Showing papers by "Wageningen University and Research Centre published in 2019"
Northern Arizona University1, National Institutes of Health2, University of Minnesota3, Woods Hole Oceanographic Institution4, University of California, Davis5, Massachusetts Institute of Technology6, University of Copenhagen7, University of Trento8, Chinese Academy of Sciences9, University of California, San Francisco10, University of Pennsylvania11, Pacific Northwest National Laboratory12, North Carolina State University13, University of California, San Diego14, Institute for Systems Biology15, Dalhousie University16, University of British Columbia17, Statens Serum Institut18, Anschutz Medical Campus19, University of Washington20, Michigan State University21, Stanford University22, Broad Institute23, Harvard University24, Australian National University25, University of Düsseldorf26, University of New South Wales27, Sookmyung Women's University28, San Diego State University29, Howard Hughes Medical Institute30, Cornell University31, Max Planck Society32, Colorado State University33, Google34, Syracuse University35, Webster University36, United States Department of Agriculture37, University of Arkansas for Medical Sciences38, Colorado School of Mines39, University of Southern Mississippi40, National Oceanic and Atmospheric Administration41, University of California, Merced42, Wageningen University and Research Centre43, University of Arizona44, Environment Agency45, University of Florida46, Merck & Co.47
TL;DR: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Abstract: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.
8,821 citations
Harvard University1, Potsdam Institute for Climate Impact Research2, Stockholm Resilience Centre3, University of Oxford4, City University London5, Chatham House6, World Wide Fund for Nature7, Environmental Change Institute8, University of California, Santa Barbara9, University of Minnesota10, CGIAR11, Johns Hopkins University12, American University of Beirut13, Wageningen University and Research Centre14, Institute for Health Metrics and Evaluation15, ETH Zurich16, Indian Institute of Technology Kanpur17, Commonwealth Scientific and Industrial Research Organisation18, University of Indonesia19, World Health Organization20, Food and Agriculture Organization21, International Food Policy Research Institute22, Royal Swedish Academy of Sciences23, University of Auckland24, Public Health Foundation of India25, Centre for Science and Environment26
TL;DR: Food in the Anthropocene : the EAT-Lancet Commission on healthy diets from sustainable food systems focuses on meat, fish, vegetables and fruit as sources of protein.
4,710 citations
TL;DR: AntiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-Ri PPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines and provides more detailed predictions for type II polyketide synthase-encoding gene clusters.
Abstract: Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.
2,084 citations
TL;DR: More high quality data is needed on the occurrence of microplastics in drinking water, to better understand potential exposure and to inform human health risk assessments, and there is a significant need to improve quality assurance ofmicroplastic sampling and analysis in water samples.
1,148 citations
TL;DR: In this article, Akkermansia muciniphila, a gut microbe previously associated with metabolic health in preclinical models, is safe and well tolerated in humans and may improve metabolic parameters in overweight and obese patients.
Abstract: Metabolic syndrome is characterized by a constellation of comorbidities that predispose individuals to an increased risk of developing cardiovascular pathologies as well as type 2 diabetes mellitus1. The gut microbiota is a new key contributor involved in the onset of obesity-related disorders2. In humans, studies have provided evidence for a negative correlation between Akkermansia muciniphila abundance and overweight, obesity, untreated type 2 diabetes mellitus or hypertension3–8. Since the administration of A. muciniphila has never been investigated in humans, we conducted a randomized, double-blind, placebo-controlled pilot study in overweight/obese insulin-resistant volunteers; 40 were enrolled and 32 completed the trial. The primary end points were safety, tolerability and metabolic parameters (that is, insulin resistance, circulating lipids, visceral adiposity and body mass). Secondary outcomes were gut barrier function (that is, plasma lipopolysaccharides) and gut microbiota composition. In this single-center study, we demonstrated that daily oral supplementation of 1010 A. muciniphila bacteria either live or pasteurized for three months was safe and well tolerated. Compared to placebo, pasteurized A. muciniphila improved insulin sensitivity (+28.62 ± 7.02%, P = 0.002), and reduced insulinemia (−34.08 ± 7.12%, P = 0.006) and plasma total cholesterol (−8.68 ± 2.38%, P = 0.02). Pasteurized A. muciniphila supplementation slightly decreased body weight (−2.27 ± 0.92 kg, P = 0.091) compared to the placebo group, and fat mass (−1.37 ± 0.82 kg, P = 0.092) and hip circumference (−2.63 ± 1.14 cm, P = 0.091) compared to baseline. After three months of supplementation, A. muciniphila reduced the levels of the relevant blood markers for liver dysfunction and inflammation while the overall gut microbiome structure was unaffected. In conclusion, this proof-of-concept study (clinical trial no. NCT02637115) shows that the intervention was safe and well tolerated and that supplementation with A. muciniphila improves several metabolic parameters. Supplementation with Akkermansia muciniphila, a gut microbe previously associated with metabolic health in preclinical models, is safe and well tolerated in humans and may improve metabolic parameters in overweight and obese patients.
