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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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.

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.

Data from: Multi-variable approach pinpoints origin of oak wood with higher precision
Akhmetzyanov, L. ; Buras, Allan ; Sass-Klaassen, U.G.W. ; Ouden, J. den; Mohren, G.M.J. ; Groenendijk, Peter ; García-González, Ignacio - \ 2019
dendroprovenancing - earlywood vessels - latewood width - multi-variable approach - region-specific growth patterns - Quercus spp. - wood anatomy - Quercus robur - Quercus petraea - Quercus pyrenaica - Quercus faginea
Aim: Spatial variations of environmental conditions translate into biogeographic growth patterns of tree growth. This fact is used to identify the origin of timber by means of dendroprovenancing. Yet, dendroprovenancing attempts are based on ring-widths measurements, and neglect additional tree-ring parameters. To explore the effect of including additional variables in dendroprovenancing, we investigate whether and, if so, why the incorporation of wood-anatomical parameters can increase the precision of identifying the origin of oak wood. Since such features reflect environmental conditions of different periods – which vary between source regions – we hypothesize that their inclusion allows more precise dendroprovenancing. Location: Europe, Spain. Taxon: Quercus robur L., Quercus petraea (Matt.) Liebl., Quercus faginea Lam., Quercus pyrenaica Willd. Methods: We sampled four oak species resembling a longitudinal and an elevational/continental gradients. We measured multiple tree-ring variables to (1) extract meaningful variables, (2) represent statistical relations among variables, (3) analyse regional-specific growth patterns in individual time series and (4) determine underlying climate-growth relationships. Leave-one-out analyses were used to test whether a combination of selected variables allows dendroprovenancing of a randomly selected tree within the area. Results: A combination of latewood width and earlywood vessels size can be used to pin-point the origin of oak wood with higher precision than latewood width only. Variation in latewood widths appointed the wood to areas across the longitudinal gradient, whereas variation in vessels assigned wood to locations along a latitudinal/topographic gradient. The climatic factors behind these gradients are respectively an East-West gradient in June-July temperature, and a North-South gradient in winter/ spring temperatures. The leave-one-out analyses supported the robustness of the results. Main conclusions: Integration of multiple tree-ring variables in combination with multivariate techniques leads to higher precision in the dendroprovenancing of ring-porous oak species.
Multi-variable approach pinpoints origin of oak wood with higher precision
Akhmetzyanov, Linar ; Buras, Allan ; Sass-Klaassen, Ute ; Ouden, Jan den; Mohren, Frits ; Groenendijk, Peter ; García-González, Ignacio - \ 2019
Journal of Biogeography 46 (2019)6. - ISSN 0305-0270 - p. 1163 - 1177.
dendroprovenancing - earlywood vessels - latewood width - multi-variable approach - Quercus spp. - region-specific growth patterns - wood anatomy

Aim: Spatial variations of environmental conditions translate into biogeographical patterns of tree growth. This fact is used to identify the origin of timber by means of dendroprovenancing. Yet, dendroprovenancing attempts are commonly only based on ring-width measurements, and largely neglect additional tree–ring variables. We explore the potential of using wood anatomy as a dendroprovenancing tool, and investigate whether it increases the precision of identifying the origin of oak wood. Since different tree–ring variables hold different information on environmental conditions prevailing at specific times of the growing season—which vary between source regions—we hypothesize that their inclusion allows more precise dendroprovenancing. Location: Europe, Spain. Taxon: Quercus robur L., Quercus petraea (Matt.) Liebl., Quercus faginea Lam., Quercus pyrenaica Willd. Methods: We sampled four oak species across Northern Spain, i.e. from the Basque country and Cantabria and—in the Basque country—from low to high elevation (topographic/latitudinal gradient). We measured multiple tree–ring variables to (a) extract complementary variables; (b) present statistical relations among them; (c) analyse region-specific variation in their patterns based on time–series of individual trees; and (d) determine underlying climate–growth relationships. Leave-one-out analysis was used to test whether a combination of selected variables allowed dendroprovenancing of a randomly selected tree within the area. Results: A combination of latewood width (LW) and earlywood vessel size was used to pinpoint the origin of oak wood with higher precision than ring width or LW only. Variation in LW pinpointed the wood to east and west areas, whereas variation in vessels assigned wood to locations along a latitudinal/topographic gradient. The climatic triggers behind these gradients are respectively an east–west gradient in June–July temperature and a north–south gradient in winter/spring temperatures. The leave-one-out analyses supported the robustness of these results. Main conclusions: Integration of multiple wood–xylem anatomical variables analysed with multivariate techniques leads to higher precision in the dendroprovenancing of ring-porous oak species.

