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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Global distribution of earthworm diversity
Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Global 3-D Simulations of the Triple Oxygen Isotope Signature Δ17O in Atmospheric CO2
Koren, Gerbrand ; Schneider, Linda ; Velde, Ivar R. van der; Schaik, Erik van; Gromov, Sergey S. ; Adnew, Getachew A. ; Mrozek Martino, Dorota J. ; Hofmann, Magdalena E.G. ; Liang, Mao Chang ; Mahata, Sasadhar ; Bergamaschi, Peter ; Laan-Luijkx, Ingrid T. van der; Krol, Maarten C. ; Röckmann, Thomas ; Peters, Wouter - \ 2019
Journal of Geophysical Research: Atmospheres (2019). - ISSN 2169-897X
O excess (ΔO) - carbon cycle - carbon dioxide (CO) - gross primary production (GPP) - mass-independent fractionation (MIF) - stable isotopes

The triple oxygen isotope signature Δ17O in atmospheric CO2, also known as its “17O excess,” has been proposed as a tracer for gross primary production (the gross uptake of CO2 by vegetation through photosynthesis). We present the first global 3-D model simulations for Δ17O in atmospheric CO2 together with a detailed model description and sensitivity analyses. In our 3-D model framework we include the stratospheric source of Δ17O in CO2 and the surface sinks from vegetation, soils, ocean, biomass burning, and fossil fuel combustion. The effect of oxidation of atmospheric CO on Δ17O in CO2 is also included in our model. We estimate that the global mean Δ17O (defined as Δ17O = ln(δ17O+1)−λRL·ln(δ18O+1) with λRL = 0.5229) of CO2 in the lowest 500 m of the atmosphere is 39.6 per meg, which is ∼20 per meg lower than estimates from existing box models. We compare our model results with a measured stratospheric Δ17O in CO2 profile from Sodankylä (Finland), which shows good agreement. In addition, we compare our model results with tropospheric measurements of Δ17O in CO2 from Göttingen (Germany) and Taipei (Taiwan), which shows some agreement but we also find substantial discrepancies that are subsequently discussed. Finally, we show model results for Zotino (Russia), Mauna Loa (United States), Manaus (Brazil), and South Pole, which we propose as possible locations for future measurements of Δ17O in tropospheric CO2 that can help to further increase our understanding of the global budget of Δ17O in atmospheric CO2.

Monitoring antimicrobial resistance trends in commensal Escherichia coli from livestock, the Netherlands, 1998 to 2016
Hesp, Ayla ; Veldman, Kees ; Goot, Jeanet van der; Mevius, Dik ; Schaik, G. van - \ 2019
Eurosurveillance 24 (2019)25. - ISSN 1025-496X
AMR - antimicrobial resistance - Escherichia coli - monitoring - quantitative - surveillance - trend analysis

BackgroundMonitoring of antimicrobial resistance (AMR) in animals is essential for public health surveillance. To enhance interpretation of monitoring data, evaluation and optimisation of AMR trend analysis is needed.AimsTo quantify and evaluate trends in AMR in commensal Escherichia coli, using data from the Dutch national AMR monitoring programme in livestock (1998-2016).MethodsFaecal samples were collected at slaughter from broilers, pigs and veal calves. Minimum inhibitory concentration values were obtained by broth microdilution for E. coli for 15 antimicrobials of eight antimicrobial classes. A Poisson regression model was applied to resistant isolate counts, with explanatory variables representing time before and after 2009 (reference year); for veal calves, sampling changed from 2012 represented by an extra explanatory variable.ResultsResistant counts increased significantly from 1998-2009 in broilers and pigs, except for tetracyclines and sulfamethoxazole in broilers and chloramphenicol and aminoglycosides in pigs. Since 2009, resistant counts decreased for all antimicrobials in broilers and for all but the phenicols in pigs. In veal calves, for most antimicrobials no significant decrease in resistant counts could be determined for 2009-16, except for sulfamethoxazole and nalidixic acid. Within animal species, antimicrobial-specific trends were similar.ConclusionsUsing Dutch monitoring data from 1998-2016, this study quantified AMR trends in broilers and slaughter pigs and showed significant trend changes in the reference year 2009. We showed that monitoring in commensal E. coli is useful to quantify trends and detect trend changes in AMR. This model is applicable to similar data from other European countries.

