Showing papers by "Wageningen University and Research Centre published in 2018"
Jeffrey D. Stanaway1, Ashkan Afshin1, Emmanuela Gakidou1, Stephen S Lim1 +1050 more•Institutions (346)
TL;DR: This study estimated levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs) by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017 and explored the relationship between development and risk exposure.
2,910 citations
Stockholm Resilience Centre1, Stockholm University2, University of Copenhagen3, University of Exeter4, Royal Swedish Academy of Sciences5, University of Arizona6, Scott Polar Research Institute7, Stanford University8, Université catholique de Louvain9, Potsdam Institute for Climate Impact Research10, Australian National University11, Wageningen University and Research Centre12, University of Potsdam13
TL;DR: The risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a “Hothouse Earth” pathway even as human emissions are reduced is explored.
Abstract: We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a "Hothouse Earth" pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System-biosphere, climate, and societies-and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values.
1,685 citations
University of Oxford1, University of Minnesota2, International Food Policy Research Institute3, Commonwealth Scientific and Industrial Research Organisation4, Potsdam Institute for Climate Impact Research5, Technical University of Madrid6, Wageningen University and Research Centre7, Chatham House8, Stockholm Resilience Centre9, Royal Swedish Academy of Sciences10, Bioversity International11, American University of Beirut12, Johns Hopkins University13, University of California, Santa Barbara14, Harvard University15
TL;DR: A global model finds that the environmental impacts of the food system could increase by 60–90% by 2050, and that dietary changes, improvements in technologies and management, and reductions in food loss and waste will all be needed to mitigate these impacts.
Abstract: The food system is a major driver of climate change, changes in land use, depletion of freshwater resources, and pollution of aquatic and terrestrial ecosystems through excessive nitrogen and phosphorus inputs. Here we show that between 2010 and 2050, as a result of expected changes in population and income levels, the environmental effects of the food system could increase by 50–90% in the absence of technological changes and dedicated mitigation measures, reaching levels that are beyond the planetary boundaries that define a safe operating space for humanity. We analyse several options for reducing the environmental effects of the food system, including dietary changes towards healthier, more plant-based diets, improvements in technologies and management, and reductions in food loss and waste. We find that no single measure is enough to keep these effects within all planetary boundaries simultaneously, and that a synergistic combination of measures will be needed to sufficiently mitigate the projected increase in environmental pressures.
1,521 citations
University of East Anglia1, University of Exeter2, Alfred Wegener Institute for Polar and Marine Research3, Ludwig Maximilian University of Munich4, Max Planck Society5, Commonwealth Scientific and Industrial Research Organisation6, Karlsruhe Institute of Technology7, Atlantic Oceanographic and Meteorological Laboratory8, Cooperative Institute for Marine and Atmospheric Studies9, École Normale Supérieure10, Centre national de la recherche scientifique11, University of Maryland, College Park12, University of Virginia13, Flanders Marine Institute14, Oak Ridge National Laboratory15, Woods Hole Research Center16, University of Illinois at Urbana–Champaign17, Geophysical Institute, University of Bergen18, Met Office19, University of California, San Diego20, Utrecht University21, Netherlands Environmental Assessment Agency22, University of Paris23, Oeschger Centre for Climate Change Research24, Tsinghua University25, National Center for Atmospheric Research26, Institute of Arctic and Alpine Research27, National Institute for Environmental Studies28, Hobart Corporation29, Cooperative Research Centre30, Japan Agency for Marine-Earth Science and Technology31, Wageningen University and Research Centre32, University of Groningen33, Bjerknes Centre for Climate Research34, Goddard Space Flight Center35, Leibniz Institute for Baltic Sea Research36, Princeton University37, Leibniz Institute of Marine Sciences38, National Oceanic and Atmospheric Administration39, Auburn University40, Food and Agriculture Organization41, VU University Amsterdam42
TL;DR: In this article, the authors describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties, including emissions from land use and land-use change data and bookkeeping models.
