Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Toward the improvement of total nitrogen deposition budgets in the United States
Walker, J.T. ; Beachley, G. ; Amos, H.M. ; Baron, J.S. ; Bash, J. ; Baumgardner, R. ; Bell, M.D. ; Benedict, K.B. ; Chen, X. ; Clow, D.W. ; Cole, A. ; Coughlin, J.G. ; Cruz, K. ; Daly, R.W. ; Decina, S.M. ; Elliott, E.M. ; Fenn, M.E. ; Ganzeveld, L. ; Gebhart, K. ; Isil, S.S. ; Kerschner, B.M. ; Larson, R.S. ; Lavery, T. ; Lear, G.G. ; Macy, T. ; Mast, M.A. ; Mishoe, K. ; Morris, K.H. ; Padgett, P.E. ; Pouyat, R.V. ; Puchalski, M. ; Pye, H.O.T. ; Rea, A.W. ; Rhodes, M.F. ; Rogers, C.M. ; Saylor, R. ; Scheffe, R. ; Schichtel, B.A. ; Schwede, D.B. ; Sexstone, G.A. ; Sive, B.C. ; Sosa, R. ; Templer, P.H. ; Thompson, T. ; Tong, D. ; Wetherbee, G.A. ; Whitlow, T.H. ; Wu, Z. ; Yu, Z. ; Zhang, L. - \ 2019
Science of the Total Environment 691 (2019). - ISSN 0048-9697 - p. 1328 - 1352.
Ammonia - Dry deposition - Organic nitrogen - Oxidized nitrogen - Reactive nitrogen - Wet deposition

Frameworks for limiting ecosystem exposure to excess nutrients and acidity require accurate and complete deposition budgets of reactive nitrogen (Nr). While much progress has been made in developing total Nr deposition budgets for the U.S., current budgets remain limited by key data and knowledge gaps. Analysis of National Atmospheric Deposition Program Total Deposition (NADP/TDep) data illustrates several aspects of current Nr deposition that motivate additional research. Averaged across the continental U.S., dry deposition contributes slightly more (55%) to total deposition than wet deposition and is the dominant process (>90%) over broad areas of the Southwest and other arid regions of the West. Lack of dry deposition measurements imposes a reliance on models, resulting in a much higher degree of uncertainty relative to wet deposition which is routinely measured. As nitrogen oxide (NOx) emissions continue to decline, reduced forms of inorganic nitrogen (NHx = NH3 + NH4 +) now contribute >50% of total Nr deposition over large areas of the U.S. Expanded monitoring and additional process-level research are needed to better understand NHx deposition, its contribution to total Nr deposition budgets, and the processes by which reduced N deposits to ecosystems. Urban and suburban areas are hotspots where routine monitoring of oxidized and reduced Nr deposition is needed. Finally, deposition budgets have incomplete information about the speciation of atmospheric nitrogen; monitoring networks do not capture important forms of Nr such as organic nitrogen. Building on these themes, we detail the state of the science of Nr deposition budgets in the U.S. and highlight research priorities to improve deposition budgets in terms of monitoring and flux measurements, leaf- to regional-scale modeling, source apportionment, and characterization of deposition trends and patterns.

