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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Successful Host Adaptation of IncK2 Plasmids
Rozwandowicz, Marta ; Brouwer, Michael S.M. ; Mughini-Gras, Lapo ; Wagenaar, Jaap A. ; Gonzalez-Zorn, Bruno ; Mevius, Dik J. ; Hordijk, Joost - \ 2019
Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
chicken - conjugation - IncK2 - plasmid - sigma-32

The IncK plasmid group can be divided into two separate lineages named IncK1 and IncK2. IncK2 is found predominantly in poultry while IncK1 was reported in various mammals, including animals and humans. The physiological basis of this distinction is not known. In this manuscript we examined fitness cost of IncK1 and IncK2 plasmids at 37 and 42°C, which resembles mammalian and chicken body temperatures, respectively. We analyzed conjugation frequency, plasmid copy number and plasmid fitness cost in direct competition. Additionally, we measured levels of σ-32 in Escherichia coli carrying either wild type or conjugation-deficient IncK plasmids. The results show that IncK2 plasmids have a higher conjugation frequency and lower copy number at 42°C compared to IncK1. While the overall fitness cost to the host bacterium of IncK2 plasmids was higher than that of IncK1, it was not affected by the temperature while the fitness cost of IncK1 was shown to increase at 42°C compared to 37°C. These differences correlate with an increased expression of σ-32, a regulator of heat-shock protein expression, in E. coli with IncK2 compared to cells containing IncK1. This effect was not seen in cells containing conjugation deficient plasmids. Therefore, it is hypothesized that the assembly of the functional T4S may lead to these increased levels of σ–32. Increased activation of CpxR at 42°C may explain why IncK2 plasmids, and not IncK1, are predominantly found in chicken isolates.

High throughput cultivation-based screening on the MicroDish platform allows targeted isolation of antibiotic resistant human gut bacteria
Versluis, Dennis ; Bello Gonzalez, Teresita ; Zoetendal, Erwin ; Passel, Mark van; Smidt, Hauke - \ 2019
Wageningen University
PRJEB27463 - ERP109543
The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on MicroDish porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput screening of growth communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance.
SoilGrids: consistent soil information to assess and map soil functions at global scale
Poggio, Laura ; Duque Moreira de Sousa, Luïs ; Heuvelink, G.B.M. ; Kempen, B. ; Batjes, N.H. ; Leenaars, J.G.B. ; Mantel, S. ; Bai, Z.G. ; Turdukulov, Ulan ; Ruiperez Gonzalez, M. ; Carvalho Ribeiro, E.D. ; Rossiter, David ; Bosch, H. van den - \ 2019
In: Wageningen Soil Conference: Understanding Soil Functions. - Wageningen : ISRIC - p. 50 - 51.
When a Few Clicks Make All the Difference: Improving Weakly-Supervised Wildlife Detection in UAV Images
Kellenberger, B.A. ; Marcos Gonzalez, D. ; Tuia, D. - \ 2019
In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR) Workshops Institute of Electrical and Electronics Engineers Inc. - 9 p.
Experimental trials in Europe 2019 edition
Garnica, I. ; Lezaun, J.A. ; Gonzalez-Andujar, J.L. ; Pedraza Jimenez, V. ; Antichi, D. ; Frasconi, C. ; Carlesi, S. ; Lazzaro, M. ; Leoni, F. ; Moonen, A.C. ; Huiting, H.F. ; Riemens, M.M. ; Chiarini, F. ; Zanche, A. De - \ 2019
Veneto Agricoltura - 150 p.
Modulatory Effect of Protein and Carotene Dietary Levels on Pig gut Microbiota
González-Prendes, Rayner ; Pena, Ramona Natacha ; Solé, Emma ; Seradj, Ahmad Reza ; Estany, Joan ; Ramayo-Caldas, Yuliaxis - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

In this study we investigated the impact of dietary protein and carotene levels on microbial functions and composition during the last month of purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points of live, 165 (T1) and 195 (T2) days. From 70 to 165 days of age, 32 pigs were divided into two groups fed either a standard-protein (SP) or a low-protein (LP) diet. In the last month (165–195 days), all pigs received a LP diet, either carotene-enriched (CE) or not (NC). Significant differences were observed between T1 and T2 at Amplicon Sequences Variants (ASVs), phylum and genus levels. In T1 group, Prevotella, Faecalibacterium and Treponema were the genera most influenced by dietary protein, together with predicted functions related with the degradation of protein. In contrast, the CE diet did not impact the microbiome diversity, although 160 ASVs were differentially abundant between CE and NC groups at T2. Weak stability of enterotype clusters across time-points was observed as consequence of medium-term dietary interventions. Our results suggest that during the last month of fattening, dietary protein have a stronger effect than carotenes on the modulation of the compositional and functional structure of the pig microbiota.

