Introducing the Biodiversity Conservation Collection

  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

 

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).

 

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Stem Cell Plasticity in Tissue Repair and Regeneration Collection

 

We are excited to publish a collection entitled Stem Cell Plasticity in Tissue Repair and Regeneration, which results from a PLOS ONE’s call for papers announced last year. We encouraged submissions spanning a broad range of biomedical topics, including basic stem cell biology, preclinical research and biomedical engineering. The papers included in the collection provide examples of how the dynamic functions of stem cells can be harnessed to regenerate damaged or lost tissues. Regenerative approaches may offer a unique therapeutic opportunity for diseases where with no established treatments exist.

 

In line with PLOS ONE publication ethos, we welcomed solid and clearly reported studies regardless of the perceived impact and positive nature of the main findings. We think that in the fast-paced field of stem cell research, addressing publication bias is particularly important to advance knowledge and bring new therapies to the clinic.

 

Two studies included in the collection reported the role and regenerative ability of adult mesenchymal stem cells (MSCs). Chung et al. showed the regenerative potential of human MSCs in a rat model of bladder disease. They also identified the bladder submucosa as the most effective route of MSC administration. In a clinical study among patients with acute respiratory distress syndrome, Patry et al. found that extracorporeal membrane oxygenation increased the number of circulating MSCs, although further research is needed to establish the regenerative potential of these cells in the context of pulmonary disease.

 


Bladder tissue regeneration identified via IHC staining pone.0226390

 

Two methodological papers focused on the differentiation of human induced pluripotent stem cells (hiPSCs) into cardiac cells. This rapidly evolving research area aims at overcoming the current challenges in generating mature cells in large quantity and high purity for tissue engineering applications. Rupert et al. described practical methods for the optimization of hiPSC-cardiomyocyte differentiation, highlighting the key role of metabolic selection. Chu et al. demonstrated that cardiac differentiation can be achieved by co-culturing hiPSCs with mature cardiomyocytes, without the addition of exogenous pharmacological agents.

 


Workflows for cardiac differentiation of stem cells pone.0230001

 

This collection was made possible thanks to the fantastic work of our Guest Editors – Michelina Iacovino, Scott D. Olson and Che Connon – who helped develop the scope of the call for papers and evaluated all submitted research for inclusion in the collection. We are also extremely grateful to the members of our editorial board and external peer-reviewers for dedicating their time and expertise to the evaluation of submissions.

 

We will add new papers to the Collection as they are published, so we invite you to check back the collection webpage in the coming weeks. If you are interested in keeping up to date with the latest stem cell research from the broader literature, check out our PLOS Channel too.

 

Guest Editors

Scott D. Olson

Scott Olson is a mesenchymal stem cell (MSC) Biologist working in the Children’s Program in Regenerative Medicine in the Department of Pediatric Surgery at McGovern School of Medicine. Dr. Olson completed his doctorate in the lab of Dr. Darwin Prockop at Tulane University’s Center for Gene Therapy studying novel methods by which MSCs can contribute to tissue repair. At University of California at Davis’s Health Sciences Institute for Regenerative Cures with Dr. Jan Nolta, Dr. Olson worked to apply MSCs as a platform to develop new treatments for Huntington’s Disease. Dr. Olson joined UTHealth in September 2011.

 

Dr. Olson is involved in developing and transitioning studies with direct translational applications. At UT Health, his primary focus is bringing his expertise in the field of adult stem cells, specifically MSCs, to explore their potential in the treatment of Traumatic Brain Injury (TBI) and in trauma-associated neuroinflammation in general. MSCs have been used in a number of completed, ongoing, and proposed clinical trials with reported therapeutic benefits. Dr. Olson strives to better describe the role of MSCs in injuries of the central nervous system, highlighting their innate therapeutic abilities in an effort to create an improved treatment for TBI.

 

Michelina Iacovino

Michelina Iacovino is an Assistant Professor at the David Geffen School of Medicine at The University of California, Los Angeles (UCLA), and a Principal Investigator at Los Angeles Biomedical Research Institute (LABioMed) at Harbor-UCLA in the Pediatrics Department.

She obtained her Doctorate in Italy in Biochemistry and Applied Chemistry working on mitochondrial DNA inheritance in yeast in collaboration with Dr. Ronal Butow at the University of Texas Southwestern Medical Center. She then trained in the field of hematopoietic stem cells with Dr. Michael Kyba during her postdoctoral fellowship, studying the role of Hox genes during blood development. She joined LABioMed in 2012, extending her expertise of stem cell biology to develop treatments for rare lysosomal disorders that affect brain function. She is currently developing a stem cell therapy for Sanfilippo syndrome, an incurable and rare lysosomal disorder, using neural progenitor cells.

 

Che Connon

Che Connon obtained his PhD in Biophysics from the Open University Oxford Research Unit in 2000, during which time (under the supervision of Professor Keith Meek) he investigated corneal wound healing and transparency. He subsequently obtained a JSPS post-doctoral fellowship to work with Professor Shigeru Kinoshita in Kyoto, Japan for two years studying corneal stem cell transplantation. Upon his return to the UK he was awarded a Royal Society Fellowship to investigate the use of biomaterials in stem cell therapies. He obtained his first permanent position in 2007 at University of Reading, School of Pharmacy and since 2014 he has held the position of Professor of Tissue Engineering at Newcastle University.

Professor Connon’s research team seeks to engineer functional replacement and temporary ‘bridge’ tissues using a modular approach while also developing model systems to study physiological and pathophysiological corneal tissue formation. He is currently working with smart (cell responsive) biomaterials, characterizing the mechanical and geometric environment of the corneal stem cell niche and 3D printing the corneal stroma.

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Introducing the Life in Extreme Environments Collection

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.

