases in the digital age. PLoS ONE 14(9): e0215794. https://doi.org/10.1371/journal.pone.0215794

Callaghan CT, Rowley JJL, Cornwell WK, Poore AGB, Major RE (2019) Improving big citizen science data: Moving beyond haphazard sampling. PLoS Biol 17(6): e3000357. https://doi.org/10.1371/journal.pbio.3000357

Can ÖE, D’Cruze N, Balaskas M, Macdonald DW (2017) Scientific crowdsourcing in wildlife research and conservation: Tigers (Panthera tigris) as a case study. PLoS Biol 15(3): e2001001. https://doi.org/10.1371/journal.pbio.2001001

Chiovitti A, Thorpe F, Gorman C, Cuxson JL, Robevska G, Szwed C, et al. (2019) A citizen science model for implementing statewide educational DNA barcoding. PLoS ONE 14(1): e0208604. https://doi.org/10.1371/journal.pone.0208604

Falk S, Foster G, Comont R, Conroy J, Bostock H, Salisbury A, et al. (2019) Evaluating the ability of citizen scientists to identify bumblebee (Bombus) species. PLoS ONE 14(6): e0218614. https://doi.org/10.1371/journal.pone.0218614

Gibson KJ, Streich MK, Topping TS, Stunz GW (2019) Utility of citizen science data: A case study in land-based shark fishing. PLoS ONE 14(12): e0226782. https://doi.org/10.1371/journal.pone.0226782

Gouraguine A, Moranta J, Ruiz-Frau A, Hinz H, Reñones O, Ferse SCA, et al. (2019) Citizen science in data and resource-limited areas: A tool to detect long-term ecosystem changes. PLoS ONE 14(1): e0210007. https://doi.org/10.1371/journal.pone.0210007

Hallmann CA, Sorg M, Jongejans E, Siepel H, Hofland N, Schwan H, et al. (2017) More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLoS ONE 12(10): e0185809. https://doi.org/10.1371/journal.pone.0185809

Larson RN, Brown JL, Karels T, Riley SPD (2020) Effects of urbanization on resource use and individual specialization in coyotes (Canis latrans) in southern California. PLoS ONE 15(2): e0228881. https://doi.org/10.1371/journal.pone.0228881

Lyons E, Zhang L (2019) Trade-offs in motivating volunteer effort: Experimental evidence on voluntary contributions to science. PLoS ONE 14(11): e0224946. https://doi.org/10.1371/journal.pone.0224946

Ožana S, Burda M, Hykel M, Malina M, Prášek M, Bárta D, et al. (2019) Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science. PLoS ONE 14(1): e0210370. https://doi.org/10.1371/journal.pone.0210370

Pescott OL, Walker KJ, Harris F, New H, Cheffings CM, Newton N, et al. (2019) The design, launch and assessment of a new volunteer-based plant monitoring scheme for the United Kingdom. PLoS ONE 14(4): e0215891. https://doi.org/10.1371/journal.pone.0215891

Rasmussen SL, Nielsen JL, Jones OR, Berg TB, Pertoldi C (2020) Genetic structure of the European hedgehog (Erinaceus europaeus) in Denmark. PLoS ONE 15(1): e0227205. https://doi.org/10.1371/journal.pone.0227205

Siljamo P, Ashbrook K, Comont RF, Skjøth CA (2020) Do atmospheric events explain the arrival of an invasive ladybird (Harmonia axyridis) in the UK? PLoS ONE 15(1): e0219335. https://doi.org/10.1371/journal.pone.0219335

Torre M, Nakayama S, Tolbert TJ, Porfiri M (2019) Producing knowledge by admitting ignorance: Enhancing data quality through an “I don’t know” option in citizen science. PLoS ONE 14(2): e0211907. https://doi.org/10.1371/journal.pone.0211907

Wepprich T, Adrion JR, Ries L, Wiedmann J, Haddad NM (2019) Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA. PLoS ONE 14(7): e0216270. https://doi.org/10.1371/journal.pone.0216270

All images used under Pixabay licence.

The post Maximizing the rigor and reproducibility of citizen science in ecological research appeared first on EveryONE.