BrAPI-an application programming interface for plant breeding applications
Selby, Peter ; Abbeloos, Rafael ; Backlund, Jan Erik ; Basterrechea Salido, Martin ; Bauchet, Guillaume ; Benites-Alfaro, Omar E. ; Birkett, Clay ; Calaminos, Viana C. ; Carceller, Pierre ; Cornut, Guillaume ; Vasques Costa, Bruno ; Edwards, Jeremy D. ; Finkers, Richard ; Yanxin Gao, Star ; Ghaffar, Mehmood ; Glaser, Philip ; Guignon, Valentin ; Hok, Puthick ; Kilian, Andrzej ; König, Patrick ; Lagare, Jack Elendil B. ; Lange, Matthias ; Laporte, Marie Angélique ; Larmande, Pierre ; LeBauer, David S. ; Lyon, David A. ; Marshall, David S. ; Matthews, Dave ; Milne, Iain ; Mistry, Naymesh ; Morales, Nicolas ; Mueller, Lukas A. ; Neveu, Pascal ; Papoutsoglou, Evangelia ; Pearce, Brian ; Perez-Masias, Ivan ; Pommier, Cyril ; Ramírez-González, Ricardo H. ; Rathore, Abhishek ; Raquel, Angel Manica ; Raubach, Sebastian ; Rife, Trevor ; Robbins, Kelly ; Rouard, Mathieu ; Sarma, Chaitanya ; Scholz, Uwe ; Sempéré, Guilhem ; Shaw, Paul D. ; Simon, Reinhard ; Verouden, Maikel - \ 2019
Bioinformatics 35 (2019)20. - ISSN 1367-4803 - p. 4147 - 4155.

MOTIVATION: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. RESULTS: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. AVAILABILITY AND IMPLEMENTATION: More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.

The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data
Wittenburg, Peter ; Sustkova, Hana Pergl ; Montesanti, Annalisa ; Bloemers, Margreet ; Waard, S.H. de; Musen, Mark A. ; Graybeal, John ; Hettne, Kristina M. ; Jacobsen, Annika ; Pergl, Robert ; Hooft, Rob W.W. ; Staiger, Christine ; Gelder, Celia W.G. van; Knijnenburg, Sebastiaan L. ; Arkel, A.C. van; Meerman, Bert ; Wilkinson, Mark D. ; Sansone, S.A. ; Rocca-Serra, Philippe ; McQuilton, Peter ; Gonzalez-Beltran, Alejandra N. ; Aben, G.J.C. ; Henning, P. ; Menezes Alencar, Maria Simone de; Ribeiro, C. ; Silva, C.R.L. ; Sayao, Luis ; Sales, Luana ; Veiga, Viviane ; Lima, Jefferson ; Dib, Simone ; Xavier dos Santos, Paula dos; Murtinho, R. ; Tendel, Jakob ; Schaap, B.F. ; Brouwer, P.M. ; Gavai, A.K. ; Bouzembrak, Yamine ; Marvin, Hans J.P. ; Mons, Albert ; Kuhn, Tobias ; Gambardella, A.A. ; Miranda Azevedo, Ricardo de; Muhonen, Vesa ; Naald, Mira van der; Smit, N.W. ; Buys, M.J. ; Bruin, Taco F. de; Schoots, Fieke ; Goodson, H.J.E. ; Rzepa, Henry S. ; Jeffery, Keith G. ; Shanahan, Hugh P. ; Axton, M. ; Tkachenko, Veniamin ; Deslattes Maya, Anne ; Meyers, Natalie ; Conlon, Michael ; Haak, Laurel L. ; Schultes, Erik - \ 2019
arXiv - 13 p.
There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.
Eerdere krimp leverde varkensboeren geld op
Hoste, R. ; Galen, M.A. van; Jongeneel, R.A. ; Gonzalez Martinez, Ana ; Wattel, C.J. - \ 2019
Post-fire soil erosion mitigation at the scale of swales using forest logging residues at a reduced application rate
Prats, Sergio A. ; González-Pelayo, Óscar ; Silva, Flavio C. ; Bokhorst, Koen J. ; Baartman, Jantiene E.M. ; Keizer, Jan J. - \ 2019
Earth Surface Processes and Landforms 44 (2019)14. - ISSN 0197-9337 - p. 2837 - 2848.
effectiveness - erosion - mulch - organic matter - wildfire

