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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Hoofed animals bad for Veluwe forests
Ramirez Chiriboga, J.I. - \ 2019
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.

Wild ungulates as forest engineers
Ramírez Chiriboga, Juan Ignacio - \ 2019
Wageningen University. Promotor(en): L. Poorter, co-promotor(en): J. den Ouden; P.A. Jansen. - Wageningen : Wageningen University - ISBN 9789463951074 - 159
Speckle pattern analysis of crumpled papers
Rad, Vahideh Farzam ; Ramírez-Miquet, Evelio E. ; Cabrera, Humberto ; Habibi, Mehdi ; Moradi, Ali Reza - \ 2019
Applied Optics 58 (2019)24. - ISSN 1559-128X - p. 6549 - 6554.

In this paper, we show that laser speckle analysis (LSA) can provide valuable information about the structure of crumpled thin sheets. Crumpling and folding of slender objects are present in several phenomena and in various ranges of size, e.g., paper compaction, cortical folding in brains, DNA packing in viral capsids, and flower buds, to name a few. The analysis of laser speckles, both numerical and graphical, is a source of information about the activity of biological or non-biological materials, and the development of digital electronics, which brought the ease of image processing, has opened new perspectives for a spectrum of LSA applications. LSA is applied on randomly crumpled and one-, two-, and three-times folded papers, and appreciable differences in LSA parameters are observed. The methodology can be applied for easy-to-implement quantitative assessment of similar phenomena and samples.

Author Correction: Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems
Guerrero-Ramírez, Nathaly R. ; Craven, Dylan ; Reich, Peter B. ; Ewel, John J. ; Isbell, Forest ; Koricheva, Julia ; Parrotta, John A. ; Auge, Harald ; Erickson, Heather E. ; Forrester, David I. ; Hector, Andy ; Joshi, Jasmin ; Montagnini, Florencia ; Palmborg, Cecilia ; Piotto, Daniel ; Potvin, Catherine ; Roscher, Christiane ; Ruijven, Jasper van; Tilman, David ; Wilsey, Brian ; Eisenhauer, Nico - \ 2019
Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1365 - 1365.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep
Thomas, Nadine A. ; Olvera-Ramírez, Andrea M. ; Abecia, Leticia ; Adam, Clare L. ; Edwards, Joan E. ; Cox, Georgina F. ; Findlay, Patricia A. ; Destables, Elodie ; Wood, Tracy A. ; McEwan, Neil R. - \ 2019
Archives of Microbiology 201 (2019)7. - ISSN 0302-8933 - p. 889 - 896.
Anaerobic fungi - Bacteria - Ciliated protozoa - Day length - Digestive tract - Soay sheep

Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal ‘by-pass’ nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.

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

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

Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants
Wilschut, Rutger A. ; Geisen, Stefan ; Martens, Henk ; Kostenko, Olga ; Hollander, Mattias de; Hooven, Freddy C. ten; Weser, Carolin ; Snoek, L.B. ; Bloem, Janneke ; Caković, Danka ; Čelik, Tatjana ; Koorem, Kadri ; Krigas, Nikos ; Manrubia, Marta ; Ramirez, Kelly S. ; Tsiafouli, Maria A. ; Vreš, Branko ; Putten, Wim H. van der - \ 2019
Global Change Biology 25 (2019)8. - ISSN 1354-1013 - p. 2714 - 2726.
Centaurea stoebe - enemy release hypothesis - plant-pathogenic nematodes - range expansion - range-expanding plant species - root-feeding nematodes

Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change-driven intracontinental range-expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range-expanding and four congeneric native species along a 2,000 km latitudinal transect from South-Eastern to North-Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range-expanding plant species than in congeneric natives and that in their new range, range-expanding plant species accumulate fewest root-feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range-expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range-expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root-feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range-expanding and native plant species and that some range-expanding plant species may become released from root-feeding nematodes in the new range.

Range-expansion effects on the belowground plant microbiome
Ramirez, Kelly S. ; Snoek, L.B. ; Koorem, Kadri ; Geisen, Stefan ; Bloem, L.J. ; Hooven, Freddy ten; Kostenko, Olga ; Krigas, Nikos ; Manrubia, Marta ; Caković, Danka ; Raaij, Debbie van; Tsiafouli, Maria A. ; Vreš, Branko ; Čelik, Tatjana ; Weser, Carolin ; Wilschut, Rutger A. ; Putten, Wim H. van der - \ 2019
Nature Ecology & Evolution 3 (2019)4. - ISSN 2397-334X - p. 604 - 611.

Plant range expansion is occurring at a rapid pace, largely in response to human-induced climate warming. Although the movement of plants along latitudinal and altitudinal gradients is well-documented, effects on belowground microbial communities remain largely unknown. Furthermore, for range expansion, not all plant species are equal: in a new range, the relatedness between range-expanding plant species and native flora can influence plant–microorganism interactions. Here we use a latitudinal gradient spanning 3,000 km across Europe to examine bacterial and fungal communities in the rhizosphere and surrounding soils of range-expanding plant species. We selected range-expanding plants with and without congeneric native species in the new range and, as a control, the congeneric native species, totalling 382 plant individuals collected across Europe. In general, the status of a plant as a range-expanding plant was a weak predictor of the composition of bacterial and fungal communities. However, microbial communities of range-expanding plant species became more similar to each other further from their original range. Range-expanding plants that were unrelated to the native community also experienced a decrease in the ratio of plant pathogens to symbionts, giving weak support to the enemy release hypothesis. Even at a continental scale, the effects of plant range expansion on the belowground microbiome are detectable, although changes to specific taxa remain difficult to decipher.

Phytochrome a protects tomato plants from injuries induced by continuous light
Velez-Ramirez, Aaron I. ; Vreugdenhil, Dick ; Millenaar, Frank F. ; Ieperen, Wim van - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
Continuous light - Far-red light - Photosynthesis down-regulation - Phytochrome - Solanum lycopersicum - Tomato

Plants perceive and transduce information about light quantity, quality, direction and photoperiod via several photoreceptors and use it to adjust their growth and development. A role for photoreceptors has been hypothesized in the injuries that tomato plants develop when exposed to continuous light as the light spectral distribution influences the injury severity. Up to now, however, only indirect clues suggested that phytochromes (PHY), red/far-red photoreceptors, are involved in the continuous-light-induced injuries in tomato. In this study, therefore, we exposed mutant and transgenic tomato plants lacking or over-expressing phytochromes to continuous light, with and without far-red light enrichment. The results show that PHYA over-expression confers complete tolerance to continuous light regardless the light spectrum. Under continuous light with low far-red content, PHYB1 and PHYB2 diminished and enhanced the injury, respectively, yet the effects were small. These results confirm that phytochrome signaling networks are involved in the induction of injury under continuous light. HIGHLIGHTS-PHYA over-expression confers tolerance to continuous light regardless the light spectrum.-In the absence of far-red light, PHYB1 slightly diminishes the continuous light-induced injury.-Continuous light down-regulates photosynthesis genes in sensitive tomato lines.

Assessment of browsed plants in a sub-tropical forest frontier by means of fuzzy inference
Dechnik-Vázquez, Yanus A. ; García-Barrios, Luis ; Ramírez-Marcial, Neptalí ; Noordwijk, Meine van; Alayón-Gamboa, Armando - \ 2019
Journal of Environmental Management 236 (2019). - ISSN 0301-4797 - p. 163 - 181.
Agroforestry - Browsing - Cattle - Fuzzy inference - Silvopastoral systems

Browsing of forest frontiers by cattle in sub-tropical landscapes is detrimental to ecosystem health, but essential to smallholder livelihoods. We described a silvopastoral landscape, searching for browsed plants to assess how much of the forest is actually used for this end, and also searching for potential new useful species for silvopastoral purposes. The first objective was accomplished through a floristic description, making observations of individuals with browsing marks. Information from interviews, bromatological analyses and vegetative propagation tests further complemented this information to achieve the second objective. We classified the results using Fuzzy Inference Systems (FISs). A great variety of nutritious browsed plants was found, distributed across various types of vegetation, growth habits and taxonomic groups: forest frontiers already are like silvopastoral systems. Various plants like Acalypha leptopoda, Montanoa tomentosa and Verbesina perymenioides are interesting prospects for further intensification of silvopastoral systems.