Applying ecosystem services for pre-market environmental risk assessments of regulated stressors
Devos, Y. ; Munns Jr., W.R. ; Forbes, V.E. ; Maltby, Lorraine ; Stenseke, Marie ; Brussaard, L. ; Streissl, F. ; Hardy, A. - \ 2019
In: Proceedings of the Third EFSA Scientific Conference: Science, Food and Society Guest / Devos, Y., Elliott, K.C., Hardy, A., John Wiley and Sons (EFSA Journal S1)
Ecosystem services (ES) are the benefits that people obtain from ecosystems. Investigating the environment through an ES framework has gained wide acceptance in the international scientific community and is applied by policymakers to protect biodiversity and safeguard the sustainability of ecosystems. This approach can enhance the ecological and societal relevance of pre‐market/prospective environmental risk assessments (ERAs) of regulated stressors by: (1) informing the derivation of operational protection goals; (2) enabling the integration of environmental and human health risk assessments; (3) facilitating horizontal integration of policies and regulations; (4) leading to more comprehensive and consistent environmental protection; (5) articulating the utility of, and trade‐offs involved in, environmental decisions; and (6) enhancing the transparency of risk assessment results and the decisions based upon them. Realisation of these advantages will require challenges that impede acceptance of an ES approach to be overcome. Particularly, there is concern that, if biodiversity only matters to the extent that it benefits humans, the intrinsic value of nature is ignored. Moreover, our understanding of linkages among ecological components and the processes that ultimately deliver ES is incomplete, valuing ES is complex, and there is no standard ES lexicon and limited familiarity with the approach. To help overcome these challenges, we encourage: (1) further research to establish biodiversity–ES relationships; (2) the development of approaches that (i) quantitatively translate responses to chemical stressors by organisms and groups of organisms to ES delivery across different spatial and temporal scales, (ii) measure cultural ES and ease their integration into ES valuations, and (iii) appropriately value changes in ES delivery so that trade‐offs among different management options can be assessed; (3) the establishment of a standard ES lexicon; and (4) building capacity in ES science and how to apply ES to ERAs. These development needs should not prevent movement towards implementation of an ES approach in ERAs, as the advantages we perceive of using this approach render it more than worthwhile to tackle those challenges. Society and the environment stand to benefit from this shift in how we conduct the ERA of regulated stressors.
New records and updated checklist of mosquitoes (Diptera: Culicidae) from Lao People's Democratic Republic, with special emphasis on adult and larval surveillance in Khammuane Province
Motoki, Maysa T. ; Vongphayloth, Khamsing ; Rueda, Leopoldo M. ; Miot, Elliott F. ; Hiscox, Alexandra ; Hertz, Jeffrey C. ; Brey, Paul T. - \ 2019
Journal of Vector Ecology 44 (2019)1. - ISSN 1081-1710 - p. 76 - 88.
Culicidae - DNA barcode - Khammuane Province - Lao PDR - mosquito species list - mosquito surveillance

A list of mosquitoes from the Nakai Nam Theun National Protected Area along the Nam Theun, Nam Mon, Nam Noy, and Nam On rivers, Nakai District, Khammuane Province, Lao People's Democratic Republic (Lao PDR) is presented. Fifty-four mosquito taxa were identified, including 15 new records in the Lao PDR. A fragment of the mtDNA cytochrome c oxidase subunit I (COI) gene, barcode region, was generated for 34 specimens, and together with four specimens already published, it represented 23 species in eight genera. In addition, an updated checklist of 170 mosquito taxa from Lao PDR is provided based on field collections from Khammuane Province, the literature, and specimens deposited in the Smithsonian Institution, National Museum of Natural History (SI-NMNH), Washington, DC, U.S.A. This paper provides additional information about the biodiversity of mosquito fauna in Lao PDR.

The Global Gridded Crop Model Intercomparison phase 1 simulation dataset
Müller, Christoph ; Elliott, Joshua ; Kelly, David ; Arneth, Almut ; Balkovic, Juraj ; Ciais, Philippe ; Deryng, Delphine ; Folberth, Christian ; Hoek, Steven ; Izaurralde, Roberto C. ; Jones, Curtis D. ; Khabarov, Nikolay ; Lawrence, Peter ; Liu, Wenfeng ; Olin, Stefan ; Pugh, Thomas A.M. ; Reddy, Ashwan ; Rosenzweig, Cynthia ; Ruane, Alex C. ; Sakurai, Gen ; Schmid, Erwin ; Skalsky, Rastislav ; Wang, Xuhui ; Wit, Allard de; Yang, Hong - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463 - 22 p.

The Global Gridded Crop Model Intercomparison (GGCMI) phase 1 dataset of the Agricultural Model Intercomparison and Improvement Project (AgMIP) provides an unprecedentedly large dataset of crop model simulations covering the global ice-free land surface. The dataset consists of annual data fields at a spatial resolution of 0.5 arc-degree longitude and latitude. Fourteen crop modeling groups provided output for up to 11 historical input datasets spanning 1901 to 2012, and for up to three different management harmonization levels. Each group submitted data for up to 15 different crops and for up to 14 output variables. All simulations were conducted for purely rainfed and near-perfectly irrigated conditions on all land areas irrespective of whether the crop or irrigation system is currently used there. With the publication of the GGCMI phase 1 dataset we aim to promote further analyses and understanding of crop model performance, potential relationships between productivity and environmental impacts, and insights on how to further improve global gridded crop model frameworks. We describe dataset characteristics and individual model setup narratives.