Mulching with forest residues has proved to be highly effective in reducing post-fire soil losses at the plot scale. However, its effectiveness has not been quantified at the application rates that are typically used in operational post-fire land management (2–3 Mg ha-1 using straw), as well as at scales larger than 100 m2. The present study compared post-fire erosion rates for six convergent hillslopes or swales of 500 to 800 m2, three of which were left untreated while the other three were mulched immediately after the fire with shredded eucalypt bark at a rate of 2.4 Mg ha-1. Erosion rates were monitored at irregular intervals during the first three post-fire years, whilst ground cover was assessed yearly. Selected topsoil properties (0–2 cm) such as organic matter content and aggregate stability were determined at a single occasion – two years after the wildfire, for three micro-environments separately: bare soil, and under mulch/litter and vegetation. Soil losses on the untreated swales decreased with post-fire year from 2.2 to 0.4 and 0.11 Mg ha-1 yr-1 (respectively for the first, second and third post-fire years), while the mulched swales produced 84%, 77% and 38% less soil losses than the untreated swales. Soil losses also depended on slope aspect, with the north-facing swales producing less erosion than the west-facing ones. This could be linked to their significant differences in bare soil, vegetation and stone cover, or a combination thereof. The type of micro-environment also played a significant role in topsoil properties (stone content, bulk density, resistance to penetration/shear stress, porosity and organic matter content). The present results add to the increasing evidence that forest residues should be duly considered for operational post-fire land management. Forest residues were highly effective in reducing erosion from swales at application rates as low as the typical 2 Mg ha-1 of post-fire straw mulch.

Robustness of trait connections across environmental gradients and growth forms
Flores-Moreno, Habacuc ; Fazayeli, Farideh ; Banerjee, Arindam ; Datta, Abhirup ; Kattge, Jens ; Butler, Ethan E. ; Atkin, Owen K. ; Wythers, Kirk ; Chen, Ming ; Anand, Madhur ; Bahn, Michael ; Byun, Chaeho ; Cornelissen, Hans C. ; Craine, Joseph ; Gonzalez-Melo, Andres ; Hattingh, Wesley N. ; Jansen, Steven ; Kraft, Nathan J.B. ; Kramer, Koen ; Laughlin, Daniel C. ; Minden, Vanessa ; Niinemets, Ülo ; Onipchenko, Vladimir ; Peñuelas, Josep ; Soudzilovskaia, Nadejda A. ; Dalrymple, Rhiannon L. ; Reich, Peter B. - \ 2019
Global Ecology and Biogeography 28 (2019)12. - ISSN 1466-822X - p. 1806 - 1826.
leaf traits - plant functional traits - plant strategy integration - seed traits - stem traits - trait interdependence - trait networks

Aim: Plant trait databases often contain traits that are correlated, but for whom direct (undirected statistical dependency) and indirect (mediated by other traits) connections may be confounded. The confounding of correlation and connection hinders our understanding of plant strategies, and how these vary among growth forms and climate zones. We identified the direct and indirect connections across plant traits relevant to competition, resource acquisition and reproductive strategies using a global database and explored whether connections within and between traits from different tissue types vary across climates and growth forms. Location: Global. Major taxa studied: Plants. Time period: Present. Methods: We used probabilistic graphical models and a database of 10 plant traits (leaf area, specific leaf area, mass- and area-based leaf nitrogen and phosphorous content, leaf life span, plant height, stem specific density and seed mass) with 16,281 records to describe direct and indirect connections across woody and non-woody plants across tropical, temperate, arid, cold and polar regions. Results: Trait networks based on direct connections are sparser than those based on correlations. Land plants had high connectivity across traits within and between tissue types; leaf life span and stem specific density shared direct connections with all other traits. For both growth forms, two groups of traits form modules of more highly connected traits; one related to resource acquisition, the other to plant architecture and reproduction. Woody species had higher trait network modularity in polar compared to temperate and tropical climates, while non-woody species did not show significant differences in modularity across climate regions. Main conclusions: Plant traits are highly connected both within and across tissue types, yet traits segregate into persistent modules of traits. Variation in the modularity of trait networks suggests that trait connectivity is shaped by prevailing environmental conditions and demonstrates that plants of different growth forms use alternative strategies to cope with local conditions.