Robust soil mapping at the farm scale with vis–NIR spectroscopy
Ramirez-Lopez, L. ; Wadoux, A.M.J.C. ; Franceschini, M.H.D. ; Terra, F.S. ; Marques, K.P.P. ; Sayão, V.M. ; Demattê, J.A.M. - \ 2019
European Journal of Soil Science 70 (2019)2. - ISSN 1351-0754 - p. 378 - 393.

Sustainable agriculture practices are often hampered by the prohibitive costs associated with the generation of fine-resolution soil maps. Recently, several papers have been published highlighting how visible and near infrared (vis–NIR) reflectance spectroscopy may offer an alternative to address this problem by increasing the density of soil sampling and by reducing the number of conventional laboratory analyses needed. However, for farm-scale soil mapping, previous studies rarely focused on sample optimization for the calibration of vis–NIR models or on robust modelling of the spatial variation of soil properties predicted by vis–NIR spectroscopy. In the present study, we used soil vis–NIR spectroscopy models optimized in terms of both number of calibration samples and accuracy for high-resolution robust farm-scale soil mapping and addressed some of the most common pitfalls identified in previous research. We collected 910 samples from 458 locations at two depths (A, 0–0.20 m; B, 0.80–1.0 m) in the state of São Paulo, Brazil. All soil samples were analysed by conventional methods and scanned in the vis–NIR spectral range. With the vis–NIR spectra only, we inferred statistically the optimal set size and the best samples with which to calibrate vis–NIR models. The calibrated vis–NIR models were validated and used to predict soil properties for the rest of the samples. The prediction error of the spectroscopic model was propagated through the spatial analysis, in which robust block kriging was used to predict particle-size fractions and exchangeable calcium content for each depth. The results indicated that statistical selection of the calibration samples based on vis–NIR spectra considerably decreased the need for conventional chemical analysis for a given level of mapping accuracy. The methods tested in this research were developed and implemented using open-source software. All codes and data are provided for reproducible research purposes. Highlights: Vis–NIR spectroscopy enables an increase in sampling density with little additional cost. Guided selection of vis–NIR calibration samples reduced the need for conventional soil analysis. Error of spectroscopic model prediction was propagated by spatial analysis. Maps from the vis–NIR augmented dataset were almost as accurate as those from conventional soil analysis.

Defining and applying the concept of Favourable Reference Values for species habitats under the EU Birds and Habitats Directives : examples of setting favourable reference values
Bijlsma, R.J. ; Agrillo, E. ; Attorre, F. ; Boitani, L. ; Brunner, A. ; Evans, P. ; Foppen, R. ; Gubbay, S. ; Janssen, J.A.M. ; Kleunen, A. van; Langhout, W. ; Pacifici, M. ; Ramirez, I. ; Rondinini, C. ; Roomen, M. van; Siepel, H. ; Swaaij, C.A.M. van; Winter, H.V. - \ 2019
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2929) - 219
Defining and applying the concept of Favourable Reference Values for species habitats under the EU Birds and Habitats Directives : technical report
Bijlsma, R.J. ; Agrillo, E. ; Attorre, F. ; Boitani, L. ; Brunner, A. ; Evans, P. ; Foppen, R. ; Gubbay, S. ; Janssen, J.A.M. ; Kleunen, A. van; Langhout, W. ; Noordhuis, R. ; Pacifici, M. ; Ramirez, I. ; Rondinini, C. ; Roomen, M. van; Siepel, H. ; Winter, H.V. - \ 2019
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2928) - 93
Recent insights on uncertainties present in integrated catchment water quality modelling
Tscheikner-Gratl, Franz ; Bellos, Vasilis ; Schellart, Alma ; Moreno-Rodenas, Antonio ; Muthusamy, Manoranjan ; Langeveld, Jeroen ; Clemens, Francois ; Benedetti, Lorenzo ; Rico-Ramirez, Miguel Angel ; Carvalho, Rita Fernandes de; Breuer, Lutz ; Shucksmith, James ; Heuvelink, Gerard B.M. ; Tait, Simon - \ 2019
Water Research 150 (2019). - ISSN 0043-1354 - p. 368 - 379.
Complexity management - Integrated catchment modelling - Sub-models of integrated modelling - Uncertainty - Water quality

This paper aims to stimulate discussion based on the experiences derived from the QUICS project (Quantifying Uncertainty in Integrated Catchment Studies). First it briefly discusses the current state of knowledge on uncertainties in sub-models of integrated catchment models and the existing frameworks for analysing uncertainty. Furthermore, it compares the relative approaches of both building and calibrating fully integrated models or linking separate sub-models. It also discusses the implications of model linkage on overall uncertainty and how to define an acceptable level of model complexity. This discussion includes, whether we should shift our attention from uncertainties due to linkage, when using linked models, to uncertainties in model structure by necessary simplification or by using more parameters. This discussion attempts to address the question as to whether there is an increase in uncertainty by linking these models or if a compensation effect could take place and that overall uncertainty in key water quality parameters actually decreases. Finally, challenges in the application of uncertainty analysis in integrated catchment water quality modelling, as encountered in this project, are discussed and recommendations for future research areas are highlighted.