Gut microbiota from infant with cow’s milk allergy promotes clinical and immune features of atopy in a murine model
Mauras, Aurélie ; Wopereis, Harm ; Yeop, Intan ; Esber, Nathalie ; Delannoy, Johanne ; Labellie, Chantal ; Reygner, Julie ; Kapel, Nathalie ; Slump, Rob ; Eijndthoven, Tiemen van; Rutten, Lieke ; Knol, Jan ; Garssen, Johan ; Harthoorn, Lucien F. ; Butel, Marie José ; Bajaj-Elliott, Mona ; Hartog, Anita ; Waligora-Dupriet, Anne Judith - \ 2019
Allergy 74 (2019)9. - ISSN 0105-4538 - p. 1790 - 1793.
State-of-the-art global models underestimate impacts from climate extremes
Schewe, Jacob ; Gosling, Simon N. ; Reyer, Christopher ; Zhao, Fang ; Ciais, Philippe ; Elliott, Joshua ; Francois, Louis ; Huber, Veronika ; Lotze, Heike K. ; Seneviratne, Sonia I. ; Vliet, Michelle T.H. Van; Vautard, Robert ; Wada, Yoshihide ; Breuer, Lutz ; Büchner, Matthias ; Carozza, David A. ; Chang, Jinfeng ; Coll, Marta ; Deryng, Delphine ; Wit, Allard De; Eddy, Tyler D. ; Folberth, Christian ; Frieler, Katja ; Friend, Andrew D. ; Gerten, Dieter ; Gudmundsson, Lukas ; Hanasaki, Naota ; Ito, Akihiko ; Khabarov, Nikolay ; Kim, Hyungjun ; Lawrence, Peter ; Morfopoulos, Catherine ; Müller, Christoph ; Müller Schmied, Hannes ; Orth, René ; Ostberg, Sebastian ; Pokhrel, Yadu ; Pugh, Thomas A.M. ; Sakurai, Gen ; Satoh, Yusuke ; Schmid, Erwin ; Stacke, Tobias ; Steenbeek, Jeroen ; Steinkamp, Jörg ; Tang, Qiuhong ; Tian, Hanqin ; Tittensor, Derek P. ; Volkholz, Jan ; Wang, Xuhui ; Warszawski, Lila - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723
Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought.
A cool comparison of black and white pepper grades
Ruth, Saskia M. van; Silvis, Isabelle C.J. ; Ramos, Manuel Esbri ; Luning, Pieternel A. ; Jansen, Marc ; Elliott, Christopher T. ; Alewijn, Martin - \ 2019
Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 106 (2019). - ISSN 0023-6438 - p. 122 - 127.
Adulteration - Fraud - PTR-MS - Quality - Volatiles

Black pepper (BP) is globally the most widely used spice and is appreciated for its aroma and taste qualities. Its aroma is influenced by various factors. In the current study, we examined a reference set of 90 quality BP and 40 quality white pepper (WP) samples from the EU spice industry for their volatile organic compounds (VOC) by Proton Transfer Reaction - Mass Spectrometry, as well as 10 low-grade pepper (LG) samples (light berries, rejects, spent). Furthermore, 50 retail BP and 30 WP samples were compared with the reference set. The predominant VOC measured were terpenes. BP presented the most abundant VOC profiles, followed by the WP group, and - at some distance - by the LG pepper material. Reference BP exhibited significantly higher intensities for 41% of the masses compared to WP, and the LG group lower intensities than both BP and WP for 27% of the masses. When using mass 137, the monoterpenes marker, retail samples presented significantly lower VOC intensities than their reference counterparts in case of 42% of the retail BP and 70% of the WP samples. Those samples may have suffered from poor storage conditions during production or potential adulteration or substitution with LG material.

What agricultural practices are most likely to deliver “sustainable intensification” in the UK?
Dicks, Lynn V. ; Rose, David C. ; Ang, Frederic ; Aston, Stephen ; Birch, A.N.E. ; Boatman, Nigel ; Bowles, Elizabeth L. ; Chadwick, David ; Dinsdale, Alex ; Durham, Sam ; Elliott, John ; Firbank, Les ; Humphreys, Stephen ; Jarvis, Phil ; Jones, Dewi ; Kindred, Daniel ; Knight, Stuart M. ; Lee, Michael R.F. ; Leifert, Carlo ; Lobley, Matt ; Matthews, Kim ; Midmer, Alice ; Moore, Mark ; Morris, Carol ; Mortimer, Simon ; Murray, T.C. ; Norman, Keith ; Ramsden, Stephen ; Roberts, Dave ; Smith, Laurence G. ; Soffe, Richard ; Stoate, Chris ; Taylor, Bryony ; Tinker, David ; Topliff, Mark ; Wallace, John ; Williams, Prysor ; Wilson, Paul ; Winter, Michael ; Sutherland, William J. - \ 2019
Food and Energy Security 8 (2019)1. - ISSN 2048-3694