Introducing the Life in Extreme Environments Collection

Posted on March 10, 2020 by Jamie Males

Written by Daniel Colman (Guest Editor, Montana State University), Ruth Blake (Guest Editor, Yale University) and Hanna Landenmark (Associate Editor, PLOS ONE). We are delighted to introduce a Collection entitled Life in Extreme Environments, consisting

Introducing the Life in Extreme Environments Collection

Posted on March 10, 2020 by Jamie Males

Introducing the Life in Extreme Environments Collection

Posted on March 10, 2020 by Jamie Males

Written by Daniel Colman (Guest Editor, Montana State University), Ruth Blake (Guest Editor, Yale University) and Hanna Landenmark (Associate Editor, PLOS ONE).

We are delighted to introduce a Collection entitled Life in Extreme Environments, consisting of papers published in PLOS Biology and PLOS ONE. This interdisciplinary Collection helps us better understand the diversity of life on Earth in addition to the biological processes, geochemistry, and nutrient cycling taking place in many of the Earth’s most inhospitable environments, while also enabling us to make inferences about the potential for life beyond Earth. Microorganisms and other life in extreme environments are fundamental agents of geochemical and nutrient cycling in many of the most poorly understood environments on Earth. While we tend to think of these environments as lying at the boundaries of what life is capable of dealing with, many organisms are uniquely adapted to thrive in habitats at the extremes of temperatures, pressures, water availability, salinity, and other environmental characteristics. Indeed, these environments are certainly not “extreme” to these organisms, but represent their unique niches within ecosystems on Earth. The papers included in this Collection bring together research from different disciplines including the biosciences, geosciences, planetary sciences, and oceanography in order to shed light on this crucial topic.

We are immensely grateful to our Guest Editor team- Paola Di Donato (Università degli Studi di Napoli “Parthenope”), Jiasong Fang (Hawaii Pacific University), David Pearce (Northumbria University), Anna Metaxas (Dalhousie University), Henrik Sass (Cardiff University), Ruth Blake (Yale University), Daniel Colman (Montana State University), Karen Olsson-Francis (The Open University), Frank Reith (The University of Adelaide), Felipe Gómez (Centro de Astrobiología, Instituto Nacional de Técnica Aeronáutica)- for curating this Collection.

The importance of studying life in extreme environments

It is important to study life in extreme environments in order to establish life’s limits – both physical and geographic (e.g., the depth of life beneath the seafloor), as well as the capacity of life to withstand and adapt to change. Besides significantly expanding our understanding of the limits of familiar and extreme life on Earth, studies in extreme environments have also revised our understanding of the nature of the earliest life on our planet, as well as providing the possibility of discovering new industrially useful organisms or biological products. Moreover, if there is life on other planetary bodies in our solar system or elsewhere, they will almost certainly be living in what we consider “extreme environments” on Earth. Thus, understanding how life copes with what we consider extreme conditions can provide insight into how life may be able to persist on other planetary bodies, perhaps in the subsurface oceans of Saturn’s moon, Enceladus, or Jupiter’s moon, Europa.

Investigating extreme life

One of the most exciting aspects of researching extreme life is the exploration of the unknown and discovery of new things in unexpected places that expands our very way of thinking. Microbial life, in particular, has evolved to find a way to exist and even thrive pretty much everywhere we have looked so far. Moreover, contemporary research of extremophiles is happening at an exciting time when the lines between scientific fields have been increasingly blurred. The more we understand about how environments not only influence life in extreme environments, but how life also influences those environments, the more apparent it becomes that extreme ecosystems are dynamic systems with feedback between biological activities and ecosystem properties. These interdisciplinary perspectives certainly invigorate the study of extreme life.

Extremophile research is often interdisciplinary by nature, perhaps due to the close association with biological organisms and their ecosystems, and thus the need to consider environmental, geologic, ecological, physiological, and even evolutionary considerations when investigating how organisms are able to push the limits of life. The challenges can be considerable due to the need to integrate across many disciplines, which requires expertise in a number of areas (and requiring scientists across disciplines to productively engage one another). But the reward for conducting this type of research is that it can transform how we view the relationships between living organisms and their environments. These insights can be profound in terms of our understanding of organismal biology and broader evolutionary processes of adaptation.

