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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    Biased-corrected richness estimates for the Amazonian tree flora
    Steege, Hans ter; Prado, Paulo I. ; Lima, Renato A.F. de; Pos, Edwin ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Martins, Maria Pires ; Sabatier, Daniel ; Irume, Mariana Victória ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Ramos, José Ferreira ; Monteagudo Mendoza, Abel ; Venticinque, Eduardo Martins ; Luize, Bruno Garcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Leão Novo, Evlyn Márcia Moraes de; Reis, Neidiane Farias Costa ; Terborgh, John ; Manzatto, Angelo Gilberto ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Duque, Alvaro ; Costa, Flávia R.C. ; Castaño Arboleda, Nicolás ; Schöngart, Jochen ; Zartman, Charles Eugene ; Killeen, Timothy J. ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Feldpausch, Ted R. ; Engel, Julien ; Petronelli, Pascal ; Baraloto, Chris ; Assis, Rafael L. ; Castellanos, Hernán ; Simon, Marcelo Fragomeni ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Laurance, Susan G.W. ; Rincón, Lorena M. ; Andrade, Ana ; Sousa, Thaiane R. ; Camargo, José Luís ; Schietti, Juliana ; Laurance, William F. ; Queiroz, Helder Lima de; Nascimento, Henrique Eduardo Mendonça ; Lopes, Maria Aparecida ; Sousa Farias, Emanuelle de; Magalhães, José Leonardo Lima ; Brienen, Roel ; Aymard C, Gerardo A. ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Lopes, Aline ; García-Villacorta, Roosevelt ; Draper, Freddie ; Vicentini, Alberto ; Cornejo Valverde, Fernando ; Lloyd, Jon ; Gomes, Vitor H.F. ; Neill, David ; Alonso, Alfonso ; Dallmeier, Francisco ; Souza, Fernanda Coelho de; Maas, Paul ; Baker, Tim R. ; Andel, Tinde R. van; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Malhi, Yadvinder ; Tirado, Milton ; Wang, Ophelia ; Nascimento, Marcelo Trindade ; Flores, Bernardo Monteiro - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322

    Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

    A schematic sampling protocol for contaminant monitoring in raptors
    Espín, Silvia ; Andevski, Jovan ; Duke, Guy ; Eulaers, Igor ; Gómez-Ramírez, Pilar ; Hallgrimsson, Gunnar Thor ; Helander, Björn ; Herzke, Dorte ; Jaspers, Veerle L.B. ; Krone, Oliver ; Lourenço, Rui ; María-Mojica, Pedro ; Martínez-López, Emma ; Mateo, Rafael ; Movalli, Paola ; Sánchez-Virosta, Pablo ; Shore, Richard F. ; Sonne, Christian ; Brink, Nico W. van den; Hattum, Bert van; Vrezec, Al ; Wernham, Chris ; García-Fernández, Antonio J. - \ 2020
    Ambio (2020). - ISSN 0044-7447
    Best practices - Birds of prey - Falcons - Large-scale biomonitoring - Owls - Pan-European network

    Birds of prey, owls and falcons are widely used as sentinel species in raptor biomonitoring programmes. A major current challenge is to facilitate large-scale biomonitoring by coordinating contaminant monitoring activities and by building capacity across countries. This requires sharing, dissemination and adoption of best practices addressed by the Networking Programme Research and Monitoring for and with Raptors in Europe (EURAPMON) and now being advanced by the ongoing international COST Action European Raptor Biomonitoring Facility. The present perspective introduces a schematic sampling protocol for contaminant monitoring in raptors. We provide guidance on sample collection with a view to increasing sampling capacity across countries, ensuring appropriate quality of samples and facilitating harmonization of procedures to maximize the reliability, comparability and interoperability of data. The here presented protocol can be used by professionals and volunteers as a standard guide to ensure harmonised sampling methods for contaminant monitoring in raptors.

    Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs
    García-Contreras, Consolación ; Madsen, Ole ; Groenen, Martien A.M. ; López-García, Adrián ; Vázquez-Gómez, Marta ; Astiz, Susana ; Núñez, Yolanda ; Benítez, Rita ; Fernández, Almudena ; Isabel, Beatriz ; Rey, Ana Isabel ; González-Bulnes, Antonio ; Óvilo, Cristina - \ 2020
    PLoS ONE 15 (2020)1. - ISSN 1932-6203

    Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype∗weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.

    Key knowledge gaps to achieve global sustainability goals
    Mastrángelo, Matías E. ; Pérez-Harguindeguy, Natalia ; Enrico, Lucas ; Bennett, Elena ; Lavorel, Sandra ; Cumming, Graeme S. ; Abeygunawardane, Dilini ; Amarilla, Leonardo D. ; Burkhard, Benjamin ; Egoh, Benis N. ; Frishkoff, Luke ; Galetto, Leonardo ; Huber, Sibyl ; Karp, Daniel S. ; Ke, Alison ; Kowaljow, Esteban ; Kronenburg-García, Angela ; Locatelli, Bruno ; Martín-López, Berta ; Meyfroidt, Patrick ; Mwampamba, Tuyeni H. ; Nel, Jeanne ; Nicholas, Kimberly A. ; Nicholson, Charles ; Oteros-Rozas, Elisa ; Rahlao, Sebataolo J. ; Raudsepp-Hearne, Ciara ; Ricketts, Taylor ; Shrestha, Uttam B. ; Torres, Carolina ; Winkler, Klara J. ; Zoeller, Kim - \ 2019
    Nature Sustainability 2 (2019). - ISSN 2398-9629 - p. 1115 - 1121.

    Regional and global assessments periodically update what we know, and highlight what remains to be known, about the linkages between people and nature that both define and depend upon the state of the environment. To guide research that better informs policy and practice, we systematically synthesize knowledge gaps from recent assessments of four regions of the globe and three key themes by the Intergovernmental Science-Policy Platform for Biodiversity and Ecosystem Services. We assess their relevance to global sustainability goals and trace their evolution relative to those identified in the Millennium Ecosystem Assessment. We found that global sustainability goals cannot be achieved without improved knowledge on feedbacks between social and ecological systems, effectiveness of governance systems and the influence of institutions on the social distribution of ecosystem services. These top research priorities have persisted for the 14 years since the Millennium Ecosystem Assessment. Our analysis also reveals limited understanding of the role of indigenous and local knowledge in sustaining nature’s benefits to people. Our findings contribute to a policy-relevant and solution-oriented agenda for global, long-term social-ecological research.

