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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Genome editing, gene drives, and synthetic biology: Will they contribute to disease-resistant crops, and who will benefit?
Pixley, Kevin V. ; Falck-Zepeda, Jose B. ; Giller, Ken E. ; Glenna, Leland L. ; Gould, Fred ; Mallory-Smith, Carol A. ; Stelly, David M. ; Stewart, C.N. - \ 2019
Annual Review of Phytopathology 57 (2019). - ISSN 0066-4286 - p. 165 - 188.
gene drives - Gene editing - Genetically engineered crops - Science and society - Social equity - Synthetic biology

Genetically engineered crops have been grown for more than 20 years, resulting in widespread albeit variable benefits for farmers and consumers. We review current, likely, and potential genetic engineering (GE) applications for the development of disease-resistant crop cultivars. Gene editing, gene drives, and synthetic biology offer novel opportunities to control viral, bacterial, and fungal pathogens, parasitic weeds, and insect vectors of plant pathogens. We conclude that there will be no shortage of GE applications totackle disease resistance and other farmer and consumer priorities for agricultural crops. Beyond reviewing scientific prospects for genetically engineered crops, we address the social institutional forces that are commonly overlooked by biological scientists. Intellectual property regimes, technology regulatory frameworks, the balance of funding between public-and private-sector research, and advocacy by concerned civil society groups interact to define who uses which GE technologies, on which crops, and for the benefit of whom. Ensuring equitable access to the benefits of genetically engineered crops requires affirmative policies, targeted investments, and excellent science.

Current climate, isolation and history drive global patterns of tree phylogenetic endemism
Sandel, Brody ; Weigelt, Patrick ; Kreft, Holger ; Keppel, Gunnar ; Sande, Masha T. van der; Levin, Sam ; Smith, Stephen ; Craven, Dylan ; Knight, Tiffany M. - \ 2019
Global Ecology and Biogeography (2019). - ISSN 1466-822X
biogeography - climate stability - historical contingency - islands - isolation - phylogenetic endemism - trees

Aim: We mapped global patterns of tree phylogenetic endemism (PE) to identify hotspots and test hypotheses about possible drivers. Specifically, we tested hypotheses related to current climate, geographical characteristics and historical conditions and assessed their relative importance in shaping PE patterns. Location: Global. Time period: We used the present distribution of trees, and predictors covering conditions from the mid-Miocene to present. Major taxa studied: All seed-bearing trees. Methods: We compiled distributions for 58,542 tree species across 463 regions worldwide, matched these to a recent phylogeny of seed plants and calculated PE for each region. We used a suite of predictor variables describing current climate (e.g., mean annual temperature), geographical characteristics (e.g., isolation) and historical conditions (e.g., tree cover at the Last Glacial Maximum) in a spatial regression model to explain variation in PE. Results: Tree PE was highest on islands, and was higher closer to the equator. All three groups of predictor variables contributed substantially to the PE pattern. Isolation and topographic heterogeneity promoted high PE, as did high current tree cover. Among mainland regions, temperature seasonality was strongly negatively related to PE, while mean annual temperature was positively related to PE on islands. Some relationships differed among the major floristic regions. For example, tree cover at the Last Glacial Maximum was a positive predictor of PE in the Palaeotropics, while tree cover at the Miocene was a negative predictor of PE in the Neotropics. Main conclusions: Globally, PE can be explained by a combination of geographical, historical and current factors. Some geographical variables appear to be key predictors of PE. However, the impact of historic and current climate variables differs considerably among the major floristic regions, reflecting their unique histories. Hence, the current distribution of trees is the result of globally relevant geographical drivers and regional climatic histories.