Sustainable intensification is a process by which agricultural productivity is enhanced whilst also creating environmental and social benefits. We aimed to identify practices likely to deliver sustainable intensification, currently available for UK farms but not yet widely adopted. We compiled a list of 18 farm management practices with the greatest potential to deliver sustainable intensification in the UK, following a well-developed stepwise methodology for identifying priority solutions, using a group decision-making technique with key agricultural experts. The list of priority management practices can provide the focal point of efforts to achieve sustainable intensification of agriculture, as the UK develops post-Brexit agricultural policy, and pursues the second Sustainable Development Goal, which aims to end hunger and promote sustainable agriculture. The practices largely reflect a technological, production-focused view of sustainable intensification, including for example, precision farming and animal health diagnostics, with less emphasis on the social and environmental aspects of sustainability. However, they do reflect an integrated approach to farming, covering many different aspects, from business organization and planning, to soil and crop management, to landscape and nature conservation. For a subset of 10 of the priority practices, we gathered data on the level of existing uptake in English and Welsh farms through a stratified survey in seven focal regions. We find substantial existing uptake of most of the priority practices, indicating that UK farming is an innovative sector. The data identify two specific practices for which uptake is relatively low, but which some UK farmers find appealing and would consider adopting. These practices are: prediction of pest and disease outbreaks, especially for livestock farms; staff training on environmental issues, especially on arable farms.

Addressing global ruminant agricultural challenges through understanding the rumen microbiome : Past, present, and future
Huws, Sharon A. ; Creevey, Christopher J. ; Oyama, Linda B. ; Mizrahi, Itzhak ; Denman, Stuart E. ; Popova, Milka ; Muñoz-Tamayo, Rafael ; Forano, Evelyne ; Waters, Sinead M. ; Hess, Matthias ; Tapio, Ilma ; Smidt, Hauke ; Krizsan, Sophie J. ; Yáñez-Ruiz, David R. ; Belanche, Alejandro ; Guan, Leluo ; Gruninger, Robert J. ; McAllister, Tim A. ; Newbold, C.J. ; Roehe, Rainer ; Dewhurst, Richard J. ; Snelling, Tim J. ; Watson, Mick ; Suen, Garret ; Hart, Elizabeth H. ; Kingston-Smith, Alison H. ; Scollan, Nigel D. ; Prado, Rodolpho M. Do; Pilau, Eduardo J. ; Mantovani, Hilario C. ; Attwood, Graeme T. ; Edwards, Joan E. ; McEwan, Neil R. ; Morrisson, Steven ; Mayorga, Olga L. ; Elliott, Christopher ; Morgavi, Diego P. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X
Diet - Host - Methane - Microbiome - Omics - Production - Rumen

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in "omic" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent "omics" approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Using 'omic approaches to compare temporal bacterial colonization of lolium perenne, lotus corniculatus, and trifolium pratensein the Rumen
Elliott, Christopher L. ; Edwards, Joan E. ; Wilkinson, Toby J. ; Allison, Gordon G. ; McCaffrey, Kayleigh ; Scott, Mark B. ; Rees-Stevens, Pauline ; Kingston-Smith, Alison H. ; Huws, Sharon A. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X - 16 p.
16S rRNA gene - Birds foot trefoil - CowPI - FTIR - Microbiome - Perennial ryegrass - Red clover - Rumen

Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

What are the scientific challenges in moving from targeted to non-targeted methods for food fraud testing and how can they be addressed? – Spectroscopy case study
McGrath, Terry F. ; Haughey, Simon A. ; Patterson, Jenny ; Fauhl-Hassek, Carsten ; Donarski, James ; Alewijn, Martin ; Ruth, Saskia van; Elliott, Christopher T. - \ 2018
Trends in Food Science and Technology 76 (2018). - ISSN 0924-2244 - p. 38 - 55.
Chemometric model - Food authenticity - Harmonisation - Non-targeted - Scientific opinion - Spectroscopy
Background: The authenticity of foodstuffs and associated fraud has become an important area. It is estimated that global food fraud costs approximately $US49b annually. In relation to testing for this malpractice, analytical technologies exist to detect fraud but are usually expensive and lab based. However, recently there has been a move towards non-targeted methods as means for detecting food fraud but the question arises if these techniques will ever be accepted as routine. Scope and approach: In this opinion paper, many aspects relating to the role of non-targeted spectroscopy based methods for food fraud detection are considered: (i) a review of the current non-targeted spectroscopic methods to include the general differences with targeted techniques; (ii) overview of in-house validation procedures including samples, data processing and chemometric techniques with a view to recommending a harmonized procedure; (iii) quality assessments including QC samples, ring trials and reference materials; (iv) use of “big data” including recording, validation, sharing and joint usage of databases. Key findings and conclusions: In order to keep pace with those who perpetrate food fraud there is clearly a need for robust and reliable non-targeted methods that are available to many stakeholders. Key challenges faced by the research and routine testing communities include: a lack of guidelines and legislation governing both the development and validation of non-targeted methodologies, no common definition of terms, difficulty in obtaining authentic samples with full traceability for model building; the lack of a single chemometric modelling software that offers all the algorithms required by developers.
Development and in-house validation of a rapid and simple to use ELISA for the detection and measurement of the mycotoxin sterigmatocystin
Oplatowska-Stachowiak, Michalina ; Reiring, Claudine ; Sajic, Nermin ; Haasnoot, Willem ; Brabet, Catherine ; Campbell, Katrina ; Elliott, Christopher T. ; Salden, Martin - \ 2018
Analytical and Bioanalytical Chemistry 410 (2018)12. - ISSN 1618-2642 - p. 3017 - 3023.
Enzyme-linked immunosorbent assay - Food safety - Immunoassay - Mycotoxin
Sterigmatocystin (STG) is a highly toxic secondary fungal metabolite structurally closely related to the well-known carcinogenic aflatoxins. Its presence has been reported in grains and grain-based products as well as in other foodstuffs like nuts, green coffee beans, spices, beer and cheese. Due to the lack of suitable data on the occurrence of STG, in 2013, the European Food Safety Authority (EFSA) could not characterise its risk for human health and recommended that more data on STG in food and feed needed to be collected. In order to provide a new tool for the specific detection of STG, a competitive enzyme-linked immunosorbent assay (ELISA) was developed, optimised and validated in this study based on a sensitive monoclonal antibody specific to STG with no cross-reactivity with aflatoxins. The sample preparation method for rice, wheat and maize was based on a modified QuEChERS (quick, easy, cheap, effective, rugged and safe) approach. The assay was validated for the detection of STG in rice, wheat and maize in accordance with the guidelines for validation of semi-quantitative screening methods included in Commission Regulation (EU) 519/2014. The screening target concentration (STC) was set at 1.5 μg/kg. The cutoffs for rice, wheat and maize were 1.2, 1.2 and 1.3 μg/kg and the false suspected rates were 0.34, 1.15 and 0.78%, respectively. Good correlation was found between the results obtained by the STG ELISA and LC-MS/MS method for naturally contaminated rice samples. This validated method can be applied as a sensitive and high-throughput screening for the presence of STG in a range of agricultural commodities. [Figure not available: see fulltext.]
Detecting macroecological patterns in bacterial communities across independent studies of global soils
Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Development and validation of a maleimide-based enzyme-linked immunosorbent assay for the detection of tetrodotoxin in oysters and mussels
Reverté, Laia ; Rambla-Alegre, Maria ; Leonardo, Sandra ; Bellés, Carlos ; Campbell, Katrina ; Elliott, Christopher T. ; Gerssen, Arjen ; Klijnstra, Mirjam D. ; Diogène, Jorge ; Campàs, Mònica - \ 2018
Talanta 176 (2018). - ISSN 0039-9140 - p. 659 - 666.
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) - Maleimide-based enzyme-linked immunosorbent assay (mELISA) - Mussel - Oyster - Solid-phase extraction (SPE) clean-up - Tetrodotoxin (TTX)

The recent detection of tetrodotoxins (TTXs) in puffer fish and shellfish in Europe highlights the necessity to monitor the levels of TTXs in seafood by rapid, specific, sensitive and reliable methods in order to protect human consumers. A previous immunoassay for TTX detection in puffer fish, based on the use of self-assembled monolayers (SAMs) for the immobilization of TTX on maleimide plates (mELISA), has been modified and adapted to the analysis of oyster and mussel samples. Changing dithiol for cysteamine-based SAMs enabled reductions in the assay time and cost, while maintaining the sensitivity of the assay. The mELISA showed high selectivity for TTX since the antibody did not cross-react with co-occurring paralytic shellfish poisoning (PSP) toxins and no interferences were observed from arginine (Arg). Moreover, TTX-coated maleimide plates stored for 3 months at −20 °C and 4 °C were stable, thus when pre-prepared, the time to perform the assay is reduced. When analyzing shellfish samples, matrix effects and toxin recovery values strongly depended on the shellfish type and the sample treatment. Blank oyster extracts could be directly analyzed without solid-phase extraction (SPE) clean-up, whereas blank mussel extracts showed strong matrix effects and SPE and subsequent solvent evaporation were required for removal. However, the SPE clean-up and evaporation resulted in toxin loss. Toxin recovery values were taken as correction factors (CFs) and were applied to the quantification of TTX contents in the analysis of naturally-contaminated shellfish samples by mELISA. The lowest effective limits of detection (eLODs) were about 20 and 50 µg/kg for oyster extracts without and with SPE clean-up, respectively, and about 30 µg/kg for mussel extracts with both protocols, all of them substantially below the eLOD attained in the previous mELISA for puffer fish (230 µg/kg). Analysis of naturally-contaminated samples by mELISA and comparison with LC-MS/MS quantifications demonstrated the viability of the approach. This mELISA is a selective and sensitive tool for the rapid detection of TTX in oyster and mussel samples showing promise to be implemented in routine monitoring programs to protect human health.