Yet, by their very nature, extreme environments pose significant challenges for studying biological life within them. This can be due to their remote locations (e.g., deep sea environments, high altitude environments), or to specific dangers associated with studying them (e.g., geothermal fields or other volcanic environments). Indeed, the reason that these environments are considered “extreme” is because they are not amenable to humans spending much time within them. It takes serious dedication and preparation to execute scientific research under such conditions.

The future of extremophile research

The last 30-40 years have reshaped our understanding of life in extreme environments, but much remains to be discovered. As one example, we’re still only beginning to understand what types of microbial life can exist in extreme environments, let alone what the physiological adaptations of these organisms might be. One of the greatest questions in the study of life in extreme environments i whether life is present in other “extreme environments” of the Universe beyond our planet. While we cannot know whether answers to this question will be forthcoming in the near future, great strides are being made in pointing us in what may be the most likely directions.

The Life in Extreme Environments Collection

This Collection showcases a wide variety of research on how life, from microorganisms like bacteria, archaea, diatoms, and algae, through to macroorganisms like humans, survive and flourish in diverse extreme environments, ranging from hydrothermal vents and the deep ocean to permafrosts and hypersaline lakes, and from the high Andes to deep space. Many papers illustrate highly interdisciplinary approaches and collaborations, and provide important insights into the limits of life on Earth in truly extreme environments. As indicated above, extremophiles provide insight into far-ranging topics like the limits of life on Earth, biogeochemical cycling in extreme but globally important environments, insights into early life on Earth, and how organisms cope with conditions that push the boundaries of organismal physiology.

A critical component of extremophile research is understanding how extremophiles are distributed across environments in both contemporary settings as well as over geologic time. Serpentinizing environments are considered to be analogs for the environments where life originated on Earth (and that may also support life on other planetary bodies). The investigation of fully serpentinized rocks by Khilyas et al. document the endolithic (i.e., within-rock dwelling) microbial diversity within these unique environments, their associations with their mineral environments, and contrast their findings with those of active serpentinizing aqueous environments. Such studies examining the connection between extreme environments and their native microbiomes can be critical for understanding how organisms have and continue to interact with their environments over time. Another study in the Collection by Kiel and Peckmann provides new insights into the association of macrofauna with hydrothermal vents over the past ~550 million years. Their survey of dominant brachiopod and bivalve fossils over this period challenge the pre-existing hypotheses that these two groups competed for the same resources, with the latter group ultimately gaining prominence in the last ~100 million years. However, the authors show that the two groups likely inhabited different vent environments altogether, with brachiopods inhabiting hydrocarbon seeps and bivalves preferring sulfide-producing vents in association with their symbiotic sulfide oxidizing bacteria. To better understand the contemporary distributions of important marine microorganisms, Ferreira da Silva et al. documented how diatom communities are associated with macroalgae in the waters near the South Shetland Islands of Antarctica, revealing a potential role of the unique Antarctic climate in determining the biogeography of diatoms and their associated macroalgae. Indeed, the relationships among organisms may be critical for the habitation of extreme environments. In another investigation of cross-taxa associations in extreme environments, Gallet et al. evaluated the diversity of microbiota associated with enigmatic bioluminescent lantern fish species, and found that the latter might interact with its microbiome to inhabit the extreme environment of deep southern oceans. The data provide a better understanding of these important associations in key species involved in the ecosystem function of extreme deep sea environments.

Although extreme environments are often considered marginal habitats of mostly local influence, the functions of some extreme environments, and the organisms inhabiting them, can have particularly important implications for global biogeochemical cycling. For example, Nayak et al. document new insights into the functioning of one of the most important microbial enzymes involved in global carbon cycling, the methyl-coenzyme M reductase protein of methanogens, which catalyzes the key step of methanogenesis allowing the biological production of methane, which contributes to a significant portion of global methane production. In the authors’ investigation, they show how the protein is post-translationally modified by a previously unknown mechanism, and that this ‘tuning’ of methyl-coenzyme M reductase has profound impacts on the adaptation of methanogens to various environmental conditions. Anoxic peatlands are one such environment where methanogens play critical roles in biogeochemical cycling. These anoxic peatland environments are extreme environments that are important for global biogeochemical cycling, despite only occupying a small fraction of the total land space. Kluber et al. used an experimental warming approach to investigate how deep, anoxic peatland reserves would respond to fluctuating environmental conditions. The authors document that temperature is a key parameter that could drastically affect the decomposition of peatland nutrient stocks and their contribution to global biogeochemical cycling.