Invasive moth facilitates use of a native food plant by other native and invasive arthropods
Harvey, Jeffrey A. ; Gols, Rieta ; Smith, Brittany ; Ode, Paul J. - \ 2019
Ecological Research 34 (2019)5. - ISSN 0912-3814 - p. 659 - 666.
cow parsnip - ecosystem engineer - facilitation - invasive moth - small hogweed

Organisms that invade new habitats exploit new resources or niches and influence native species. Here, we examine how an invasive moth, the parsnip webworm (Depressaria radiella, formerly D. pastinacella), facilitates interactions with other arthropods in spatially separated populations of native cow parsnip (Heracleum maximum) in the Rocky Mountains (New Mexico and Colorado). We compare this with results on small hogweed (Heracleum sphondylium) in the Netherlands, where both the plant and herbivore are native. Larvae of D. radiella feed in webs on ripening fruits of their food plants. Mature caterpillars descend the hollow stems into which they chew a hole, enter the stem and pupate. Other arthropods enter the stems through these holes. Plants in all populations of cow parsnip/hogweed contained either moth pupae and/or webworms mummified by their main parasitoid, Copidosoma sosares that also been introduced into parts of the United States. In both countries, earwigs (Forficula auricularia), which are also invasive in the United States, were the dominant arthropod to utilize webworm-perforated stems, although there was more within-site variability in abundance of earwigs in the United States than in the Netherlands. The woodlouse, Porcelio scaber, which is native to Eurasia but also established in the United States, was abundant in stems of Dutch hogweeds but absent in stems of American cow parsnips. Other native herbivores (e.g., mirid bugs), were collected in stems at sites in both continents. Moreover, the number of various arthropods found in perforated stems correlate positively with the number of holes found in these stems.

Bog Bodies in Context: Developing a Best Practice Approach
Beek, R. van; Chapman, Henry ; Gearey, Ben ; Jennings, Ben ; Smith, D. ; Helt Nielsen, Nina ; Zein Elabdin, Zena - \ 2019
European Journal of Archaeology (2019). - ISSN 1461-9571 - p. 1 - 23.
Bog bodies are among the best-known archaeological finds worldwide. Much of the work on these often extremely well-preserved human remains has focused on forensics, whereas the environmental setting of the finds has been largely overlooked. This applies to both the ‘physical’ and ‘cultural’ landscape and
constitutes a significant problem since the vast spatial and temporal scales over which the practice appeared demonstrate that contextual assessments are of the utmost importance for our explanatory frameworks.
In this article we develop best practice guidelines for the contextual analysis of bog bodies, after assessing the current state of research and presenting the results of three recent case studies including the well-known finds of Lindow Man in the United Kingdom, Bjældskovdal (Tollund Man and Elling Woman) in Denmark, and Yde Girl in the Netherlands. Three spatial and chronological scales
are distinguished and linked to specific research questions and methods. This provides a basis for further discussion and a starting point for developing approaches to bog body finds and future discoveries, while facilitating and optimizing the re-analysis of previous studies, making it possible to compare deposition sites across time and space.
Achtergrondrapportage Programmeringsstudies Landbouw, Water en Voedsel: Noordzee en Visserij
Smith, S. ; Steins, N.A. ; Bogaart, L. van den; Bos, O.G. ; Maarse, M. ; Rijn, J. van; Schadeberg, A. ; Tamis, J. ; Tatman, S. - \ 2019
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C075/19) - 153
Characterising permanent grassland-based farming systems in Europe
Korevaar, H. ; Sacco, Dario ; Ravetto Enri, Simone ; Lombardi, Giampiero ; Berge, H.F.M. ten; Bufe, Conny ; Whittingham, Mark J. ; Smith, Pete ; Vanwalleghem, Tom ; Lellei-kovács, Eszter ; Stypinski, Piotr ; Hejduk, Stanislav ; Tonn, Bettina ; Newell Price, Paul J. - \ 2019
In: Improving sown grasslands through breeding and management Wageningen Academic Publishers (Grassland Science in Europe ) - p. 164 - 166.
Basic Phytochrome B Calculations
Smith, Robert W. ; Fleck, Christian - \ 2019
In: Phytochromes / Hiltbrunner, Andreas, Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493996117 - p. 121 - 133.
Computer programming - Mathematical modeling - Ordinary differential equations - Phytochromes

Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to calculate the steady-state amounts of phytochrome subspecies relative to the total phytochrome molecule population. Starting from a simplified two-state system we expand and apply the technique to the extended phytochrome dimer model. Additionally, we provide a Python package that can automatically calculate the proportion of phytochrome B in a particular state given specific experimental conditions.