Defining scenarios of future vectors of change in marine life and associated economic sectors
Groeneveld, Rolf A. ; Bosello, Francesco ; Butenschön, Momme ; Elliott, Mike ; Peck, Myron A. ; Pinnegar, John K. - \ 2018
Estuarine Coastal and Shelf Science 201 (2018). - ISSN 0272-7714 - p. 164 - 171.
Climatic changes - Ecosystem management - International policy - Scenarios - Socioeconomic aspects
Addressing the multitude of challenges in marine policy requires an integrated approach that considers the multitude of drivers, pressures, and interests, from several disciplinary angles. Scenarios are needed to harmonise the analyses of different components of the marine system, and to deal with the uncertainty and complexity of the societal and biogeophysical dynamics in the system. This study considers a set of socio-economic scenarios to (1) explore possible futures in relation to marine invasive species, outbreak forming species, and gradual changes in species distribution and productivity; and (2) harmonise the projection modelling performed within associated studies. The exercise demonstrates that developing interdisciplinary scenarios as developed in this study is particularly complicated due to (1) the wide variety in endogeneity or exogeneity of variables in the different analyses involved; (2) the dual role of policy decisions as variables in a scenario or decisions to be evaluated and compared to other decisions; and (3) the substantial difference in time scale between societal and physical drivers.
T-2 toxin/HT-2 toxin and ochratoxin A ELISAs development and in-house validation in food in accordance with the commission regulation (EU) no 519/2014
Oplatowska-Stachowiak, Michalina ; Kleintjens, Tim ; Sajic, Nermin ; Haasnoot, Willem ; Campbell, Katrina ; Elliott, Christopher T. ; Salden, Martin - \ 2017
Toxins 9 (2017)12. - ISSN 2072-6651
Enzyme-linked immunosorbent assay - Immunoassay - Mycotoxins - Screening
T-2 toxin/HT-2 toxin (T-2/HT-2) and ochratoxin A (OTA) are mycotoxins that can contaminate a variety of agricultural commodities. To protect consumers’ health, indicative limits for T-2/HT-2 and maximum limits for OTA have been set by the European Commission, requiring food business operators and controlling agencies to conduct routine checks for the presence of these harmful contaminants. Screening methods are increasingly used for monitoring purposes. Due to the demand for new and improved screening tools, two individual detection methods, T-2/HT-2 and OTA enzyme-linked immunosorbent assays (ELISAs), were developed in this study. The T-2/HT-2 ELISA was based on a T-2 monoclonal antibody with an IC50(50% inhibitory concentration) of 0.28 ng/mL and 125% cross-reactivity with HT-2. As regards the OTA ELISA, a new sensitive monoclonal antibody specific to OTA with an IC50 of 0.13 ng/mL was produced. Both developed ELISA tests were then validated in agricultural commodities in accordance with the new performance criteria guidelines for the validation of screening methods for mycotoxins included in Commission Regulation (EU) No 519/2014. The T-2/HT-2 ELISA was demonstrated to be suitable for the detection of T-2/HT-2 in cereals and baby food at and above the screening target concentration (STC) of 12.5 μg/kg and 7.5 μg/kg, respectively. The OTA ELISA was shown to be applicable for the detection of OTA in cereals, coffee, cocoa and wine at and above the STC of 2 μg/kg, 2.5 μg/kg, 2.5 μg/kg and 0.4 ng/mL, respectively. The accuracy of both ELISAs was further confirmed by analysing proficiency test and reference samples. The developed methods can be used for sensitive and high-throughput screening for the presence of T-2/HT-2 and OTA in agricultural commodities.
Assessing the impacts of 1.5°C global warming - Simulation protocol of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2b)
Frieler, Katja ; Lange, Stefan ; Piontek, Franziska ; Reyer, Christopher P.O. ; Schewe, Jacob ; Warszawski, Lila ; Zhao, Fang ; Chini, Louise ; Denvil, Sebastien ; Emanuel, Kerry ; Geiger, Tobias ; Halladay, Kate ; Hurtt, George ; Mengel, Matthias ; Murakami, Daisgbre ; Ostberg, Sebastian ; Popp, Alexander ; Riva, Riccardo ; Stevanovic, Miodrag ; SuzGBRi, Tatsuo ; Volkholz, Jan ; Burke, Eleanor ; Ciais, Philippe ; Ebi, Kristie ; Eddy, Tyler D. ; Elliott, Joshua ; Galbraith, Eric ; Gosling, Simon N. ; Hattermann, Fred ; Hickler, Thomas ; Hinkel, Jochen ; Hof, Christian ; Huber, Veronika ; Jägermeyr, Jonas ; Krysanova, Valentina ; Marcé, Rafael ; Müller Schmied, Hannes ; Mouratiadou, Ioanna ; Pierson, Don ; Tittensor, Derek P. ; Vautard, Robert ; Vliet, Michelle Van; Biber, Matthias F. ; Betts, Richard A. ; Leon Bodirsky, Benjamin ; Deryng, Delphine ; Frolking, Steve ; Jones, Chris D. ; Lotze, Heike K. ; Lotze-Campen, Hermann ; Sahajpal, Ritvik ; Thonicke, Kirsten ; Tian, Hanqin ; Yamagata, Yoshiki - \ 2017