Key to the interaction between organisms and extreme environments are the adaptations that extreme environments impose upon organisms. The Collection features a number of investigations documenting the unique adaptations of microorganisms and macroorganisms to habitats ranging from hydrothermal vents to space at both the genomic and physiological levels. One of the most enigmatic discoveries of extreme environments over the past half century was the identification of entire ecosystems that dwell on or around hydrothermal vents at the ocean floor that are sustained by inorganic chemical synthesis from hydrothermal vent fluid chemicals. The paper within this Collection by Zhu et al. provides new evidence for the genetic mechanisms that allow the habitation of vent ecosystems by two distinct shrimp species that characteristically inhabit different thermal regions of vents. Using transcriptomic approaches, the authors identified new molecular mechanisms underlying how macrofauna can adapt to different hydrothermal niches within these extreme systems. Likewise, Díaz-Riaño et al. used transcriptomics to identify the mechanisms of ultraviolet radiation resistance (UVR) within high UVR bacterial strains that were isolated from high altitudes within the Colombian Andes. These new insights provide much needed resolution into the RNA-based regulatory mechanisms underlying UVR in organisms, which represents a fundamental knowledge-gap in our understanding of organismal adaptations to extreme altitude environments.

While life that persists continuously under extreme environments provide valuable information to understand the physiological limits of life, it is also critical to understand how life adapted to more ‘normal’ environments can withstand excursions to extreme environments over prolonged periods of time. One such example are oxygen minimum zones that occur in deep oceans where oxygen levels have been depleted to levels thought to not be able to support higher life, in what is termed ‘hypoxic conditions’. Nevertheless, some higher organisms are capable of living in such environments, although their adaptations to this lifestyle are not currently clear. One such species is the bluntnose sixgill shark that can tolerate very low levels of oxygen. Using an array of biologging techniques that allowed them to monitor the physiological and behavioral activities of these sharks, Coffey et al. provide evidence for their migratory behavior and long periods of exposure to hypoxic conditions in the deep sea. In addition to elucidating how sixgill sharks cope with extreme deep sea conditions, the new ecophysiological logging techniques provide a new platform for future studies of organisms adapted to the extremes of deep oceans. Among the possible excursions of life to extreme environments, none are potentially more problematic than the travel of humans to space. A common physiological effect of space transit is the bone mineral density (BMD) loss that is experienced by astronauts. In a paper within the Collection, Axpe et al., performed a modeling analysis based on BMD loss by previous astronauts involved in long-term missions in order to evaluate the potential for these harmful effects on trips that might become targets for longer manned missions to Mars or elsewhere. The study thus provides critical new data to inform these important missions.

As exemplified by the papers within this Collection, unique adaptations allow life to persist in extreme environments. These adaptations can also be useful in biotechnological applications, as several other papers in the Collection demonstrate. Halophiles that inhabit extremely saline environments have long been a source for bioprospecting due to their unique adaptations that allow them to maintain osmotic balance within environments that most types of life could not survive in. Notably, halophiles often concentrate unique biomolecules in order to overcome the abiotic stress of hypersaline environments. In their manuscript, Abdollahnia et al. explore the previously little-investigated ability of halophiles to concentrate nanoparticles, finding evidence for the unique ability to concentrate metal nanoparticles within archaeal and bacterial species. Importantly, these organisms could represent a potential environmentally-friendly means of synthesizing unique metal nanoparticles. Thus, the identification of new bio-resources is an area of ongoing and intense interest in the investigation of extreme life.

As is evident by the diverse range of topics, organisms, and environments within the papers of this Collection, the investigation of extreme life incorporates numerous fields of study and a wealth of methods to understand the limits to life on Earth. We’ll be adding new papers to the Collection as they are published, so please do keep checking back.