Assessment of ecosystem services from permanent grassland systems
Korevaar, H. ; Berge, H.F.M. ten; Bufe, Conny ; Whittingham, Mark J. ; Smith, Pete ; Vanwalleghem, Tom ; Lellei-kovács, Eszter ; Stypinski, Piotr ; Hejduk, Stanislav ; Tonn, Bettina ; Sacco, Dario ; Newell-Price, Paul P. - \ 2019
In: Proceedings of the joint BGS/BSSS Winter meeting Improving grassland performance: managing soil structure and organic matter, 19th March 2019: 23-24. - British Grassland Society - p. 23 - 24.
The vulnerabilities of agricultural land and food production to future water scarcity
Fitton, N. ; Alexander, P. ; Arnell, N. ; Bajzelj, B. ; Calvin, K. ; Doelman, J. ; Gerber, J.S. ; Havlik, P. ; Hasegawa, T. ; Herrero, M. ; Krisztin, T. ; Meijl, H. van; Powell, T. ; Sands, R. ; Stehfest, E. ; West, P.C. ; Smith, P. - \ 2019
Global environmental change : human and policy dimensions 58 (2019). - ISSN 0959-3780
Food security - Land use - Shared socio-economic pathways - Water availability

Rapidly increasing populations coupled with increased food demand requires either an expansion of agricultural land or sufficient production gains from current resources. However, in a changing world, reduced water availability might undermine improvements in crop and grass productivity and may disproportionately affect different parts of the world. Using multi-model studies, the potential trends, risks and uncertainties to land use and land availability that may arise from reductions in water availability are examined here. In addition, the impacts of different policy interventions on pressures from emerging risks are examined. Results indicate that globally, approximately 11% and 10% of current crop- and grass-lands could be vulnerable to reduction in water availability and may lose some productive capacity, with Africa and the Middle East, China, Europe and Asia particularly at risk. While uncertainties remain, reduction in agricultural land area associated with dietary changes (reduction of food waste and decreased meat consumption) offers the greatest buffer against land loss and food insecurity.

Duurzame Visserij: programmeringsstudie Landbouw, Water en Voedsel
Smith, Sarah - \ 2019
1928088 NS/IH
Twenty-three unsolved problems in hydrology (UPH)–a community perspective
Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

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.

Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Nature and mental health: An ecosystem service perspective
Bratman, Gregory N. ; Anderson, Christopher B. ; Berman, Marc G. ; Cochran, Bobby ; Vries, Sjerp De; Flanders, Jon ; Folke, Carl ; Frumkin, Howard ; Gross, James J. ; Hartig, Terry ; Kahn, Peter H. ; Kuo, Ming ; Lawler, Joshua J. ; Levin, Phillip S. ; Lindahl, Therese ; Meyer-lindenberg, Andreas ; Mitchell, Richard ; Ouyang, Zhiyun ; Roe, Jenny ; Scarlett, Lynn ; Smith, Jeffrey R. ; Bosch, Matilda Van Den; Wheeler, Benedict W. ; White, Mathew P. ; Zheng, Hua ; Daily, Gretchen C. - \ 2019
Science Advances 5 (2019)7. - ISSN 2375-2548 - 15 p.
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.
The Lemon Car Game Across Cultures: Evidence of Relational Rationality
Hofstede, G.J. ; Jonker, Catholijn ; Verwaart, T. ; Yorke-Smith, Neil - \ 2019
Group Decision and Negotiation 28 (2019)5. - ISSN 0926-2644 - p. 849 - 877.
Negotiation - Culture - Experimental studies - Power distance - Long-term orientation - Lemon car
In cross-cultural business negotiation, culture is known to influence negotiation processes. As a lens to study this effect we deployed the Lemon Car Game, an online negotiation game developed for this purpose (Hofstede et al. in: Proceedings of 39th international simulation and gaming association conference (ISAGA). Technologia, Kaunas, pp 39–46, 2009a; Hofstede et al. in: David, Sichman (eds) Multi-agent-based simulation IX, international workshop, MABS 2008, revised selected papers, LNAI 5269. Springer, Berlin, pp 1–16, 2009b). In this article we report the results from the game, obtained from over 800 players from more than 70 countries. We employ several complementary analyses in a mixed-methods approach.Our findings show that to make sense of the players’ actions during negotiation, economic rationality falls short. A pan-cultural individual-level analysis of actions and stated intentions also fails to yield a coherent picture. Within countries, however, actions and intentions do cohere, as shown by an ecological country-level factor analysis, from which three factors emerge for the sellers at country level: trustworthiness, opportunism, and fairness. We conclude from these findings that, in this game, players are driven by what we call relational rationality: they are rational from the perspective of the social world in which they live, with interpersonal relationships weighing heavily. Relational rationality changes players’ perspective of economic rationality, and thus their observed behaviour in negotiation. Based on this evidence, we extrapolate that relational rationality significantly influences negotiation processes in all cultures.
Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum
Vossenberg, Bart T.L.H. van de; Warris, Sven ; Nguyen, Hai D.T. ; Gent-Pelzer, Marga P.E. van; Joly, David L. ; Geest, Henri C. van de; Bonants, Peter J.M. ; Smith, Donna S. ; Lévesque, André C. ; Lee, Theo A.J. van der - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.

