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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.

Tropical Montane Cloud Forests : Hydrometeorological variability in three neighbouring catchments with different forest cover
Ramirez Correal, Beatriz ; Teuling, Adriaan J. ; Ganzeveld, Laurens ; Hegger, Zita ; Leemans, Rik - \ 2017
Journal of Hydrology 552 (2017). - ISSN 0022-1694 - p. 151 - 167.
Andean catchments - Continental Tropical Montane Cloud Forests - Elevation gradients - Orinoco river basin - Streamflow uncertainty - Water balance

Mountain areas are characterized by a large heterogeneity in hydrological and meteorological conditions. This heterogeneity is currently poorly represented by gauging networks and by the coarse scale of global and regional climate and hydrological models. Tropical Montane Cloud Forests (TMCFs) are found in a narrow elevation range and are characterized by persistent fog. Their water balance depends on local and upwind temperatures and moisture, therefore, changes in these parameters will alter TMCF hydrology. Until recently the hydrological functioning of TMCFs was mainly studied in coastal regions, while continental TMCFs were largely ignored. This study contributes to fill this gap by focusing on a TMCF which is located on the northern eastern Andes at an elevation of 1550–2300 m asl, in the Orinoco river basin highlands. In this study, we describe the spatial and seasonal meteorological variability, analyse the corresponding catchment hydrological response to different land cover, and perform a sensitivity analysis on uncertainties related to rainfall interpolation, catchment area estimation and streamflow measurements. Hydro-meteorological measurements, including hourly solar radiation, temperature, relative humidity, wind speed, precipitation, soil moisture and streamflow, were collected from June 2013 to May 2014 at three gauged neighbouring catchments with contrasting TMCF/grassland cover and less than 250 m elevation difference. We found wetter and less seasonally contrasting conditions at higher elevations, indicating a positive relation between elevation and fog or rainfall persistence. This pattern is similar to that of other eastern Andean TMCFs, however, the study site had higher wet season rainfall and lower dry season rainfall suggesting that upwind contrasts in land cover and moisture can influence the meteorological conditions at eastern Andean TMCFs. Contrasting streamflow dynamics between the studied catchments reflect the overall system response as a function of the catchments’ elevation and land cover. The forested catchment, located at the higher elevations, had the highest seasonal streamflows. During the wet season, different land covers at the lower elevations were important in defining the streamflow responses between the deforested catchment and the catchment with intermediate forest cover. Streamflows were higher and the rainfall-runoff responses were faster in the deforested catchment than in the intermediate forest cover catchment. During the dry season, the catchments’ elevation defined streamflows due to higher water inputs and lower evaporative demand at the higher elevations.

Two maize Kip-related proteins differentially interact with, inhibit and are phosphorylated by cyclin D-cyclin-dependent kinase complexes
Godínez-Palma, Silvia K. ; Rosas-Bringas, Fernando R. ; Rosas-Bringas, Omar G. ; García-Ramírez, Elpidio ; Zamora-Zaragoza, Jorge ; Vázquez-Ramos, Jorge M. - \ 2017
Journal of Experimental Botany 68 (2017)7. - ISSN 0022-0957 - p. 1585 - 1597.
CDKs - Cyclins D - ICK/KRPs - Kinase inhibition - KRP phosphorylation - Zea mays

The family of maize Kip-related proteins (KRPs) has been studied and a nomenclature based on the relationship to rice KRP genes is proposed. Expression studies of KRP genes indicate that all are expressed at 24 h of seed germination but expression is differential in the different tissues of maize plantlets. Recombinant KRP1;1 and KRP4;2 proteins, members of different KRP classes, were used to study association to and inhibitory activity on different maize cyclin D (CycD)-cyclin-dependent kinase (CDK) complexes. Kinase activity in CycD2;2-CDK, CycD4;2-CDK, and CycD5;3- CDK complexes was inhibited by both KRPs; however, only KRP1;1 inhibited activity in the CycD6;1-CDK complex, not KRP4;2. Whereas KRP1;1 associated with either CycD2;2 or CycD6;1, and to cyclin-dependent kinase A (CDKA) recombinant proteins, forming ternary complexes, KRP4;2 bound CDKA and CycD2;2 but did not bind CycD6;1, establishing a differential association capacity. All CycD-CDK complexes included here phosphorylated both the retinoblastoma- related (RBR) protein and the two KRPs; interestingly, while KRP4;2 phosphorylated by the CycD2;2-CDK complex increased its inhibitory capacity, when phosphorylated by the CycD6;1-CDK complex the inhibitory capacity was reduced or eliminated. Evidence suggests that the phosphorylated residues in KRP4;2 may be different for every kinase, and this would influence its performance as a cyclin-CDK inhibitor.