Abstract: . Accurate assessment of anthropogenic carbon dioxide
( CO2 ) emissions and their redistribution among the atmosphere,
ocean, and terrestrial biosphere – the “global carbon budget” – is
important to better understand the global carbon cycle, support the
development of climate policies, and project future climate change. Here we
describe data sets and methodology to quantify the five major components of
the global carbon budget and their uncertainties. Fossil CO2
emissions ( EFF ) are based on energy statistics and cement
production data, while emissions from land use and land-use change ( ELUC ),
mainly deforestation, are based on land use and land-use change data and
bookkeeping models. Atmospheric CO2 concentration is measured
directly and its growth rate ( GATM ) is computed from the annual
changes in concentration. The ocean CO2 sink ( SOCEAN )
and terrestrial CO2 sink ( SLAND ) are estimated with
global process models constrained by observations. The resulting carbon
budget imbalance ( BIM ), the difference between the estimated
total emissions and the estimated changes in the atmosphere, ocean, and
terrestrial biosphere, is a measure of imperfect data and understanding of
the contemporary carbon cycle. All uncertainties are reported as ±1σ . For the last decade available (2008–2017), EFF was
9.4±0.5 GtC yr −1 , ELUC 1.5±0.7 GtC yr −1 , GATM 4.7±0.02 GtC yr −1 ,
SOCEAN 2.4±0.5 GtC yr −1 , and SLAND 3.2±0.8 GtC yr −1 , with a budget imbalance BIM of
0.5 GtC yr −1 indicating overestimated emissions and/or underestimated
sinks. For the year 2017 alone, the growth in EFF was about 1.6 %
and emissions increased to 9.9±0.5 GtC yr −1 . Also for 2017,
ELUC was 1.4±0.7 GtC yr −1 , GATM was 4.6±0.2 GtC yr −1 , SOCEAN was 2.5±0.5 GtC yr −1 , and SLAND was 3.8±0.8 GtC yr −1 ,
with a BIM of 0.3 GtC. The global atmospheric
CO2 concentration reached 405.0±0.1 ppm averaged over 2017.
For 2018, preliminary data for the first 6–9 months indicate a renewed
growth in EFF of + 2.7 % (range of 1.8 % to 3.7 %) based
on national emission projections for China, the US, the EU, and India and
projections of gross domestic product corrected for recent changes in the
carbon intensity of the economy for the rest of the world. The analysis
presented here shows that the mean and trend in the five components of the
global carbon budget are consistently estimated over the period of 1959–2017,
but discrepancies of up to 1 GtC yr −1 persist for the representation
of semi-decadal variability in CO2 fluxes. A detailed comparison
among individual estimates and the introduction of a broad range of
observations show (1) no consensus in the mean and trend in land-use change
emissions, (2) a persistent low agreement among the different methods on
the magnitude of the land CO2 flux in the northern extra-tropics,
and (3) an apparent underestimation of the CO2 variability by ocean
models, originating outside the tropics. This living data update documents
changes in the methods and data sets used in this new global carbon budget
and the progress in understanding the global carbon cycle compared with
previous publications of this data set (Le Quere et al., 2018, 2016,
2015a, b, 2014, 2013). All results presented here can be downloaded from
https://doi.org/10.18160/GCP-2018 .
1,458 citations
TL;DR: It is found that explicit evaluation of soil quality with respect to specific soil threats, soil functions and ecosystem services has rarely been implemented, and few approaches providing clear interpretation schemes of measured indicator values limits their adoption by land managers as well as policy.
Abstract: Sampling and analysis or visual examination of soil to assess its status and use potential is widely practiced from plot to national scales. However, the choice of relevant soil attributes and interpretation of measurements are not straightforward, because of the complexity and site-specificity of soils, legacy effects of previous land use, and trade-offs between ecosystem services. Here we review soil quality and related concepts, in terms of definition, assessment approaches, and indicator selection and interpretation. We identify the most frequently used soil quality indicators under agricultural land use. We find that explicit evaluation of soil quality with respect to specific soil threats, soil functions and ecosystem services has rarely been implemented, and few approaches provide clear interpretation schemes of measured indicator values. This limits their adoption by land managers as well as policy. We also consider novel indicators that address currently neglected though important soil properties and processes, and we list the crucial steps in the development of a soil quality assessment procedure that is scientifically sound and supports management and policy decisions that account for the multi-functionality of soil. This requires the involvement of the pertinent actors, stakeholders and end-users to a much larger degree than practiced to date.