1,107 citations
University of Exeter1, École Normale Supérieure2, Norwich Research Park3, Alfred Wegener Institute for Polar and Marine Research4, Wageningen University and Research Centre5, University of Groningen6, Max Planck Society7, Ludwig Maximilian University of Munich8, Commonwealth Scientific and Industrial Research Organisation9, Centre national de la recherche scientifique10, Stanford University11, Karlsruhe Institute of Technology12, Atlantic Oceanographic and Meteorological Laboratory13, Cooperative Institute for Marine and Atmospheric Studies14, Bjerknes Centre for Climate Research15, Geophysical Institute, University of Bergen16, Japan Agency for Marine-Earth Science and Technology17, University of Maryland, College Park18, National Institute of Water and Atmospheric Research19, National Oceanic and Atmospheric Administration20, Appalachian State University21, Flanders Marine Institute22, Augsburg College23, ETH Zurich24, Leibniz Institute of Marine Sciences25, University of East Anglia26, Woods Hole Research Center27, University of Illinois at Urbana–Champaign28, University of Hong Kong29, Utrecht University30, Netherlands Environmental Assessment Agency31, University of Paris32, University of Tasmania33, Hobart Corporation34, University of Bern35, National Center for Atmospheric Research36, University of Reading37, Cooperative Institute for Research in Environmental Sciences38, National Institute for Environmental Studies39, Russian Academy of Sciences40, Goddard Space Flight Center41, Leibniz Institute for Baltic Sea Research42, Princeton University43, Met Office44, Lund University45, Auburn University46, Food and Agriculture Organization47, VU University Amsterdam48
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, and show that 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.
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 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 (2009–2018), EFF was 9.5±0.5 GtC yr −1 ,
ELUC 1.5±0.7 GtC yr −1 , GATM 4.9±0.02 GtC yr −1 ( 2.3±0.01 ppm yr −1 ), SOCEAN 2.5±0.6 GtC yr −1 , and SLAND 3.2±0.6 GtC yr −1 , with a budget
imbalance BIM of 0.4 GtC yr −1 indicating overestimated emissions
and/or underestimated sinks. For the year 2018 alone, the growth in EFF was
about 2.1 % and fossil emissions increased to 10.0±0.5 GtC yr −1 , reaching 10 GtC yr −1 for the first time in history,
ELUC was 1.5±0.7 GtC yr −1 , for total anthropogenic
CO2 emissions of 11.5±0.9 GtC yr −1 ( 42.5±3.3 GtCO2 ). Also for 2018, GATM was 5.1±0.2 GtC yr −1 ( 2.4±0.1 ppm yr −1 ), SOCEAN was 2.6±0.6 GtC yr −1 , and SLAND was 3.5±0.7 GtC yr −1 , with a BIM of 0.3 GtC. The global atmospheric CO2 concentration reached 407.38±0.1 ppm averaged over 2018. For 2019, preliminary data for the first 6–10 months indicate a reduced growth in EFF of +0.6 % (range of
−0.2 % to 1.5 %) based on national emissions projections for China, the
USA, 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. Overall, the mean and trend in the five components of the global
carbon budget are consistently estimated over the period 1959–2018, 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
shows (1) no consensus in the mean and trend in land use change emissions
over the last decade, (2) a persistent low agreement between 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 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 of the global carbon cycle
compared with previous publications of this data set (Le Quere et
al., 2018a, b, 2016, 2015a, b, 2014, 2013). The data generated by
this work are available at https://doi.org/10.18160/gcp-2019 (Friedlingstein
et al., 2019).