Effect of mass rearing on the genetic diversity of the predatory mite Amblyseius swirskii
Paspati, Angeliki ; Ferguson, Kim B. ; Verhulst, Eveline C. ; Urbaneja, Alberto ; González‐Cabrera, Joel ; Pannebakker, Bart A. - \ 2019
Entomologia Experimentalis et Applicata 167 (2019)7. - ISSN 0013-8703 - p. 670 - 681.
Amblyseius swirskii Athias‐Henriot (Acari: Phytoseiidae) is a predatory mite used to control whiteflies and thrips in protected crops. This biocontrol agent, originating from the Eastern Mediterranean region, has been mass‐reared for commercial use since 2005 and is widely used in augmentative biocontrol programs. As a polyphagous predator, it has to cope with different biotic and abiotic factors. However, possible adaptation to mass rearing for production might be hindering its resilience and capacity for optimum performance in the field. In this study, we investigated the effect of long‐term mass rearing on the genetic diversity of A. swirskii. We identified six microsatellite loci from whole‐genome nanopore sequencing of A. swirskii and used these in a comparative analysis of the genetic diversity and differentiation in eight wild populations collected from Israel in 2017 and a commercially available population. Our results indicate that the commercial population is 2.5× less heterozygous than the wild A. swirskii. Furthermore, the commercial population has the highest genetic differentiation from all the natural populations, as indicated by higher pairwise Fst values. Overall, we show that commercially reared A. swirskii have reduced genetic variation compared to their wild counterparts, which may reduce their performance when released to control pests in an integrated pest management (IPM) context.
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology (2019). - ISSN 1087-0156

In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

Neonicotinoids in excretion product of phloem-feeding insects kill beneficial insects
Calvo-Agudo, Miguel ; González-Cabrera, Joel ; Picó, Yolanda ; Calatayud-Vernich, Pau ; Urbaneja, Alberto ; Dicke, Marcel ; Tena, Alejandro - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)34. - ISSN 0027-8424 - p. 16817 - 16822.
Pest control in agriculture is mainly based on the application of insecticides, which may impact nontarget beneficial organisms leading to undesirable ecological effects. Neonicotinoids are among the most widely used insecticides. However, they have important negative side effects, especially for pollinators and other beneficial insects feeding on nectar. Here, we identify a more accessible exposure route: Neonicotinoids reach and kill beneficial insects that feed on the most abundant carbohydrate source for insects in agroecosystems, honeydew. Honeydew is the excretion product of phloem-feeding hemipteran insects such as aphids, mealybugs, whiteflies, and psyllids. We allowed parasitic wasps and pollinating hoverflies to feed on honeydew from hemipterans feeding on trees treated with thiamethoxam or imidacloprid, the most commonly used neonicotinoids. LC-MS/MS analyses demonstrated that both neonicotinoids were present in honeydew. Honeydew with thiamethoxam was highly toxic to both species of beneficial insects, and honeydew with imidacloprid was moderately toxic to hoverflies. Collectively, our data provide strong evidence for honeydew as a route of insecticide exposure that may cause acute or chronic deleterious effects on nontarget organisms. This route should be considered in future environmental risk assessments of neonicotinoid applications.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
Genera of phytopathogenic fungi: GOPHY 3
Marin-Felix, Y. ; Hernández-Restrepo, M. ; Iturrieta-González, I. ; García, D. ; Gené, J. ; Groenewald, J.Z. ; Cai, L. ; Chen, Q. ; Quaedvlieg, W. ; Schumacher, R.K. ; Taylor, P.W.J. ; Ambers, C. ; Bonthond, G. ; Edwards, J. ; Krueger-Hadfield, S.A. ; Luangsa-ard, J.J. ; Morton, L. ; Moslemi, A. ; Sandoval-Denis, M. ; Tan, Y.P. ; Thangavel, R. ; Vaghefi, N. ; Cheewangkoon, R. ; Crous, P.W. - \ 2019
Studies in Mycology 94 (2019). - ISSN 0166-0616 - p. 1 - 124.
DNA barcodes - Fungal systematics - New taxa

This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.

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.

The problem of water use in rural areas of Southwestern Spain: A local perspective
Pulido, Manuel ; Barrena-González, Jesús ; Alfonso-Torreño, Alberto ; Robina-Ramírez, Rafael ; Keesstra, Saskia - \ 2019
Water 11 (2019)6. - ISSN 2073-4441
Drinking water - Irrigation - Leisure facilities - Local perception