1,257 citations
Swedish University of Agricultural Sciences1, Uppsala University2, University of Tartu3, Charité4, Max Delbrück Center for Molecular Medicine5, Leiden University6, University of Wisconsin-Madison7, Braunschweig University of Technology8, Technical University of Madrid9, Wageningen University and Research Centre10, University of California, Riverside11, University of Oslo12, Lund University13, ETH Zurich14, American Museum of Natural History15, University of Würzburg16
TL;DR: It is shown that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance, and that the relative contributions of these microorganisms to global nutrient cycling varies spatially.
Abstract: Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1–4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial–fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.
1,108 citations
TL;DR: A first systematic analysis of microbiota changes in the ileum and colon using multiple diets and investigating both fecal and mucosal samples demonstrates correlations between the microbiota and dysfunctions of gut, adipose tissue, and liver, independent of a specific disease-inducing diet.
Abstract: Development of non-alcoholic fatty liver disease (NAFLD) is linked to obesity, adipose tissue inflammation, and gut dysfunction, all of which depend on diet. So far, studies have mainly focused on diet-related fecal microbiota changes, but other compartments may be more informative on host health. We present a first systematic analysis of microbiota changes in the ileum and colon using multiple diets and investigating both fecal and mucosal samples. Ldlr−/−.Leiden mice received one of three different energy-dense (ED)-diets (n = 15/group) for 15 weeks. All of the ED diets induced obesity and metabolic risk factors, altered short-chain fatty acids (SCFA), and increased gut permeability and NAFLD to various extents. ED diets reduced the diversity of high-abundant bacteria and increased the diversity of low-abundant bacteria in all of the gut compartments. The ED groups showed highly variable, partially overlapping microbiota compositions that differed significantly from chow. Correlation analyses demonstrated that (1) specific groups of bacteria correlate with metabolic risk factors, organ dysfunction, and NAFLD endpoints, (2) colon mucosa had greater predictive value than other compartments, (3) correlating bacteria differed per compartment, and (4) some bacteria correlated with plasma SCFA levels. In conclusion, this comprehensive microbiota analysis demonstrates correlations between the microbiota and dysfunctions of gut, adipose tissue, and liver, independent of a specific disease-inducing diet.
1,097 citations
Northern Arizona University1, University of Minnesota2, University of California, Davis3, Woods Hole Oceanographic Institution4, Massachusetts Institute of Technology5, University of Copenhagen6, University of Trento7, Chinese Academy of Sciences8, University of California, San Francisco9, Children's Hospital of Philadelphia10, Pacific Northwest National Laboratory11, North Carolina State University12, University of Montana13, Dalhousie University14, University of British Columbia15, Shedd Aquarium16, University of Colorado Denver17, University of California, San Diego18, Michigan State University19, Stanford University20, Broad Institute21, Harvard University22, Australian National University23, University of Düsseldorf24, Sookmyung Women's University25, San Diego State University26, Howard Hughes Medical Institute27, Cornell University28, Max Planck Society29, University of Washington30, Colorado State University31, Google32, Syracuse University33, Webster University34, United States Department of Agriculture35, University of Arkansas for Medical Sciences36, Colorado School of Mines37, Atlantic Oceanographic and Meteorological Laboratory38, University of Southern Mississippi39, University of California, Merced40, Wageningen University and Research Centre41, University of Arizona42, Environment Agency43, University of Florida44, Merck & Co.45
TL;DR: QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Abstract: We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
875 citations
TL;DR: The sources of plastic particles in agroecosystems, the mechanisms, constraints and dynamic behaviour of plastic during aging on land, and the responses of soil organisms and plants at different levels of biological organisation to plastic particles of micro and nano-scale are discussed.
754 citations
18 Jun 2018
TL;DR: The DeepGlobe 2018 Satellite Image Understanding Challenge is presented, which includes three public competitions for segmentation, detection, and classification tasks on satellite images, and characteristics of each dataset are analyzed, and evaluation criteria for each task are defined.
Abstract: We present the DeepGlobe 2018 Satellite Image Understanding Challenge, which includes three public competitions for segmentation, detection, and classification tasks on satellite images (Figure 1). Similar to other challenges in computer vision domain such as DAVIS[21] and COCO[33], DeepGlobe proposes three datasets and corresponding evaluation methodologies, coherently bundled in three competitions with a dedicated workshop co-located with CVPR 2018. We observed that satellite imagery is a rich and structured source of information, yet it is less investigated than everyday images by computer vision researchers. However, bridging modern computer vision with remote sensing data analysis could have critical impact to the way we understand our environment and lead to major breakthroughs in global urban planning or climate change research. Keeping such bridging objective in mind, DeepGlobe aims to bring together researchers from different domains to raise awareness of remote sensing in the computer vision community and vice-versa. We aim to improve and evaluate state-of-the-art satellite image understanding approaches, which can hopefully serve as reference benchmarks for future research in the same topic. In this paper, we analyze characteristics of each dataset, define the evaluation criteria of the competitions, and provide baselines for each task.