981 citations
TL;DR: Improved brine management strategies are required to limit the negative environmental impacts and reduce the economic cost of disposal, thereby stimulating further developments in desalination facilities to safeguard water supplies for current and future generations.
932 citations
Stanford University1, University of Chicago2, Willamette University3, Wageningen University and Research Centre4, University of Bristol5, Bat Conservation International6, Royal Swedish Academy of Sciences7, Stockholm Resilience Centre8, University of Washington9, Wellcome Trust10, Uppsala University11, University of Illinois at Urbana–Champaign12, The Nature Conservancy13, Heidelberg University14, University of Glasgow15, Chinese Academy of Sciences16, University of Virginia17, University of British Columbia18, University of Exeter19
TL;DR: It is shown how ecosystem service assessments can be expanded to include mental health, and a heuristic, conceptual model for doing so is provided.
Abstract: A growing body of empirical evidence is revealing the value of nature experience for mental health. With rapid urbanization and declines in human contact with nature globally, crucial decisions must be made about how to preserve and enhance opportunities for nature experience. Here, we first provide points of consensus across the natural, social, and health sciences on the impacts of nature experience on cognitive functioning, emotional well-being, and other dimensions of mental health. We then show how ecosystem service assessments can be expanded to include mental health, and provide a heuristic, conceptual model for doing so.
736 citations
TL;DR: The results indicate that microplastic counts increase over time where successive sludge applications are performed, and stress the relevance of sludge as a driver of soil microplastics contamination.
667 citations
TL;DR: The nature of the mode of action of antagonists requires a rethinking of data requirements for the registration of MBCAs, and risks of microbial metabolites involved in antagonistic modes of action are often assessed similar to assessments of single molecule fungicides.
Abstract: Microbial biological control agents (MBCAs) are applied to crops for biological control of plant pathogens where they act via a range of modes of action. Some MBCAs interact with plants by inducing resistance or priming plants without any direct interaction with the targeted pathogen. Other MBCAs act via nutrient competition or other mechanisms modulating the growth conditions for the pathogen. Antagonists acting through hyperparasitism and antibiosis are directly interfering with the pathogen. Such interactions are highly regulated cascades of metabolic events, often combining different modes of action. Compounds involved such as signaling compounds, enzymes and other interfering metabolites are produced in situ at low concentrations during interaction. The potential of microorganisms to produce such a compound in vitro does not necessarily correlate with their in situ antagonism. Understanding the mode of action of MBCAs is essential to achieve optimum disease control. Also understanding the mode of action is important to be able to characterize possible risks for humans or the environment and risks for resistance development against the MBCA. Preferences for certain modes of action for an envisaged application of a MBCA also have impact on the screening methods used to select new microbials. Screening of MBCAs in bioassays on plants or plant tissues has the advantage that MBCAs with multiple modes of action and their combinations potentially can be detected whereas simplified assays on nutrient media strongly bias the selection toward in vitro production of antimicrobial metabolites which may not be responsible for in situ antagonism. Risks assessments for MBCAs are relevant if they contain antimicrobial metabolites at effective concentration in the product. However, in most cases antimicrobial metabolites are produced by antagonists directly on the spot where the targeted organism is harmful. Such ubiquitous metabolites involved in natural, complex, highly regulated interactions between microbial cells and/or plants are not relevant for risk assessments. Currently, risks of microbial metabolites involved in antagonistic modes of action are often assessed similar to assessments of single molecule fungicides. The nature of the mode of action of antagonists requires a rethinking of data requirements for the registration of MBCAs.
615 citations
TL;DR: In this paper, the authors presented a paper on the African Climate and Development Initiative (ACDI) in South Africa, focusing on the effects of climate change on the local environment.