    Rarity of monodominance in hyperdiverse Amazonian forests
    Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

    Agronomic evaluation of biochar, compost and biochar-blended compost across different cropping systems: Perspective from the European project FERTIPLUS
    Sánchez-Monedero, Miguel A. ; Cayuela, María L. ; Sánchez-García, María ; Vandecasteele, Bart ; D’Hose, Tommy ; López, Guadalupe ; Martínez-Gaitán, Carolina ; Kuikman, Peter J. ; Sinicco, Tania ; Mondini, Claudio - \ 2019
    Agronomy 9 (2019)5. - ISSN 2073-4395
    Composting - Crop yield - Fertilization - Nutrient recycling - Organic waste management - Pyrolysis - Soil fertility - Soil organic matter

    This paper reports the results on the agronomic performance of organic amendments in the EU 7th FP project “FERTIPLUS—reducing mineral fertilizers and agro-chemicals by recycling treated organic waste as compost and bio-char”. Four case studies on field-scale application of biochar, compost and biochar-blended compost were established and studied for three consecutive years in four distinct cropping systems and under different agro-climatic conditions in Europe. These included the following sites: olive groves in Murcia (Spain), greenhouse grown tomatoes in Almeria (Spain), an arable crop rotation in Oost-Vlaanderen (Merelbeke, Belgium), and three vineyards in Friuli Venezia Giulia (Italy). A slow pyrolysis oak biochar was applied, either alone or in combination with organic residues: compost from olive wastes in Murcia (Spain), sheep manure in Almeria (Spain), and compost from biowaste and green waste in Belgium and Italy. The agronomical benefits were evaluated based on different aspects of soil fertility (soil total organic carbon (TOC), pH, nutrient cycling and microbial activity) and crop nutritional status and productivity. All amendments were effective in increasing soil organic C in all the field trials. On average, the increase with respect to the control was about 11% for compost, 20% for biochar-blended compost, and 36% for biochar. The amendments also raised the pH by 0.15–0.50 units in acidic soils. Only biochar had a negligible fertilization effect. On the contrary, compost and biochar-blended compost were effective in enhancing soil fertility by increasing nutrient cycling (25% mean increase in extractable organic C and 44% increase in extractable N), element availability (26% increase in available K), and soil microbial activity (26% increase in soil respiration and 2–4 fold enhancement of denitrifying activity). In general, the tested amendments did not show any negative effect on crop yield and quality. Furthermore, in vineyards and greenhouse grown tomatoes cropping systems, compost and biochar-blended compost were also effective in enhancing key crop quality parameters (9% increase in grape must acidity and 16% increase in weight, 9% increase in diameter and 8% increase in hardness of tomato fruits) important for the quality and marketability of the crops. The overall results of the project suggest that the application of a mixture of biochar and compost can benefit crops. Therefore, biochar-blended compost can support and maintain soil fertility.

    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
    Wageningen University & Research
    secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
    We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, Lourens ; Rozendaal, Danaë M.A. ; Bongers, Frans ; Almeida-Cortez, Jarcilene S. de; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo G. ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário M. ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, Catarina C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião V. ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa de; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco de; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Paz, Horacio ; Peña-Claros, Marielos ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Utrera, Luis P. ; Breugel, Michiel van; Sande, Masha T. van der; Wal, Hans van der; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vieira, Ima C.G. ; Villa, Pedro Manuel ; Williamson, G.B. ; Wright, S.J. ; Zanini, Kátia J. ; Zimmerman, Jess K. ; Westoby, Mark - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 928 - 934.

    Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

    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.

    Corrigendum to “Opinion paper about organic trace pollutants in wastewater: Toxicity assessment in a European perspective"
    Pedrazzani, Roberta ; Bertanza, Giorgio ; Brnardić, Ivan ; Cetecioglu, Zeynep ; Dries, Jan ; Dvarionienė, Jolanta ; García-Fernández, Antonio J. ; Langenhoff, Alette ; Libralato, Giovanni ; Lofrano, Giusy ; Škrbić, Biljana ; Martínez-López, Emma ; Meriç, Süreyya ; Mutavdžić Pavlović, Dragana ; Papa, Matteo ; Schröder, Peter ; Tsagarakis, Konstantinos P. ; Vogelsang, Christian - \ 2019
    Science of the Total Environment 669 (2019). - ISSN 0048-9697 - p. 1062 - 1062.

    The authors regret that, despite thoroughly reviewing the manuscript, the content of a paragraph has been duplicated and has to be ignored .

    Opinion paper about organic trace pollutants in wastewater : Toxicity assessment in a European perspective
    Pedrazzani, Roberta ; Bertanza, Giorgio ; Brnardić, Ivan ; Cetecioglu, Zeynep ; Dries, Jan ; Dvarionienė, Jolanta ; García-Fernández, Antonio J. ; Langenhoff, Alette ; Libralato, Giovanni ; Lofrano, Giusy ; Škrbić, Biljana ; Martínez-López, Emma ; Meriç, Süreyya ; Pavlović, Dragana Mutavdžić ; Papa, Matteo ; Schröder, Peter ; Tsagarakis, Konstantinos P. ; Vogelsang, Christian - \ 2019
    Science of the Total Environment 651 (2019). - ISSN 0048-9697 - p. 3202 - 3221.
    Aquatic ecosystem - Bioassays - Ecotoxicity - Micro-pollutants - Risk assessment - Wastewater treatment

    This opinion paper focuses on the role of eco-toxicological tools in the assessment of possible impacts of emerging contaminants on the aquatic ecosystem, hence, on human health. Indeed, organic trace pollutants present in raw and treated wastewater are the pivot targets: a multidisciplinary approach allows defining the basic principles for managing this issue, from setting a proper monitoring campaign up to evaluating the optimal process treatment. Giving hints on trace pollutants fate and behaviour, attention is focused on the choice of the bioassay(s), by analysing the meaning of possible biological answers. Data interpretation and exploitation are detailed with the final goal of providing criteria in order to be able to select the best targeted treatment options. The manuscript deals with conventional and innovative analytical approaches for assessing toxicity, by reviewing laboratory and field assays; illustrative real scale and laboratory applications integrate and exemplify the proposed approach.

    Technologies for the bioconversion of methane into more valuable products
    Cantera, Sara ; Muñoz, Raúl ; Lebrero, Raquel ; López, Juan Carlos ; Rodríguez, Yadira ; García-Encina, Pedro Antonio - \ 2018
    Current Opinion in Biotechnology 50 (2018). - ISSN 0958-1669 - p. 128 - 135.

    Methane, with a global warming potential twenty five times higher than that of CO 2 is the second most important greenhouse gas emitted nowadays. Its bioconversion into microbial molecules with a high retail value in the industry offers a potential cost-efficient and environmentally friendly solution for mitigating anthropogenic diluted CH 4 -laden streams. Methane bio-refinery for the production of different compounds such as ectoine, feed proteins, biofuels, bioplastics and polysaccharides, apart from new bioproducts characteristic of methanotrophic bacteria, has been recently tested in discontinuous and continuous bioreactors with promising results. This review constitutes a critical discussion about the state-of-the-art of the potential and research niches of biotechnologies applied in a CH 4 biorefinery approach.