About the Guest Editors

Ruth Blake

Ruth Blake is a Professor in the departments of Geology & Geophysics and Environmental Engineering, and in the School of Forestry & Environmental Studies at Yale University. Dr. Blake’s areas of expertise include marine biogeochemistry, stable isotope geochemistry and geomicrobiology. Her recent work focuses on developing new stable isotope tools, geochemical proxies and biomarkers to study marine/microbial phosphorus cycling and evolution of the phosphorus cycle from pre-biotic to recent.

Dr. Blake is engaged in a range of studies on co- evolution of earth and life and the impacts of both on biogeochemical processes occurring in the oceans, deep-sea sediments, seafloor hydrothermal systems and the sub-seafloor deep biosphere. Dr. Blake has participated in several ocean exploration/ research expeditions including cruises to: FeMO observatory at Loihi undersea volcano, 9°N EPR, Orca Basin in the Gulf of Mexico and North Pond in the mid-Atlantic. She has also served as shipboard scientist on Ocean Drilling Program and R/V Atlantis /DSV ALVIN platforms. Ruth Blake graduated from the University of Michigan in 1998 with a PhD in geochemistry.

Daniel Colman

Dan is currently an assistant research professor at Montana State University and is an environmental microbiologist with primary research interests in broadly understanding how microbial populations interact with one another and with their environments. To investigate these broad topics, he uses a suite of interdisciplinary techniques at the intersection of environmental microbiology, biogeochemistry, geomicrobiology, microbial physiology, geochemistry, hydrology, and microbial evolution.

In particular, his work leverages environmental genomics methods coupled to in situ and laboratory experiments along with geochemical insights from hydrological and geochemical analyses to understand 1) how and why environments structure micobial communities, 2) how microbial communities shape their environments, and 3) how environments and microbial populations have co- evolved through time. In particular, he has largely focused on evaluating these questions in extreme environments, and especially hydrothermal systems, which represent an excellent platform to deconvolute microbial-environment relationships across substantial environmental gradients.

Paola Di Donato

Graduated in Chemistry, Paola received her PhD in 2002 and since 2008 she is a Researcher in Biochemistry at the Department of Science and Technology of University of Naples “Parthenope”; in 2016 she has been appointed as the Dean’s delegate to managing the Institutional Repository of the University “Parthenope”.

Her research interests are the valorisation of waste vegetable biomass and the study of extremophilic bacteria. With regard to the first topic, her research focuses on the recovery of value added chemicals (polysaccharides and polyphenols) and the production of energy (bioethanol) from wastes of vegetables food industry and of dedicated crops (giant reed, cardoon). With regard to the study of extremophilic bacteria, her research activity is aimed at studying the biotechnologically useful biomolecules (enzymes and exopolysaccharides) produced by these bacteria; in the last seven years, particular attention has been paid to the study of extremophiles in relation to Astrobiology, the multidisciplinary approach to the study of origin and evolution of life on Earth and in the Universe.

Felipe Gómez

Dr. Felipe Gómez is a senior staff scientist at the CAB. His research work focuses on the study of extreme environments, limits of life and, by extrapolation, development of habitability potential in adverse environments. He participates in Mars exploration space missions to search for traces of life and study the habitability potential of the red planet. He is currently part of the scientific team (Co-Investigator) of the Rover Environmental Monitoring Station (REMS) instrument aboard the NASA Curiosity-MSL rover that is studying the surface of Mars at this time. Dr. Felipe Gómez is Co-I of MEDA instrument that will be onboard Mars2020 NASA mission to Mars.

He has been part of the scientific team of several campaigns of astrobiological interest in studying different extreme environments. The project M.A.R.T.E. (Mars Analogue Research and Technology Development) began in 2003 and extended until 2006. Its principal investigator was Dr. Carol Stocker of NASA Ames Research Center. This project was funded by NASA within NASA’s ASTEP program for the development of technology for future space missions. This project was developed with the collaboration of several institutions in the United States and CAB. It consisted in the study of the subterranean environment of the zone of origin of the Tinto River (Huelva) where several perforations were made (160 m deeper) until reaching the anoxic zone isolated from the surface. The ultimate goal of the project was the design and development of an automatic platform for drilling without direct human intervention (automatic drilling) on ??the surface of Mars. This project was the beginning of research into the development of automatic drilling instruments for this purpose. It was developed in three phases: first and second year with non-automatic perforations and “in situ” study of the samples that were obtained in real time. In the third year, the automatic platform was implemented.