Abstract: 1 Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA 2 School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia 3 Conservation Biology Institute, 136 SW Washington Avenue, Suite 202, Corvallis, OR 97333, USA 4 African Climate and Development Initiative, University of Cape Town, Cape Town, 7700, South Africa. 5 The Fletcher School and Global Development and Environment Institute, Tufts University, Medford, MA, USA
ETH Zurich1, University of California, Davis2, Bielefeld University3, Nanyang Technological University4, Wageningen University and Research Centre5, Brigham Young University6, Aligarh Muslim University7, Colorado State University8, University of Manchester9, University of Cologne10, University of La Rioja11, University of Brasília12, Queen's University Belfast13, Nanjing Agricultural University14, University of Minho15, Empresa Brasileira de Pesquisa Agropecuária16, Zealand Institute of Business and Technology17, Spanish National Research Council18, Scotland's Rural College19, American Museum of Natural History20, Russian Academy of Sciences21, Swedish University of Agricultural Sciences22, University of Göttingen23, Chinese Academy of Sciences24, University of Catania25, University of Nebraska–Lincoln26, James Hutton Institute27, Vietnam Academy of Science and Technology28, University of Sydney29, Bulgarian Academy of Sciences30, Universidade Federal de Lavras31, University of Helsinki32, University of Montpellier33, Aarhus University34, Lancaster University35, National Taiwan University36
TL;DR: High-resolution spatial maps of the global abundance of soil nematodes and the composition of functional groups show that soil nematode are found in higher abundances in sub-Arctic regions, than in temperate or tropical regions.
Abstract: Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios.
TL;DR: It is suggested that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR.
Abstract: Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
TL;DR: The presence of mixtures of pesticide residues in soils are the rule rather than the exception, indicating that environmental risk assessment procedures should be adapted accordingly to minimize related risks to soil life and beyond.
TL;DR: This review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
Abstract: Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
TL;DR: The results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.
Abstract: Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.
TL;DR: The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
Günter Blöschl1, Marc F. P. Bierkens2, António Chambel3, Christophe Cudennec4 +209 more•Institutions (124)
TL;DR: In this article, a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts is described. But despite the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work.
Abstract: This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.
Imperial College London1, German Aerospace Center2, Wageningen University and Research Centre3, Clarkson University4, University of Valencia5, VU University Amsterdam6, Potsdam Institute for Climate Impact Research7, University of California, San Diego8, Carnegie Mellon University9, Max Planck Society10, University of Copenhagen11, University of Amsterdam12, Oeschger Centre for Climate Change Research13, University of Bern14, ETH Zurich15
TL;DR: An overview of causal inference frameworks is given, promising applications and methodological challenges are identified, and a causality benchmark platform is initiated to close the gap between method users and developers.
Abstract: The heart of the scientific enterprise is a rational effort to understand the causes behind the phenomena we observe. In large-scale complex dynamical systems such as the Earth system, real experiments are rarely feasible. However, a rapidly increasing amount of observational and simulated data opens up the use of novel data-driven causal methods beyond the commonly adopted correlation techniques. Here, we give an overview of causal inference frameworks and identify promising generic application cases common in Earth system sciences and beyond. We discuss challenges and initiate the benchmark platform causeme.net to close the gap between method users and developers.
TL;DR: In this paper, the authors present seventeen articles dealing with social, economic and institutional dynamics of precision farming, digital agriculture, smart farming or agriculture 4.0, and reveal new insights on the link between digital agriculture and farm diversity, new economic, business and institutional arrangements both on-farm, in the value chain and food system, and in the innovation system.
