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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    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    Opportunities for seaweed biorefinery
    Lange, Lene ; Grandorf Bak, Urd ; Cole Brandstrup Hansen, Steffen ; Gregersen, Olavur ; Harmsen, Paulien ; Nordberg Karlsson, Eva ; Meyer, Anne ; Mikkelsen, Maria D. ; Broek, Ben van den; Óli Hreggviðsson, Guðmundur - \ 2020
    In: Sustainable Seaweed Technologies / Dolores Torres, M., Kraan, S., Dominguez, H., Elsevier (Advances in Green Chemistry ) - ISBN 9780128179437 - p. 3 - 31.
    This introductory chapter provides an overview of seaweed biorefinery opportunities, providing basis for multiple value chains, contributing to nutrition and health of a growing global population, to local job generation and development, to ecosystem services, and not the least to climate change mitigation and adaptation. A unique and rich diversity of the seaweed components provides the basis for the broad spectrum of value-chains described here. Red, brown, and green seaweeds are phylogenetically very different and this is reflected in their differences in growth, structure, and biochemical composition. Stable supply and high quality of feedstock are essential for unlocking the value-adding potential of seaweeds. A special focus of the chapter is to provide an overview of the range of different methods of seaweed production (through cultivation or from natural growth, collected or cut at the shore). Furthermore, the results of dedicated efforts to develop new deep-sea cultivation technologies of brown seaweed are highlighted. The chapter has a dual message with regard to seaweed processing: the need to develop more environmentally benign biological processing (to replace chemical processing); the advantage (regarding resource efficiency) and opportunities (social and economic) of designing seaweed biorefineries according to the cascading principle. Making optimized use of all valuable components of seaweed biomass, cascading from high-value products, such as skin care, health-promoting food and feed supplements and functional food ingredients; to lower-value products, such as plant stimulants, soil improvers, and bioenergy. Lastly, this introductory chapter provides global perspectives for future development of sustainable seaweed utilization, contributing to the UN-SDGs, providing livelihood and health for more.
    Nest attentiveness drives nest predation in arctic sandpipers
    Meyer, Nicolas ; Bollache, Loïc ; Dechaume-Moncharmont, François Xavier ; Moreau, Jérôme ; Afonso, Eve ; Angerbjörn, Anders ; Bêty, Joël ; Ehrich, Dorothée ; Gilg, Vladimir ; Giroux, Marie Andrée ; Hansen, Jannik ; Lanctot, Richard B. ; Lang, Johannes ; Lecomte, Nicolas ; McKinnon, Laura ; Reneerkens, Jeroen ; Saalfeld, Sarah T. ; Sabard, Brigitte ; Schmidt, Niels M. ; Sittler, Benoît ; Smith, Paul ; Sokolov, Aleksandr ; Sokolov, Vasiliy ; Sokolova, Natalia ; Bemmelen, Rob van; Gilg, Olivier - \ 2020
    Oikos (2020). - ISSN 0030-1299
    Arctic shorebirds - breeding behaviour - incubation recesses - incubation strategy - nest survival - parental care

    Most birds incubate their eggs to allow embryo development. This behaviour limits the ability of adults to perform other activities. Hence, incubating adults trade off incubation and nest protection with foraging to meet their own needs. Parents can either cooperate to sustain this tradeoff or incubate alone. The main cause of reproductive failure at this reproductive stage is predation and adults reduce this risk by keeping the nest location secret. Arctic sandpipers are interesting biological models to investigate parental care evolution as they may use several parental care strategies. The three main incubation strategies include both parents sharing incubation duties (‘biparental’), one parent incubating alone (‘uniparental’), or a flexible strategy with both uniparental and biparental incubation within a population (‘mixed’). By monitoring the incubation behaviour in 714 nests of seven sandpiper species across 12 arctic sites, we studied the relationship between incubation strategy and nest predation. First, we described how the frequency of incubation recesses (NR), their mean duration (MDR), and the daily total duration of recesses (TDR) vary among strategies. Then, we examined how the relationship between the daily predation rate and these components of incubation behaviour varies across strategies using two complementary survival analysis. For uniparental and biparental species, the daily predation rate increased with the daily total duration of recesses and with the mean duration of recesses. In contrast, daily predation rate increased with the daily number of recesses for biparental species only. These patterns may be attributed to two independent mechanisms: cryptic incubating adults are more difficult to locate than unattended nests and adults departing the nest or feeding close to the nest can draw predators’ attention. Our results demonstrate that incubation behaviour as mediated by incubation strategy has important consequences for sandpipers’ reproductive success.