Balanced nuclear and cytoplasmic distribution is required for activation of Gpa2 mediated cell death induced by the potato cyst nematode effector RBP 1
Zheng, Qi ; Slootweg, E.J. ; Sukarta, O.C.A. ; Schaik, C.C. van; Smant, G. ; Goverse, A. - \ 2019
Resistance-gene independent variation in susceptibility to the root-knot nematode Meloidogyne incognita in Solanum lycopersicum
Sterken, M.G. ; Warmerdam, S. ; Guarneri, Nina ; Schaik, C.C. van; Oortwijn, M.E.P. ; Steenbrugge, Joris van; Lozano Torres, J.L. ; Goverse, A. ; Smant, G. - \ 2019
Quantifying calf mortality on dairy farms: Challenges and solutions
Santman-Berends, I.M.G.A. ; Schukken, Y.H. ; Schaik, G. van - \ 2019
Journal of Dairy Science 102 (2019)7. - ISSN 0022-0302 - p. 6404 - 6417.
census data - dairy calves - monitoring - mortality

In the Netherlands, the mortality rate of ear-tagged calves <1 yr is one of the indicators that is continuously monitored in census data and is defined as the number of deceased calves relative to the number of calf-days-at-risk. In 2017, yearly calf mortality rates were published in the lay press and resulted in discussions about the calculation of this parameter among stakeholders because the same parameter appeared to be calculated in many different ways by different organizations. These diverse definitions of calf mortality answered different aims such as early detection of deviations, monitoring trends, or providing insight into herd-specific results, but were difficult to understand by stakeholders. The aim of this study was to evaluate several definitions of calf mortality for scientific validity, usefulness for policymakers, and comprehensibility by farmers. Based on expert consultations, 10 definitions for calf mortality were evaluated that assessed different age categories, time periods, and denominators. Differences in definitions appeared to have a large effect on the magnitude of mortality. For example, with the original mortality parameter, the mortality rate was 16.5% per year. When the first year of life was subdivided into 3 age categories, the mortality rate was 3.3, 4.5, and 3.1% for postnatal calves (≤14 d), preweaned calves (15–55 d), and weaned calves (56 d–1 yr), respectively. Although it was logical that these mortality rates were lower than the original, the sum of the 3 separate mortality rates was also lower than the original mortality rate. The reason was that the number of calves present in a herd and the risk of mortality are not randomly distributed over a calf's first year of life and the conditional nature of mortality rates when calculated for different age categories. Ultimately, 4 parameters to monitor calf mortality in Dutch dairy herds were chosen based on scientific value, usefulness for monitoring of trends, and comprehensibility by farmers: perinatal calf mortality risk (i.e., mortality before, during, or shortly after the moment of birth up to the moment of ear-tagging), postnatal calf mortality risk (≤14 d), preweaned calf mortality rate (15–55 d), and weaned calf mortality rate (56 d–1 yr). Slight differences in definitions of parameters can have a major effect on results, and many factors have to be taken into account when defining an important health indicator such as mortality. Our evaluation resulted in a more thorough understanding of the definitions of the selected parameters and agreement by the stakeholders to use these key indicators to monitor calf mortality.

Three genes identified by genome wide association mapping of root-knot nematode susceptibility in Arabidopsis
Sterken, M.G. ; Warmerdam, S. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Lozano Torres, J.L. ; Bakker, J. ; Smant, G. - \ 2019
Root-knot nematodes are devastating plant-pathogens affecting agricultural productivity of major food crops world-wide. Current control strategies depend on a limited supply of nematode resistance genes. Hence, there is need for alternative control strategies. Here, we show that more subtle quantitative trait loci could be used as additional genetic resource for nematode control.