652 citations
Vrije Universiteit Brussel1, University of Copenhagen2, University of Gothenburg3, New York University4, University of Pennsylvania5, Wageningen University and Research Centre6, University of Helsinki7, King's College London8, Institut national de la recherche agronomique9, University of Maryland, Baltimore10, Waseda University11, Harvard University12, University College Cork13, University of Minnesota14, University of Texas at Austin15, University of Warwick16, Veterans Health Administration17, Stanford University18, ETH Zurich19, Shanghai Jiao Tong University20, Katholieke Universiteit Leuven21, Molecular Medicine Partnership Unit22, Max Delbrück Center for Molecular Medicine23
TL;DR: The concept of enterotypes and their use to characterize the gut microbiome are debated, a classifier and standardized methodology is provided to aid cross-study comparisons, and a balanced application of the concept is encouraged.
Abstract: Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
TL;DR: The results showed that macro- and micro- plastic residues affected both above-ground and below-ground parts of the wheat plant during both vegetative and reproductive growth and the type of plastic mulch films used had a strong effect on wheat growth.
TL;DR: The potential of Nature based solutions (NBSs) as a cost-effective long term solution for hydrological risks and land degradation is shown and these services directly feed into the realization of the Sustainable Development Goals of the United Nations.
TL;DR: This paper pleads in the short term for a pragmatic form of agriculture that is adaptable, non-dogmatic and combines the sustainability gain from all types of agriculture and pest management methods, and proposes to move to “conscious agriculture”.
Abstract: In augmentative biological control (ABC), invertebrate and microbial organisms are seasonally released in large numbers to reduce pests. Today it is applied on more than 30 million ha worldwide. Europe is the largest commercial market for invertebrate biological control agents, while North America has the largest sales of microbials. A strong growth in use of ABC, particularly of microbial agents, is taking place in Latin America, followed by Asia. The current popularity of ABC is due to (1) its inherent positive characteristics (healthier for farm workers and persons living in farming communities, no harvesting interval or waiting period after release of agents, sustainable as there is no development of resistance against arthropod natural enemies, no phytotoxic damage to plants, better yields and a healthier product, reduced pesticide residues [well below the legal Maximum Residue Levels (MRLs)], (2) professionalism of the biological control industry (inexpensive large scale mass production, proper quality control, efficient packaging, distribution and release methods, and availability of many (>440 species) control agents for numerous pests), (3) a number of recent successes showing how biological control can save agricultural production when pesticides fail or are not available, (4) several non-governmental organizations (NGOs), consumers, and retailers demanding pesticide residues far below the legal MRLs, and (5) policy developments in several regions of the world aimed at reduction and replacement of synthetic pesticides by more sustainable methods of pest management. We are convinced, however, that ABC can be applied on a much larger area than it is today. We plead in the short term for a pragmatic form of agriculture that is adaptable, non-dogmatic and combines the sustainability gain from all types of agriculture and pest management methods. We then propose to move to “conscious agriculture”, which involves participation of all stakeholders in the production and consumer chain, and respects the environment and resource availability for future generations. Were “conscious agriculture” to be considered a serious alternative to conventional farming, ABC would face an even brighter future.
University of Oxford1, Royal Berkshire Hospital2, Clinical Trial Service Unit3, University of Groningen4, McMaster University5, Population Health Research Institute6, Mario Negri Institute for Pharmacological Research7, Quintiles8, Wageningen University and Research Centre9, National Institute for Health Research10, Sorbonne11, National Institutes of Health12
TL;DR: This meta-analysis demonstrated that omega-3 fatty acids had no significant association with fatal or nonfatal coronary heart disease or any major vascular events, and provides no support for current recommendations for the use of such supplements in people with a history of coronaryHeart disease.