    Dataset for the model of a municipality competitiveness in relation to the geothermal resources exploitation in Poland
    Kurek, Katarzyna A. ; Heijman, Wim ; Ophem, Johan van; Gędek, Stanisław ; Strojny, Jacek - \ 2020
    Data in Brief 31 (2020). - ISSN 2352-3409
    Analytical Hierarchy Process - Geothermal energy - Local competitiveness - Multicriteria decision analysis - Socioeconomic indicators

    This dataset corresponds with the manuscript “The impact of geothermal resources on the competitiveness of municipalities: evidence from Poland” [1]. In the paper, the geothermal resources are assumed as a local competitive advantage for the municipalities that exploit them. In order to examine the relation between the exploitation of the geothermal resources and local competitiveness we determine a model of municipality competitiveness in Poland. Concept of the local competitiveness is referred to place-based measures (Lovering [2], Mytelka and Farinelli [3], Plummer and Taylor [4], Kitson et al. [5]) and it is related to the management of local resources (Malecki [6], Turok [7]). Literature review suggests that the local competitiveness is best reflected in the indicators of economic welfare and sustainability (Meyer-Stamer [8], Audretsch et al. [9]). Therefore, we use an expert method to build the model of a municipality competitiveness indicators on the example of Poland. Throughout the Analytical Hierarchy Process (AHP) method engaged experts select the 24 indicators of local competitiveness. This method serves in situations of a problem complexity (Kamenetzky [10], Saaty [11]) and as a multicriteria method in the regional studies (Dinc et al. [12]). Aggregation of the AHP selected indicators yields a synthetic competitiveness index for each of the municipalities that we examine. This index constitutes the model dependent variable in the related research article. This procedure of building municipality competitiveness model sets an example of approaching a complex phenomenon such as the local competitiveness definition. The versatility of this method enables its application into related research cases.

    Give CRISPR a Chance : the GeneSprout Initiative
    Vangheluwe, Nick ; Swinnen, Gwen ; Koning, Ramon de; Meyer, Prisca ; Houben, Maarten ; Huybrechts, Michiel ; Sajeev, Nikita ; Rienstra, Juriaan ; Boer, Damian - \ 2020
    Trends in Plant Science 25 (2020)7. - ISSN 1360-1385 - p. 624 - 627.
    CRISPR - policy - science communication - young researcher

    Did you know that a group of early-career researchers launched an initiative enabling open dialog on new plant breeding techniques, such as genome editing? We developed a wide-ranging initiative that aims to facilitate public engagement and provide a platform for young plant scientists to encourage participation in science communication.

    Vissen in Zeeland
    Calle, P. ; Calle, L. ; Kranenbarg, J. ; Velden, J.A. van der; Meyer, A.J.M. ; Boois, I.J. de; Dubbeldam, M. ; Jacobusse, C. - \ 2020
    Stichting Het Zeeuwse Landschap (Fauna Zeelandica IX) - ISBN 9789080637009 - 301 p.
    In dit boek worden alle ooit waargenomen vissoorten (177) in Zeeland uitgebreid beschreven en geïllustreerd met fantastische foto’s. Samen met vele partners en vrijwilligers is na jaren van veldonderzoek, digitalisering van oude data en data-analyse een aantrekkelijk en toegankelijk boek gerealiseerd voor iedereen die van vis houdt.
    Policy Coordination and Integration: A Research Agenda
    Trein, Philipp ; Biesbroek, Robbert ; Bolognesi, Thomas ; Cejudo, Guillermo M. ; Duffy, Robert ; Hustedt, Thurid ; Meyer, Iris - \ 2020
    Public Administration Review (2020). - ISSN 0033-3352