Introducing the Mathematical Modelling of Infectious Disease Dynamics Collection

In recent months, the words “infection” and “outbreak” have not been far from anyone’s mind as we’ve faced the emergence of a new coronavirus, COVID-19. Across the globe, efforts are underway to control and limit

Announcing the PLOS ONE Collection: Early Diagnosis and Treatment of Alzheimer’s Disease

PLOS ONE is excited to publish the Early Diagnosis and Treatment of Alzheimer’s Disease Collection. As the global population ages, the impact and prevalence on Alzheimer’s disease is predicted to rise, making early diagnosis and treatment crucial. PLOS ONE launched a call for papers last year inviting submissions in this important area. This Collection showcases the submissions chosen for inclusion by the guest editors.

We received over 50 submissions, covering topics related to both the diagnosis and treatment of the disease using preclinical methods and clinical data.

Much of the preclinical work in the Collection provides insights that will be valuable for development of future therapeutics, with topics including gene delivery of modified antibodies and possible mechanisms for genes known to act as risk factors for Alzheimer’s. Further studies investigate the potential role of inflammatory responses as risk factors for the disease and the effects of modulation of the immune system in treating pre-symptomatic Alzheimer’s disease in an animal model.

These works are complemented by several clinical papers, many of which bring us closer to early detection of Alzheimer’s disease. This includes studies detecting Alzheimer’s disease with blood-based biomarkers and the correlation between Amyloid-? PET imaging results and cerebrospinal fluid biomarkers.

A number of the papers also make use of machine learning and other computational techniques to analyse genetic, PET imaging and MRI datasets, demonstrating how these can be used to improve detection of the disease.

At launch, the Collection includes 20 papers, with several more to be added as they reach publication. We invite you to revisit the Collection again to read the latest research on this topic.

To celebrate its launch the Guest Editors have selected some of their favourite papers featured in the Collection and provided a short summary.

 

Yona Levites, University of Florida, USA


Image credit: pone.0226245

This study by Elmer and Collegues assesses effects of single chain variable fragment coupled with mutated Fc domain retaining FcRn binding, but lacking Fc gamma receptor (Fc?R) binding (silent scFv-IgG) on amyloid accumulation and aggregation in Alzheimer’s disease transgenic mouse model. The molecule has increased affinity to amyloid as compared to scFv, but toxicity. Interestingly, peripheral AAV delivery resulted in detectable levels of scFv-IgG in the brain. Intracranial injection of anti-amyloid scFv IgG resulted in significant reduction of amyloid burden in TgAPP mice. Future studies will potentially focus on improving the effects of silent scFv-IgG delivered peripherally.

 

Jussi Tohka, University of Eastern Finland, Finland


Image credit: pone.0226784

The current diagnostic criteria allow the use of Cerebro Spinal Fluid (CSF) biomarkers to provide pathophysiological support for the diagnosis of AD. The paper  by Rhodius-Meester and colleagues argues that diagnostic guidelines do not specify which patients should receive CSF testing and the appropriate use criteria, which have been proposed as a guideline, are challenging to translate to clinical practice.  Hence, this study evaluated a computerized decision support system to select patients for CSF biomarker (CSF beta-amyloid 1–42 (AB42), total tau and tau phosphorylated at threonine 181 (p-tau)) determination. In the computerized decision support approach of the study, diagnosis is first attempted using only neuropsychology, MRI and APOE data.  Depending on the confidence of the first diagnosis, the clinician can decide either not to order CSF testing or visualize the effects of the simulated normal and AD-like CSF values on the workflow. Only if the potential change in the confidence of the diagnosis due to CSF is large enough, the clinician orders CSF testing.  The study indicated that this approach could support clinicians in making a balanced decision in ordering additional CSF testing. Specifically, the computerized decision support approach of the study restricted CSF testing to only 26% of cases, without compromising diagnostic accuracy.

Roberta Diaz Brinton, The University of Arizona


Image credit: pone.0222921

The computational analysis by Potashkin, Bottero, Santiago and Quinn yielded new insights regarding gene networks affected in Alzheimer’s while also strengthening the role of metabolic networks in the pathophysiology of the disease. Each of the gene networks identified by this team, glucose homeostasis, glucocorticoid signaling, sleep regulation, and memory, are familiar to those working in the field. The critical insight derived from this analysis is that multiple gene networks are involved in Alzheimer’s and by extension that a single therapeutic target does not address the complexity of the disease. The gene network analyses were conducted on postmortem brain tissue and thus represent the brain in the end stages of the disease. A challenge for the field is to develop accessible and predictive biomarkers of earlier stages of the disease when therapeutic interventions can potentially delay or reverse the disease process. The findings provided by Potashkin and colleagues provide a platform on which to build just such predictive biomarkers.

Michael Weiner, University of California San Francisco, USA


Image credit: pone.0221365

In this paper  comparing amyloid PET with Flutemetamol and measurements of A?42 in cerebrospinal fluid, Müller and co-workers found a significant correlation between 18F-Flutemetamol PET classification and the three CSF biomarkers. The highest correlation was between A?42 and 18F-Flutemetamol PET. Good correlations between CSF A?42   and amyloid PET have been previously reported in many studies.  An  “optimal cut-off value for A?42 “ was used and yielded an improvement in sensitivity, while maintaining a high specificity, for a positive 18F-Flutemetamol PET. 18F-Flutemetamol PET was found to be the best predictor of a clinical AD diagnosis. The authors stated that  “whether biomarkers are to be included in the clinical criteria to further improve their sensitivity is still under investigation.”

 

 

 

 

 

 

 

The post Announcing the PLOS ONE Collection: Early Diagnosis and Treatment of Alzheimer’s Disease appeared first on EveryONE.