Geoscientific Model Development 10 (2017)12. - ISSN 1991-959X - p. 4321 - 4345.
In Paris, France, December 2015, the Conference of the Parties (COP) to the United Nations Framework Convention on Climate Change (UNFCCC) invited the Intergovernmental Panel on Climate Change (IPCC) to provide a special report in 2018 on the impacts of global warming of 1.5ĝ€°C above pre-industrial levels and related global greenhouse gas emission pathways. In Nairobi, Kenya, April 2016, the IPCC panel accepted the invitation. Here we describe the response devised within the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) to provide tailored, cross-sectorally consistent impact projections to broaden the scientific basis for the report. The simulation protocol is designed to allow for (1) separation of the impacts of historical warming starting from pre-industrial conditions from impacts of other drivers such as historical land-use changes (based on pre-industrial and historical impact model simulations); (2) quantification of the impacts of additional warming up to 1.5ĝ€°C, including a potential overshoot and long-term impacts up to 2299, and comparison to higher levels of global mean temperature change (based on the low-emissions Representative Concentration Pathway RCP2.6 and a no-mitigation pathway RCP6.0) with socio-economic conditions fixed at 2005 levels; and (3) assessment of the climate effects based on the same climate scenarios while accounting for simultaneous changes in socio-economic conditions following the middle-of-the-road Shared Socioeconomic Pathway (SSP2, Fricko et al., 2016) and in particular differential bioenergy requirements associated with the transformation of the energy system to comply with RCP2.6 compared to RCP6.0. With the aim of providing the scientific basis for an aggregation of impacts across sectors and analysis of cross-sectoral interactions that may dampen or amplify sectoral impacts, the protocol is designed to facilitate consistent impact projections from a range of impact models across different sectors (global and regional hydrology, lakes, global crops, global vegetation, regional forests, global and regional marine ecosystems and fisheries, global and regional coastal infrastructure, energy supply and demand, temperature-related mortality, and global terrestrial biodiversity).
Voluntary "New Approach" Technical Standards are Subject to Judicial Scrutiny by the CJEU! - The Remarkable CJEU judgment "Elliott" On Private Standards
Purnhagen, K. - \ 2017
European Journal of Risk Regulation 8 (2017)3. - ISSN 1867-299X - p. 586 - 598.
The CJEU has developed some remarkable answers on pertinent questions of EU private law with a view on “new approach” standards. “New approach” standards are “acts” in the meaning of Art. 267(b) TFEU by virtue of their public law effect and EU law framing. “New approach” Directives regulate only market access at the border, not behind the border, where Member State regulations apply. For this reason, EU law also does not require transferring the conformity presumption pars pro toto to the interpretation of rules from national contract law. I will illustrate the impact of this judgment on access to justice, the making of EU private law and transnational contract law, liability of standardisation organisations and on the private standards debate in WTO law.
Global gridded crop model evaluation : Benchmarking, skills, deficiencies and implications
Müller, Christoph ; Elliott, Joshua ; Chryssanthacopoulos, James ; Arneth, Almut ; Balkovic, Juraj ; Ciais, Philippe ; Deryng, Delphine ; Folberth, Christian ; Glotter, Michael ; Hoek, Steven ; Iizumi, Toshichika ; Izaurralde, Roberto C. ; Jones, Curtis ; Khabarov, Nikolay ; Lawrence, Peter ; Liu, Wenfeng ; Olin, Stefan ; Pugh, Thomas A.M. ; Ray, Deepak K. ; Reddy, Ashwan ; Rosenzweig, Cynthia ; Ruane, Alex C. ; Sakurai, Gen ; Schmid, Erwin ; Skalsky, Rastislav ; Song, Carol X. ; Wang, Xuhui ; Wit, Allard De; Yang, Hong - \ 2017
Geoscientific Model Development 10 (2017)4. - ISSN 1991-959X - p. 1403 - 1422.