Arsenic in Argentina: Occurrence, human health, legislation and determination
Litter, Marta I. ; Ingallinella, Ana M. ; Olmos, Valentina ; Savio, Marianela ; Difeo, Gonzalo ; Botto, Lía ; Farfán Torres, Elsa Mónica ; 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 676 (2019). - ISSN 0048-9697 - p. 756 - 766.
Analytical determination - Argentina - Arsenic - Health - Occurrence - Regulations

An overview about the presence of arsenic (As) in groundwaters of Argentina, made by a transdisciplinary group of experts is presented. Aspects on As occurrence, effects of As on human health, regulations regarding the maximum allowable amount of As in drinking water as well as bottled water, and analytical techniques for As determination are presented. The most affected region in Argentina is the Chaco-Pampean plain, covering around 10 million km 2 , where approximately 88% of 86 groundwater samples collected in 2007 exceeded the World Health Organization (WHO) guideline value. In the Salí river basin, As concentrations ranged from 11.4 to 1660 μg/L, with 100% of the samples above the WHO guideline value. In the Argentine Altiplano (Puna) and Subandean valleys, 61% of 62 samples collected from surface and groundwaters exceeded the WHO limit. Thus, it can be estimated that, at present, the population at risk in Argentina reaches around four million people. Pathologies derived from the chronic consumption of As, the metabolism of As in the human body and the effects of the different As chemical forms, gathered under the name HACRE (hidroarsenicismo crónico regional endémico in Spanish, for chronic regional endemic hydroarsenicism) are described. Regarding the regulations, the 10 μg/L limit recommended by the WHO and the United States Environmental Protection Agency has been incorporated in the Argentine Food Code, but the application is still on hold. In addition, there is disparity regarding the maximal admitted values in several provinces. Considerations about the As concentrations in bottled water are also presented. A survey indicates that there are several Argentine laboratories with the suitable equipment for As determination at 10 μg/L, although 66% of them are concentrated in Buenos Aires City, and in the Santa Fe, Córdoba and Buenos Aires provinces. Conclusions and recommendations of this first part are provided.

sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds
Nunes-Nesi, Adriano ; Alseekh, Saleh ; Oliveira Silva, Franklin Magnum de; Omranian, Nooshin ; Lichtenstein, Gabriel ; Mirnezhad, Mohammad ; González, Roman R.R. ; y Garcia, Julia Sabio ; Conte, Mariana ; Leiss, Kirsten A. ; Klinkhamer, Peter G.L. ; Nikoloski, Zoran ; Carrari, Fernando ; Fernie, Alisdair R. - \ 2019
Metabolomics 15 (2019)4. - ISSN 1573-3882
Leaf metabolism - Metabolite network - Metabolite QTL - Tomato

Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

Biodiversity recovery of Neotropical secondary forests
Rozendaal, Danaë M.A. ; Bongers, Frans ; Aide, T.M. ; Alvarez-Dávila, Esteban ; Ascarrunz, Nataly ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; Calvo-Rodriguez, Sofia ; Chave, Jerome ; César, Ricardo G. ; Chazdon, Robin L. ; Condit, Richard ; Dallinga, Jorn S. ; Almeida-Cortez, Jarcilene S. De; Jong, Ben de; Oliveira, Alexandre De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Dutrieux, Loïc P. ; Espírito-Santo, Mario M. ; Fandino, María C. ; Fernandes, G.W. ; Finegan, Bryan ; García, Hernando ; Gonzalez, Noel ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Hubbell, Stephen ; Jakovac, Catarina C. ; Hernández, Alma Johanna ; Junqueira, André B. ; Kennard, Deborah ; Larpin, Denis ; Letcher, Susan G. ; Licona, Juan-Carlos ; Lebrija-trejos, Edwin ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita C.G. ; Mora, Francisco ; Müller, Sandra C. ; Muñoz, Rodrigo ; Oliveira Neto, Silvio Nolasco De; Norden, Natalia ; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Ortiz-Malavassi, Edgar ; Ostertag, Rebecca ; Peña-Caros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Powers, Jennifer S. ; Aguilar-Cano, José ; Rodriguez-Buritica, Susana ; Rodríguez-Velázquez, Jorge ; Romero-Romero, Marco Antonio ; Ruíz, Jorge ; Sanchez-Azofeifa, Arturo ; Almeida, Arlete Silva De; Silver, Whendee L. ; Schwartz, Naomi B. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Sá Sampaio, Everardo Valadares De; Breugel, Michiel van; Wal, Hans van der; Martins, Sebastião Venâncio ; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vicentini, Alberto ; Vieira, Ima C.G. ; Villa, Pedro ; Williamson, G.B. ; Zanini, Kátia J. ; Zimmerman, Jess ; Poorter, Lourens - \ 2019
Science Advances 5 (2019)3. - ISSN 2375-2548 - 10 p.
Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.
Erratum to: The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
GigaScience 7 (2018)12. - ISSN 2047-217X
Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research 63 (2018)1. - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Guide to evaluation of quality of surface water in coffee river basins of Colombia
Rodríguez Valencia, Nelson ; Quintero Yepes, Laura Vanessa ; Gómez Zuluaga, Gustavo Adolfo ; Bohórquez Zapata, Viviana Lorena ; González Durán, Cristy Mayerly ; Osorio Ocampo, Andrés Felipe ; Miguel García, Ángel de; Harmsen, Joop ; Wolters, W. ; Miguel Ayala, L. - \ 2018
Bogota : APC Columbia - 206
Guía para la evaluación de la calidad del agua superficial en microcuencas cafeteras de Colombia
Rodríguez Valencia, Nelson ; Quintero Yepes, Laura Vanessa ; Gómez Zuluaga, Gustavo Adolfo ; Bohórquez Zapata, Viviana Lorena ; González Durán, Cristy Mayerly ; Osorio Ocampo, Andrés Felipe ; Miguel García, Ángel de; Harmsen, Joop ; Wolters, W. ; Miguel Ayala, L. - \ 2018
Bogota : APC Columbia - ISBN 9789588490304 - 206
Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, Patrick ; Knudsen, Berith Elkær ; Lukjancenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Aarestrup, Frank M. ; Graveland, Haitske ; Essen, Alieda van; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Munk, Patrick ; Knudsen, Berith Elkær ; Lukjacenko, Oksana ; Duarte, Ana Sofia Ribeiro ; Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Smit, Lidwien A.M. ; Schmitt, Heike ; Garcia, Alejandro Dorado ; Hansen, Rasmus Borup ; Petersen, Thomas Nordahl ; Bossers, Alex ; Ruppé, Etienne ; Graveland, Haitske ; Essen, Alieda van; Gonzalez-Zorn, Bruno ; Moyano, Gabriel ; Sanders, Pascal ; Chauvin, Claire ; David, Julie ; Battisti, Antonio ; Caprioli, Andrea ; Dewulf, Jeroen ; Blaha, Thomas ; Wadepohl, Katharina ; Brandt, Maximiliane ; Wasyl, Dariusz ; Skarzyńska, Magdalena ; Zajac, Magdalena ; Daskalov, Hristo ; Saatkamp, Helmut W. ; Stärk, Katharina D.C. ; Lund, Ole ; Hald, Tine ; Pamp, Sünje Johanna ; Vigre, Håkan ; Heederik, Dick ; Wagenaar, Jaap A. ; Mevius, Dik ; Aarestrup, Frank M. - \ 2018
Nature Microbiology 3 (2018)8. - ISSN 2058-5276 - p. 898 - 908.

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.