    Coordinating and integrating different policies and public sector organizations is a major challenge for practitioners and a continuing topic of interest for researchers. This Viewpoint essay argues that research on this topic needs reorientation to provide better insights for practice and theory of policy making, as well as policy implementation. The authors offer four suggestions on how future research could advance: (1) combining existing conceptual and epistemological approaches more systematically; (2) complementing case studies and surveys with large‐N analyses and novel research tools and methods; (3) more systematic analysis of the causal mechanisms in policy coordination and integration; and (4) more thorough study of the real‐world impact of policy coordination and integration

    Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches : a review
    Swanson, K.S. ; Vos, W.M. de; Martens, E.C. ; Gilbert, J.A. ; Menon, R.S. ; Soto-Vaca, A. ; Hautvast, J. ; Meyer, P.D. ; Borewicz, K. ; Vaughan, E.E. ; Slavin, J.L. - \ 2020
    Beneficial Microbes 11 (2020)2. - ISSN 1876-2883 - p. 101 - 129.
    health - intestine - inulin - microbiota - nutrition

    The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest. Research and collective initiatives to determine the composition and diversity of the human gut microbiota have increased over the past decade due to great advances in high-throughput technologies, particularly the 16S ribosomal RNA (rRNA) sequencing. Here we reviewed the application of 16S rRNA-based molecular technologies, both community wide (sequencing and phylogenetic microarrays) and targeted methodologies (quantitative PCR, fluorescent in situ hybridisation) to study the effect of chicory inulin-type fructans, NDOs and specific added fibres, such as resistant starches, on the human intestinal microbiota. Overall, such technologies facilitated the monitoring of microbiota shifts due to prebiotic/fibre consumption, though there are limited community-wide sequencing studies so far. Molecular studies confirmed the selective bifidogenic effect of fructans and galactooligosaccharides (GOS) in human intervention studies. Fructans only occasionally decreased relative abundance of Bacteroidetes or stimulated other groups. The sequencing studies for various resistant starches, polydextrose and beta-glucan showed broader effects with more and different types of gut microbial species being enhanced, often including phylotypes of Ruminococcaceae. There was substantial variation in terms of magnitude of response and in individual responses to a specific fibre or NDO which may be due to numerous factors, such as initial presence and relative abundance of a microbial type, diet, genetics of the host, and intervention parameters, such as intervention duration and fibre dose. The field will clearly benefit from a more systematic approach that will support defining the impact of prebiotics and fibres on the gut microbiome, identify biomarkers that link gut microbes to health, and address the personalised response of an individual's microbiota to prebiotics and dietary fibres.

    Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    Following publication of this Data Descriptor it was found that the affiliation of Oliver Purschke was stated incorrectly. The correct affiliations are stated below: Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden Biodiversity, Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden This has been corrected in both the HTML and PDF versions.

    Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands
    Buzhdygan, Oksana Y. ; Meyer, Sebastian T. ; Weisser, Wolfgang W. ; Eisenhauer, Nico ; Ebeling, Anne ; Borrett, Stuart R. ; Buchmann, Nina ; Cortois, Roeland ; Deyn, Gerlinde B. De; Kroon, Hans de; Gleixner, Gerd ; Hertzog, Lionel R. ; Hines, Jes ; Lange, Markus ; Mommer, Liesje ; Ravenek, Janneke ; Scherber, Christoph ; Scherer-Lorenzen, Michael ; Scheu, Stefan ; Schmid, Bernhard ; Steinauer, Katja ; Strecker, Tanja ; Tietjen, Britta ; Vogel, Anja ; Weigelt, Alexandra ; Petermann, Jana S. - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 393 - 405.

    The continuing loss of global biodiversity has raised questions about the risk that species extinctions pose for the functioning of natural ecosystems and the services that they provide for human wellbeing. There is consensus that, on single trophic levels, biodiversity sustains functions; however, to understand the full range of biodiversity effects, a holistic and multitrophic perspective is needed. Here, we apply methods from ecosystem ecology that quantify the structure and dynamics of the trophic network using ecosystem energetics to data from a large grassland biodiversity experiment. We show that higher plant diversity leads to more energy stored, greater energy flow and higher community-energy-use efficiency across the entire trophic network. These effects of biodiversity on energy dynamics were not restricted to only plants but were also expressed by other trophic groups and, to a similar degree, in aboveground and belowground parts of the ecosystem, even though plants are by far the dominating group in the system. The positive effects of biodiversity on one trophic level were not counteracted by the negative effects on adjacent levels. Trophic levels jointly increased the performance of the community, indicating ecosystem-wide multitrophic complementarity, which is potentially an important prerequisite for the provisioning of ecosystem services.