Long-term effects of wild ungulates on the structure, composition and succession of temperate forests
Ramirez Chiriboga, J.I. ; Jansen, P.A. ; Ouden, J. den; Goudzwaard, L. ; Poorter, L. - \ 2019
Forest Ecology and Management 432 (2019). - ISSN 0378-1127 - p. 478 - 488.
Ungulates in temperate regions are increasing in range and abundance, leading to concerns that browsing and trampling reach levels that hamper tree recruitment and forest regeneration. However, studies that actually quantify the long-term effects of ungulates on forest succession are scarce. Here, we use a chronosequence of ungulate exclosures (fenced) and control (unfenced) plots to assess the long-term effects of ungulates on forest structure, diversity and litter depth in forests on poor sandy soils at the Veluwe, the Netherlands, which have moderate ungulate densities ( = 13.6 ungulates km−2). We surveyed the vegetation in 27 paired fenced and unfenced plots that ranged from 1 to 33 years old, and measured seven variables to characterize forest structure (stem density, canopy cover and understory vegetation cover), composition (Shannon diversity, species richness and conifer proportion) and leaf litter depth. We found on average that fencing compared to unfencing reduced understory vegetation cover (fenced = 64.3 ± 20.2%, unfenced = 80.3 ± 19.4%), increased canopy cover (fenced = 47.4 ± 30.1%, unfenced = 29.3 ± 21.1%), tree species richness (fenced = 4.5 ± 1.3 spp., unfenced = 2.7 ± 1.2 spp.), tree Shannon diversity (fenced = 1.1 ± 0.3 index, unfenced = 0.7 ± 0.3 index) and litter layer depth (fenced = 4.4 ± 1.4 cm, unfenced = 2.4 ± 1.1 cm). While fenced plots developed woody vegetation with palatable broadleaved species such as Betula pendula, Betula pubescens, Prunus serotina, and Quercus robur, unfenced plots were not associated with any particular tree species. Our results show that current ungulate densities in this system have pronounced long-term effects on forest structure, composition and litter depth, implying that ungulates can slow down natural succession of temperate forest, from light demanding to shade tolerant species, by keeping the system in an arrested state consisting of light demanding species.
Small Fish and Food Security : Towards innovative integration of small fish in African food systems to improve nutrition
Kolding, Jeppe ; Overa, Ragnhild ; Kjellevold, Marian ; Zwieten, P.A.M. van; Pucher, Johannes ; Yaro, Joseph ; Njiru, James ; Taabu-Munyaho, Anthony - \ 2018
In: WSFC 3rd world small-scale fisheries congress, Chiang Mai, Thailand, October 22-26, 2018. - - p. 57 - 57.
Study on the approaches to management for data-poor stocks in mixed fisheries : DRuMFISH : final report - Study
Poos, J.J. ; Oliveira, José De; Ulrich, C. ; Brunel, T.P.A. ; Plet-Hansen, Kristian ; Mildenberger, Tobias ; Nielsen, J.R. ; Kokkalis, A. ; Minto, Coilín ; Pawlowski, Lionel ; Robert, Marianne ; Macher, Claire ; Merzereaud, Mathieu ; Garcia, Dorleta ; Ibaibarriaga, L. ; Bertignac, Michel ; Vermard, Youen ; Fischer, Simon ; Carpi, Piera ; Walker, Nicola ; Earl, Timothy ; Davie, Sarah ; Haslob, Holger ; Kempf, A. ; Taylor, Marc ; Martin, Paloma ; Maynou, Francesc ; Recasens, Laura ; Ramirez, John Gabriel ; Lleonart, Jordi ; Garriga, Mariona ; Tserpes, George ; Sgardeli, Viki ; Coro, Gianpolo ; Scarcella, Giuseppe ; Angelini, Silvia - \ 2018
EU - ISBN 9789292024062 - 84 p.
This is the final report of the European Commission funded research project "DRuMFISH" (service contract n° EASME/EMFF/2014/l.3.2.4/ SI2.721116). The main aim of the project was to develop models and strategies for providing advice for mixed fisheries that account for: (i) fishing mortality ranges consistent with MSY, (ii) all fish caught being landed, and (iii) significant components of the marine fish ecosystem lacking key biological information. In order to meet this aim, DRuMFISH delivered a review of assessment approaches for data-poor stocks, extended mixed fisheries simulation frameworks to include data-poor stocks. The assessment approaches and simulation frameworks were implemented in 7 case studies. These case studies were mixed fisheries in the Baltic Sea, the North Sea, the Celtic Sea, the Bay of Biscay, the Western Mediterranean, the Adriatic Sea, and the Aegean Sea. Within the case studies, 35 data-poor stock assessments were done. These assessments provided exploitation status of data-poor stocks. Different harvest control rules were subsequently tested for their expected yields and stock biomasses from the mixed fisheries in the simulation frameworks. Now that data-poor stocks can be incorporated with in the mixed fisheries simulation frameworks, the design of new management plans can account for data-poor stocks in mixed fisheries.
Opportunities for soil sustainability in Europe
Putten, W.H. van der; Ramirez, Kelly S. ; Poesen, Jean ; Winding, A. ; Lemanceau, Philippe ; Lisa, Lenka ; Simek, Miloslaw ; Moora, M. ; Setala, Heikki ; Zaitsev, A. ; Economou-Eliopoulos, Maria ; Hornung, E. ; Wall, David ; Angelis, P. de; Lipiec, Jerzy ; Briones, M.J.I. ; Hedlund, Katarina ; Heijden, M. ; Six, Johan ; Bardgett, Richard D. ; Powlson, D. ; Goulding, K. ; Norton, Michael - \ 2018
European Academies Science Advisory Council (EASAC) (EASAC policy report 36) - ISBN 9783804738980 - 48 p.
Reduction in nutritional quality and growing area suitability of common bean under climate change induced drought stress in Africa
Hummel, Marijke ; Hallahan, Brendan F. ; Brychkova, Galina ; Ramirez-Villegas, Julian ; Guwela, Veronica ; Chataika, Bartholomew ; Curley, Edna ; McKeown, Peter C. ; Morrison, Liam ; Talsma, Elise F. ; Beebe, Steve ; Jarvis, Andy ; Chirwa, Rowland ; Spillane, Charles - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322 - 11 p.

Climate change impacts on food security will involve negative impacts on crop yields, and potentially on the nutritional quality of staple crops. Common bean is the most important grain legume staple crop for human diets and nutrition worldwide. We demonstrate by crop modeling that the majority of current common bean growing areas in southeastern Africa will become unsuitable for bean cultivation by the year 2050. We further demonstrate reductions in yields of available common bean varieties in a field trial that is a climate analogue site for future predicted drought conditions. Little is known regarding the impact of climate change induced abiotic stresses on the nutritional quality of common beans. Our analysis of nutritional and antinutritional compounds reveals that iron levels in common bean grains are reduced under future climate-scenario relevant drought stress conditions. In contrast, the levels of protein, zinc, lead and phytic acid increase in the beans under such drought stress conditions. This indicates that under climate-change induced drought scenarios, future bean servings by 2050 will likely have lower nutritional quality, posing challenges for ongoing climate-proofing of bean production for yields, nutritional quality, human health, and food security.

A framework for priority-setting in climate smart agriculture research
Thornton, Philip K. ; Whitbread, Anthony ; Baedeker, Tobias ; Cairns, Jill ; Claessens, Lieven ; Baethgen, Walter ; Bunn, Christian ; Friedmann, Michael ; Giller, Ken E. ; Herrero, Mario ; Howden, Mark ; Kilcline, Kevin ; Nangia, Vinay ; Ramirez-Villegas, Julian ; Kumar, Shalander ; West, Paul C. ; Keating, Brian - \ 2018
Agricultural Systems 167 (2018). - ISSN 0308-521X - p. 161 - 175.
Adaptation - Agriculture - Climate change - Mitigation - Research

Climate-smart agriculture (CSA) is widely promoted as an approach for reorienting agricultural development under the realities of climate change. Prioritising research-for-development activities is crucial, given the need to utilise scarce resources as effectively as possible. However, no framework exists for assessing and comparing different CSA research investments. Several aspects make it challenging to prioritise CSA research, including its multi-dimensional nature (productivity, adaptation and mitigation), the uncertainty surrounding many climate impacts, and the scale and temporal dependencies that may affect the benefits and costs of CSA adoption. Here we propose a framework for prioritising agricultural research investments across scales and review different approaches to setting priorities among agricultural research projects. Many priority-setting case studies address the short- to medium-term and at relatively local scales. We suggest that a mix of actions that span spatial and temporal time scales is needed to be adaptive to a changing climate, address immediate problems and create enabling conditions for enduring change.

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
Symmetry-reversals in chiral active matter
Workamp, Marcel ; Ramirez, Gustavo ; Daniels, Karen E. ; Dijksman, Joshua A. - \ 2018
Soft Matter 14 (2018)27. - ISSN 1744-683X - p. 5572 - 5580.

We perform experiments on an active granular material composed of individually-driven, spinning disks confined within a circular arena. Small bumps at the outer edges of the disks provide a variable amount of interparticle coupling in the form of geometric friction. The disks each spin counter-clockwise, but undergo a transition in their collective circulation around the center of the arena, from a clockwise orbit to a counter-clockwise orbit, as a function of packing fraction φ. We identify that, unlike for vibrated granular gases, the particles' velocity distributions are Gaussian over a large range of φ. By fitting the speed distribution to a Maxwell-Boltzmann distribution, we identify a temperature-like parameter which is a universal function of φ; this parameter is also equal to the mean translational energy of the particles. We quantify the collective circulation via its solid-body-like rotation rate, and find that this is a universal function centered around a critical packing fraction. In addition, the ratio of orbital kinetic energy to spin kinetic energy is also a universal function for non-zero geometric friction. These findings highlight the important role of both the type of driving and the interparticle interactions (here, geometric friction) in controlling the collective behavior of active granular systems.

Network Analyses Can Advance Above-Belowground Ecology
Ramirez, Kelly S. ; Geisen, Stefan ; Morriën, Elly ; Snoek, Basten L. ; Putten, Wim H. van der - \ 2018
Trends in Plant Science 23 (2018)9. - ISSN 1360-1385 - p. 759 - 768.
community ecology - global change - species interactions - terrestrial ecology

An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.