Abstract: Importance Current guidelines advocate the use of marine-derived omega-3 fatty acids supplements for the prevention of coronary heart disease and major vascular events in people with prior coronary heart disease, but large trials of omega-3 fatty acids have produced conflicting results. Objective To conduct a meta-analysis of all large trials assessing the associations of omega-3 fatty acid supplements with the risk of fatal and nonfatal coronary heart disease and major vascular events in the full study population and prespecified subgroups. Data Sources and Study Selection This meta-analysis included randomized trials that involved at least 500 participants and a treatment duration of at least 1 year and that assessed associations of omega-3 fatty acids with the risk of vascular events. Data Extraction and Synthesis Aggregated study-level data were obtained from 10 large randomized clinical trials. Rate ratios for each trial were synthesized using observed minus expected statistics and variances. Summary rate ratios were estimated by a fixed-effects meta-analysis using 95% confidence intervals for major diseases and 99% confidence intervals for all subgroups. Main Outcomes and Measures The main outcomes included fatal coronary heart disease, nonfatal myocardial infarction, stroke, major vascular events, and all-cause mortality, as well as major vascular events in study population subgroups. Results Of the 77 917 high-risk individuals participating in the 10 trials, 47 803 (61.4%) were men, and the mean age at entry was 64.0 years; the trials lasted a mean of 4.4 years. The associations of treatment with outcomes were assessed on 6273 coronary heart disease events (2695 coronary heart disease deaths and 2276 nonfatal myocardial infarctions) and 12 001 major vascular events. Randomization to omega-3 fatty acid supplementation (eicosapentaenoic acid dose range, 226-1800 mg/d) had no significant associations with coronary heart disease death (rate ratio [RR], 0.93; 99% CI, 0.83-1.03; P = .05), nonfatal myocardial infarction (RR, 0.97; 99% CI, 0.87-1.08; P = .43) or any coronary heart disease events (RR, 0.96; 95% CI, 0.90-1.01; P = .12). Neither did randomization to omega-3 fatty acid supplementation have any significant associations with major vascular events (RR, 0.97; 95% CI, 0.93-1.01; P = .10), overall or in any subgroups, including subgroups composed of persons with prior coronary heart disease, diabetes, lipid levels greater than a given cutoff level, or statin use. Conclusions and Relevance This meta-analysis demonstrated that omega-3 fatty acids had no significant association with fatal or nonfatal coronary heart disease or any major vascular events. It provides no support for current recommendations for the use of such supplements in people with a history of coronary heart disease.
École Polytechnique de Montréal1, Université de Sherbrooke2, United States Environmental Protection Agency3, Technical University of Berlin4, University of British Columbia5, University of Padua6, National Institute of Advanced Industrial Science and Technology7, Wageningen University and Research Centre8, International Institute of Minnesota9, University of the Free State10, Commonwealth Scientific and Industrial Research Organisation11, University of Tokyo12, ETH Zurich13
TL;DR: This method represents the state of the art of the current knowledge on how to assess potential impacts from water use in LCA, assessing both human and ecosystem users’ potential deprivation, at the midpoint level, and provides a consensus-based methodology for the calculation of a water scarcity footprint as per ISO 14046.
Abstract: Life cycle assessment (LCA) has been used to assess freshwater-related impacts according to a new water footprint framework formalized in the ISO 14046 standard. To date, no consensus-based approach exists for applying this standard and results are not always comparable when different scarcity or stress indicators are used for characterization of impacts. This paper presents the outcome of a 2-year consensus building process by the Water Use in Life Cycle Assessment (WULCA), a working group of the UNEP-SETAC Life Cycle Initiative, on a water scarcity midpoint method for use in LCA and for water scarcity footprint assessments. In the previous work, the question to be answered was identified and different expert workshops around the world led to three different proposals. After eliminating one proposal showing low relevance for the question to be answered, the remaining two were evaluated against four criteria: stakeholder acceptance, robustness with closed basins, main normative choice, and physical meaning. The recommended method, AWARE, is based on the quantification of the relative available water remaining per area once the demand of humans and aquatic ecosystems has been met, answering the question “What is the potential to deprive another user (human or ecosystem) when consuming water in this area?” The resulting characterization factor (CF) ranges between 0.1 and 100 and can be used to calculate water scarcity footprints as defined in the ISO standard. After 8 years of development on water use impact assessment methods, and 2 years of consensus building, this method represents the state of the art of the current knowledge on how to assess potential impacts from water use in LCA, assessing both human and ecosystem users’ potential deprivation, at the midpoint level, and provides a consensus-based methodology for the calculation of a water scarcity footprint as per ISO 14046.