    A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

    SnRK2 protein kinases and mRNA decapping machinery control root development and response to salt
    Kawa, Dorota ; Meyer, A.J. ; Dekker, Henk L. ; Abd-El-Haliem, Ahmed ; Gevaert, Kris ; De Slijke, Eveline Van; Maszkowska, Justyna ; Bucholc, Maria ; Dobrowolska, Grazyna ; Jaeger, Geert de; Schuurink, Robert C. ; Haring, Michel A. ; Testerink, Christa - \ 2020
    Plant Physiology 182 (2020)1. - ISSN 0032-0889
    SNF1-RELATED PROTEIN KINASES 2 (SnRK2) are important components of early osmotic and salt stress signaling pathways in plants. The Arabidopsis (Arabidopsis thaliana) SnRK2 family comprises the abscisic acid (ABA)-activated protein kinases SnRK2.2, SnRK2.3, SnRK2.6, SnRK2.7, and SnRK2.8, and the ABA-independent subclass 1 protein kinases SnRK2.1, SnRK2.4, SnRK2.5, SnRK2.9, and SnRK2.10. ABA-independent SnRK2s act at the post-transcriptional level via phosphorylation of VARICOSE (VCS), a member of the mRNA decapping complex, that catalyzes the first step of 5'mRNA decay. Here, we identified VCS and VARICOSE RELATED (VCR) as interactors and phosphorylation targets of SnRK2.5, SnRK2.6, and SnRK2.10. All three protein kinases phosphorylated Ser645 and Ser1156 of VCS, while SnRK2.6 and SnRK2.10 also phosphorylated VCS Ser692 and Ser680 of VCR. We showed that subclass 1 SnRK2s, VCS, and 5' EXORIBONUCLEASE 4 (XRN4) are involved in regulating root growth under control conditions as well as modulating root system architecture in response to salt stress. Our results suggest interesting patterns of redundancy within subclass 1 SnRK2 protein kinases, with SnRK2.1, SnRK2.5 and SnRK2.9 controlling root growth under non-stress conditions and SnRK2.4 and SnRK2.10 acting mostly in response to salinity. We propose that subclass 1 SnRK2s function in root development under salt stress by affecting the transcript levels of aquaporins, as well as CYP79B2, an enzyme involved in auxin biosynthesis.
    Halotropism requires phospholipase Dζ1-mediated modulation of cellular polarity of auxin transport carriers
    Korver, Ruud A. ; Berg, Thea van den; Meyer, Jessica A. ; Galvan-Ampudia, Carlos S. ; Tusscher, Kirsten H.W.J. ten; Testerink, Christa - \ 2020
    Plant, Cell & Environment 43 (2020)1. - ISSN 0140-7791 - p. 143 - 158.

    Endocytosis and relocalization of auxin carriers represent important mechanisms for adaptive plant growth and developmental responses. Both root gravitropism and halotropism have been shown to be dependent on relocalization of auxin transporters. Following their homology to mammalian phospholipase Ds (PLDs), plant PLDζ-type enzymes are likely candidates to regulate auxin carrier endocytosis. We investigated root tropic responses for an Arabidopsis pldζ1-KO mutant and its effect on the dynamics of two auxin transporters during salt stress, that is, PIN2 and AUX1. We found altered root growth and halotropic and gravitropic responses in the absence of PLDζ1 and report a role for PLDζ1 in the polar localization of PIN2. Additionally, irrespective of the genetic background, salt stress induced changes in AUX1 polarity. Utilizing our previous computational model, we found that these novel salt-induced AUX1 changes contribute to halotropic auxin asymmetry. We also report the formation of “osmotic stress-induced membrane structures.” These large membrane structures are formed at the plasma membrane shortly after NaCl or sorbitol treatment and have a prolonged presence in a pldζ1 mutant. Taken together, these results show a crucial role for PLDζ1 in both ionic and osmotic stress-induced auxin carrier dynamics during salt stress.