We mapped the genetic architecture of susceptibility in 340 natural isolates of Arabidopsis thaliana to Meloidogyne incognitia. We found ample genetic variation in M. incognita reproduction on these plants, with a narrow-sense heritability of 0.52. By genome wide association 19 associated loci were identified. Three loci were investigated by characterizing nine T-DNA knock-out mutants of candidate genes, identifying three (co-)regulators of nematode susceptibility in Arabidopsis: BZR1, FRNI1, and ERF6.

Our results suggest that allelic variation in susceptibility genes could be used to improve nematode resistance of plants, paving the way to investigate these traits in food-crops.
Three genes identified by genome wide association mapping of root-knot nematode susceptibility in Arabidopsis
Sterken, M.G. ; Warmerdam, S. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Lozano Torres, J.L. ; Bakker, J. ; Goverse, A. ; Smant, G. - \ 2019
Root-knot nematodes are devastating plant-pathogens affecting the agricultural productivity of major food crops world-wide. The major control strategy nowadays is through incorporating major-effect resistance-genes in food-crops. However, the supply of nematode resistance genes available for breeding is very limited. Hence, there is need for alternative control strategies. Here, we show that more subtle quantitative trait loci could be used as an additional genetic resource for nematode control.We mapped the genetic architecture of susceptibility of the model plant Arabidopsis thaliana to Meloidogyne incognitia using a set of 340 natural isolates. These isolates represent the world-wide genetic variation in this plant. Each of these isolates was tested in at least four technical replicates, the average number of egg-masses per plant ranged from five to 45. We found ample genetic variation in M. incognita reproduction on these plants, with a narrow-sense heritability of 0.52. Subsequently, we mapped quantitative trait loci by genome wide association, explaining genetic variation in nematode reproduction. At a permissive significance threshold of LOD > 4, we identified 19 associated loci. We investigated three loci by characterizing nine T-DNA knock-out mutants of candidate genes. This way, three genes that function as (co-)regulators of nematode susceptibility in Arabidopsis were identified: BRASSINAZOLE RESISTANT1, an F-box familiy protein, and ETHYLENE RESPONSE FACTOR 6. Our results show that there is quantitative genetic variation in the host-plant affecting nematode reproduction. Furthermore, our results suggest that allelic variation in these susceptibility genes could be used to improve the resistance of crops to root-knot nematodes. Our results pave the way to investigate these traits in food-crops.
Nucleocytoplastic distribution is required for activation of Gpa-2 resistance ageinst Globodera pallida
Zheng, Qi ; Slootweg, E.J. ; Sukarta, O.C.A. ; Schaik, C.C. van; Smant, G. ; Goverse, A. - \ 2019
Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463

Intramammary antimicrobial treatment of subclinical mastitis and cow performance later in lactation
Borne, Bart H.P. van den; Schaik, Gerdien van; Lam, Theo J.G.M. ; Nielen, Mirjam ; Frankena, Klaas - \ 2019
Journal of Dairy Science 102 (2019)5. - ISSN 0022-0302 - p. 4441 - 4451.
antimicrobial - clinical mastitis - dairy cow - milk yield - somatic cell count

The aim of this study was to evaluate long-term therapeutic effects of antimicrobial treatment of recently acquired subclinical mastitis (RASCM) during lactation. Quarter-level clinical mastitis (CM) follow-up, composite somatic cell counts (SCC), and cow-level milk yield later in lactation were evaluated using follow-up data from 2 previously published linked randomized field trials. The first trial randomly assigned antimicrobial treatment with any intramammary product or negative control to culture-positive quarters of cows having a first elevated composite SCC after 2 consecutive low composite SCC measurements. Untreated cows that had a second elevated composite SCC at the next measurement and were staphylococci-positive (i.e., Staphylococcus aureus or non-aureus staphylococci) were randomly assigned to treatment or control. Quarter-level CM cases were reported by the participating herd personnel, and milk yield and composite SCC data were obtained from the regular test-day recording. Frailty survival models were used to evaluate the long-term therapeutic effects of antimicrobial treatment of RASCM on quarter-level CM follow-up. Mixed linear regression models were applied to quantify the effect on milk yield and composite SCC. Data of 638 quarters from 486 cows in 38 herds were available for statistical analyses, of which 229 quarters of 175 cows received antimicrobial treatment for RASCM. Antimicrobial treatment culminated in reduced composite SCC levels later in lactation but did not result in different milk yield levels or CM follow-up compared with control cows. Antimicrobial treatment of cows with RASCM should therefore only be considered in exceptional situations given the current focus on antimicrobial usage reduction in animal husbandry.