Impact of lincosamides antibiotics on the composition of the rat gut microbiota and the metabolite profile of plasma and feces
Behr, C. ; Ramírez-Hincapié, S. ; Cameron, H.J. ; Strauss, V. ; Walk, T. ; Herold, M. ; Beekmann, K. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2018
Toxicology Letters 296 (2018). - ISSN 0378-4274 - p. 139 - 151.
Antibiotics - Gut microbiome - Metabolomics - Microbiome-related metabolites - Repeated dose oral toxicity study - Taxonomic profiling

The importance of the gut microorganisms and their wide range of interactions with the host are well-acknowledged. In this study, lincomycin and clindamycin were used to modulate microbial communities of Wistar rats to gain a comprehensive understanding of the implications of microbiome alterations. A metabolomics approach and taxonomic profiling were applied to characterize the effects of these antibiotics on the functionality of the microbiome and to identify microbiome-related metabolites. After treatment, the diversity of the microbial community was drastically reduced. Bacteroidetes and Verrucomicrobia were drastically reduced, Tenericutes and Deferribacteres completely disappeared, while abundance of Firmicutes and Proteobacteria were highly increased. Changes in plasma and feces metabolites were observed for metabolites belonging mainly to the class of complex lipids, fatty acids and related metabolites as well as amino acids and related compounds. Bile acid metabolism was markedly affected: taurocholic acid, glycochenodeoxycholic acid and cholic acid presented abrupt changes showing a specific metabolite pattern indicating disruption of the microbial community. In both plasma and feces taurocholic acid was highly upregulated upon treatment whereas glycochenodeoxycholic acid was downregulated. Cholic acid was upregulated in feces but downregulated in plasma. These results show that changes in the gut microbial community lead to alterations of the metabolic profile in blood and feces of the host and can be used to identify potentially microbiome-related metabolites. This implies that metabolomics could be a suitable tool to estimate the extent of changes induced in the intestinal microbiome with respect to consequences for the host.