Collective irrigation reloaded. Re-collection and re-moralization of water management after privatization in Spain
González-Sanchis, María ; Boelens, R.A. ; Garcia-Molla, Marta - \ 2017
Geoforum 87 (2017). - ISSN 0016-7185 - p. 38 - 47.
In recent decades, water has been subjected to different commodification and de-collectivization processes. Increasingly, this is also affecting collective irrigation water management. Critical analysis of this privatization and de-collectivization wave in the irrigation sector has mainly focused on neoliberal institutional policies and market-oriented legislation. However, subtly and silently but equally determinant, the adoption of water-saving technologies is fostering the penetration of private enterprise and market-based governance into these hydro-social settings. This paper discusses this phenomenon through a case study of the community of Senyera in Valencia, Spain, tracking the privatization and subsequent contestation and re-takeover of water management by irrigation system users. The article shows how privatization removes users’ autonomy in the name of common well-being, and increases irrigation costs in a context of little transparency. But the case also highlights users’ capacity to re-value and re-signify their past collective action, remembering and ‘re-membering to’ the collective. Senyera water users critically and reflexively analyse privatization, reconstruct societal relationships around and embedded inside the new technology, and re-collectivize and re-moralize irrigation management in a new hydro-social scenario.
The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
GigaScience 6 (2017)10. - ISSN 2047-217X
16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
Are forest disturbances amplifying or canceling out climate change-induced productivity changes in European forests?
Reyer, Christopher Paul Oliver ; Bathgate, Stephan ; Blennow, K. ; Borges, J.G. ; Bugmann, Harald ; Delzon, Sylvain ; Faias, Sonia P. ; Garcia-Gonzalo, Jordi ; Gardiner, Barry ; Gonzalez-Olabarria, J.R. ; Gracia, Carlos ; Guerra Hernandez, Jordi ; Kellomaki, Seppo ; Kramer, K. ; Lexer, M.J. ; Lindner, Marcus ; Maaten, Ernest van der; Maroschek, M. ; Muys, Bart ; Nicoll, B. ; Palahi, M. ; Palma, J.H.N. ; Paulo, Joana A. ; Peltola, H. ; Pukkala, T. ; Rammer, W. ; Ray, D. ; Sabaté, S. ; Schelhaas, M. ; Seidl, R. ; Temperli, Christian ; Tomé, Margarida ; Yousefpour, R. ; Zimmerman, N.E. ; Hanewinkel, Marc - \ 2017
Environmental Research Letters 12 (2017)3. - ISSN 1748-9326
Recent studies projecting future climate change impacts on forests mainly consider either the effects of climate change on productivity or on disturbances. However, productivity and disturbances are intrinsically linked because 1) disturbances directly affect forest productivity (e.g. via a reduction in leaf area, growing stock or resource-use efficiency), and 2) disturbance susceptibility is often coupled to a certain development phase of the forest with productivity determining the time a forest is in this specific phase of susceptibility. The objective of this paper is to provide an overview of forest productivity changes in different forest regions in Europe under climate change, and partition these changes into effects induced by climate change alone and by climate change and disturbances. We present projections of climate change impacts on forest productivity from state-of-the-art forest models that dynamically simulate forest productivity and the effects of the main European disturbance agents (fire, storm, insects), driven by the same climate scenario in seven forest case studies along a large climatic gradient throughout Europe. Our study shows that, in most cases, including disturbances in the simulations exaggerate ongoing productivity declines or cancel out productivity gains in response to climate change. In fewer cases, disturbances also increase productivity or buffer climate-change induced productivity losses, e.g. because low severity fires can alleviate resource competition and increase fertilization. Even though our results cannot simply be extrapolated to other types of forests and disturbances, we argue that it is necessary to interpret climate change-induced productivity and disturbance changes jointly to capture the full range of climate change impacts on forests and to plan adaptation measures.
System-wide Benefits of Intermeal Fasting by Autophagy
Martinez-Lopez, Nuria ; Tarabra, Elena ; Toledo, Miriam ; Garcia-Macia, Marina ; Sahu, Srabani ; Coletto, Luisa ; Batista-Gonzalez, Ana ; Barzilai, Nir ; Pessin, Jeffrey E. ; Schwartz, Gary J. ; Kersten, Sander ; Singh, Rajat - \ 2017
Cell Metabolism 26 (2017)6. - ISSN 1550-4131 - p. 856 - 871.e5.
Aging - Autophagy - Caloric restriction - Circadian - Fatty liver - Gluconeogenesis - Metabolic syndrome - Myogenic progenitors - POMC - Twice-a-day feeding

Autophagy failure is associated with metabolic insufficiency. Although caloric restriction (CR) extends healthspan, its adherence in humans is poor. We established an isocaloric twice-a-day (ITAD) feeding model wherein ITAD-fed mice consume the same food amount as ad libitum controls but at two short windows early and late in the diurnal cycle. We hypothesized that ITAD feeding will provide two intervals of intermeal fasting per circadian period and induce autophagy. We show that ITAD feeding modifies circadian autophagy and glucose/lipid metabolism that correlate with feeding-driven changes in circulating insulin. ITAD feeding decreases adiposity and, unlike CR, enhances muscle mass. ITAD feeding drives energy expenditure, lowers lipid levels, suppresses gluconeogenesis, and prevents age/obesity-associated metabolic defects. Using liver-, adipose-, myogenic-, and proopiomelanocortin neuron-specific autophagy-null mice, we mapped the contribution of tissue-specific autophagy to system-wide benefits of ITAD feeding. Our studies suggest that consuming two meals a day without CR could prevent the metabolic syndrome. Our studies suggest that consuming two meals a day with complete food restriction in between the meals is sufficient to lower blood glucose and lipid levels. This simple dietary approach activates a cell “cleansing system“ called autophagy in liver, fat, brain, and muscle that helps prevent obesity and diabetes.