Assessing the potential of soil carbonation and enhanced weathering through Life Cycle Assessment: A case study for Sao Paulo State, Brazil
Lefebvre, David ; Goglio, Pietro ; Williams, Adrian ; Manning, David A.C. ; Azevedo, Antonio Carlos de; Bergmann, Magda ; Meersmans, Jeroen ; Smith, Pete - \ 2019
Journal of Cleaner Production 233 (2019). - ISSN 0959-6526 - p. 468 - 481.
Carbonation - Enhanced weathering - LCA - Life cycle assessment - NET - Sao paulo

Enhanced silicate rock weathering for long-term carbon dioxide sequestration has considerable potential, but depends on the availability of suitable rocks coupled with proximity to suitable locations for field application. In this paper, we investigate the established mining industry that extracts basaltic rocks for construction from the Paraná Basin, Sao Paulo State, Brazil. Through a Life Cycle Assessment, we determine the balance of carbon dioxide emissions involved in the use of this material, the relative contribution of soil carbonation and enhanced weathering, and the potential carbon dioxide removal of Sao Paulo agricultural land through enhanced weathering of basalt rock. Our results show that enhanced weathering and carbonation respectively emit around 75 and 135 kg carbon dioxide equivalent per tonne of carbon dioxide equivalent removed (considering a quarry to field distance of 65 km). We underline transportation as the principal process negatively affecting the practice and uncover a limiting road travel distance from the quarry to the field of 540 ± 65 km for carbonation and 990 ± 116 km for enhanced weathering, above which the emissions offset the potential capture. Regarding Sao Paulo State, the application of crushed basalt at 1 t/ha to all of the State's 12 million hectares of agricultural land could capture around 1.3 to 2.4 Mt carbon dioxide equivalent through carbonation and enhanced weathering, respectively. This study suggests a lower sequestration estimate than previous studies and emphasizes the need to consider all process stages through a Life Cycle Assessment methodology, to provide more reliable estimates of the sequestration potential of greenhouse gas removal technologies.

Nitrogen Surplus Benchmarks for Controlling N Pollution in the Main Cropping Systems of China
Zhang, Chong ; Ju, Xiaotang ; Powlson, David ; Oenema, Oene ; Smith, Pete - \ 2019
Environmental Science and Technology 53 (2019)12. - ISSN 0013-936X - p. 6678 - 6687.

Nitrogen (N) surplus is a useful indicator for improving agricultural N management and controlling N pollution. Few studies have developed benchmark values for cropping systems in China, a country with the largest N fertilizer use in the world. We established N surplus benchmarks for 13 main cropping systems, at optimal N management, using results from >4500 on-farm field experiments and a soil surface balance approach. These cropping systems accounted for about 50% of total N fertilizer consumption in Chinese agriculture in 2009. The results showed that N surplus benchmarks for single cropping systems ranged from 40 to 100 kg N ha-1 yr-1 (average 73 kg N ha-1 yr-1), and for double cropping systems from 110 to 190 kg N ha-1 yr-1 (average 160 kg N ha-1 yr-1), roughly twice that of single cropping systems. These N surplus benchmarks may be further refined, following further decreases in N deposition rates and reactive N losses as a result of strict implementation of "4R-nutrient stewardship" and improvements in fertilization techniques and agronomic managements. Our N surplus benchmarks could serve as realistic targets to improve the N management of current conventional practices, and thereby could lay the foundations for a more sustainable N management in China.