Tropical Montane Cloud Forests in the Orinoco River basin : Inferring fog interception from through-fall dynamics
Ramírez, Beatriz H. ; Melsen, Lieke A. ; Ganzeveld, Laurens ; Leemans, Rik ; Teuling, Adriaan J. - \ 2018
Agricultural and Forest Meteorology 260-261 (2018). - ISSN 0168-1923 - p. 17 - 30.
Eastern Andes - Forest succession - Hydrology - Interception - Rutter model
The interaction between vegetation and the atmosphere is highly complex in fog affected ecosystems like Tropical Montane Cloud Forests (TMCFs). Despite acknowledging fog effects on the canopy's water balance, quantifying their influence remains challenging. While the reduction in potential evaporation that is caused by fog presence, is largely independent of land cover, fog interception itself strongly depends on the land-cover's vegetation characteristics. A better understanding of how these two fog related processes affect the water balance is highly relevant under current land-use and climate-change pressures. In this study we evaluate the different fog effects on TMCFs’ canopy interception combining model simulations and high temporal resolution (10 min) observations that were collected in different TMCF regeneration stages: early succession, secondary and old-growth TMCFs. We also analyse the difficulties in closing catchment water balances caused by limitations on the interpretation of throughfall data to properly represent these fog effects. Results show that different fog frequencies along elevation affect potential evaporation. The higher elevation old-growth TMCFs have a lower simulated evaporation and a lower dry canopy frequency than the low elevation secondary and early succession forests. Furthermore, we show that fog water inputs during fog-only events, even though higher at the higher elevation, are irrelevant as water inputs (from 0.8% to 1.6% of measured rainfall), but fog's contribution to through-fall during foggy rainfall events can be more relevant (from 5.8%–12.8% of measured rainfall). Additional to the fog trends along the elevation, we also uncover variable fog-vegetation interactions controlled by differences in canopy water storages as a function of forest cover. Each evaluated process has associated uncertainties, which together cumulatively explain why closing a water budget in TMCF catchments is limited by data collection methods that probably do not capture all relevant fog effects. In addition, this study also indicates that the temporal resolution of measured rainfall and through-fall and compensating effects of canopy parameters that are estimated by the commonly used Rutter canopy-rainfall interception model, pose an additional challenge to understand and quantify fog effects in the water budgets of TMCFs.
Effects of wild ungulates on the regeneration, structure and functioning of temperate forests: A semi-quantitative review
Ramirez Chiriboga, J.I. ; Jansen, P.A. ; Poorter, L. - \ 2018
Forest Ecology and Management 424 (2018). - ISSN 0378-1127 - p. 406 - 419.
Wild ungulates such as red deer, roe deer and wild boar are key drivers of forest ecosystems. Across the northern hemisphere, their range and abundance is increasing, while at the same time forest conversion and habitat fragmentation have led to a large variation in ungulate density and composition among areas. Understanding ungulate density impacts are important in order to prevent shifts towards undesired states, such as from forest to heathland. Here, we assess the effects of ungulate density on forest regeneration, development and functioning. We carried out a systematic literature review of 433 published studies in temperate forests, and used the data to model dose-response curves of the effects of ungulate density on three sets of forest attributes; tree regeneration (abundance, species richness and composition), forest structure (horizontal and vertical), and forest functioning (nutrient cycling in soil, timber and food production). Ungulate density averaged 23.6 km−2 across studies. Ungulates had a negative effect on forest regeneration, structure and functioning in 70% of the evaluated cases. The dose-response curves had a sigmoidal, rather than a unimodal shape. Critical tipping points, where ungulates started to have a negative effect on forest regeneration, were found at an ungulate metabolic weight density of 115 kg km−2 for forest regeneration, 141 kg km−2 for forest structure, and 251 kg km−2 for forest functioning, which is roughly equivalent to 10, 13 and 23 roe deer per km−2. Forest regeneration was most sensitive to immediate browsing and trampling impacts of small seedlings, while forest functioning was least sensitive because of time lags. However, these effects may build up over time. We suggest research priorities for studying ungulate-plant interactions in temperate forests, and make management recommendations how to balance wildlife with a functioning forest.
Fusarium riograndense sp. nov., a new species in the Fusarium solani species complex causing fungal rhinosinusitis
Dallé Rosa, P. ; Ramirez-Castrillon, M. ; Valente, P. ; Meneghello Fuentefria, A. ; Diepeningen, A.D. Van; Goldani, L.Z. - \ 2018
Journal de Mycologie Medicale 28 (2018)1. - ISSN 1156-5233 - p. 29 - 35.
Antifungal susceptibility - Fusarium - MLST - Molecular phylogeny - Morphology
Invasive fusariosis has a high mortality and is predominantly observed in patients with leukemia. We report the first case of a novel species of Fusarium, Fusarium riograndense sp. nov, isolated from a lesion in the nasal cavity lesion of a patient with acute lymphoblastic leukemia. The etiological agent was identified by Multilocus Sequencing Typing (MLST), including RPB2, TEF-1α, and ITS-LSU sequences, the gold standard technique to identify new species of Fusarium. MLST and phenotypic data strongly supported its inclusion in the F. solani species complex (FSSC). The new species produced a red pigment in the Sabouraud Dextrose Agar similar to other members of the complex. The macroconiodia developed from phialides on multibranched conidiophores which merge to form effuse sporodochia with a basal foot-cell instead of papilla in basal cell shape. The microconidia were ellipsoidal, 0-1-septated, produced from long monophialides. Chlamydospores were produced singly or in pairs. Amphotericin B (MIC 1. μg/mL) was the most active drug, followed by voriconazole (MIC 8. μg/mL). The patient was successfully treated with voriconazole. Our findings indicate another lineage within FSSC capable causing of invasive human infection.
Mycokey round table discussions of future directions in research on chemical detection methods, genetics and biodiversity of mycotoxins
Leslie, John F. ; Lattanzio, Veronica ; Audenaert, Kris ; Battilani, Paola ; Cary, Jeffrey ; Chulze, Sofia N. ; Saeger, Sarah De; Gerardino, Annamaria ; Karlovsky, Petr ; Liao, Yu Cai ; Maragos, Chris M. ; Meca, Giuseppe ; Medina, Angel ; Moretti, Antonio ; Munkvold, Gary ; Mulè, Giuseppina ; Njobeh, Patrick ; Pecorelli, Ivan ; Perrone, Giancarlo ; Pietri, Amedeo ; Palazzini, Juan M. ; Proctor, Robert H. ; Rahayu, Endang S. ; Ramírez, Maria L. ; Samson, Robert ; Stroka, Jörg ; Sulyok, Michael ; Sumarah, Mark ; Waalwijk, Cees ; Zhang, Qi ; Zhang, Hao ; Logrieco, Antonio F. - \ 2018
Toxins 10 (2018)3. - ISSN 2072-6651
Antibodies - Biological control - Communication with non-scientists - Metabolomics - Microbiome - Multi-mycotoxin detection protocols - Nominal group discussion technique - Proteomics - Transcriptomics
MycoKey, an EU-funded Horizon 2020 project, includes a series of “Roundtable Discussions” to gather information on trending research areas in the field of mycotoxicology. This paper includes summaries of the Roundtable Discussions on Chemical Detection and Monitoring of mycotoxins and on the role of genetics and biodiversity in mycotoxin production. Discussions were managed by using the nominal group discussion technique, which generates numerous ideas and provides a ranking for those identified as the most important. Four questions were posed for each research area, as well as two questions that were common to both discussions. Test kits, usually antibody based, were one major focus of the discussions at the Chemical Detection and Monitoring roundtable because of their many favorable features, e.g., cost, speed and ease of use. The second area of focus for this roundtable was multi-mycotoxin detection protocols and the challenges still to be met to enable these protocols to become methods of choice for regulated mycotoxins. For the genetic and biodiversity group, both the depth and the breadth of trending research areas were notable. For some areas, e.g., microbiome studies, the suggested research questions were primarily of a descriptive nature. In other areas, multiple experimental approaches, e.g., transcriptomics, proteomics, RNAi and gene deletions, are needed to understand the regulation of toxin production and mechanisms underlying successful biological controls. Answers to the research questions will provide starting points for developing acceptable prevention and remediation processes. Forging a partnership between scientists and appropriately-placed communications experts was recognized by both groups as an essential step to communicating risks, while retaining overall confidence in the safety of the food supply and the integrity of the food production chain.
Role of cell surface composition and lysis in static biofilm formation by Lactobacillus plantarum WCFS1
Fernández Ramírez, Mónica D. ; Nierop Groot, Masja N. ; Smid, Eddy J. ; Hols, Pascal ; Kleerebezem, Michiel ; Abee, Tjakko - \ 2018
International Journal of Food Microbiology 271 (2018). - ISSN 0168-1605 - p. 15 - 23.
Autolysis - Capsular polysaccharides - Extracellular DNA - Sortase A
Next to applications in fermentations, Lactobacillus plantarum is recognized as a food spoilage organism, and its dispersal from biofilms in food processing environments might be implicated in contamination or recontamination of food products. This study provides new insights into biofilm development by L. plantarum WCFS1 through comparative analysis of wild type and mutants affected in cell surface composition, including mutants deficient in the production of Sortase A involved in the covalent attachment of 27 predicted surface proteins to the cell wall peptidoglycan (ΔsrtA) and mutants deficient in the production of capsular polysaccharides (CPS1–4, Δcps1–4). Surface adhesion and biofilm formation studies revealed none of the imposed cell surface modifications to affect the initial attachment of cells to polystyrene while biofilm formation based on Crystal Violet (CV) staining was severely reduced in the ΔsrtA mutant and significantly increased in mutants lacking the cps1 cluster, compared to the wild-type strain. Fluorescence microscopy analysis of biofilm samples pointed to a higher presence of extracellular DNA (eDNA) in cps1 mutants and this corresponded with increased autolysis activity. Subsequent studies using Δacm2 and ΔlytA derivatives affected in lytic behaviour revealed reduced biofilm formation measured by CV staining, confirming the relevance of lysis for the build-up of the biofilm matrix with eDNA.
Field methods for sampling tree height for tropical forest biomass estimation
Sullivan, Martin J.P. ; Lewis, Simon L. ; Hubau, Wannes ; Qie, Lan ; Baker, Timothy R. ; Banin, Lindsay F. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Feldpausch, Ted R. ; Lopez-Gonzalez, Gabriela ; Arets, Eric ; Ashton, Peter ; Bastin, Jean François ; Berry, Nicholas J. ; Bogaert, Jan ; Boot, Rene ; Brearley, Francis Q. ; Brienen, Roel ; Burslem, David F.R.P. ; Canniere, Charles de; Chudomelová, Markéta ; Dančák, Martin ; Ewango, Corneille ; Hédl, Radim ; Lloyd, Jon ; Makana, Jean Remy ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Junior, Ben Hur Marimon ; Metali, Faizah ; Moore, Sam ; Nagy, Laszlo ; Vargas, Percy Nuñez ; Pendry, Colin A. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Rutishauser, Ervan ; Salim, Kamariah Abu ; Sonké, Bonaventure ; Sukri, Rahayu S. ; Sunderland, Terry ; Svátek, Martin ; Umunay, Peter M. ; Martinez, Rodolfo Vasquez ; Vernimmen, Ronald R.E. ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Phillips, Oliver L. - \ 2018
Methods in Ecology and Evolution 9 (2018)5. - ISSN 2041-210X - p. 1179 - 1189.
Above-ground biomass estimation - Allometry - Carbon stocks - Forest inventory - Forest structure - Sample size
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.
Relatedness with plant species in native community influences ecological consequences of range expansions
Koorem, K. ; Kostenko, O. ; Snoek, L.B. ; Weser, Carolin ; Ramirez, Kelly ; Wilschut, Rutger ; Putten, W.H. van der - \ 2018
Oikos 127 (2018)7. - ISSN 0030-1299 - p. 981 - 990.
Global warming is enabling many plant species to expand their range to higher latitudes and altitudes, where they may suffer less from natural aboveground and belowground enemies. Reduced control by natural enemies can enable climate warming-induced range expanders to get an advantage in competition with natives and become disproportionally abundant in their new range. However, so far studies have examined individual growth of range expanders, which have common congeneric plant species in their new range. Thus it is not known how general is this reduced effect of above- and belowground enemies and how it operates in communities, where multiple plant species also interact with each other. Here we show that range-expanding plant species with and without congenerics in the invaded habitats differ in their ecological interactions in the new range. In a community-level experiment, range-expanding plant species, both with and without congenerics, suppressed the growth of a herbivore. However, only range expanders without congenerics reduced biomass production of the native plant species. In the present study, range expanders without congenerics allocated more biomass aboveground compared to native plant species, which can explain their competitive advantage. Competitive interaction and also biomass allocation of native plants and their congeneric range expanders were similar. Our results highlight that information about species phylogenetic relatedness with native flora can be crucial for improving predictions about the consequences of climate warming-induced range expansions.
Hydro-meteorological functioning of tropical montane cloud forests in the Orinoco River basin
Ramírez Correal, Beatriz Helena - \ 2018
Wageningen University. Promotor(en): R. Leemans, co-promotor(en): L.N. Ganzeveld; A.J. Teuling. - Wageningen : Wageningen University - ISBN 9789463432153 - 206

The hydrologic interactions between the atmosphere, land cover and soil largely determine water availability to sustain ecosystems’and anthropogenic demands. Therefore, understanding how these interactions operate is required to design strategies to reduce or cope with the potential hydrological impacts of land-use and climate change. A particularly vulnerable ecosystem to changes in land use and climate is the Tropical Montane Cloud Forest (TMCF). The hydrology of this ecosystem is determined by the interactions between fog affected meteorology and land cover; both of which present a large spatio-temporal variability. This thesis aims to improve our understanding on TMCFs’ hydrological functioning in the seasonal Orinoco River basin headwaters located in the Colombian eastern Andes. This information is fundamental to anticipate the hydrological consequences of climate and land-use change.