Aarhus University1, University of Edinburgh2, University of Colorado Boulder3, Institute of Arctic and Alpine Research4, National Ecological Observatory Network5, Smithsonian Institution6, Lund University7, VU University Amsterdam8, University of Lapland9, Northern Arizona University10, Bigelow Laboratory For Ocean Sciences11, University of British Columbia12, University of Washington13, Grand Valley State University14, Swiss Federal Institute for Forest, Snow and Landscape Research15, Max Planck Society16, University of Zurich17, Université de Sherbrooke18, University of Greifswald19, University of Parma20, Memorial University of Newfoundland21, Université du Québec à Trois-Rivières22, University of Gothenburg23, Leiden University24, University of California, Riverside25, Qatar University26, Mississippi State University27, University of Barcelona28, Utrecht University29, Umeå University30, University of Alaska Anchorage31, Adam Mickiewicz University in Poznań32, Wageningen University and Research Centre33, Alaska Department of Fish and Game34, University of Tromsø35, University of Vienna36, University of Copenhagen37, Helmholtz Centre for Environmental Research - UFZ38, University of Oulu39, Spanish National Research Council40, Queen's University41, Saint Mary's University42, Oak Ridge National Laboratory43, University of Aberdeen44, University of Saskatchewan45, Vrije Universiteit Brussel46, University of Victoria47, Swiss Federal Institute of Aquatic Science and Technology48, Norwegian University of Science and Technology49, Research Institute for Nature and Forest50, Florida International University51, Moscow State University52, University of Alaska Fairbanks53, University of Waterloo54, Laval University55, Deakin University56, University of Bonn57, United States Forest Service58, Simon Fraser University59, University Centre in Svalbard60, University of Iceland61, United States Fish and Wildlife Service62, Colorado State University63, University of Texas at El Paso64, University of Stirling65, University of Innsbruck66, Rocky Mountain Biological Laboratory67, University of Oxford68, Pacific Northwest National Laboratory69, University of Camerino70, University of Insubria71, University of New South Wales72, University of Manchester73, National University of Cordoba74, Santa Fe Institute75, University of Arizona76, Harvard University77, King Juan Carlos University78, Estonian University of Life Sciences79, Kyoto University80, World Agroforestry Centre81, Radboud University Nijmegen82, Macquarie University83, Forschungszentrum Jülich84, University of Regensburg85, University of Minnesota86, University of Sydney87, Santa Clara University88, Algoma University89, Komarov Botanical Institute90, University of Wisconsin–Eau Claire91
TL;DR: Biome-wide relationships between temperature, moisture and seven key plant functional traits across the tundra and over time show that community height increased with warming across all sites, whereas other traits lagged behind predicted rates of change.
Abstract: The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.
TL;DR: In this article, the authors report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture.
Abstract: In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
Daniel S. Karp1, Rebecca Chaplin-Kramer2, Timothy D. Meehan3, Emily A. Martin4 +153 more•Institutions (81)
TL;DR: Analysis of the largest pest-control database of its kind shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others.
Abstract: The idea that noncrop habitat enhances pest control and represents a win-win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win-win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies.
TL;DR: In this review, the state of the art knowledge concerning anthocyanins in the Solanaceous vegetables, i.e., pepper, tomato, eggplant, and potato, is discussed, including biochemistry and biological function of anthcyanins, as well as their genetic and environmental regulation.
Abstract: Anthocyanins are a group of polyphenolic pigments that are ubiquitously found in the plant kingdom. In plants, anthocyanins play a role not only in reproduction, by attracting pollinators and seed dispersers, but also in protection against various abiotic and biotic stresses. There is accumulating evidence that anthocyanins have health-promoting properties, which makes anthocyanin metabolism an interesting target for breeders and researchers. In this review, the state of the art knowledge concerning anthocyanins in the Solanaceous vegetables, i.e., pepper, tomato, eggplant, and potato, is discussed, including biochemistry and biological function of anthocyanins, as well as their genetic and environmental regulation. Anthocyanin accumulation is determined by the balance between biosynthesis and degradation. Although the anthocyanin biosynthetic pathway has been well-studied in Solanaceous vegetables, more research is needed on the inhibition of biosynthesis and, in particular, the anthocyanin degradation mechanisms if we want to control anthocyanin content of Solanaceous vegetables. In addition, anthocyanin metabolism is distinctly affected by environmental conditions, but the molecular regulation of these effects is poorly understood. Existing knowledge is summarized and current gaps in our understanding are highlighted and discussed, to create opportunities for the development of anthocyanin-rich crops through breeding and environmental management.