Data from: The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agro-ecosystem services across Europe
Martin, Emily A. ; Dainese, Matteo ; Clough, Yann ; Báldi, András ; Bommarco, R. ; Gagic, Vesna ; Garratt, Michael P.D. ; Holzschuh, Andrea ; Kleijn, D. ; Kovács-Hostyánszki, Anikó ; Marini, Lorenzo ; Potts, Simon G. ; Smith, Henrik G. ; Hassan, Diab Al; Albrecht, Matthias ; Andersson, Georg K.S. ; Asís, Josep D. ; Aviron, Stéphanie ; Balzan, M.V. ; Baños-Picón, Laura ; Bartomeus, Ignasi ; Batáry, Péter ; Burel, Francoise ; Caballero-lópez, Berta ; Concepción, Elena D. ; Coudrain, Valérie ; Dänhardt, Juliana ; Diaz, Mario ; Diekötter, Tim ; Dormann, Carsten F. ; Duflot, Rémi ; Entling, Martin H. ; Farwig, Nina ; Fischer, Christina ; Frank, Thomas ; Garibaldi, Lucas A. ; Hermann, John ; Herzog, Felix ; Inclán, Diego J. ; Jacot, Katja ; Jauker, Frank ; Jeanneret, Philippe ; Kaiser, Marina ; Krauss, Jochen ; Féon, Violette Le; Marshall, Jon ; Moonen, Anna Camilla ; Moreno, Gerardo ; Riedinger, Verena ; Rundlöf, Maj ; Rusch, Adrien ; Scheper, J.A. ; Schneider, Gudrun ; Schüepp, Christof ; Stutz, Sonja ; Sutter, Louis ; Tamburini, Giovanni ; Thies, Carsten ; Tormos, José ; Tscharntke, Teja ; Tschumi, Matthias ; Uzman, Deniz ; Wagner, Christian ; Zubair Anjum, Muhammad ; Steffan-Dewenter, Ingolf - \ 2019
biodiversity - agroecosystem - landscape composition - landscape configuration - functional traits - arthropods - natural pest control - pollination - yields
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.
Science-based wildlife disease response
Vicente, Joaquín ; Apollonio, Marco ; Blanco-Aguiar, Jose A. ; Borowik, Tomasz ; Brivio, Francesca ; Casaer, Jim ; Croft, Simon ; Ericsson, Göran ; Ferroglio, Ezio ; Gavier-Widen, Dolores ; Gortázar, Christian ; Jansen, Patrick A. ; Keuling, Oliver ; Kowalczyk, Rafał ; Petrovic, Karolina ; Plhal, Radim ; Podgórski, Tomasz ; Sange, Marie ; Scandura, Massimo ; Schmidt, Krzysztof ; Smith, Graham C. ; Soriguer, Ramon ; Thulke, Hans Hermann ; Zanet, Stefania ; Acevedo, Pelayo - \ 2019
Science 364 (2019)6444. - ISSN 0036-8075 - p. 943 - 944.
Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise
Keizer, Emma M. ; Bastian, Björn ; Smith, Robert W. ; Grima, Ramon ; Fleck, Christian - \ 2019
Physical Review. E, Statistical nonlinear, and soft matter physics 99 (2019)5. - ISSN 2470-0045

It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. While there are many methods to study the effect of intrinsic noise on the system dynamics, few exist to study the influence of both types of noise. Here we show how one can extend the conventional linear-noise approximation to allow for the rapid evaluation of the molecule numbers statistics of a biochemical network influenced by intrinsic noise and by slow lognormally distributed extrinsic noise. The theory is applied to simple models of gene regulatory networks and its validity confirmed by comparison with exact stochastic simulations. In particular, we consider three important biological examples. First, we investigate how extrinsic noise modifies the dependence of the variance of the molecule number fluctuations on the rate constants. Second, we show how the mutual information between input and output of a network motif is affected by extrinsic noise. And third, we study the robustness of the ubiquitously found feed-forward loop motifs when subjected to extrinsic noise.

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