Initially, the hydrometeorological spatio-temporal variability was evaluated in three neighboring catchments with contrasting forest cover and the corresponding hydrological responses of soil moisture and streamflow were assessed (Chapter 2). Results revealed a positive relation of fog/rainfall with elevation that steepened during the dry season. Therefore, hydrological responses were modulated by the interaction of seasonality, land cover and elevation. From these analyses, two key processes that could potentially explain the seasonal contrasts between the water budgets of the studied catchments, were identified.

The first was the water storage and release from organic soil layers. The hydrological role of these organic layers was assessed for different land-cover and climate conditions by combining field and laboratory data with modelling of vertical water flows under variable climate conditions (Chapter 3). From a land-use change perspective the storage loss caused by organic layer removal following deforestation largely explains the higher peak flows in the deforested catchment during the wet season. From the climate change perspective, simulated transpiration was limited by soil moisture during an observed severe dry season and continued to decline under expected climate change with the prolongation of dry spells. These results indicate that the organic layers have to be considered when evaluating hydrological impacts in TMCF catchments due to land-use and climate change.

The second identified key process was the potential fog influence on the catchments’ water budgets through its effect on the canopy water budget. Therefore, the fog’s effect on the canopy water budget was analyzed in three TMCF successional stages by combining hydrometeorological data on a high temporal resolution (i.e. 10 minutes) with modelling (Chapter 4). This approach helped to quantify, albeit a high uncertainty, the fog effects on the canopy-water balance. Even though additional water inputs by fog interception are not significant in relation to total rainfall, the fog’s effect in reducing potential evaporation plays a key role in sustaining canopy and overall system moisture. An improved understanding of the hydrological functioning in TMCFs in the Orinoco River basin, allowed to identify current and potential climate and land-use change impacts on the catchment water balances (Chapter 5). This information will be relevant in guiding future research on TMCF hydrological functioning and in supporting local and regional land-use planning policies and climate-change adaptation plans (Chapter 6).

Detecting macroecological patterns in bacterial communities across independent studies of global soils
Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Analysing intermediary organisations and their influence on upgrading in emerging agricultural clusters
Ramirez, Matias ; Clarke, Ian ; Klerkx, Laurens - \ 2018
Environment and Planning A 50 (2018)6. - ISSN 0308-518X - p. 1314 - 1335.
This paper analyses intermediary organisations in developing economy agricultural clusters. The paper critically engages with a growing narrative in studies of intermediaries that have stressed the ownership structure of intermediaries as a key driver for enabling knowledge transfer, inter-firm learning and upgrading of small producers in clusters. Two case studies of Latin American clusters are presented and discussed. The study suggests that in addition to ownership structure, cluster governance and the embeddedness of intermediaries in clusters are critical factors that need to be taken into account in understanding the influence of intermediaries in the upgrading of small producers in clusters.
Response of young bearing olive trees to irrigation-induced salinity
Ben-Gal, A. ; Beiersdorf, I. ; Yermiyahu, U. ; Soda, N. ; Presnov, E. ; Zipori, I. ; Ramirez Crisostomo, R. ; Dag, A. - \ 2017
Irrigation Science 35 (2017)2. - ISSN 0342-7188 - p. 99 - 109.

Expansion of irrigated olives, combined with prevalence of water containing dissolved salts, leads to irrigation-induced exposure of olive trees to salinity. Root zone salinity can rise either as a function of increasing input irrigation water salinity (ECi) or relative reductions in water for leaching. We investigated five ECi levels from 0.5 to 11.0 dS m−1 with a constant leaching fraction (LF) of 0.29 and five leaching levels from 0.05 to 0.44 (drainage: irrigation ratio) with water of ECi = 5.0 dS m−1 on young bearing Olea europaea cv Barnea olive trees grown in 2.5 m3 weighing-drainage lysimeters over three years. Tree-scale response to increased salinity did not demonstrate any sign of a threshold value and was not differentiated by the cause of salinity, be it changes in input irrigation water salt concentrations or changes in LF. Soil salinity, measured as electrical conductivity of saturated soil paste extract (ECe) and maintained at stable levels over time, decreased tree water consumption and tree size measured as trunk area or above-ground biomass by 40–60 % as it increased from 1.2 to around 3.5–4.0 dS m−1. Further increases in ECe to as high as 7.5 dS m−1 brought these parameters to 20–30 % of the treatment with low salinity. Fruit yield also decreased with increasing salinity, albeit with less drastic relative effects. An analytical model calculating water and salt balance and subsequent evapotranspiration or biomass as a function of irrigation water quantity and salinity successfully predicted the measured results.