Abstract: While there is a lot of literature from a natural or technical sciences perspective on different forms of digitalization in agriculture (big data, internet of things, augmented reality, robotics, sensors, 3D printing, system integration, ubiquitous connectivity, artificial intelligence, digital twins, and blockchain among others), social science researchers have recently started investigating different aspects of digital agriculture in relation to farm production systems, value chains and food systems. This has led to a burgeoning but scattered social science body of literature. There is hence lack of overview of how this field of study is developing, and what are established, emerging, and new themes and topics. This is where this article aims to make a contribution, beyond introducing this special issue which presents seventeen articles dealing with social, economic and institutional dynamics of precision farming, digital agriculture, smart farming or agriculture 4.0. An exploratory literature review shows that five thematic clusters of extant social science literature on digitalization in agriculture can be identified: 1) Adoption, uses and adaptation of digital technologies on farm; 2) Effects of digitalization on farmer identity, farmer skills, and farm work; 3) Power, ownership, privacy and ethics in digitalizing agricultural production systems and value chains; 4) Digitalization and agricultural knowledge and innovation systems (AKIS); and 5) Economics and management of digitalized agricultural production systems and value chains. The main contributions of the special issue articles are mapped against these thematic clusters, revealing new insights on the link between digital agriculture and farm diversity, new economic, business and institutional arrangements both on-farm, in the value chain and food system, and in the innovation system, and emerging ways to ethically govern digital agriculture. Emerging lines of social science enquiry within these thematic clusters are identified and new lines are suggested to create a future research agenda on digital agriculture, smart farming and agriculture 4.0. Also, four potential new thematic social science clusters are also identified, which so far seem weakly developed: 1) Digital agriculture socio-cyber-physical-ecological systems conceptualizations; 2) Digital agriculture policy processes; 3) Digitally enabled agricultural transition pathways; and 4) Global geography of digital agriculture development. This future research agenda provides ample scope for future interdisciplinary and transdisciplinary science on precision farming, digital agriculture, smart farming and agriculture 4.0.
University of Würzburg1, National University of Comahue2, Spanish National Research Council3, Swedish University of Agricultural Sciences4, University of Lisbon5, Universidade Federal de Goiás6, Stanford University7, Commonwealth Scientific and Industrial Research Organisation8, National University of Río Negro9, ETH Zurich10, Cornell University11, University of California, Davis12, The Nature Conservancy13, Wageningen University and Research Centre14, University of British Columbia15, Great Lakes Bioenergy Research Center16, University of California, Santa Cruz17, University of Padua18, University of New England (Australia)19, Lund University20, University of Göttingen21, University of La Rochelle22, Institut national de la recherche agronomique23, Federal University of Ceará24, University of Freiburg25, Concordia University Wisconsin26, University of Belgrade27, National University of Tucumán28, Michigan State University29, University of Brasília30, University of Greenwich31, University of Reading32, University of Wisconsin-Madison33, National Institute of Amazonian Research34, Boise State University35, University of Texas at Austin36, University of Haifa37, Kansas State University38, University of Hamburg39, Bioversity International40, University of California, Santa Barbara41, Seattle University42, University of Vienna43, University of Florida44, Centro Agronómico Tropical de Investigación y Enseñanza45, National Audubon Society46, University of Buenos Aires47, Virginia Tech48, University of Bordeaux49, University of Auckland50, University of California, Berkeley51, University College Dublin52, Trinity College, Dublin53, University of Tokyo54, Federal University of Bahia55, Lincoln University (New Zealand)56, National Institute for Environmental Studies57, International Food Policy Research Institute58, Xi'an Jiaotong-Liverpool University59
TL;DR: Using a global database from 89 studies (with 1475 locations), the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change is partitioned.
Abstract: Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.
TL;DR: The goal of the perspective is not to present a convincing answer to these questions, but to assess the scientific progress to date, while highlighting new and innovative avenues to keep advancing the understanding in the future.
Abstract: Droughts and heatwaves cause agricultural loss, forest mortality, and drinking water scarcity, especially when they occur simultaneously as combined events. Their predicted increase in recurrence and intensity poses serious threats to future food security. Still today, the knowledge of how droughts and heatwaves start and evolve remains limited, and so does our understanding of how climate change may affect them. Droughts and heatwaves have been suggested to intensify and propagate via land-atmosphere feedbacks. However, a global capacity to observe these processes is still lacking, and climate and forecast models are immature when it comes to representing the influences of land on temperature and rainfall. Key open questions remain in our goal to uncover the real importance of these feedbacks: What is the impact of the extreme meteorological conditions on ecosystem evaporation? How do these anomalies regulate the atmospheric boundary layer state (event self-intensification) and contribute to the inflow of heat and moisture to other regions (event self-propagation)? Can this knowledge on the role of land feedbacks, when available, be exploited to develop geo-engineering mitigation strategies that prevent these events from aggravating during their early stages? The goal of our perspective is not to present a convincing answer to these questions, but to assess the scientific progress to date, while highlighting new and innovative avenues to keep advancing our understanding in the future.