Distinct roles for strigolactones in cyst nematode parasitism of Arabidopsis roots
Escudero Martinez, Carmen M. ; Guarneri, Nina ; Overmars, Hein ; Schaik, Casper van; Bouwmeester, Harro ; Ruyter-spira, Carolien ; Goverse, Aska - \ 2019
European Journal of Plant Pathology 154 (2019)1. - ISSN 0929-1873 - p. 129 - 140.
Phytohormones play an essential role in different stages of plant-nematode interactions. Strigolactones (SLs) are a novel class of plant hormones which play an important role in plant development. Furthermore, certain soil-inhabiting organisms exploit this plant molecule as allelochemical. However, whether SLs play a role in plant parasitism by nematodes is as yet unknown. This prompted us to investigate the potential role of SLs in different stages of the nematode life cycle using the beet cyst nematode Heterodera schachtii and Arabidopsis as a model system. We analyzed the effect of SLs on cyst nematode hatching, host attraction and invasion, and the establishment of a feeding relation upon infection of the SL deficient mutant max4-1 and the SL signaling mutant max2-1. In addition, infection assays were performed under phosphate shortage to enhance SL production and in the presence of the synthetic SL analog GR24. From this study, we can conclude that SLs do not contribute to cyst nematode hatching at the levels tested but that they do play a role in host attraction and subsequent invasion in a MAX2 dependent manner. Furthermore, we observed that increased levels of exogenous and endogenous SLs change the root invasion zone. Upon root infection, cyst nematode development was enhanced in both the max2-1 and max4-1 mutants due to the formation of enlarged feeding cells. These data provide evidence for distinct roles of SLs during cyst nematode parasitism of plant roots.
Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
Warmerdam, Sonja ; Sterken, Mark G. ; Schaik, Casper van; Oortwijn, Marian E.P. ; Lozano-Torres, Jose L. ; Bakker, Jaap ; Goverse, Aska ; Smant, Geert - \ 2019
Molecular Plant Pathology 20 (2019)1. - ISSN 1464-6722 - p. 137 - 152.
abiotic stress - Arabidopsis thaliana - ERF6 - genome-wide association mapping - Meloidogyne incognita - root-knot nematodes - transcription factor

Root-knot nematodes transform vascular host cells into permanent feeding structures to selectively withdraw their nutrients from host plants during the course of several weeks. The susceptibility of host plants to root-knot nematode infections is thought to be a complex trait involving many genetic loci. However, genome-wide association (GWA) analysis has so far revealed only four quantitative trait loci (QTLs) linked to the reproductive success of the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana, which suggests that the genetic architecture underlying host susceptibility could be much simpler than previously thought. Here, we report that, by using a relaxed stringency approach in a GWA analysis, we could identify 15 additional loci linked to quantitative variation in the reproductive success of M. incognita in Arabidopsis. To test the robustness of our analysis, we functionally characterized six genes located in a QTL with the lowest acceptable statistical support and smallest effect size. This led us to identify ETHYLENE RESPONSE FACTOR 6 (ERF6) as a novel susceptibility gene for M. incognita in Arabidopsis. ERF6 functions as a transcriptional activator and suppressor of genes in response to various abiotic stresses independent of ethylene signalling. However, whole-transcriptome analysis of nematode-infected roots of the Arabidopsis erf6-1 knockout mutant line showed that allelic variation at this locus may regulate the conversion of aminocyclopropane-1-carboxylate (ACC) into ethylene by altering the expression of 1-aminocyclopropane-1-carboxylate oxidase 3 (ACO3). Our data further suggest that tolerance to abiotic stress mediated by ERF6 forms a novel layer of control in the susceptibility of Arabidopsis to M. incognita.