Existing modeling platforms for biomass supply in Europe
Elbersen, B.S. ; Forsell, Nicklas ; Leduc, S. ; Staritsky, I.G. ; Witzke, P. ; Ramirez Almeyda, Jacqueline - \ 2017
In: Modelling and Optimisation of Biomass Supply Chains / Panoutsou, C., Academic Press - ISBN 9780128123034 - p. 25 - 54.
Biomass availability is related to the prevailing land use patterns in a region as these deliver different types and quantities of feedstocks. Robust modeling frameworks are required to predict future land use changes and biomass availability for given demands in terms of the production of crops, livestock, timber, bioenergy, biochemical, and biomaterials. This chapter presents two important modeling frameworks, CAPRI, and GLOBIOM and explains how they are used respectively to assess cost supply of domestic biomass potential from agriculture and forestry in Europe and cost-supply potential for biomass imports from the rest of the world. Recent work demonstrates that both model structure and consistency in input data are imperative to ensure the validity of biomass assessments but there are also limitations deriving from the inconsistency of statistical databases, the increasingly complex assumptions, variable feedstock types, and geographical levels. Regular updates and model improvements will be necessary to internalize further the evolving key issues determining biomass supply for biobased economy in Europe.
Assessing the potentials for nonfood crops
Ramirez Almeyda, Jacqueline ; Elbersen, B.S. ; Monti, M. ; Staritsky, I.G. ; Panoutsou, P. ; Alexopoulou, E. ; Schrijver, R.A.M. ; Elbersen, H.W. - \ 2017
In: Modelling and Optimisation of Biomass Supply Chains / Panoutsou, C., Academic Press - ISBN 9780128123034 - p. 219 - 251.
Given the ambitious EU targets to further decarbonize the economy, it can be expected that demand for lignocellulosic biomass will continue to grow. Provisioning of part of this biomass by dedicated biomass crops becomes an option. This chapter presents yields and cost levels that can be reached in Europe with different perennial crops in different climatic, soil, and management situations. The AquaCrop model developed by FAO was used and fed with phenological parameters per crop and detailed weather data to simulate the crop growth in all European NUTS3 regions. Yield levels were simulated for a maximum and a water limited yield situation and further converted to match with low, medium, and high input management systems. Low input systems are suitable for the lower quality soils often characterized as “marginal” because of their low suitability to be used for annual (rotational) cropping. In addition, suitability maps specific per crop were prepared according to important limiting factors such as killing frost, length of growing season, and slope. The cost productions were assessed with an activity-based costing (ABC) model, developed to assess the roadside Net Present Value (NPV) cost per ton of biomass. The yield, crop suitability, and cost simulation results were then combined to identify the best performing crop–management mix per region.
MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
Latrasse, David ; Jégu, Teddy ; Li, H. ; Zelicourt, Axel de; Raynaud, Cécile ; Legras, Stéphanie ; Gust, Andrea ; Samajova, Olga ; Veluchamy, Alaguraj ; Rayapuram, Naganand ; Ramirez-Prado, Juan Sebastian ; Kulikova, O. ; Colcombet, Jean ; Genot, Baptiste ; Bisseling, A.H.J. ; Benhamed, Moussa ; Hirt, Heribert - \ 2017
GSE99936 - Arabidopsis thaliana - PRJNA390146
Microbial-associated molecular patterns (MAMPs) activate several MAP Kinases (MAPKs), which are major regulators of the innate immune response in Arabidopsis that induce large-scale changes in gene expression. Here, we determined whether MAMP-triggered gene expression involves chromatin modifications at the chromosomal level. Our results show that histone acetylation and deacetylation are major regulators of MAMP-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defense gene expression and innate immunity. The MAPK MPK3 directly interacts with and phosphorylates HD2B, thereby regulating the intra-nuclear compartmentalization and function of the histone deacetylase. By studying a number of gene loci that undergo MAMP-dependent activation or repression, our data reveal a mechanistic model for how protein kinase signaling directly impacts chromatin reprogramming in plant defense.
MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
Latrasse, David ; Jégu, Teddy ; Li, H. ; Zelicourt, Axel de; Raynaud, Cécile ; Legras, Stéphanie ; Gust, Andrea ; Samajova, Olga ; Veluchamy, Alaguraj ; Rayapuram, Naganand ; Ramirez-Prado, Juan Sebastian ; Kulikova, O. ; Colcombet, Jean ; Bigeard, Jean ; Genot, Baptiste ; Bisseling, A.H.J. ; Benhamed, Moussa ; Hirt, Heribert - \ 2017
defence gene expression - chromatin reprogramming - pattern-triggered gene expression - histone deactylase - MAP kinase MPK 3 - microbial-associated - phosphorylates HD 2B - histone deactylase HD 2B - histone acetylation - MAPK-triggered chromatin reprogramming - regulator - immunity
Data from: Relatedness with plant species in native community influences ecological consequences of range expansions
Koorem, K. ; Kostenko, O. ; Snoek, L.B. ; Weser, Carolin ; Ramirez, Kelly ; Wilschut, Rutger ; Putten, W.H. van der - \ 2017
climate change - plant-plant interaction - plant-herbivore interaction - plant-soil interaction
Global warming is enabling many plant species to expand their range to higher latitudes and altitudes, where they may suffer less from natural aboveground and belowground enemies. Reduced control by natural enemies can enable climate warming-induced range expanders to get an advantage in competition with natives and become disproportionally abundant in their new range. However, so far studies have examined individual growth of range expanders, which have common congeneric plant species in their new range. Thus it is not known how general is this reduced effect of above- and belowground enemies and how it operates in communities, where multiple plant species also interact with each other. Here we show that range-expanding plant species with and without congenerics in the invaded habitats differ in their ecological interactions in the new range. In a community-level experiment, range-expanding plant species, both with and without congenerics, suppressed the growth of a herbivore. However, only range expanders without congenerics reduced biomass production of the native plant species. In the present study, range expanders without congenerics allocated more biomass aboveground compared to native plant species, which can explain their competitive advantage. Competitive interaction and also biomass allocation of native plants and their congeneric range expanders were similar. Our results highlight that information about species phylogenetic relatedness with native flora can be crucial for improving predictions about the consequences of climate warming-induced range expansions.
Case study of algae production integration into wastewater treatment: the Climate-KIC MAB2.0 project
Gyalai-Korpos, Miklós ; Broek, L.A.M. van den; Ramirez, Andrea ; Abiusi, Fabian ; Reith, J.H. - \ 2017
Water-soluble polysaccharide extracts from the oyster culinary-medicinal mushroom pleurotus ostreatus (Agaricomycetes) with HMGCR inhibitory activity
Gil-Ramírez, Alicia ; Smiderle, Fhernanda R. ; Morales, Diego ; Govers, Coen ; Synytsya, Andriy ; Wichers, Harry J. ; Iacomini, Marcello ; Soler-Rivas, Cristina - \ 2017
International Journal of Medicinal Mushrooms 19 (2017)10. - ISSN 1521-9437 - p. 879 - 892.
Caco2 - Cholesterol - HMGCR - Medicinal mushrooms - Pleurotus ostreatus - Polysaccharides - β-glucans
Water extracts from Pleurotus ostreatus containing no statins showed 3-hydroxy-3-methyl-glutaryl CoA reductase (HMGCR) inhibitory activity (in vitro) that might be due to specific water-soluble polysaccharides (WSPs); when isolated and deproteinized, increasing concentrations of the WSP extract induced higher inhibition. The WSP extract contained mainly β-glucans, mannogalactans, and glycogen (e.g., α-glucans), although derivatives or fragments with lower molecular weights (between 14 and 3.5 kDa) were present and were able to induce the inhibitory activity. The extract contained more β-(1→3)-glucans than β-(1→3),(1→6)-glucans, and they partially survived digestion and managed to pass through Caco2 cell monolayers to the lower compartment after in vitro digestion and transport experiments. The WSP might also modulate Caco2 membrane integrity.
Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems
Guerrero-Ramírez, Nathaly R. ; Craven, Dylan ; Reich, Peter B. ; Ewel, John J. ; Isbell, Forest ; Koricheva, Julia ; Parrotta, John A. ; Auge, Harald ; Erickson, Heather E. ; Forrester, David Ian ; Hector, Andy ; Joshi, Jasmin ; Montagnini, Florencia ; Palmborg, Cecilia ; Piotto, Daniel ; Potvin, Catherine ; Roscher, Christiane ; Ruijven, Jasper van; Tilman, David ; Wilsey, Brian ; Eisenhauer, Nico - \ 2017
Nature Ecology & Evolution 1 (2017). - ISSN 2397-334X - p. 1639 - 1642.
The effects of biodiversity on ecosystem functioning generally increase over time, but the underlying processes remain unclear. Using 26 long-term grassland and forest experimental ecosystems, we demonstrate that biodiversity–ecosystem functioning relationships strengthen mainly by greater increases in functioning in high-diversity communities in grasslands and forests. In grasslands, biodiversity effects also strengthen due to decreases in functioning in low-diversity communities. Contrasting trends across grasslands are associated with differences in soil characteristics.
Sucrose and Starch Content Negatively Correlates with PSII Maximum Quantum Efficiency in Tomato (Solanum lycopersicum) Exposed to Abnormal Light/Dark Cycles and Continuous Light"
Velez Ramirez, A.I. ; Carreno Quintero, N. ; Vreugdenhil, D. ; Millenaar, Frank F. ; Ieperen, W. van - \ 2017
Plant and Cell Physiology 58 (2017)8. - ISSN 0032-0781 - p. 1339 - 1349.
Light is most important to plants as it fuels photosynthesis and provides clues about the environment. If provided in unnatural long photoperiods, however, it can be harmful and even lethal. Tomato (Solanum lycopersicum), for example, develops mottled chlorosis and necrosis when exposed to continuous light. Understanding the mechanism of these injuries is valuable, as important pathways regulating photosynthesis, such as circadian, retrograde and light signaling pathways are probably involved. Here, we use non-targeted metabolomics and transcriptomics analysis as well as hypothesis-driven experiments with continuous light-tolerant and -sensitive tomato lines to explore the long-standing proposed role of carbohydrate accumulation in this disorder. Analysis of metabolomics and transcriptomics data reveals a clear effect of continuous light on sugar metabolism and photosynthesis. A strong negative correlation between sucrose and starch content with the severity of continuous light-induced damage quantified as the maximum quantum efficiency of PSII (Fv/Fm) was found across several abnormal light/dark cycles, supporting the hypothesis that carbohydrates play an important role in the continuous light-induced injury. We postulate that the continuous light-induced injury in tomato is caused by down-regulation of photosynthesis, showing characteristics of both cytokinin-regulated senescence and light-modulated retrograde signaling. Molecular mechanisms linking carbohydrate accumulation with down-regulation of carbon-fixing enzymes are discussed.
Sampling design optimisation for rainfall prediction using a non-stationary geostatistical model
Wadoux, Alexandre M.J.C. ; Brus, Dick J. ; Rico-Ramirez, Miguel A. ; Heuvelink, Gerard B.M. - \ 2017
Advances in Water Resources 107 (2017). - ISSN 0309-1708 - p. 126 - 138.
Geostatistics - Kriging - Non-stationary variance - Radar-gauge merging - Rainfall - Sampling design optimisation - Spatial Simulated Annealing
The accuracy of spatial predictions of rainfall by merging rain-gauge and radar data is partly determined by the sampling design of the rain-gauge network. Optimising the locations of the rain-gauges may increase the accuracy of the predictions. Existing spatial sampling design optimisation methods are based on minimisation of the spatially averaged prediction error variance under the assumption of intrinsic stationarity. Over the past years, substantial progress has been made to deal with non-stationary spatial processes in kriging. Various well-documented geostatistical models relax the assumption of stationarity in the mean, while recent studies show the importance of considering non-stationarity in the variance for environmental processes occurring in complex landscapes. We optimised the sampling locations of rain-gauges using an extension of the Kriging with External Drift (KED) model for prediction of rainfall fields. The model incorporates both non-stationarity in the mean and in the variance, which are modelled as functions of external covariates such as radar imagery, distance to radar station and radar beam blockage. Spatial predictions are made repeatedly over time, each time recalibrating the model. The space-time averaged KED variance was minimised by Spatial Simulated Annealing (SSA). The methodology was tested using a case study predicting daily rainfall in the north of England for a one-year period. Results show that (i) the proposed non-stationary variance model outperforms the stationary variance model, and (ii) a small but significant decrease of the rainfall prediction error variance is obtained with the optimised rain-gauge network. In particular, it pays off to place rain-gauges at locations where the radar imagery is inaccurate, while keeping the distribution over the study area sufficiently uniform.
Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
Pérez-Jaramillo, Juan E. ; Carrión, Víctor J. ; Bosse, Mirte ; Ferrão, Luiz F.V. ; Hollander, Mattias de; Garcia, Antonio Augusto Franco ; Ramírez, Camilo A. ; Mendes, Rodrigo ; Raaijmakers, Jos M. - \ 2017
ISME Journal 11 (2017)10. - ISSN 1751-7362 - p. 2244 - 2257.
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.
Biosynthesis, localization and ecological role of pyrethrins and linked secondary metabolites in pyrethrum
Jongsma, M.A. ; Ramirez, A. - \ 2017
In: 2nd International Symposium on Pyrethrum International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611658 - p. 101 - 111.
The perennial herbaceous plant Tanacetum cinerariifolium, also known as pyrethrum, is a daisy-like flower with an inherent ability to produce considerable amounts of biologically active metabolites, especially pyrethrins, probably intended for self-defence. The discovery of pyrethrin toxicity towards insect pests triggered the exploitation of pyrethrum for commercial purposes in the late 19th century. Despite having a long history of safe and effective use as a source of a versatile botanical insecticide, pyrethrum lost its popularity when, in the mid-20th century, more cost-effective, active and persistent synthetic variants became available. In recent years, a shift in general consumer preferences towards more selective, safer, non-persistent and more environment-friendly pesticides has renewed interest in the use of pyrethrum, renewing pyrethrum's economic significance. Despite the fact that the plant has been under commercial cultivation in many parts of the world for the last 160 years, surprisingly little breeding, ecological and genetic work has been performed to achieve important economic targets of the industry. Increasing the yield of pyrethrins in its natural host, or the mass production of pyrethrins in cultured cells or even a microbial host, would offer new possibilities to the pyrethrin industry that could potentially contribute to placing pyrethrins in a more favourable competitive position in today's insecticide market. Similarly, insights into the biological role of secondary metabolites found in pyrethrum could potentially greatly benefit the economics of the pyrethrum industry. However, in an era in which advanced breeding and genetic modification techniques are not the limiting factor, the lack of basic biochemical information, such as the identification and isolation of key enzymes involved in the formation of pyrethrins and sesquiterpene lactones, constitutes the major hurdle in the genetic engineering of these secondary metabolites, in either the natural host or other species. Genes encoding enzymes involved in the biosynthesis of certain metabolites are expected to be actively transcribed at specific moments and/or specific tissues; hence, the determination of the exact site of accumulation and synthesis of secondary metabolites constitutes a necessary tool to help pick out genes of interest. Developing knowledge around different aspects of pyrethrum secondary metabolism will, therefore, contribute to generating the necessary tools for breeding and/or engineering of varieties with enhanced pyrethrin content and decreased content of unwanted metabolites. Potentially, in the longer run, it will also be possible to engineer the biosynthesis of pyrethrins into other crop species. Ideally, such crops would then no longer require the external application of pesticides to protect them against microbial diseases and pests. Here, we will discuss the most important findings obtained in our lab, ranging from localization and biochemical aspects of the synthesis of pyrethrum defence compounds to their possible biological role in the young emerging seedling as well as in the adult plant.
XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED
Zhao, Chengsong ; Lasses, Theres ; Bako, Laszlo ; Kong, Danyu ; Zhao, Bingyu ; Chanda, Bidisha ; Bombarely, Aureliano ; Cruz-Ramírez, Alfredo ; Scheres, Ben ; Brunner, Amy M. ; Beers, Eric P. - \ 2017
New Phytologist 216 (2017)1. - ISSN 0028-646X - p. 76 - 89.
Arabidopsis thaliana - Angiosperm - Differentiation - LXCXE - NAC domain - Retinoblastoma - Xylem