    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    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
    Monitoreo climático: herramienta al servicio de la caficultura Colombiana
    Sarmiento, Ninibeth ; Ramírez, Carolina ; Jaramillo, Álvaro ; Restrepo, Alexander ; García López, Juan Carlos ; Wolters, W. ; Miguel Ayala, L. - \ 2018
    Bogota : APC Columbia - ISBN 9789588490298 - 110
    OliveCan : A process-based model of development, growth and yield of olive orchards
    López-Bernal, Álvaro ; Morales, Alejandro ; García-Tejera, Omar ; Testi, Luca ; Orgaz, Francisco ; Melo-Abreu, J.P. De; Villalobos, Francisco J. - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    Carbon assimilation - Crop model - Olea europaea L. - SPAC model - Water stress - Water uptake
    Several simulation models of the olive crop have been formulated so far, but none of them is capable of analyzing the impact of environmental conditions and management practices on water relations, growth and productivity under both well-irrigated and water-limiting irrigation strategies. This paper presents and tests OliveCan, a process-oriented model conceived for those purposes. In short, OliveCan is composed of three main model components simulating the principal elements of the water and carbon balances of olive orchards and the impacts of some management operations. To assess its predictive power, OliveCan was tested against independent data collected in two 3-year field experiments conducted in Córdoba, Spain, each of them applying different irrigation treatments. An acceptable level of agreement was found between measured and simulated values of seasonal evapotranspiration (ET, range 393 to 1016 mm year−1; RMSE of 89 mm year−1), daily transpiration (Ep, range 0.14–3.63 mm d−1; RMSE of 0.32 mm d−1) and oil yield (Yoil, range 13–357 g m−2; RMSE of 63 g m−2). Finally, knowledge gaps identified during the formulation of the model and further testing needs are discussed, highlighting that there is additional room for improving its robustness. It is concluded that OliveCan has a strong potential as a simulation platform for a variety of research applications.
    Species Distribution Modelling: Contrasting presence-only models with plot abundance data
    Gomes, Vitor H.F. ; Ijff, Stéphanie D. ; Raes, Niels ; Amaral, Iêda Leão ; Salomão, Rafael P. ; Coelho, Luiz De Souza ; Matos, Francisca Dionízia De Almeida ; Castilho, Carolina V. ; Filho, Diogenes De Andrade Lima ; López, Dairon Cárdenas ; Guevara, Juan Ernesto ; Magnusson, William E. ; Phillips, Oliver L. ; Wittmann, Florian ; Carim, Marcelo De Jesus Veiga ; Martins, Maria Pires ; Irume, Mariana Victória ; Sabatier, Daniel ; Molino, Jean François ; Bánki, Olaf S. ; Guimarães, José Renan Da Silva ; Pitman, Nigel C.A. ; Piedade, Maria Teresa Fernandez ; Mendoza, Abel Monteagudo ; Luize, Bruno Garcia ; Venticinque, Eduardo Martins ; de Leão Novo, E.M.M. ; Vargas, Percy Núñez ; Silva, Thiago Sanna Freire ; Manzatto, Angelo Gilberto ; Terborgh, John ; Reis, Neidiane Farias Costa ; Montero, Juan Carlos ; Montero, Juan Carlos ; Casula, Katia Regina ; Marimon, Beatriz S. ; Marimon, Ben Hur ; Honorio Coronado, Euridice N. ; Feldpausch, Ted R. ; Duque, Alvaro ; Zartman, Charles Eugene ; Arboleda, Nicolás Castaño ; Killeen, Timothy J. ; Mostacedo, Bonifacio ; Vasquez, Rodolfo ; Schöngart, Jochen ; Assis, Rafael L. ; Medeiros, Marcelo Brilhante ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Laurance, William F. ; Camargo, José Luís ; Demarchi, Layon O. ; Laurance, Susan G.W. ; Farias, Emanuelle De Sousa ; Nascimento, Henrique Eduardo Mendonça ; Revilla, Juan David Cardenas ; Quaresma, Adriano ; Costa, Flavia R.C. ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Cintra, Bruno Barçante Ladvocat ; Castellanos, Hernán ; Brienen, Roel ; Stevenson, Pablo R. ; Feitosa, Yuri ; Duivenvoorden, Joost F. ; Aymard, Gerardo A.C. ; Mogollón, Hugo F. ; Targhetta, Natalia ; Comiskey, James A. ; Vicentini, Alberto ; Lopes, Aline ; Damasco, Gabriel ; Dávila, Nállarett ; García-Villacorta, Roosevelt ; Levis, Carolina ; Schietti, Juliana ; Souza, Priscila ; Emilio, Thaise ; Alonso, Alfonso ; Neill, David ; Dallmeier, Francisco ; Ferreira, Leandro Valle ; Araujo-Murakami, Alejandro ; Praia, Daniel ; Amaral, Dário Dantas Do; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho De - \ 2018
    Scientific Reports 8 (2018)1. - ISSN 2045-2322
    Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
    (Dis) integrated valuation – Assessing the information gaps in ecosystem service appraisals for governance support
    Barton, D.N. ; Kelemen, E. ; Dick, J. ; Martin-Lopez, B. ; Gómez-Baggethun, E. ; Jacobs, S. ; Hendriks, C.M.A. ; Termansen, M. ; García- Llorente, M. ; Primmer, E. ; Dunford, R. ; Harrison, P.A. ; Turkelboom, F. ; Saarikoski, H. ; Dijk, J. Van; Rusch, G.M. ; Palomo, I. ; Yli-Pelkonen, V.J. ; Carvalho, L. ; Baró, F. ; Langemeyer, J. ; Tjalling Van Der Wal, J. ; Mederly, P. ; Priess, J.A. ; Luque, S. ; Berry, P. ; Santos, R. ; Odee, D. ; Martines Pastur, G. ; García Blanco, G. ; Saarela, S.R. ; Silaghi, D. ; Pataki, G. ; Masi, F. ; Vădineanu, A. ; Mukhopadhyay, R. ; Lapola, D.M. - \ 2018
    Ecosystem Services 29 (2018)pt. C. - ISSN 2212-0416 - p. 529 - 541.
    Integrated valuation - Ecosystem service appraisal - Ecosystem service governance - Information costs - Uncertainty - Valuation - Ecosystem services cascade
    The operational challenges of integrated ecosystem service (ES) appraisals are determined by study purpose, system complexity and uncertainty, decision-makers’ requirements for reliability and accuracy of methods, and approaches to stakeholder–science interaction in different decision contexts. To explore these factors we defined an information gap hypothesis, based on a theory of cumulative uncertainty in ES appraisals. When decision context requirements for accuracy and reliability increase, and the expected uncertainty of the ES appraisal methods also increases, the likelihood of methods being used is expected to drop, creating a potential information gap in governance. In order to test this information gap hypothesis, we evaluate 26 case studies and 80 ecosystem services appraisals in a large integrated EU research project. We find some support for a decreasing likelihood of ES appraisal methods coinciding with increasing accuracy and reliability requirements of the decision-support context, and with increasing uncertainty. We do not find that information costs are the explanation for this information gap, but rather that the research project interacted mostly with stakeholders outside the most decision-relevant contexts. The paper discusses how alternative definitions of integrated valuation can lead to different interpretations of decision-support information, and different governance approaches to dealing with uncertainty.
    Integrating methods for ecosystem service assessment : Experiences from real world situations