Jiasong Fang

Jiasong Fang is a professor in the College of Natural and Computational Sciences of Hawaii Pacific University, Distinguished Chair Professor in the College of Marine Sciences of Shanghai Ocean University, and Director of the Shanghai Engineering Research Center of Hadal Science and Technology. Dr. Fang received his Ph.D. in oceanography from Texas A&M University and did his postdoctoral training at the Department of Microbiology of Miami University.

His scientific interests are primarily in the areas of high-pressure microbiology and biogeochemistry, focusing on piezophilic microorganisms and their role in mediating biogeochemical cycles in the deep ocean and the deep biosphere. He has co-authored 100 scientific publications.

Anna Metaxas

Dr. Anna Metaxas is a Professor in Oceanography at Dalhousie University. She received a B.Sc. in Biology from McGill University in 1986, a MSc in Oceanography from the University of British Columbia in 1989 and a PhD from Dalhousie University in 1994. She was a Postdoctoral Fellow at Harbor Branch Oceanographic Institution from 1995 to 1997, and a Postdoctoral Scholar at Woods Hole Oceanographic Institution from 1997 to 1999.

Her research focuses on the factors that regulate populations of benthic marine invertebrates, particularly early in their life history. She uses a combination of approaches, such as field sampling, laboratory experiments and mathematical modelling, to study organisms of ecological and economic importance, including invasive species. She has worked in a variety of habitats from shallow rocky subtidal regions to the deep-sea, including hydrothermal vents and deep- water corals, in temperate and tropical regions of the world. Her research has implications for marine conservation, such as the establishment and success of conservation areas for benthic populations.

Karen Olsson-Francis

Dr. Karen Olsson-Francis is a Senior Lecturer at the Open University, in the United Kingdom. Her research focuses on understanding the role that microorganisms play in biogeochemical cycling in extreme environments. She is interested in this from a diversity and functional prospective. In particular, she has focused on studying terrestrial analogue sites and utilizing this information to understand how, and where, potential evidence of life can be found elsewhere in the Solar System.

David Pearce

The underlying theme of David Pearce’s research is to use microbiology (and in particular novel molecular techniques applied to microbial ecology, microbial biodiversity and activity, environmental genomics, biogeochemical cycling and model extremophiles) to understand Polar ecosystem function and the potential for shifts in biogeochemical activity that may result from environmental change. He has taken the lead in the development of new frontiers of research in metagenomics, chemosynthetic communities, sediment sequestration of carbon and subglacial lake environments and have initiated new interdisciplinary approaches on the aerial environment (with chemists), ice nucleation activity (with physicists) and in the biogeochemistry of ice (with glaciologists).

Frank Reith

Frank Reith is an Associate Professor in geomicrobiology at the School of Biological Sciences at University of Adelaide and CSIRO Land and Water, where he heads the Microbes and Heavy Metal Research Group. He holds a PhD in Earth Sciences from the Australian National University. He is interested in microbial processes that affect metal cycling and the formation of new minerals. In turn, he also studies how microbes are affected by elevated concentrations of heavy metals in extreme environments. His particular interests lie in the biomediated cycling of noble/heavy metals, e.g., gold, silver, platinum, uranium, osmium and iridium.

An important aim of the fundamental processes understanding created by his research is to use it to develop tools for industry, e.g., biosensors and bioindicators for mineral exploration, as well as biotechnological methods for mineral processing and resource recovery from electronic waste. Thereby, his approach is highly multidisciplinary and covers field expeditions to remote corners of the Earth, synchrotron research, meta-genomic and proteomic approaches as well as statistical-, geochemical- and reactive transport modelling.

We were very saddened to hear of Frank’s passing before this Collection published. We are immensely grateful for his contributions to PLOS and to his field of research, as well as for his enthusiasm and kindness. Our thoughts go out to his family and friends.

Henrik Sass

Dr. Henrik Sass is senior lecturer in Geomicrobiology at the School of Earth and Ocean Sciences of Cardiff University. He received his PhD from the University of Oldenburg (Germany).