Apoplastic venom allergen-like proteins of plant-parasitic nematodes modulate the activation of plant innate immunity by cell surface receptors
Lozano Torres, J.L. ; Wilbers, R.H.P. ; Warmerdam, S. ; Varossieau, K. ; Willig, J. ; Schaik, C.C. van; Asojo, Oluwatoyin A. ; Darwiche, Rabih ; Schneiter, Roger ; Drurey, Claire ; Maizels, Rick M. ; Goverse, A. ; Schots, A. ; Smant, G. - \ 2018
Despite causing considerable damage to host tissue during parasitism, nematodes establish persistent infections in both animals and plants. An elaborate repertoire of nematode effectors modulates damage-triggered immune responses of the host. However, the nature and mode of action of most of nematode immunomodulatory compounds is not well understood. We discovered that the nematode effectors named the venom allergen-like proteins (VAPs) selectively suppress host immunity during the onset of parasitism in plants. VAPs are uniquely conserved in secretions of all animal- and plant-parasitic nematodes, but their role in parasitism has remained elusive. Knocking-down the expression of Gr-VAP1 hampered the infectivity of the potato cyst nematode Globodera rostochiensis. By contrast, heterologous expression of Gr-VAP1 and VAPs from the beet cyst nematode Heterodera schachtii, in Arabidopsis, resulted in the loss of basal immunity to multiple pathogens. Surprisingly, VAPs only affect the defence responses mediated by surface-localised immune receptors. The modulation of basal immunity by ectopic expression of VAPs involves extracellular protease-based host defences and jasmonic acid responses. Crystal structures of VAPs revealed lipid binding motifs. In these cavities VAPs can bind palmitate and sterol both in vitro and in vivo. The delivery of VAPs into host tissue coincides with large modifications in the extracellular matrix by migratory nematodes. We, therefore, conclude that parasitic nematodes most likely utilise VAPs to suppress the activation of defences by immunogenic breakdown products in damaged host tissue.
Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
Warmerdam, S. ; Sterken, M.G. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Lozano Torres, J.L. ; Dicke, M. ; Helder, J. ; Kammenga, J.E. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth, and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focussed on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance genes. To study the genetic architecture of susceptibility to M. incognita in plants, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed thirty-six quantitative trait loci (QTLs) in the genome of A. thaliana significantly associated with reproductive success of M. incognita. Mutant analysis of candidate genes located in four QTLs revealed various novel proteins functioning as (co-)regulators of susceptibility to M. incognita in Arabidopsis. Our data further suggests that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.
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Rijgersberg, Hajo ; Geijn, Frank van de; Schaik, Alex van; Willems, Don ; Hogeveen, Esther - \ 2018
Wageningen : Wageningen Food & Biobased Research (Wageningen Food &amp; Biobased Research rapport 1877) - ISBN 9789463435536 - 29
Changes in surface hydrology, soil moisture, and Gross Primary Productivity in the Amazon during the 2015/2016 El Niño
Laan-Luijkx, I.T. van der - \ 2018
This zip file contains XX individual NetCDF files with the data used for the publication of van Schaik et al. 2018 in the Philosophical transactions of the Royal Society. Full description of the methodology used to create these numbers is available from the publication and its Supplement.
Custom Amazon Sun-Induced Fluorescence dataset used in Koren et al., (2018) publication
Peters, W. ; Koren, G.B. ; Schaik, Erik van - \ 2018
This dataset was used to create the results in the paper of Koren et al., (2018) published by the journal "Philosophical Transactions of the Royal Society B". It contains SIF data for the region of South America retrieved from GOME-2A radiances using a modified version of the SIFTERv2 algorithm developed at the Royal Dutch Meteorological Office (KNMI). The dataset spans 10 years (2007-2016) and is at 0.5x0.5 degrees resolution. Details are provided as attributes in the NetCDF file.
Changes in surface hydrology, soil moisture and gross primary production in the Amazon during the 2015/2016 El Niño
Schaik, Erik van; Killaars, Lars ; Smith, Naomi E. ; Koren, Gerbrand ; Beek, L.P.H. van; Peters, Wouter ; Laan-Luijkx, Ingrid T. van der - \ 2018
Philosophical Transactions of the Royal Society B. Biological sciences 373 (2018)1760. - ISSN 0962-8436 - 9 p.
Amazon - El Niño - gross primary productivity - river discharge - soil moisture - tropical terrestrial carbon cycle