    Dunford, Rob ; Harrison, Paula ; Smith, Alison ; Dick, Jan ; Barton, David N. ; Martin-Lopez, Berta ; Kelemen, Ezsther ; Jacobs, Sander ; Saarikoski, Heli ; Turkelboom, Francis ; Verheyden, Wim ; Hauck, Jennifer ; Antunes, Paula ; Aszalós, Réka ; Badea, Ovidu ; Baró, Francesc ; Berry, Pam ; Carvalho, Laurence ; Conte, Giulio ; Czúcz, Bálint ; Garcia Blanco, Gemma ; Howard, Dave ; Giuca, Relu ; Gomez-Baggethun, Erik ; Grizetti, Bruna ; Izakovicova, Zita ; Kopperoinen, Leena ; Langemeyer, Johannes ; Luque, Sandra ; Lapola, David M. ; Martinez-Pastur, Guillermo ; Mukhopadhyay, Raktima ; Roy, S.B. ; Niemelä, Jari ; Norton, Lisa ; Ochieng, John ; Odee, David ; Palomo, Ignacio ; Pinho, Patricia ; Priess, Joerg ; Rusch, Graciella ; Saarela, Sanna Riikka ; Santos, Rui ; Wal, Jan Tjalling van der; Vadineanu, Angheluta ; Vári, Ágnes ; Woods, Helen ; Yli-Pelkonen, Vesa - \ 2018
    Ecosystem Services 29 (2018)pt. C. - ISSN 2212-0416 - p. 499 - 514.
    The Ecosystem Services (ES) concept highlights the varied contributions the environment provides to humans and there are a wide range of methods/tools available to assess ES. However, in real-world decision contexts a single tool is rarely sufficient and methods must be combined to meet practitioner needs. Here, results from the OpenNESS project are presented to illustrate the methods selected to meet the needs of 24 real-world case studies and better understand why and how methods are combined to meet practical needs. Results showed that within the cases methods were combined to: i) address a range of ES; ii) assess both supply and demand of ES; iii) assess a range of value types; iv) reach different stakeholder groups v) cover weaknesses in other methods used and vi) to meet specific decision context needs. Methods were linked in a variety of ways: i) as input-output chains of methods; ii) through learning; iii) through method development and iv) through comparison/triangulation of results. The paper synthesises these case study-based experiences to provide insight to others working in practical contexts as to where, and in what contexts, different methods can be combined and how this can add value to case study analyses.
    Stakeholders’ perspectives on the operationalisation of the ecosystem service concept: Results from 27 case studies
    Dick, Jan ; Turkelboom, Francis ; Woods, Helen ; Iniesta-Arandia, Irene ; Primmer, Eeva ; Saarela, Sanna-Riikka ; Bezák, Peter ; Mederly, Peter ; Leone, Michael ; Verheyden, Wim ; Kelemen, Eszter ; Hauck, Jennifer ; Andrews, Chris ; Antunes, Paula ; Aszalós, Réka ; Baró, Francesc ; Barton, David N. ; Berry, Pam ; Bugter, Rob ; Carvalho, Laurence ; Czúcz, Bálint ; Dunford, Rob ; Garcia Blanco, Gemma ; Geamănă, Nicoleta ; Giucă, Relu ; Grizzetti, Bruna ; Izakovičová, Zita ; Kertész, Miklós ; Kopperoinen, Leena ; Langemeyer, Johannes ; Montenegro Lapola, David ; Liquete, Camino ; Luque, Sandra ; Martínez Pastur, Guillermo ; Martin-Lopez, Berta ; Mukhopadhyay, Raktima ; Niemela, Jari ; Odee, David ; Peri, Pablo Luis ; Pinho, Patricia ; Patrício-Roberto, Gleiciani Bürger ; Preda, Elena ; Priess, Joerg ; Röckmann, Christine ; Santos, Rui ; Silaghi, Diana ; Smith, Ron ; Vădineanu, Angheluţă ; Wal, Jan Tjalling van der; Arany, Ildikó ; Badea, Ovidiu ; Bela, Györgyi ; Boros, Emil ; Bucur, Magdalena ; Blumentrath, Stefan ; Calvache, Marta ; Carmen, Esther ; Clemente, Pedro ; Fernandes, João ; Ferraz, Diogo ; Fongar, Claudia ; García-Llorente, Marina ; Gómez-Baggethun, Erik ; Gundersen, Vegard ; Haavardsholm, Oscar ; Kalóczkai, Ágnes ; Khalalwe, Thalma ; Kiss, Gabriella ; Köhler, Berit ; Lazányi, Orsolya ; Lellei-Kovács, Eszter ; Lichungu, Rael ; Lindhjem, Henrik ; Magare, Charles ; Mustajoki, Jyri ; Ndege, Charles ; Nowell, Megan ; Nuss Girona, Sergi ; Ochieng, John ; Often, Anders ; Palomo, Ignacio ; Pataki, György ; Reinvang, Rasmus ; Rusch, Graciela ; Saarikoski, Heli ; Smith, Alison ; Soy Massoni, Emma ; Stange, Erik ; Vågnes Traaholt, Nora ; Vári, Ágnes ; Verweij, Peter ; Vikström, Suvi ; Yli-Pelkonen, Vesa ; Zulian, Grazia - \ 2018
    Ecosystem Services 29 (2018)pt. C. - ISSN 2212-0416 - p. 552 - 565.
    The ecosystem service (ES) concept is becoming mainstream in policy and planning, but operational influence on practice is seldom reported. Here, we report the practitioners’ perspectives on the practical implementation of the ES concept in 27 case studies. A standardised anonymous survey (n = 246), was used, focusing on the science-practice interaction process, perceived impact and expected use of the case study assessments. Operationalisation of the concept was shown to achieve a gradual change in practices: 13% of the case studies reported a change in action (e.g. management or policy change), and a further 40% anticipated that a change would result from the work. To a large extent the impact was attributed to a well conducted science-practice interaction process (>70%). The main reported advantages of the concept included: increased concept awareness and communication; enhanced participation and collaboration; production of comprehensive science-based knowledge; and production of spatially referenced knowledge for input to planning (91% indicated they had acquired new knowledge). The limitations were mostly case-specific and centred on methodology, data, and challenges with result implementation. The survey highlighted the crucial role of communication, participation and collaboration across different stakeholders, to implement the ES concept and enhance the democratisation of nature and landscape planning.
    Selecting methods for ecosystem service assessment : A decision tree approach
    Harrison, Paula A. ; Dunford, Rob ; Barton, David N. ; Kelemen, Eszter ; Martín-López, Berta ; Norton, Lisa ; Termansen, Mette ; Saarikoski, Heli ; Hendriks, Kees ; Gómez-Baggethun, Erik ; Czúcz, Bálint ; García-Llorente, Marina ; Howard, David ; Jacobs, Sander ; Karlsen, Martin ; Kopperoinen, Leena ; Madsen, Andes ; Rusch, Graciela M. ; Eupen, Michiel van; Verweij, Peter ; Smith, Ron ; Tuomasjukka, Diana ; Zulian, Grazia - \ 2018
    Ecosystem Services 29 (2018)pt. C. - ISSN 2212-0416 - p. 481 - 498.
    Biophysical - Decision trees - Guidance - Method - Monetary - Socio-cultural - Tool
    A range of methods are available for assessing ecosystem services. Methods differ in their aims; from mapping and modelling the supply and demand of ecosystem services to appraising their economic and non-economic importance through valuation techniques. Comprehensive guidance for the selection of appropriate ecosystem service assessment methods that address the requirements of different decision-making contexts is lacking. This paper tackles this gap using the experience from 27 case studies which applied different biophysical, socio-cultural and monetary valuation methods to operationalise the ecosystem service concept towards sustainable land, water and urban management. A survey of the reasons why the case study teams selected particular methods revealed that stakeholder-oriented reasons, such as stakeholder participation, inclusion of local knowledge and ease of communication, and decision-oriented reasons, such as the purpose of the case study and the ecosystem services at stake, were key considerations in selecting a method. Pragmatic reasons such as available data, resources and expertise were also important factors. This information was used to develop a set of linked decision trees, which aim to provide guidance to researchers and practitioners in choosing ecosystem service assessment methods that are suitable for their context.
    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.
    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.