Henrik is a biogeochemist, geomicrobiologist and microbial physiologist with a special interest in anaerobic processes and the prokaryotes involved, such as the strictly anaerobic sulphate reducers and methanogens. He has been working on anaerobic metabolism and described new metabolic pathways in methanogens. One main topic of his research is life in the extreme environments, particularly life in the deep biosphere and in deep-sea anoxic brine lakes. These studies aim to reveal how anaerobes adapt to their particular ecological niches (e.g. oxygen tolerance of sulphate reducers). His work utilizes a range of different approaches including in situ activity measurements and the estimation of viable population sizes, but also culture-based laboratory experiments. Another aspect of his work has been the use of biomarkers, including dipicolinic acid for the detection of endospores in environmental samples.

The post Introducing the Life in Extreme Environments Collection appeared first on EveryONE.

It’s the little things- An interview with the Guest Editors of our Microbial Ecology of Changing Environments Call for Papers

Posted on January 24, 2020 by Jamie Males

PLOS ONE has an open Call for Papers on the Microbial Ecology of Changing Environments, with selected submissions to be featured in an upcoming Collection. We aim to highlight a range of interdisciplinary articles showcasing

It’s the little things- An interview with the Guest Editors of our Microbial Ecology of Changing Environments Call for Papers

Posted on January 24, 2020 by Jamie Males

PLOS ONE has an open Call for Papers on the Microbial Ecology of Changing Environments, with selected submissions to be featured in an upcoming Collection. We aim to highlight a range of interdisciplinary articles showcasing the diversity of systems, scales, interactions and applications in this dynamic field of research.

We spoke to the Guest Editors for this project, Melissa Cregger and Stephanie Kivlin, about what motivates their research and the challenges and opportunities faced by microbial ecologists.

What makes microbes so interesting?

MC: Microorganisms are everywhere and are important members of all of the ecosystems they inhabit. There are microorganisms in soils, oceans, lakes, and even within our bodies. Within all of these habitats they are performing really important functions. In lakes, oceans, and soils, microorganisms are key to moving nutrients around. Within our bodies, they aid in things like digestion and disease prevention.

SK: Microorganisms are fascinating in how genetically diverse and numerous they are. Microorganisms can be found in almost every habitat on Earth and are often the first to respond to environmental disturbance and global change. Thus, microorganisms likely hold the key to solving most of Earth’s problems as we face global climate change.

How is microbial ecology relevant to major environmental and societal issues like climate change and food security?

MC: Given how ubiquitous microorganisms are across the world, understanding how they function is key if we want to understand and mitigate the consequences of climatic change and if we want to grow food more sustainably and in marginal lands. For instance, if we can get a better understanding of microbial carbon cycling, we can potentially use biological carbon capture as a mitigation strategy to help combat rising levels of atmospheric carbon dioxide. Additionally, researchers around the world are trying to understand how plants interact with microbial communities in an effort to harness these microbes to increase food production and the ability of plants to withstand changing abiotic conditions.

SK: Microorganisms are the key for innovating nature-based solutions to climate change. For example, specific fungal symbionts of plants can be tailored to increase agricultural plant drought tolerance. Other microorganisms may be deployed to remediate oil spills or other man-made pollutants. Finally, engineering plant-microbial associations may lead to a larger terrestrial carbon sink to offset atmospheric CO2 concentrations, creating a negative feedback to climate change itself.

Tell us a bit about your own research and how it ties in with some of these issues.

MC: A large portion of my research is focused on understanding how to use beneficial microbes to increase plant productivity and tolerance to drought, and also in understanding how these communities function in the soil environment with the ultimate goal of using them to enhance ecosystem stability. I am part of two large multi-disciplinary teams at Oak Ridge National Laboratory that are specifically focused on plant-microbe interactions in the potential biofuel feedstock, Populus. We are trying to characterize basic principles governing plant-microbe interactions in the hope of making Populus a better biofuel that can grow in marginal lands with limited input of fertilizer and water.

SK: Research in the Kivlin Lab aims to create distribution models for terrestrial microorganisms and their functions. Our current focus is on arbuscular mycorrhizal (AM) fungi, as these plant symbionts are the main providers of nutrients and drought tolerance to agricultural plants. We are interested in where these fungi are, the ecosystem-level carbon and nutrient cycling they promote and how sensitive these plant-fungal interactions may be to climate change. To address these questions, we both compile data on AM fungal distributions worldwide, but also examine plant-AM fungal interactions along altitudinal gradients that serve as a space for time substitution for climate change and in long-term climate change experiments.