    Effectiveness of Panama as an intercontinental land bridge for large mammals
    Meyer, Ninon F.V. ; Moreno, Ricardo ; Sutherland, Christopher ; Torre, J.A. de la; Esser, Helen J. ; Jordan, Christopher A. ; Olmos, Melva ; Ortega, Josué ; Reyna-Hurtado, Rafael ; Valdes, Samuel ; Jansen, Patrick A. - \ 2020
    Conservation Biology 34 (2020)1. - ISSN 0888-8892 - p. 207 - 219.
    Bayesian statistics - community-level distribution - hierarchical occupancy modeling - landscape connectivity - Mesoamerican Biological Corridor - Neotropical forest

    Habitat fragmentation is a primary driver of wildlife loss, and establishment of biological corridors is a common strategy to mitigate this problem. A flagship example is the Mesoamerican Biological Corridor (MBC), which aims to connect protected forest areas between Mexico and Panama to allow dispersal and gene flow of forest organisms. Because forests across Central America have continued to degrade, the functioning of the MBC has been questioned, but reliable estimates of species occurrence were unavailable. Large mammals are suitable indicators of forest functioning, so we assessed their conservation status across the Isthmus of Panama, the narrowest section of the MBC. We used large-scale camera-trap surveys and hierarchical multispecies occupancy models in a Bayesian framework to estimate the occupancy of 9 medium to large mammals and developed an occupancy-weighted connectivity metric to evaluate species-specific functional connectivity. White-lipped peccary (Tayassu pecari), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), white-tailed deer (Odocoileus virginianus), and tapir (Tapirus bairdii) had low expected occupancy along the MBC in Panama. Puma (Puma concolor), red brocket deer (Mazama temama), ocelot (Leopardus pardalis), and collared peccary (Pecari tajacu), which are more adaptable, had higher occupancy, even in areas with low forest cover near infrastructure. However, the majority of species were subject to ≥1 gap that was larger than their known dispersal distances, suggesting poor connectivity along the MBC in Panama. Based on our results, forests in Darien, Donoso–Santa Fe, and La Amistad International Park are critical for survival of large terrestrial mammals in Panama and 2 areas need restoration.