    Seasonal drought limits tree species across the Neotropics
    Esquivel-Muelbert, Adriane ; Baker, Timothy R. ; Dexter, Kyle G. ; Lewis, Simon L. ; Steege, Hans ter; Lopez-Gonzalez, Gabriela ; Monteagudo Mendoza, Abel ; Brienen, Roel ; Feldpausch, Ted R. ; Pitman, Nigel ; Alonso, Alfonso ; Heijden, Geertje van der; Peña-Claros, Marielos ; Ahuite, Manuel ; Alexiaides, Miguel ; Álvarez Dávila, Esteban ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Aulestia, Milton ; Balslev, Henrik ; Barroso, Jorcely ; Boot, Rene ; Cano, Angela ; Chama Moscoso, Victor ; Comiskey, James A. ; Cornejo, Fernando ; Dallmeier, Francisco ; Daly, Douglas C. ; Dávila, Nallarett ; Duivenvoorden, Joost F. ; Duque Montoya, Alvaro Javier ; Erwin, Terry ; Fiore, Anthony Di; Fredericksen, Todd ; Fuentes, Alfredo ; García-Villacorta, Roosevelt ; Gonzales, Therany ; Guevara Andino, Juan Ernesto ; Honorio Coronado, Euridice N. ; Huamantupa-Chuquimaco, Isau ; Killeen, Timothy J. ; Malhi, Yadvinder ; Mendoza, Casimiro ; Mogollón, Hugo ; Jørgensen, Peter Møller ; Montero, Juan Carlos ; Mostacedo, Bonifacio ; Nauray, William ; Neill, David ; Vargas, Percy Núñez ; Palacios, Sonia ; Palacios Cuenca, Walter ; Pallqui Camacho, Nadir Carolina ; Peacock, Julie ; Phillips, Juan Fernando ; Pickavance, Georgia ; Quesada, Carlos Alberto ; Ramírez-Angulo, Hirma ; Restrepo, Zorayda ; Reynel Rodriguez, Carlos ; Paredes, Marcos Ríos ; Sierra, Rodrigo ; Silveira, Marcos ; Stevenson, Pablo ; Stropp, Juliana ; Terborgh, John ; Tirado, Milton ; Toledo, Marisol ; Torres-Lezama, Armando ; Umaña, María Natalia ; Urrego, Ligia Estela ; Vasquez Martinez, Rodolfo ; Gamarra, Luis Valenzuela ; Vela, César I.A. ; Vilanova Torre, Emilio ; Vos, Vincent ; Hildebrand, Patricio von; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Zartman, Charles Eugene ; Phillips, Oliver L. - \ 2017
    Ecography 40 (2017)5. - ISSN 0906-7590 - p. 618 - 629.
    Within the tropics, the species richness of tree communities is strongly and positively associated with precipitation. Previous research has suggested that this macroecological pattern is driven by the negative effect of water-stress on the physiological processes of most tree species. This implies that the range limits of inventory plots of closed canopy forest distributed across the western Neotropics taxa are defined by their ability to occur under dry conditions, and thus in terms of species distributions predicts a nested pattern of taxa distribution from wet to dry areas. However, this 'dry-tolerance' hypothesis has yet to be adequately tested at large spatial and taxonomic scales. Here, using a dataset of 531 we investigated how precipitation, evaluated both as mean annual precipitation and as the maximum climatological water deficit, influences the distribution of tropical tree species, genera and families. We find that the distributions of tree taxa are indeed nested along precipitation gradients in the western Neotropics. Taxa tolerant to seasonal drought are disproportionally widespread across the precipitation gradient, with most reaching even the wettest climates sampled; however, most taxa analysed are restricted to wet areas. Our results suggest that the 'dry tolerance' hypothesis has broad applicability in the world's most species-rich forests. In addition, the large number of species restricted to wetter conditions strongly indicates that an increased frequency of drought could severely threaten biodiversity in this region. Overall, this study establishes a baseline for exploring how tropical forest tree composition may change in response to current and future environmental changes in this region.
    Tracking pan-continental trends in environmental contamination using sentinel raptors—what types of samples should we use?
    Espín, S. ; García-Fernández, A.J. ; Herzke, D. ; Shore, R.F. ; Hattum, B. van; Martínez-López, E. ; Coeurdassier, M. ; Eulaers, I. ; Fritsch, C. ; Gómez-Ramírez, P. ; Jaspers, V.L.B. ; Krone, O. ; Duke, G. ; Helander, B. ; Mateo, R. ; Movalli, P. ; Sonne, C. ; Den Brink, N.W. van - \ 2016
    Ecotoxicology (2016). - ISSN 0963-9292 - p. 777 - 801.
    Bird of prey - Contaminant - Matrix - Monitoring - Sample type