The 2015/2016 El Niño event caused severe changes in precipitation across the tropics. This impacted surface hydrology, such as river run-off and soil moisture availability, thereby triggering reductions in gross primary production (GPP). Many biosphere models lack the detailed hydrological component required to accurately quantify anomalies in surface hydrology and GPP during droughts in tropical regions. Here, we take the novel approach of coupling the biosphere model SiBCASA with the advanced hydrological model PCR-GLOBWB to attempt such a quantification across the Amazon basin during the drought in 2015/2016. We calculate 30-40% reduced river discharge in the Amazon starting in October 2015, lagging behind the precipitation anomaly by approximately one month and in good agreement with river gauge observations. Soil moisture shows distinctly asymmetrical spatial anomalies with large reductions across the north-eastern part of the basin, which persisted into the following dry season. This added to drought stress in vegetation, already present owing to vapour pressure deficits at the leaf, resulting in a loss of GPP of 0.95 (0.69 to 1.20) PgC between October 2015 and March 2016 compared with the 2007-2014 average. Only 11% (10-12%) of the reduction in GPP was found in the (wetter) north-western part of the basin, whereas the north-eastern and southern regions were affected more strongly, with 56% (54-56%) and 33% (31-33%) of the total, respectively. Uncertainty on this anomaly mostly reflects the unknown rooting depths of vegetation.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Widespread reduction in sun-induced fluorescence from the Amazon during the 2015/2016 El Niño
Koren, Gerbrand ; Schaik, Erik van; Araújo, Alessandro C. ; Boersma, K.F. ; Gärtner, Antje ; Killaars, Lars ; Kooreman, Maurits L. ; Kruijt, Bart ; Laan-Luijkx, Ingrid T. van der; Randow, Celso von; Smith, Naomi E. ; Peters, Wouter - \ 2018
Philosophical Transactions of the Royal Society B. Biological sciences 373 (2018)1760. - ISSN 0962-8436 - 10 p.
Amazon rainforest - drought response - El Niño-Southern Oscillation - gross primary production - sun-induced fluorescence - tropical terrestrial carbon cycle

The tropical carbon balance dominates year-to-year variations in the CO2 exchange with the atmosphere through photosynthesis, respiration and fires. Because of its high correlation with gross primary productivity (GPP), observations of sun-induced fluorescence (SIF) are of great interest. We developed a new remotely sensed SIF product with improved signal-to-noise in the tropics, and use it here to quantify the impact of the 2015/2016 El Niño Amazon drought. We find that SIF was strongly suppressed over areas with anomalously high temperatures and decreased levels of water in the soil. SIF went below its climatological range starting from the end of the 2015 dry season (October) and returned to normal levels by February 2016 when atmospheric conditions returned to normal, but well before the end of anomalously low precipitation that persisted through June 2016. Impacts were not uniform across the Amazon basin, with the eastern part experiencing much larger (10-15%) SIF reductions than the western part of the basin (2-5%). We estimate the integrated loss of GPP relative to eight previous years to be 0.34-0.48 PgC in the three-month period October-November-December 2015.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

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