Water is a key strategic resource, particularly in Mediterranean climate-type areas with impermeable rocks and shallow soils like Southwestern Spain. The region of Extremadura is commonly known by its large surface occupied by big dams (30% of water dammed in Spain) although this theoretical abundance of water does not hide other problems of use. In this study, we have interviewed 132 people from the municipality of Arroyo de San Serván in order to know what the problems related to water use are, especially those that concern local people the most. Regarding the use of water at home, 90% of interviewees spend less than 60 EUR per month for water and their mean degree of satisfaction about the service is 3.7 out of 7. The reason for this low value can be the excessive content of calcium and bad taste according to 82.1%. Therefore, 64.2% of people do not usually drink water from the tap. Around two thirds of these local people usually buy water in the supermarket or drink filtered water. Concerning agricultural activities, local people gave great importance to irrigation as a source of employment (5.6/7) and inputs (4.5/7), although their satisfaction decreases about the current price of water for agriculture (0.02 EUR m-3). In addition, they are really worried about the overuse of fertilizers and herbicides (5.4/7) and they think about the necessity of taking measures to reduce these problems (6.1/7) as well as to reduce some management problems such as supply cuts. In the last few years, private (swimming pools) and public leisure facilities (swimming pool and spa) have been built in spite of not being considered important by local people (3.6-4.0/7). Nevertheless, about 60% of them consider these common facilities very positive in terms of employment, tourism attractions and entertainment for local people.

Arsenic in Argentina : Technologies for arsenic removal from groundwater sources, investment costs and waste management practices
Litter, Marta I. ; Ingallinella, Ana M. ; Olmos, Valentina ; Savio, Marianela ; Difeo, Gonzalo ; Botto, Lía ; Torres, Elsa Mónica Farfán ; Taylor, Sergio ; Frangie, Sofía ; Herkovits, Jorge ; Schalamuk, Isidoro ; González, María José ; Berardozzi, Eliana ; García Einschlag, Fernando S. ; Bhattacharya, Prosun ; Ahmad, Arslan - \ 2019
Science of the Total Environment 690 (2019). - ISSN 0048-9697 - p. 778 - 789.
Argentina - Arsenic - Drinking water - Mitigation - Removal technologies

An overview about the presence of arsenic (As) in groundwaters of Argentina, made by a transdisciplinary group of experts is presented. In this second part, the conventional and emerging technologies for As removal, management of wastes, and the initial investment costs of the proposed technologies, with emphasis on developments of local groups are described. Successful examples of real application of conventional and emerging technologies for As removal in waters for human consumption, for medium, small and rural and periurban communities are reported. In the country, the two most applied technologies for arsenic removal at a real scale are reverse osmosis and coagulation-adsorption-filtration processes using iron or aluminum salts or polyelectrolytes as coagulants. A decision tree to evaluate the possible technologies to be applied, based on the population size, the quality of the water and its intended use, is presented, including preliminary and indicative investment costs. Finally, a section discussing the treatment and final disposal of the liquid, semiliquid and solid wastes, generated by the application of the most used technologies, is included. Conclusions and recommendations, especially for isolated rural and periurban regions, have been added.

A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer : An ATPase-Mimicking Nucleoapzyme
Biniuri, Yonatan ; Shpilt, Zohar ; Albada, Bauke ; Vázquez-González, Margarita ; Wolff, Mariusz ; Hazan, Carina ; Golub, Eyal ; Gelman, Dimitri ; Willner, Itamar - \ 2019
ChemBioChem (2019). - ISSN 1439-4227 - p. 1 - 7.
catalytic DNA - DNAzymes - microscale thermophoresis - molecular dynamics - nucleic acids

Catalytic nucleic acids consisting of a bis-Zn2+-pyridyl-salen-type ([di-ZnII 3,5 bis(pyridinylimino) benzoic acid]) complex conjugated to the ATP aptamer act as ATPase-mimicking catalysts (nucleoapzymes). Direct linking of the Zn2+ complex to the 3′- or 5′-end of the aptamer (nucleoapzymes I and II) or its conjugation to the 3′- or 5′-end of the aptamer through bis-thymidine spacers (nucleoapzymes III and IV) provided a set of nucleoapzymes exhibiting variable catalytic activities. Whereas the separated bis-Zn2+-pyridyl-salen-type catalyst and the ATP aptamer do not show any noticeable catalytic activity, the 3′-catalyst-modified nucleoapzyme (nucleoapzyme IV) and, specifically, the nucleoapzyme consisting of the catalyst linked to the 3′-position through the spacer (nucleoapzyme III) reveal enhanced catalytic features in relation to the analogous nucleoapzyme substituted at the 5′-position (kcat=4.37 and 6.88 min−1, respectively). Evaluation of the binding properties of ATP to the different nucleoapzyme and complementary molecular dynamics simulations suggest that the distance separating the active site from the substrate linked to the aptamer binding site controls the catalytic activities of the different nucleoapzymes.

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