    Biomonitoring using birds of prey as sentinel species has been mooted as a way to evaluate the success of European Union directives that are designed to protect people and the environment across Europe from industrial contaminants and pesticides. No such pan-European evaluation currently exists. Coordination of such large scale monitoring would require harmonisation across multiple countries of the types of samples collected and analysed-matrices vary in the ease with which they can be collected and the information they provide. We report the first ever pan-European assessment of which raptor samples are collected across Europe and review their suitability for biomonitoring. Currently, some 182 monitoring programmes across 33 European countries collect a variety of raptor samples, and we discuss the relative merits of each for monitoring current priority and emerging compounds. Of the matrices collected, blood and liver are used most extensively for quantifying trends in recent and longer-term contaminant exposure, respectively. These matrices are potentially the most effective for pan-European biomonitoring but are not so widely and frequently collected as others. We found that failed eggs and feathers are the most widely collected samples. Because of this ubiquity, they may provide the best opportunities for widescale biomonitoring, although neither is suitable for all compounds. We advocate piloting pan-European monitoring of selected priority compounds using these matrices and developing read-across approaches to accommodate any effects that trophic pathway and species differences in accumulation may have on our ability to track environmental trends in contaminants.

    Arbuscular mycorrhizal symbiosis induces strigolactone biosynthesis under drought and improves drought tolerance in lettuce and tomato
    Ruiz-Lozano, J.M. ; Aroca, R. ; Zamarreno, A.M. ; Molina, S. ; Andreo Jimenez, B. ; Porcel, R. ; Garcia-Mina, J.M. ; Ruyter-Spira, C.P. ; Lopez-Raez, J.A. - \ 2016
    Plant, Cell & Environment 39 (2016)2. - ISSN 0140-7791 - p. 441 - 452.
    Arbuscular mycorrhizal (AM) symbiosis alleviates drought stress in plants. However, the intimate mechanisms involved, as well as its effect on the production of signalling molecules associated with the host plant–AM fungus interaction remains largely unknown. In the present work, the effects of drought on lettuce and tomato plant performance and hormone levels were investigated in non-AM and AM plants. Three different water regimes were applied, and their effects were analysed over time. AMplants showed an improved growth rate and efficiency of photosystem II than non-AM plants under drought from very early stages of plant colonization. The levels of the phytohormone abscisic acid, as well as the expression of the correspondingmarker genes, were influenced by drought stress in non-AMandAMplants. The levels of strigolactones and the expression of corresponding marker genes were affected by both AM symbiosis and drought. The results suggest that AM symbiosis alleviates drought stress by altering the hormonal profiles and affecting plant physiology in the host plant. In addition, a correlation between AM root colonization, strigolactone levels and drought severity is shown, suggesting that under these unfavourable conditions, plants might increase strigolactone production in order to promote symbiosis establishment to cope with the stress.
    Characterisation of cell-wall polysaccharides from mandarin segment membranes
    Coll-Almela, L. ; Saura-Lopez, D. ; Laencina-Sanchez, J. ; Schols, H.A. ; Voragen, A.G.J. ; Ros-García, J.M. - \ 2015
    Food Chemistry 175 (2015). - ISSN 0308-8146 - p. 36 - 42.
    hairy ramified regions - cross-flow filtration - pectolytic enzyme - citrus-fruit - pectins - degradation - extraction - skin - rhamnogalacturonase - populations
    In an attempt to develop a process of enzymatic peeling of mandarin segments suitable for use on an industrial scale, the cell wall fraction of the segment membrane of Satsuma mandarin fruits was extracted to obtain a chelating agent-soluble pectin fraction (ChSS), a dilute sodium hydroxide-soluble pectin fraction (DASS), a 1 M sodium hydroxide-soluble hemicellulose fraction (1MASS), a 4 M sodium hydroxide-soluble hemicellulose fraction (4MASS) and a cellulose-rich residue (3.1, 0.9, 0.4, 0.7 and 1.6% w/w of fresh membrane, respectively). The ChSS pectin consisted mainly of galacturonic acid followed by arabinose and galactose. The DASS fraction contained less galacturonic acid and more neutral sugars than ChSS. Eighty-nine percent of the galacturonic acid present in the segment membranes was recovered in the above two pectin fractions. The two hemicellulosic fractions consisted of two different molecular weight populations, which also differed in their sugar composition. Arabinose, xylose, mannose, galactose and glucose were the main sugar constituents of these hemicellulose fractions. In addition to an (arabino)xylan and a xyloglucan, the presence of an arabinogalactan is suggested by the sugar composition of both hemicelluloses. The pectin fractions were also characterised by their degradability by the pectic enzymes polygalacturonase, pectinmethylesterase and rhamnogalacturonan hydrolase. However the degree of degradation of the pectin fractions by enzymes differed, and the amount of the polymeric materials resistant to further degradation and the oligomeric products also differed. Using pectic enzymes it is possible to obtain peeled mandarin segments ready to eat or for canning.
    Identification in residue analysis based on liquid chromatography with tandem mass spectrometry: Experimental evidence to update performance criteria
    Mol, J.G.J. ; Zomer, P. ; Garcia Lopez, M. ; Fussell, R.J. ; Scholten, J. ; dr. Kok, A. ; Wolheim, A. ; Anastassiades, M. ; Lozano, A. ; Fernandez Alba, A. - \ 2015
    Analytica Chimica Acta 873 (2015). - ISSN 0003-2670 - p. 1 - 13.
    mycotoxin analysis - veterinary drugs - food - confirmation - extraction - pesticides - matrices
    Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is one of the most widely used techniques for identification (and quantification) of residues and contaminants across a number of different chemical domains. Although the same analytical technique is used, the parameters and criteria for identification vary depending on where in the world the analysis is performed and for what purpose (e.g. determination of pesticides, veterinary drugs, forensic toxicology, sports doping). The rationale for these differences is not clear and in most cases the criteria are essentially based on expert opinions rather than underpinned by experimental data. In the current study, the variability of the two key identification parameters, retention time and ion ratio, was assessed and compared against requirements set out in different legal and guidance documents. The study involved the analysis of 120 pesticides, representing various chemical classes, polarities, molecular weights, and detector response factors, in 21 different fruit and vegetable matrices of varying degrees of complexity. The samples were analysed non-fortified, and fortified at 10, 50 and 200µgkg(-1), in five laboratories using different LC-MS/MS instruments and conditions. In total, over 135,000 extracted-ion chromatograms were manually verified to provide an extensive data set for the assessment. The experimental data do not support relative tolerances for retention time, or different tolerances for ion ratios depending on relative abundance of the two product ions measured. Retention times in today's chromatographic systems are sufficiently stable to justify an absolute tolerance of ±0.1min. Ion ratios are stable as long as sufficient response is obtained for both product ions. Ion ratio deviations are typically within ±20% (relative), and within ±45% (relative) in case the response of product ions are close to the limit of detection. Ion ratio tolerances up to 50% did not result in false positives and reduced the false negative rate for pesticides with product ions in the low S/N range to