TL;DR: MIBiG 2.0 is presented, which encompasses major updates to the schema, the data, and the online repository itself, and improves the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases.
Abstract: Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.
TL;DR: The provided MLR guidelines will support researchers to effectively and efficiently conduct new MLRs in any area of SE and are recommended to utilize in their MLR studies and then share their lessons learned and experiences.
Abstract: Context A Multivocal Literature Review (MLR) is a form of a Systematic Literature Review (SLR) which includes the grey literature (e.g., blog posts, videos and white papers) in addition to the published (formal) literature (e.g., journal and conference papers). MLRs are useful for both researchers and practitioners since they provide summaries both the state-of-the art and –practice in a given area. MLRs are popular in other fields and have recently started to appear in software engineering (SE). As more MLR studies are conducted and reported, it is important to have a set of guidelines to ensure high quality of MLR processes and their results. Objective There are several guidelines to conduct SLR studies in SE. However, several phases of MLRs differ from those of traditional SLRs, for instance with respect to the search process and source quality assessment. Therefore, SLR guidelines are only partially useful for conducting MLR studies. Our goal in this paper is to present guidelines on how to conduct MLR studies in SE. Method To develop the MLR guidelines, we benefit from several inputs: (1) existing SLR guidelines in SE, (2), a literature survey of MLR guidelines and experience papers in other fields, and (3) our own experiences in conducting several MLRs in SE. We took the popular SLR guidelines of Kitchenham and Charters as the baseline and extended/adopted them to conduct MLR studies in SE. All derived guidelines are discussed in the context of an already-published MLR in SE as the running example. Results The resulting guidelines cover all phases of conducting and reporting MLRs in SE from the planning phase, over conducting the review to the final reporting of the review. In particular, we believe that incorporating and adopting a vast set of experience-based recommendations from MLR guidelines and experience papers in other fields have enabled us to propose a set of guidelines with solid foundations. Conclusion Having been developed on the basis of several types of experience and evidence, the provided MLR guidelines will support researchers to effectively and efficiently conduct new MLRs in any area of SE. The authors recommend the researchers to utilize these guidelines in their MLR studies and then share their lessons learned and experiences.
TL;DR: In this paper, the authors provide a transition intermediary type typology that is sensitive to the emergence, neutrality and goals of intermediary actors as well as their context and level of action.
Jeroen R. Huyghe1, Stephanie A. Bien1, Tabitha A. Harrison1, Hyun Min Kang2 +221 more•Institutions (68)
TL;DR: Genome-wide association analyses based on whole-genome sequencing and imputation identify 40 new risk variants for colorectal cancer, including a strongly protective low-frequency variant at CHD1 and loci implicating signaling and immune function in disease etiology.
Abstract: To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Kruppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
University of Würzburg1, Lund University2, Swedish University of Agricultural Sciences3, Commonwealth Scientific and Industrial Research Organisation4, University of Reading5, Wageningen University and Research Centre6, University of Padua7, University of Rennes8, University of Salamanca9, Agrocampus Ouest10, Sant'Anna School of Advanced Studies11, Spanish National Research Council12, Aix-Marseille University13, University of Kiel14, University of Freiburg15, University of Jyväskylä16, University of Koblenz and Landau17, University of Marburg18, Technische Universität München19, University of Natural Resources and Life Sciences, Vienna20, National University of Río Negro21, Instituto Nacional de Biodiversidad22, University of Giessen23, University of Belgrade24, Institut national de la recherche agronomique25, University of Extremadura26, University of Bordeaux27, University of Bern28, CABI29, University of Göttingen30, Pir Mehr Ali Shah Arid Agriculture University31
TL;DR: In landscapes with high edge density, 70% of pollinator and 44% of natural enemy species reached highest abundances and pollination and pest control improved 1.7- and 1.4-fold respectively, suggesting that enhancing edge density in European agroecosystems can promote functional biodiversity and yield-enhancing ecosystem services.