TL;DR: The versatile interactions used in adhesives secreted by sandcastle worms and mussels are explored and the variety and combinations of interactions that can be used in the design of new adhesive systems are highlighted.
Abstract: Nature has developed protein-based adhesives whose underwater performance has attracted much research attention over the last few decades. The adhesive proteins are rich in catechols combined with amphiphilic and ionic features. This combination of features constitutes a supramolecular toolbox, to provide stimuli-responsive processing of the adhesive, to secure strong adhesion to a variety of surfaces, and to control the cohesive properties of the material. Here, the versatile interactions used in adhesives secreted by sandcastle worms and mussels are explored. These biological principles are then put in a broader perspective, and synthetic adhesive systems that are based on different types of supramolecular interactions are summarized. The variety and combinations of interactions that can be used in the design of new adhesive systems are highlighted.
TL;DR: In this article, a quantitative analysis of different large-scale harvesting and dewatering systems with focus on processing cost, energy consumption and resource recovery is presented. But, due to required chemicals and loss of flocculants, these systems end at the same cost level as mechanical harvesting systems.
Abstract: Microalgal biomass is processed into products by two main process steps: 1) harvesting and dewatering; and 2) extraction, fractionation and conversion. The performance of unit operations for harvesting and dewatering is often expressed in qualitative terms, like “high energy consumption” and “low in operational cost”. Moreover, equipment is analysed as stand-alone unit operations, which do not interact in a chain of operations. This work concerns a quantitative techno-economic analysis of different large-scale harvesting and dewatering systems with focus on processing cost, energy consumption and resource recovery. Harvesting and dewatering are considered both as a single operation and as combinations of sequential operations. The economic evaluation shows that operational costs and energy consumption are in the range 0.5–2 €·kg− 1 algae and 0.2–5 kWh·kg− 1 of algae, respectively, for dilute solutions from open cultivation systems. Harvesting and dewatering of the dilute systems with flocculation results in the lowest energy requirement. However, due to required chemicals and loss of flocculants, these systems end at the same cost level as mechanical harvesting systems. For closed cultivation systems the operational costs decrease to 0.1–0.6 €·kg− 1 algae and the energy consumption to 0.1–0.7 kWh·kg− 1 algae. For all harvesting and dewatering systems, labour has a significant contribution to the total costs. The total costs can be reduced by a high level of automation, despite the higher associated investment costs. The analysis shows that a single step operation can be satisfactory if the operation reaches high biomass concentrations. Two-step operations, like pressure filtration followed by spiral plate technology or centrifugation, are attractive from an economic point of view, just as the operation chain of flocculation followed by membrane filtration and a finishing step with spiral plate technology or centrifugation.
Martin Luther University of Halle-Wittenberg1, Zürcher Fachhochschule2, University of Bayreuth3, University of Picardie Jules Verne4, University of Oviedo5, Wageningen University and Research Centre6, Masaryk University7, University of Nottingham8, University of Rostock9, Max Planck Society10, Universidade Federal do Rio Grande do Sul11, University of North Carolina at Chapel Hill12, Santa Clara University13, Leiden University14, Academy of Sciences of the Czech Republic15, Shahjalal University of Science and Technology16, Sapienza University of Rome17, Natural Resources Canada18, Florida International University19, Universidade Federal do Acre20, Ghent University21, University of Göttingen22, University of the Basque Country23, Aarhus University24, Rocky Mountain Biological Laboratory25, Environmental Change Institute26, Slovenian Academy of Sciences and Arts27, University of Nova Gorica28, King Juan Carlos University29, Czech University of Life Sciences Prague30, VU University Amsterdam31, University of Würzburg32, National University of Cordoba33, National University of Saint Anthony the Abbot in Cuzco34, Wake Forest University35, University of Exeter36, Université du Québec en Abitibi-Témiscamingue37, University of Montpellier38, University of Adelaide39, University of Chile40, IFREMER41, University of British Columbia42, Universidade do Estado de Santa Catarina43, University of Münster44, University of Hamburg45, University of Wrocław46, Swiss Federal Institute for Forest, Snow and Landscape Research47, University of Zurich48, University of Oldenburg49, University of Waikato50, University of Wyoming51, Institut national de la recherche agronomique52, Sofia University53, Royal Botanic Gardens54, University of Edinburgh55, Landcare Research56, Radboud University Nijmegen57, Spanish National Research Council58, University of Barcelona59, University of Leeds60, University of Tartu61, University of Sydney62, University of Minnesota63, University of Jena64, University of La Serena65, Peking University66, Iwokrama International Centre for Rain Forest Conservation and Development67, Aristotle University of Thessaloniki68, Bulgarian Academy of Sciences69, University of Oulu70, University of Wisconsin–Eau Claire71, International Institute of Minnesota72, American Museum of Natural History73, Leipzig University74
TL;DR: It is shown that global trait composition is captured by two main dimensions that are only weakly related to macro-environmental drivers, which reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale.