    Construction and validation of a mCherry protein vector for promoter analysis in Lactobacillus acidophilus
    Mohedano, M.L. ; Garcia-Cayuela, T. ; Perez-Ramos, A. ; Gaiser, R.A. ; Requena, T. ; Lopez, P. - \ 2015
    Journal of Industrial Microbiology and Biotechnology 42 (2015)2. - ISSN 1367-5435 - p. 247 - 253.
    lactic-acid bacteria - controlled gene-expression - streptococcus-pneumoniae - lactococcus-lactis - plasmid - cloning
    Lactobacilli are widespread in natural environments and are increasingly being investigated as potential health modulators. In this study, we have adapted the broad-host-range vector pNZ8048 to express the mCherry protein (pRCR) to expand the usage of the mCherry protein for analysis of gene expression in Lactobacillus. This vector is also able to replicate in Streptococcus pneumoniae and Escherichia coli. The usage of pRCR as a promoter probe was validated in Lactobacillus acidophilus by characterizing the regulation of lactacin B expression. The results show that the regulation is exerted at the transcriptional level, with lbaB gene expression being specifically induced by co-culture of the L. acidophilus bacteriocin producer and the S. thermophilus STY-31 inducer bacterium.
    An overview of existing raptor contaminant monitoring activities in Europe
    Gomez-Ramirez, P. ; Shore, R.F. ; Brink, N.W. van den; Hattum, B. van; Bustnes, J.O. ; Duke, G. ; Fritsch, C. ; Garcia-Fernandez, A.J. ; Helander, B.O. ; Jaspers, V. ; Krone, O. ; Martinez-Lopez, E. ; Mateo, R. ; Movalli, P. ; Sonne, C. - \ 2014
    Environment International 67 (2014). - ISSN 0160-4120 - p. 12 - 21.
    brominated flame retardants - eagles haliaeetus-albicilla - kestrel falco-tinnunculus - white-tailed eagles - long-term trends - environmental contaminants - organochlorine pesticides - southeastern spain - accipiter-gentilis - biomonitoring tool
    Biomonitoring using raptors as sentinels can provide early warning of the potential impacts of contaminants on humans and the environment and also a means of tracking the success of associated mitigation measures. Examples include detection of heavy metal-induced immune system impairment, PCB-induced altered reproductive impacts, and toxicity associated with lead in shot game. Authorisation of such releases and implementation of mitigation is now increasingly delivered through EU-wide directives but there is little established pan-European monitoring to quantify outcomes. We investigated the potential for EU-wide coordinated contaminant monitoring using raptors as sentinels. We did this using a questionnaire to ascertain the current scale of national activity across 44 European countries. According to this survey, there have been 52 different contaminant monitoring schemes with raptors over the last 50 years. There were active schemes in 15 (predominantly western European) countries and 23 schemes have been running for > 20 years; most monitoring was conducted for > 5 years. Legacy persistent organic compounds (specifically organochlorine insecticides and PCBs), and metals/metalloids were monitored in most of the 15 countries. Fungicides, flame retardants and anticoagulant rodenticides were also relatively frequently monitored (each in at least 6 countries). Common buzzard (Buteo buteo), common kestrel (Falco tinnunculus), golden eagle (Aquila chrysaetos), white-tailed sea eagle (Haliaeetus albicilla), peregrine falcon (Falco peregrinus), tawny owl (Strix aluco) and barn owl (Tyto alba) were most commonly monitored (each in 6–10 countries). Feathers and eggs were most widely analysed although many schemes also analysed body tissues. Our study reveals an existing capability across multiple European countries for contaminant monitoring using raptors. However, coordination between existing schemes and expansion of monitoring into Eastern Europe is needed. This would enable assessment of the appropriateness of the EU-regulation of substances that are hazardous to humans and the environment, the effectiveness of EU level mitigation policies, and identify pan-European spatial and temporal trends in current and emerging contaminants of concern.
    A Triple P review of the feasibility of sustainable offshore seaweed production in the North Sea
    Burg, S.W.K. van den; Stuiver, M. ; Veenstra, F.A. ; Bikker, P. ; Lopez Contreras, A.M. ; Palstra, A.P. ; Broeze, J. ; Jansen, H.M. ; Jak, R.G. ; Gerritsen, A.L. ; Harmsen, P.F.H. ; Kals, J. ; Blanco Garcia, A. ; Brandenburg, W.A. ; Krimpen, M.M. van; Duijn, A.P. van; Mulder, W.J. ; Raamsdonk, L.W.D. van - \ 2013
    Wageningen : Wageningen UR (LEI report 13-077) - ISBN 9789086156528 - 108
    zeewieren - laminaria - zeewierenteelt - zeeproducten - voer - voedingsstoffen - noordzee - biobased economy - seaweeds - laminaria - seaweed culture - marine products - feeds - nutrients - north sea - biobased economy
    This study focused on the potential of seaweed, cultivated in the North Sea, as a sustainable and profitable resource for feed and non-food applications. Seawood production can take place as part of multi-use platforms at sea (MUPS). A review of the state-of-the-art in seaweed production and its applications. Various economic, ecological and social challenges are identified, which need to be addressed to utilise this potential.
    Fluorescent protein vectors for promoter analysis in lactic acid bacteria and Escherichia coli
    García-Cayuela, T. ; Cadiñanos, L.P. de; Mohedano, M.L. ; Palencia, P.F. de; Boden, D. ; Wells, J. ; Peláez, C. ; López, P. ; Requena, T. - \ 2012
    Applied Microbiology and Biotechnology 96 (2012)1. - ISSN 0175-7598 - p. 171 - 181.
    lactococcus-lactis - streptococcus-pneumoniae - genetic tools - in-vitro - green - cremoris - red - transformation - expression - faecalis
    Fluorescent reporter genes are valuable tools for real-time monitoring of gene expression in living cells. In this study we describe the construction of novel promoter-probe vectors containing a synthetic mCherry fluorescent protein gene, codon-optimized for lactic acid bacteria, divergently linked, or not, to a gene encoding the S65T and F64L variant of the green fluorescent protein. The utility of the transcriptional fusion vectors was demonstrated by the cloning of a single or two divergent promoter regions and by the quantitative evaluation of fluorescence during growth of Lactococcus lactis, Enterococcus faecalis, and Escherichia coli.