How are technological advances opening up new opportunities in your field?

MC: Over the last 20 years there have been rapid advances in sequencing and molecular techniques that have enabled amazing opportunities in microbial and ecosystem ecology. We are finally able to identify unculturable microorganisms inhabiting diverse communities using next generation sequencing and are getting clues into their function using metagenomics, metatranscriptomics, proteomics, and metabolomics. Further, using these techniques, people are developing some new strategies to culture more microbes.

SK: It is increasingly clear that the genomics revolution has impacted microbial ecology. We now can link functional genetic potential to microorganisms in environmental microbiomes and understand how interactions among microorganisms and between microorganisms and plants control expression of these functional genes and the metabolites they code for.

How does microbial ecology benefit from interdisciplinary collaboration?

MC: Microbial communities are incredibly complex, therefore understanding their role in ecosystems really requires a systems biology approach. Because of this, having an interdisciplinary team to tackle questions at various scales is really important.

SK: Microbial ecology is inherently interdisciplinary. We collaborate with earth system modelers to scale microbial function from the organism to the globe and with geneticists to understand the genetic underpinnings of those functions. Without these collaborations, our field would be siloed to case-studies of microbial communities and lack the ability to develop first-principles theory across microbial communities and environments.

What are some of the biggest unsolved questions in microbial ecology?

MC: There are so many unsolved questions in microbial ecology that it is hard to just identify a few. We still have a limited understanding of how microbial communities fluctuate through time. How stable are they within ecosystems? Are organisms within communities functionally redundant? Does this redundancy aid in resilience of the community post disturbance? How do these communities respond to fluctuations in abiotic variables? I could really go on and on.

SK: Despite all of the vital roles that microorganisms provide in the environment, we still don’t understand (1) where microorganisms even are spatially and what abiotic and biotic processes control these distributions, or (2) how temporally dynamic microbial communities are both within and among plant growing seasons. Answering these fundamental questions will allow us to understand linkages between microbial communities and plant growth, microbial composition and ecosystem carbon and nutrient cycles, and allow us to effectively manipulate microbial consortia for societal gain in agricultural and bioremediation settings.

The post It’s the little things- An interview with the Guest Editors of our Microbial Ecology of Changing Environments Call for Papers appeared first on EveryONE.

Editors’ Picks 2019

Posted on December 31, 2019 by PLoS ONE Editors

As the end of the year draws in, PLOS ONE Staff Editors put together a list of some their favourite papers from 2019. Behavioral and Social Sciences, Neuroscience, Mental Health In an archaeological investigation, Ehud

Introducing the Urban Ecosystems Collection

Posted on December 9, 2019 by Jamie Males

We are thrilled to announce the launch of our PLOS ONE Urban Ecosystems Collection! An essential aim of this project was to draw together a diverse range of contributions. We felt it was particularly important

About Open Science

(All that comes with it, (but not by itself)

Category Archives: ecology

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

IsoBank – Stable Isotope Research + Open Data

Introducing the Microbial Ecology of Changing Environments Collection

Taking a walk on the wild side: An interview with the Guest Editors of our Rewilding & Restoration Call for Papers

Introducing the Biodiversity Conservation Collection

Introducing the Biodiversity Conservation Collection

About the Guest Editors:

Steve Beissinger

Thomas Couvreur

Carlos Duarte

Claudia Mettke-Hofmann

Stuart Pimm

Maximizing the rigor and reproducibility of citizen science in ecological research

Maximizing the rigor and reproducibility of citizen science in ecological research

References

Introducing the Life in Extreme Environments Collection

Introducing the Life in Extreme Environments Collection

Introducing the Life in Extreme Environments Collection

About the Guest Editors

It’s the little things- An interview with the Guest Editors of our Microbial Ecology of Changing Environments Call for Papers

It’s the little things- An interview with the Guest Editors of our Microbial Ecology of Changing Environments Call for Papers

Editors’ Picks 2019

Introducing the Urban Ecosystems Collection