Abstract: Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait-environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.
TL;DR: The results of this quality assessment show a dire need for stricter quality assurance in microplastic ingestion studies, and a standardized protocol for detecting microplastics in biota samples incorporating these criteria is provided.
Abstract: Data on ingestion of microplastics by marine biota are quintessential for monitoring and risk assessment of microplastics in the environment. Current studies, however, portray a wide spread in results on the occurrence of microplastic ingestion, highlighting a lack of comparability of results, which might be attributed to a lack of standardization of methods. We critically review and evaluate recent microplastic ingestion studies in aquatic biota, propose a quality assessment method for such studies, and apply the assessment method to the reviewed studies. The quality assessment method uses ten criteria: sampling method and strategy, sample size, sample processing and storage, laboratory preparation, clean air conditions, negative controls, positive controls, target component, sample (pre)treatment, and polymer identification. The results of this quality assessment show a dire need for stricter quality assurance in microplastic ingestion studies. On average, studies score 8.0 out of 20 points for "completeness of information" and 0 for "reliability". Alongside the assessment method, a standardized protocol for detecting microplastic in biota samples incorporating these criteria is provided.
TL;DR: Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity.
Abstract: Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.
Kanazawa University1, Kobe University2, Dalhousie University3, University of Düsseldorf4, University of Osnabrück5, University of Lyon6, University of Oxford7, University of Marburg8, Ghent University9, University of Würzburg10, Charles University in Prague11, Martin Luther University of Halle-Wittenberg12, Adelphi University13, University of Jena14, Leibniz Association15, University of Maryland, College Park16, National Institute of Genetics17, University of Tokyo18, Wageningen University and Research Centre19, John Innes Centre20, New York Botanical Garden21, University of Copenhagen22, University of Cologne23, University of Pretoria24, Institute of Science and Technology Austria25, University of New South Wales26, University of Toulouse27, Université Paris-Saclay28
TL;DR: Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.
Columbia University1, University of Freiburg2, Delft University of Technology3, University of Düsseldorf4, Clemson University5, University of Sheffield6, Aarhus University7, Ludwig Maximilian University of Munich8, Stony Brook University9, University of California, Irvine10, University of Groningen11, University of Ulm12, Wageningen University and Research Centre13, Johns Hopkins University14, North Carolina State University15, Dresden University of Technology16, Katholieke Universiteit Leuven17, University of Hasselt18, University of Lübeck19, University of Oxford20, Seoul National University21, Kaiserslautern University of Technology22, University of Mainz23, Institute of Molecular Biotechnology24, Arizona State University25, University of Zurich26, Braunschweig University of Technology27
TL;DR: A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes.
Abstract: Single-molecule Forster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.
TL;DR: A global attainment analysis of the feasibility of attaining SDG targets on the basis of past trends and a estimates of health-related SDG index values in countries assessed at the subnational level varied substantially, particularly in China and India, although scores in Japan and the UK were more homogeneous.
TL;DR: Results from field samples collected from North-western China prove that the method of repetitive floatation and heating can be used to extract, distinguish and quantify light density polyethylene microplastics in soils.
TL;DR: An overview of the enormous morphological, taxonomical and functional diversity of soil protists is provided, and current challenges and opportunities in soil protistology are discussed.
Abstract: Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.