    Comment on “Global pattern of nest predation is disrupted by climate change in shorebirds”
    Bulla, Martin ; Reneerkens, Jeroen ; Weiser, Emily L. ; Sokolov, Aleksandr ; Taylor, Audrey R. ; Sittler, Benoît ; McCaffery, Brian J. ; Ruthrauff, Dan R. ; Catlin, Daniel H. ; Payer, David C. ; Ward, David H. ; Solovyeva, Diana V. ; Santos, Eduardo S.A. ; Rakhimberdiev, Eldar ; Nol, Erica ; Kwon, Eunbi ; Brown, Glen S. ; Hevia, Glenda D. ; River Gates, H. ; Johnson, James A. ; Gils, Jan A. van; Hansen, Jannik ; Lamarre, Jean François ; Rausch, Jennie ; Conklin, Jesse R. ; Liebezeit, Joe ; Bêty, Joël ; Lang, Johannes ; Alves, José A. ; Fernández-Elipe, Juan ; Exo, Klaus Michael ; Bollache, Loïc ; Bertellotti, Marcelo ; Giroux, Marie Andrée ; Pol, Martijn van de; Johnson, Matthew ; Boldenow, Megan L. ; Valcu, Mihai ; Soloviev, Mikhail ; Sokolova, Natalya ; Senner, Nathan R. ; Lecomte, Nicolas ; Meyer, Nicolas ; Schmidt, Niels Martin ; Gilg, Olivier ; Smith, Paul A. ; Machín, Paula ; McGuire, Rebecca L. ; Cerboncini, Ricardo A.S. ; Ottvall, Richard ; Bemmelen, Rob S.A. van; Swift, Rose J. ; Saalfeld, Sarah T. ; Jamieson, Sarah E. ; Brown, Stephen ; Piersma, Theunis ; Albrecht, Tomas ; D’Amico, Verónica ; Lanctot, Richard B. ; Kempenaers, Bart - \ 2019
    Science 364 (2019)6445. - ISSN 0036-8075
    Kubelka et al. (Reports, 9 November 2018, p. 680) claim that climate change has disrupted patterns of nest predation in shorebirds. They report that predation rates have increased since the 1950s, especially in the Arctic. We describe methodological problems with their analyses and argue that there is no solid statistical support for their claims.
    European Weed Vegetation Database - a gap-focused vegetation-plot database
    Küzmic, Filip ; Šilc, Urban ; Lososová, Zdenka ; Mucina, Ladislav ; Chytrý, Milan ; Knollová, Ilona ; Hennekens, S.M. ; Berg, Christian ; Bergmeier, Erwin ; Biurrun, Idoia ; Fanfarillo, Emanuele ; Font, Xavier ; Iakushenko, Dmytro ; Kovacevic, Zlatan ; Meyer, Stefan ; Nagy, Katalin ; Pinke, Gyula ; Poranen, Eira ; Tereshenko, Svetlana - \ 2019
    Phytocoenologia 50 (2019)1. - ISSN 0340-269X - p. 93 - 100.
    This report presents the European Weed Vegetation Database, a new database of vegetation plots documenting short-lived vegetation of arable and ruderal habitats from Europe and Macaronesia. The database comprises the
    phytosociological classes Papaveretea rhoeadis, Sisymbrietea, Chenopodietea and Digitario sanguinalis-Eragrostietea minoris. It is a gap-focused database containing mainly plots of this vegetation from the areas not yet represented in the European Vegetation Archive (EVA), to facilitate its accessibility for researchers to answer various questions. As of the end of 2018, it contained 24,734 plots, predominantly from Southern Europe. The data can be used for phytosociological studies, various kinds of interdisciplinary research as well as for studies for agronomy, nature management and biodiversity conservation.
    Genetic Loci Associated with Early Salt Stress Responses of Roots
    Deolu-Ajayi, Ayodeji O. ; Meyer, A.J. ; Haring, Michel A. ; Julkowska, Magdalena M. ; Testerink, Christa - \ 2019
    iScience 21 (2019). - ISSN 2589-0042 - p. 458 - 473.
    Biological Sciences - Plant Biology - Plant Genetics - Plant Physiology

    Salinity is a devastating abiotic stress accounting for major crop losses yearly. Plant roots can strikingly grow away from high-salt patches. This response is termed halotropism and occurs through auxin redistribution in roots in response to a salt gradient. Here, a natural variation screen for the early and NaCl-specific halotropic response of 333 Arabidopsis accessions revealed quantitative differences in the first 24 h. These data were successfully used to identify genetic components associated with the response through Genome-Wide Association Study (GWAS). Follow-up characterization of knockout mutants in Col-0 background confirmed the role of transcription factor WRKY25, cation-proton exchanger CHX13, and a gene of unknown function DOB1 (Double Bending 1) in halotropism. In chx13 and dob1 mutants, ion accumulation and shoot biomass under salt stress were also affected. Thus, our GWAS has identified genetic components contributing to main root halotropism that provide insight into the genetic architecture underlying plant salt responses.

    Transferring biodiversity-ecosystem function research to the management of ‘real-world’ ecosystems
    Manning, P. ; Loos, Jacqueline ; Barnes, Andrew D. ; Batáry, Péter ; Bianchi, Felix J.J.A. ; Buchmann, Nina ; Deyn, Gerlinde B. De; Ebeling, Anne ; Eisenhauer, Nico ; Fischer, Markus ; Fründ, Jochen ; Grass, Ingo ; Isselstein, Johannes ; Jochum, M. ; Klein, Alexandra M. ; Klingenberg, Esther O.F. ; Landis, Douglas A. ; Lepš, Jan ; Lindborg, Regina ; Meyer, Sebastian T. ; Temperton, Vicky M. ; Westphal, Catrin ; Tscharntke, Teja - \ 2019
    In: Advances in Ecological Research Academic Press Inc. (Advances in Ecological Research ) - p. 323 - 356.
    BEF research - Biodiversity experiments - Ecosystem management - Ecosystem services - Grasslands - Knowledge transfer