On the induction of injury in tomato under continuous light : Circadian asynchrony as the main triggering factor
Velez-Ramirez, Aaron I. ; Dünner-Planella, Gabriela ; Vreugdenhil, Dick ; Millenaar, Frank F. ; Ieperen, Wim Van - \ 2017
Functional Plant Biology 44 (2017)6. - ISSN 1445-4408 - p. 597 - 611.
circadian regulation - light-induced signalling - photodamage - photoinhibition - photoperiod - quantum yield
Unlike other species, when tomato plants (Solanum lycopersicum L.) are deprived of at least 8h of darkness per day, they develop a potentially lethal injury. In an effort to understand why continuous light (CL) is injurious to tomato, we tested five factors, which potentially could be responsible for triggering the injury in CL-grown tomato: (i) differences in the light spectral distribution between sunlight and artificial light, (ii) continuous light signalling, (iii) continuous supply of light for photosynthesis, (iv) continuous photo-oxidative pressure and (v) circadian asynchrony- A mismatch between the internal circadian clock frequency and the external light/dark cycles. Our results strongly suggest that continuous-light-induced injury does not result from the unnatural spectral distribution of artificial light nor from the continuity of light per se. Instead, circadian asynchrony seems to be the main factor inducing the CL-induced injury, but the mechanism is not by the earlier hypothesised circadian pattern in sensitivity for photoinhibition. Here, however, we show for the first time diurnal fluctuations in sensitivity to photoinhibition during normal photoperiods. Similarly, we also report for the first time diurnal and circadian rhythms in the maximum quantum efficiency of PSII (Fv/Fm) and the parameter F0.
The role of belowground plant-microbe interactions in climate change induced range shifts
Ramirez, Kelly ; Snoek, L.B. ; Putten, W.H. van der - \ 2017
Geophysical Research Abstracts 19 (2017). - ISSN 1029-7006
Representing radar rainfall uncertainty with ensembles based on a time-variant geostatistical error modelling approach
Cecinati, Francesca ; Rico-Ramirez, Miguel Angel ; Heuvelink, Gerard B.M. ; Han, Dawei - \ 2017
Journal of Hydrology 548 (2017). - ISSN 0022-1694 - p. 391 - 405.
Conditional simulations - Radar ensemble - Radar QPE error model - Rainfall uncertainty propagation - Time-variant variograms

The application of radar quantitative precipitation estimation (QPE) to hydrology and water quality models can be preferred to interpolated rainfall point measurements because of the wide coverage that radars can provide, together with a good spatio-temporal resolutions. Nonetheless, it is often limited by the proneness of radar QPE to a multitude of errors. Although radar errors have been widely studied and techniques have been developed to correct most of them, residual errors are still intrinsic in radar QPE. An estimation of uncertainty of radar QPE and an assessment of uncertainty propagation in modelling applications is important to quantify the relative importance of the uncertainty associated to radar rainfall input in the overall modelling uncertainty. A suitable tool for this purpose is the generation of radar rainfall ensembles. An ensemble is the representation of the rainfall field and its uncertainty through a collection of possible alternative rainfall fields, produced according to the observed errors, their spatial characteristics, and their probability distribution. The errors are derived from a comparison between radar QPE and ground point measurements. The novelty of the proposed ensemble generator is that it is based on a geostatistical approach that assures a fast and robust generation of synthetic error fields, based on the time-variant characteristics of errors. The method is developed to meet the requirement of operational applications to large datasets. The method is applied to a case study in Northern England, using the UK Met Office NIMROD radar composites at 1 km resolution and at 1 h accumulation on an area of 180 km by 180 km. The errors are estimated using a network of 199 tipping bucket rain gauges from the Environment Agency. 183 of the rain gauges are used for the error modelling, while 16 are kept apart for validation. The validation is done by comparing the radar rainfall ensemble with the values recorded by the validation rain gauges. The validated ensemble is then tested on a hydrological case study, to show the advantage of probabilistic rainfall for uncertainty propagation. The ensemble spread only partially captures the mismatch between the modelled and the observed flow. The residual uncertainty can be attributed to other sources of uncertainty, in particular to model structural uncertainty, parameter identification uncertainty, uncertainty in other inputs, and uncertainty in the observed flow.