Alien plant invasions in European woodlands
Wagner, Viktoria ; Chytrý, Milan ; Jiménez-Alfaro, Borja ; Pergl, Jan ; Hennekens, Stephan ; Biurrun, Idoia ; Knollová, Ilona ; Berg, Christian ; Vassilev, Kiril ; Rodwell, John S. ; Škvorc, Željko ; Jandt, Ute ; Ewald, Jörg ; Jansen, Florian ; Tsiripidis, Ioannis ; Botta-Dukát, Zoltán ; Casella, Laura ; Attorre, Fabio ; Rašomavičius, Valerijus ; Ćušterevska, Renata ; Schaminée, Joop H.J. ; Brunet, Jörg ; Lenoir, Jonathan ; Svenning, Jens Christian ; Kącki, Zygmunt ; Petrášová-Šibíková, Mária ; Šilc, Urban ; García-Mijangos, Itziar ; Campos, Juan Antonio ; Fernández-González, Federico ; Wohlgemuth, Thomas ; Onyshchenko, Viktor ; Pyšek, Petr - \ 2017
Diversity and Distributions 23 (2017)9. - ISSN 1366-9516 - p. 969 - 981.
EUNIS - exotic - forest - invasive plants - life-form - neophyte - non-native - origin - tree
Aim: Woodlands make up a third of European territory and carry out important ecosystem functions, yet a comprehensive overview of their invasion by alien plants has never been undertaken across this continent. Location: Europe. Methods: We extracted data from 251,740 vegetation plots stored in the recently compiled European Vegetation Archive. After filtering (resulting in 83,396 plots; 39 regions; 1970–2015 time period), we analysed the species pool and frequency of alien vascular plants with respect to geographic origin and life-forms, and the levels of invasion across the European Nature Information System (EUNIS) woodland habitats. Results: We found a total of 386 alien plant species (comprising 7% of all recorded vascular plants). Aliens originating from outside of and from within Europe were almost equally represented in the species pool (192 vs. 181 species) but relative frequency was skewed towards the former group (77% vs. 22%) due, to some extent, to the frequent occurrence of Impatiens parviflora (21% frequency among alien plants). Phanerophytes were the most species-rich life-form (148 species) and had the highest representation in terms of relative frequency (39%) among aliens in the dataset. Apart from Europe (181 species), North America was the most important source of alien plants (109 species). At the local scale, temperate and boreal softwood riparian woodland (5%) and mire and mountain coniferous woodland (<1%) had the highest and lowest mean relative alien species richness (percentage of alien species per plot), respectively. Main conclusions: Our results indicate that European woodlands are prone to alien plant invasions especially when exposed to disturbance, fragmentation, alien propagule pressure and high soil nutrient levels. Given the persistence of these factors in the landscape, competitive alien plant species with a broad niche, including alien trees and shrubs, are likely to persist and spread further into European woodlands.
RIMA-dependent nuclear accumulation of IYO triggers auxin-irreversible cell differentiation in arabidopsis
Muñoz, Alfonso ; Mangano, Silvina ; González-García, Mary Paz ; Contreras, Ramón ; Sauer, Michael ; Rybel, Bert De; Weijers, Dolf ; Sánchez-Serrano, José Juan ; Sanmartín, Maite ; Rojo, Enrique - \ 2017
The Plant Cell 29 (2017)3. - ISSN 1040-4651 - p. 575 - 588.
The transcriptional regulator MINIYO (IYO) is essential and rate-limiting for initiating cell differentiation in Arabidopsis thaliana. Moreover, IYO moves from the cytosol into the nucleus in cells at the meristem periphery, possibly triggering their differentiation. However, the genetic mechanisms controlling IYO nuclear accumulation were unknown, and the evidence that increased nuclear IYO levels trigger differentiation remained correlative. Searching for IYO interactors, we identified RPAP2 IYO Mate (RIMA), a homolog of yeast and human proteins linked to nuclear import of selective cargo. Knockdown of RIMA causes delayed onset of cell differentiation, phenocopying the effects of IYO knockdown at the transcriptomic and developmental levels. Moreover, differentiation is completely blocked when IYO and RIMA activities are simultaneously reduced and is synergistically accelerated when IYO and RIMA are concurrently overexpressed, confirming their functional interaction. Indeed, RIMA knockdown reduces the nuclear levels of IYO and prevents its prodifferentiation activity, supporting the conclusion that RIMA-dependent nuclear IYO accumulation triggers cell differentiation in Arabidopsis. Importantly, by analyzing the effect of the IYO/RIMA pathway on xylem pole pericycle cells, we provide compelling evidence reinforcing the view that the capacity for de novo organogenesis and regeneration from mature plant tissues can reside in stem cell reservoirs.
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