Crop models are increasingly used to simulate crop yields at the global scale, but so far there is no general framework on how to assess model performance. Here we evaluate the simulation results of 14 global gridded crop modeling groups that have contributed historic crop yield simulations for maize, wheat, rice and soybean to the Global Gridded Crop Model Intercomparison (GGCMI) of the Agricultural Model Intercomparison and Improvement Project (AgMIP). Simulation results are compared to reference data at global, national and grid cell scales and we evaluate model performance with respect to time series correlation, spatial correlation and mean bias. We find that global gridded crop models (GGCMs) show mixed skill in reproducing time series correlations or spatial patterns at the different spatial scales. Generally, maize, wheat and soybean simulations of many GGCMs are capable of reproducing larger parts of observed temporal variability (time series correlation coefficients (r) of up to 0.888 for maize, 0.673 for wheat and 0.643 for soybean at the global scale) but rice yield variability cannot be well reproduced by most models. Yield variability can be well reproduced for most major producing countries by many GGCMs and for all countries by at least some. A comparison with gridded yield data and a statistical analysis of the effects of weather variability on yield variability shows that the ensemble of GGCMs can explain more of the yield variability than an ensemble of regression models for maize and soybean, but not for wheat and rice. We identify future research needs in global gridded crop modeling and for all individual crop modeling groups. In the absence of a purely observation-based benchmark for model evaluation, we propose that the best performing crop model per crop and region establishes the benchmark for all others, and modelers are encouraged to investigate how crop model performance can be increased. We make our evaluation system accessible to all crop modelers so that other modeling groups can also test their model performance against the reference data and the GGCMI benchmark.
Spatial and temporal uncertainty of crop yield aggregations
Porwollik, Vera ; Müller, Christoph ; Elliott, Joshua ; Chryssanthacopoulos, James ; Iizumi, Toshichika ; Ray, Deepak K. ; Ruane, Alex C. ; Arneth, Almut ; Balkovič, Juraj ; Ciais, Philippe ; Pugh, Thomas A.M. ; Wit, Allard de - \ 2017
European Journal of Agronomy 88 (2017). - ISSN 1161-0301 - p. 10 - 21.
Aggregation uncertainty - Crop yields - Global crop model - Gridded data - Harvested area
The aggregation of simulated gridded crop yields to national or regional scale requires information on temporal and spatial patterns of crop-specific harvested areas. This analysis estimates the uncertainty of simulated gridded yield time series related to the aggregation with four different harvested area data sets. We compare aggregated yield time series from the Global Gridded Crop Model Intercomparison project for four crop types from 14 models at global, national, and regional scale to determine aggregation-driven differences in mean yields and temporal patterns as measures of uncertainty.The quantity and spatial patterns of harvested areas differ for individual crops among the four data sets applied for the aggregation. Also simulated spatial yield patterns differ among the 14 models. These differences in harvested areas and simulated yield patterns lead to differences in aggregated productivity estimates, both in mean yield and in the temporal dynamics.Among the four investigated crops, wheat yield (17% relative difference) is most affected by the uncertainty introduced by the aggregation at the global scale. The correlation of temporal patterns of global aggregated yield time series can be as low as for soybean (r. =0.28).For the majority of countries, mean relative differences of nationally aggregated yields account for 10% or less. The spatial and temporal difference can be substantial higher for individual countries. Of the top-10 crop producers, aggregated national multi-annual mean relative difference of yields can be up to 67% (maize, South Africa), 43% (wheat, Pakistan), 51% (rice, Japan), and 427% (soybean, Bolivia). Correlations of differently aggregated yield time series can be as low as r. =0.56 (maize, India), r. =0.05 (wheat, Russia), r. =0.13 (rice, Vietnam), and r. =-0.01 (soybean, Uruguay). The aggregation to sub-national scale in comparison to country scale shows that spatial uncertainties can cancel out in countries with large harvested areas per crop type. We conclude that the aggregation uncertainty can be substantial for crop productivity and production estimations in the context of food security, impact assessment, and model evaluation exercises.
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