Tropical montane cloud forests in the Orinoco river basin: the role of soil organic layers in water storage and release
Ramirez Correal, B.H. ; Ploeg, M.J. van der; Teuling, Adriaan ; Ganzeveld, L.N. ; Leemans, H.B.J. - \ 2017
Geoderma 298 (2017). - ISSN 0016-7061 - p. 14 - 26.
The Tropical Montane Cloud Forest (TMCF) is a hydrologically unique and highly vulnerable ecosystem to changes in land-use and climate. Assessing the impacts of these changes needs to consider soil-water dynamics. In particular, the organic layer and its functioning requires attention because its difference in water retention characteristics and root density compared to the underlying mineral soils. A higher root density and a higher water storage capacity of the organic layer compared to the mineral soils suggests that most nutrient and water uptake occurs in this layer. However, hydraulic properties of mineral soils and their impact on hydrology of TMCFs have been poorly studied. Here we provide organic layer water retention curves for TMCF soils that were measured in the laboratory. With these data we assessed the potential land-use and climate change impacts on TMCF soil moisture dynamics. From the land-use change perspective, we estimated the water storage capacity loss by slash-and-burn deforestation practices. These estimates show that the storage loss ranges from 35 to 59 mm when TMCFs are converted to pastures. This is several times higher than the estimated TMCF canopy storage capacity (2 to 5 mm). Therefore, the higher peak flow observations in deforested catchments might not only be explained by a decreasing canopy water storage but also likely due to a decreasing soil water storage. From the climate change perspective, we evaluated the effect of contrasting dry season conditions on soil moisture and transpiration using a 1-D water-flow model, and assessed the sensitivity of these hydrological variables to uncertainties in saturated hydraulic conductivity. Although transpiration was not limited by soil moisture during the mild dry season, it was affected during the severe dry season and continued to decline under expected climate change with the prolongation of dry spells. Our results show that the organic layer is a key element in TMCF's hydrological functioning and call for an increased focus on the role of organic soils when evaluating effects of land-use change.
The role of native and range-expanding plant communities in buffering the effects of drought on soil functioning
Manrubia Freixa, Marta ; Ramirez, K.S. ; Geisen, Stefan ; Weser, Carolin ; Hooven, F.C. Ten; Veen, C. ; Putten, W.H. van der - \ 2017
Climate change is altering the composition of plant communities at high altitudes and latitudes by enhanced extreme events, range shifts and de-coupling of co-evolved trophic interactions. Previous research has shown that invasive plant species and abiotic stressors can change carbon and nutrient cycling at local scales. However, it remains unclear whether novel communities formed by range-expanding plant species also alter soil functions in the new ranges and what roles enhanced incidence of drought stress play in these novel communities. We tested the hypothesis that plant species that shift range from southern to northern Europe have greater resistance and resilience under extreme drought events, especially in the presence of southern soil communities.
Plant communities of range-expanding and related native species were planted in a multi-year mesocosm experiment outside. In 2016, we applied a 6-week summer drought to half of the mesocosms. Soil samples were collected before, during and after drought. We measured the functioning of soil communities (e.g. litter decomposition, carbon mineralization and soil enzymatic activities) to quantify their resistance and resilience to drought stress. Our results assess the interactions of plant range-expansion and drought stress on key ecosystem processes. Results will be presented and we will discuss how effects of climate change may interact with effects of range shifts.
Nutrition for the ageing brain: Towards evidence for an optimal diet
Vauzour, David ; Camprubi-Robles, Maria ; Miquel-Kergoat, Sophie ; Andres-Lacueva, Cristina ; Bánáti, Diána ; Barberger-Gateau, Pascale ; Bowman, Gene L. ; Caberlotto, Laura ; Clarke, Robert ; Hogervorst, Eef ; Kiliaan, Amanda J. ; Lucca, Ugo ; Manach, Claudine ; Minihane, Anne-Marie ; Mitchell, Ellen Siobhan ; Perneczky, Robert ; Perry, Hugh ; Roussel, Anne-Marie ; Schuermans, Jeroen ; Sijben, John ; Spencer, Jeremy P.E. ; Thuret, Sandrine ; De Rest, Ondine Van; Vandewoude, Maurits ; Wesnes, Keith ; Williams, Robert J. ; Williams, Robin S.B. ; Ramirez, Maria - \ 2017
Ageing Research Reviews 35 (2017). - ISSN 1568-1637 - p. 222 - 240.
As people age they become increasingly susceptible to chronic and extremely debilitating brain diseases. The precise cause of the neuronal degeneration underlying these disorders, and indeed normal brain ageing remains however elusive. Considering the limits of existing preventive methods, there is a desire to develop effective and safe strategies. Growing preclinical and clinical research in healthy individuals or at the early stage of cognitive decline has demonstrated the beneficial impact of nutrition on cognitive functions. The present review is the most recent in a series produced by the Nutrition and Mental Performance Task Force under the auspice of the International Life Sciences Institute Europe (ILSI Europe). The latest scientific advances specific to how dietary nutrients and non-nutrient may affect cognitive ageing are presented. Furthermore, several key points related to mechanisms contributing to brain ageing, pathological conditions affecting brain function, and brain biomarkers are also discussed. Overall, findings are inconsistent and fragmented and more research is warranted to determine the underlying mechanisms and to establish dose-response relationships for optimal brain maintenance in different population subgroups. Such approaches are likely to provide the necessary evidence to develop research portfolios that will inform about new dietary recommendations on how to prevent cognitive decline.