The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 (XND1) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly conserved C-terminal region containing linear motifs (CKII-acidic, LXCXE, E2FTD-like and LXCXE-mimic) predicted to interact with the cell cycle and differentiation regulator RETINOBLASTOMA-RELATED (RBR). Protein-protein interaction and functional analyses of XND1 deletion mutants were used to test the importance of RBR-interaction motifs. Deletion of either the LXCXE or the LXCXE-mimic motif reduced both the XND1-RBR interaction and XND1 efficacy as a repressor of differentiation, with loss of the LXCXE motif having the strongest negative impacts. The function of the XND1 C-terminal domain could be partially replaced by RBR fused to the N-terminal domain of XND1. XND1 also transactivated gene expression in yeast and plants. The properties of XND1, a transactivator that depends on multiple linear RBR-interaction motifs to inhibit differentiation, have not previously been described for a plant protein. XND1 harbors an apparently angiosperm-specific combination of interaction motifs potentially linking the general differentiation regulator RBR with a xylem-specific pathway for inhibition of differentiation.

MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
Latrasse, David ; Jégu, Teddy ; Li, Huchen ; Zelicourt, Axel de; Raynaud, Cécile ; Legras, Stéphanie ; Gust, Andrea ; Samajova, Olga ; Veluchamy, Alaguraj ; Rayapuram, Naganand ; Ramirez-Prado, Juan Sebastian ; Kulikova, Olga ; Colcombet, Jean ; Bigeard, Jean ; Genot, Baptiste ; Bisseling, Ton ; Benhamed, Moussa ; Hirt, Heribert - \ 2017
Genome Biology 18 (2017)1. - ISSN 1474-7596

Background: Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we determine whether microbial-associated molecular pattern-triggered gene expression involves modifications at the chromatin level. Results: Histone acetylation and deacetylation are major regulators of microbial-associated molecular pattern-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defence gene expression and innate immunity. The MAP kinase MPK3 directly interacts with and phosphorylates HD2B, thereby regulating the intra-nuclear compartmentalization and function of the histone deacetylase. Conclusions: By studying a number of gene loci that undergo microbial-associated molecular pattern-dependent activation or repression, our data reveal a mechanistic model for how protein kinase signaling directly impacts chromatin reprogramming in plant defense.

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