    Biodiversity-ecosystem functioning (BEF) research grew rapidly following concerns that biodiversity loss would negatively affect ecosystem functions and the ecosystem services they underpin. However, despite evidence that biodiversity strongly affects ecosystem functioning, the influence of BEF research upon policy and the management of ‘real-world’ ecosystems, i.e., semi-natural habitats and agroecosystems, has been limited. Here, we address this issue by classifying BEF research into three clusters based on the degree of human control over species composition and the spatial scale, in terms of grain, of the study, and discussing how the research of each cluster is best suited to inform particular fields of ecosystem management. Research in the first cluster, small-grain highly controlled studies, is best able to provide general insights into mechanisms and to inform the management of species-poor and highly managed systems such as croplands, plantations, and the restoration of heavily degraded ecosystems. Research from the second cluster, small-grain observational studies, and species removal and addition studies, may allow for direct predictions of the impacts of species loss in specific semi-natural ecosystems. Research in the third cluster, large-grain uncontrolled studies, may best inform landscape-scale management and national-scale policy. We discuss barriers to transfer within each cluster and suggest how new research and knowledge exchange mechanisms may overcome these challenges. To meet the potential for BEF research to address global challenges, we recommend transdisciplinary research that goes beyond these current clusters and considers the social-ecological context of the ecosystems in which BEF knowledge is generated. This requires recognizing the social and economic value of biodiversity for ecosystem services at scales, and in units, that matter to land managers and policy makers.

    Nature and mental health: An ecosystem service perspective
    Bratman, Gregory N. ; Anderson, Christopher B. ; Berman, Marc G. ; Cochran, Bobby ; Vries, Sjerp De; Flanders, Jon ; Folke, Carl ; Frumkin, Howard ; Gross, James J. ; Hartig, Terry ; Kahn, Peter H. ; Kuo, Ming ; Lawler, Joshua J. ; Levin, Phillip S. ; Lindahl, Therese ; Meyer-lindenberg, Andreas ; Mitchell, Richard ; Ouyang, Zhiyun ; Roe, Jenny ; Scarlett, Lynn ; Smith, Jeffrey R. ; Bosch, Matilda Van Den; Wheeler, Benedict W. ; White, Mathew P. ; Zheng, Hua ; Daily, Gretchen C. - \ 2019
    Science Advances 5 (2019)7. - ISSN 2375-2548 - 15 p.
    A growing body of empirical evidence is revealing the value of nature experience for mental health. With rapid urbanization and declines in human contact with nature globally, crucial decisions must be made about how to preserve and enhance opportunities for nature experience. Here, we first provide points of consensus across the natural, social, and health sciences on the impacts of nature experience on cognitive functioning, emotional well-being, and other dimensions of mental health. We then show how ecosystem service assessments can be expanded to include mental health, and provide a heuristic, conceptual model for doing so.
    The potential for pre-, pro- and synbiotics in the management of infants at risk of cow's milk allergy or with cow's milk allergy: An exploration of the rationale, available evidence and remaining questions
    Fox, Adam ; Bird, J.A. ; Fiocchi, Alessandro ; Knol, Jan ; Meyer, Rosan ; Salminen, Seppo ; Sitang, Gong ; Szajewska, Hania ; Papadopoulos, Nikolaos - \ 2019
    World Allergy Organization Journal 12 (2019)5. - ISSN 1939-4551
    Allergy - Anaphylaxis - Bifidobacteria - Cow's milk allergy - Dysbiosis - IgE - Lactobacilli - Microbiota - Prebiotic - Probiotic - Synbiotic - World Allergy Organization

    Cow's milk allergy is one of the most commonly reported childhood food allergies, with increasing incidence, persistence and severity in many countries across the world. The World Allergy Organization Special Committee on Food Allergy has identified cow's milk allergy as an area in need of a rationale-based approach in order to make progress against what it considered an onerous problem, with worldwide public health impact. There is growing interest in the potential role of the gut microbiota in the early programming and development of immune responses and allergy. This discussion paper considers the rationale and available evidence for modulation of the gut microbiota and for the use of synbiotics in the management of infants at risk of, or living with cow's milk allergy and summarizes remaining research questions that need to be answered for the development of evidence-based recommendations.

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