    Organohalogen exposure in a Eurasian owl (Bubo bubo) population from Southeastern Spain: Temporal-spatial trends and risk assessment
    Gomez-Ramirez, P. ; Martinez-Lopez, E. ; Garcia-Fernandez, A. ; Zweers, A.J. ; Brink, N.W. van den - \ 2012
    Chemosphere 88 (2012)8. - ISSN 0045-6535 - p. 903 - 911.
    brominated flame retardants - polybrominated diphenyl ethers - polychlorinated-biphenyls - organochlorine contaminants - haliaeetus-albicilla - hieraaetus-pennatus - breeding success - residue levels - great-lakes - eggs
    Polybrominated diphenyl ethers (PBDEs), polychlorinated biphenyls (PCBs) and organochlorine insecticides (OCs) were analysed in 58 Eurasian Eagle owl (Bubo bubo) unhatched eggs collected between 2004 and 2009 in Southeastern Spain. Levels of p,p'-DDE were found to be higher than in eggs laid by other European owls in the same decade, probably due to the greater agricultural activity in our study area. Compared to other European raptors, exposure to PCBs can be considered intermediate, but low to PBDEs. Land use differences and prey availability were the rationale to divide the study area in two subareas in further assessments. Temporal trends of HCB, p,p'-DDE, ß-HCH, PCBs and PBDEs were significantly different in each subarea, generally increasing over time in the Southern but decreasing or remaining stable in the Northern. On the contrary, levels of cyclodienes tended to decrease in both subareas. Dietary shifts with a greater amount of birds are suggested as a cause for increasing organochlorine loads in raptors. This may explain the increasing trend in the Southern territories. However, due to the proximity of most of these nests to Cartagena, an important industrial city, increasing environmental pollution cannot be ruled out. Although average levels of the compounds analysed are below threshold levels, 17% of the samples exceeded 400 pg g-1 ww (wet weight), the LOAEC for Total TEQs. Moreover, a negative correlation between TEQ concentrations and the metabolizable fraction of PCBs (Fprob = 0.0018) was found when TEQs values were above 10 pg g-1 ww. This could be indicative of hepatic enzymes induction in the birds exposed at higher concentrations, which are mainly breeding in the Southern subarea. These females could be suffering from Ah-receptor-related toxic effects, some of which have been related to altered bird reproduction. Finally, a significant negative correlation between p,p'-DDE levels and eggshell thickness (r = -0.469, p <0.001) was observed, with about 17% of eggshell thinning for eggs with p,p'-DDE levels above 100 µg g -1 lw. The persistence of this degree of thinning over a period of time has been related to population declines in other raptor species
    Evaluation trials of potential input reducing developments in 3 test locations.
    Garcia Victoria, N. ; Kempkes, F.L.K. ; Löpez Hernández, J.C. ; Baezo Romero, E.J. ; Incrocci, L. ; Pardossi, A. - \ 2012
    Almeria/Bleiswijk/Pisa : European Commission (Euphoros reports Deliverable 19 Final report) - 92
    The EUPHOROS project is co-funded by the European Commission, Directorate General for Research, within the 7th Framework Programme of RTD, Theme 2 – Biotechnology, Agriculture & Food, contract 211457. The views and opinions expressed in this Deliverable are purely those of the writers and may not in any circumstances be regarded as stating an official position of the European Commission. This Deliverable 5 Annex is the latest updated version in September 2011.
    Three European protected crops: LCA and alternatives to reduce environmental impact
    Torrellas, M. ; Antón, A. ; Baeza, E. ; López, J.C. ; Pérez Parra, J. ; Ruijs, M.N.A. ; Garcia Victoria, N. ; Montero, J.I. - \ 2011
    Organochlorine pesticides levels in eagle owl (Bubo bubo) eggs: Temporal trends and sublethal effects
    Gómez-Ramírez, P. ; Martínez-López, E. ; Maria-Mojica, P. ; Espin, S. ; Zweers, H. ; García-Fernández, A.J. ; Brink, N.W. van den - \ 2010
    Toxicology Letters 196 (2010)suppl.. - ISSN 0378-4274 - p. s129 - s129.
    According to the NRC requirements, the eagle owl could be considered a suitable sentinel species for biomonitoring organochlorine pesticides, reflecting both their use and food web transfer. In order to obtain this information from an agricultural area in Southeastern Spain, 58 unhatched eggs from the period 2004–2009 were analysed for 23 organochlorine compounds. Homogenized egg contents were processed with n-hexane, and cleaned up by GPC. Detection and quantification was performed using GC–MS. A homogeneous temporal trend was found for the total of compounds analyzed, with a significant decrease in 2008 (Chi-square = 13.31, p <0.01). On the contrary, lindane (Chi-square = 15.03, p <0.01) and DDT (Chi-square = 9.76, p <0.05) significantly increased along the whole period, reaching higher levels in 2009. Although DDT was banned in Spain in 1971, this compound has been used until 2008 for the synthesis of dicofol, an insecticide recommended for citrus farming in the study area. Previous studies in other raptor species from the same region show a positive correlation between DDT blood levels and citrus, vineyard and olive tree crops, for which dicofol was also recommended. Lindane was banned in Spain in 2000 for agricultural use, and allowed for animal use until December 2007. The increasing levels could reflect a current illegal use of this compound. Eggshell thickness is a good biomarker, inversely correlated with DDE levels in birds. A significant negative correlation was found between eggshell thickness and DDE concentration in our population (P = -0.445, p <0.01) and a 17% of thinning when DDE levels were higher than 100 µg/g (lipid weight). Although other contaminants may cause some eggshell thinning, DDE has been established as the main role.
    Trends in levels of PCBs in an Eagle Owl Bubo bubo population from Southeastern Spain
    Gómez-Ramírez, P. ; Martínez-López, E. ; María-Mojica, P. ; León-Ortega, M. ; Enrique Martínez, J. ; Francisco Calvo, J. ; Botella, F. ; Sánchez-Zapata, J.A. ; Zweers, A. ; García-Fernández, A.J. ; Brink, N.W. van den - \ 2010
    In: Proceedings of the 20th SETAC Europe congress, Seville, Spain, 23-27 May 2010. - - p. 71 - 71.
    The plasmid pGS5 from the hyperthermophilic archaeon Archaeoglobus profundus is negatively supercoiled
    Lopez-Garcia, P. ; Forterre, P. ; Oost, J. van der; Erauso, G. - \ 2000
    Journal of Bacteriology 182 (2000). - ISSN 0021-9193 - p. 4998 - 5000.
    We present evidence that, in contrast to plasmids from other hyperthermophilic archaea, which are in the relaxed to positively supercoiled state, plasmid pGS5 (2.8 kb) from Archaeoglobus profundus is negatively supercoiled. This might be due to the presence of a gyrase introducing negative supercoils, since gyrase genes are present in the genome of its close relative A. fulgidus, and suggests that gyrase activity predominates over reverse gyrase whenever the two topoisomerases coexist in cells.
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