Abstract: Managing agricultural landscapes to support biodiversity and ecosystem services is a key aim of a sustainable agriculture. However, how the spatial arrangement of crop fields and other habitats in landscapes impacts arthropods and their functions is poorly known. Synthesising data from 49 studies (1515 landscapes) across Europe, we examined effects of landscape composition (% habitats) and configuration (edge density) on arthropods in fields and their margins, pest control, pollination and yields. Configuration effects interacted with the proportions of crop and non-crop habitats, and species’ dietary, dispersal and overwintering traits led to contrasting responses to landscape variables. Overall, however, in landscapes with high edge density, 70% of pollinator and 44% of natural enemy species reached highest abundances and pollination and pest control improved 1.7- and 1.4-fold respectively. Arable-dominated landscapes with high edge densities achieved high yields. This suggests that enhancing edge density in European agroecosystems can promote functional biodiversity and yield-enhancing ecosystem services.
TL;DR: In this paper, the authors argue that current attempts to equate or subsume healthy diets within sustainability in the context of food system may be misleading and need to be challenged, and stress that trade-offs between different dimensions of sustainable food system sustainability are unavoidable.
TL;DR: A spatially explicit global map of the symbiotic status of forests, using a database of over 1.1 million forest inventory plots that collectively contain over 28,000 tree species, reveals that climate variables are the primary drivers of the distribution of different types of symbiosis.
Abstract: The identity of the dominant root-associated microbial symbionts in a forest determines the ability of trees to access limiting nutrients from atmospheric or soil pools1,2, sequester carbon3,4 and withstand the effects of climate change5,6. Characterizing the global distribution of these symbioses and identifying the factors that control this distribution are thus integral to understanding the present and future functioning of forest ecosystems. Here we generate a spatially explicit global map of the symbiotic status of forests, using a database of over 1.1 million forest inventory plots that collectively contain over 28,000 tree species. Our analyses indicate that climate variables—in particular, climatically controlled variation in the rate of decomposition—are the primary drivers of the global distribution of major symbioses. We estimate that ectomycorrhizal trees, which represent only 2% of all plant species7, constitute approximately 60% of tree stems on Earth. Ectomycorrhizal symbiosis dominates forests in which seasonally cold and dry climates inhibit decomposition, and is the predominant form of symbiosis at high latitudes and elevation. By contrast, arbuscular mycorrhizal trees dominate in aseasonal, warm tropical forests, and occur with ectomycorrhizal trees in temperate biomes in which seasonally warm-and-wet climates enhance decomposition. Continental transitions between forests dominated by ectomycorrhizal or arbuscular mycorrhizal trees occur relatively abruptly along climate-driven decomposition gradients; these transitions are probably caused by positive feedback effects between plants and microorganisms. Symbiotic nitrogen fixers—which are insensitive to climatic controls on decomposition (compared with mycorrhizal fungi)—are most abundant in arid biomes with alkaline soils and high maximum temperatures. The climatically driven global symbiosis gradient that we document provides a spatially explicit quantitative understanding of microbial symbioses at the global scale, and demonstrates the critical role of microbial mutualisms in shaping the distribution of plant species.
TL;DR: It is shown that fungicides occur widely in aquatic systems, that the accuracy of predicted environmental concentrations is debatable, and that fungicide exposure can be effectively mitigated, andThat fungicides can be highly toxic to a broad range of organisms and can pose a risk to aquatic biota.
Abstract: Fungicides are indispensable to global food security and their use is forecasted to intensify. Fungicides can reach aquatic ecosystems and occur in surface water bodies in agricultural catchments throughout the entire growing season due to their frequent, prophylactic application. However, in comparison to herbicides and insecticides, the exposure to and effects of fungicides have received less attention. We provide an overview of the risk of fungicides to aquatic ecosystems covering fungicide exposure (i.e., environmental fate, exposure modeling, and mitigation measures) as well as direct and indirect effects of fungicides on microorganisms, macrophytes, invertebrates, and vertebrates. We show that fungicides occur widely in aquatic systems, that the accuracy of predicted environmental concentrations is debatable, and that fungicide exposure can be effectively mitigated. We additionally demonstrate that fungicides can be highly toxic to a broad range of organisms and can pose a risk to aquatic biota. Finally, we outline central research gaps that currently challenge our ability to predict fungicide exposure and effects, promising research avenues, and shortcomings of the current environmental risk assessment for fungicides.