Quantitative assessment of viable cells of Lactobacillus plantarum strains in single, dual and multi-strain biofilms
Fernández Ramírez, Mónica D. ; Kostopoulos, Ioannis ; Smid, Eddy J. ; Nierop Groot, Masja N. ; Abee, Tjakko - \ 2017
International Journal of Food Microbiology 244 (2017). - ISSN 0168-1605 - p. 43 - 51.
Biofilm coculture - Competition - Food spoilage
Biofilms of Lactobacillus plantarum are a potential source for contamination and recontamination of food products. Although biofilms have been mostly studied using single species or even single strains, it is conceivable that in a range of environmental settings including food processing areas, biofilms are composed of multiple species with each species represented by multiple strains. In this study six spoilage related L. plantarum strains FBR1-FBR6 and the model strain L. plantarum WCFS1 were characterised in single, dual and multiple strain competition models. A quantitative PCR approach was used with added propidium monoazide (PMA) enabling quantification of intact cells in the biofilm, representing the viable cell fraction that determines the food spoilage risk. Our results show that the performance of individual strains in multi-strain cultures generally correlates with their performance in pure culture, and relative strain abundance in multi-strain biofilms positively correlated with the relative strain abundance in suspended (planktonic) cultures. Performance of individual strains in dual-strain biofilms was highly influenced by the presence of the secondary strain, and in most cases no correlation between the relative contributions of viable planktonic cells and viable cells in the biofilm was noted. The total biofilm quantified by CV staining of the dual and multi-strain biofilms formed was mainly correlated to CV values of the dominant strain obtained in single strain studies. However, the combination of strain FBR5 and strain WCFS1 showed significantly higher CV values compared to the individual performances of both strains indicating that total biofilm formation was higher in this specific condition. Notably, L. plantarum FBR5 was able to outgrow all other strains and showed the highest relative abundance in dual and multi-strain biofilms. All the dual and multi-strain biofilms contained a considerable number of viable cells, representing a potential source of contamination.
Directed dispersal by an abiotic vector : Wetland plants disperse their seeds selectively to suitable sites along the hydrological gradient via water
Soons, Merel B. ; Groot, Arjen de; Cuesta Ramirez, M.T. ; Fraaije, Rob G.A. ; Verhoeven, Jos T.A. ; Jager, Monique de - \ 2017
Functional Ecology 31 (2017)2. - ISSN 0269-8463 - p. 499 - 508.
Anemochory - Biodiversity - Evolutionary adaptations - Hydrochory - Hydrological niche - Plant functional traits - Riparian zones - Seed dispersal - Water dispersal - Wind dispersal
Plant species around the world invest in seed dispersal by producing large numbers of seeds, with a wide range of morphological adaptations that facilitate dispersal. Not all dispersed seeds reach suitable sites, however, and plants can significantly improve their fitness by increasing the proportion of seeds arriving at suitable sites for germination and establishment. Disproportionate dispersal to suitable sites is known as 'directed dispersal'. Yet, mechanisms of directed dispersal are only known for a limited number of animal-dispersed plant species. We tested the hypothesis that directed dispersal can also be driven by abiotic vectors, such as water or wind. We used a tiered approach, combining analyses of experimental, field and literature data on wetland plant species and evaluating the potential for evolution of directed dispersal with a spatially explicit individual-based model. The data collected demonstrate that wetland plants produce seeds with adaptations to promote transportation and deposition by water towards microsites along the hydrological gradient where they germinate and establish best. Aquatic species produce seeds that sink and are transported by water as bed load towards inundated sites. In contrast, shoreline species produce seeds that float for very long periods of time so that they are eventually entrapped by shoreline vegetation or deposited at the waterline. Our model simulations confirm that the patterns we observed in nature can evolve under natural selection through adaptations in seed buoyancy. For wind dispersal, the situation is more complex. Wind does not provide directed dispersal in the strictest sense but, rather, simply appears to be the best available dispersal vector for more terrestrial wetland plant species to reach drier areas in a wet environment. Synthesis. We show that directed dispersal towards specific, suitable microsites is not exclusive to animal-dispersed plant species, but may be far more common in plants - also in species dispersed by abiotic vectors, in particular water. As water and wind are very common dispersal vectors throughout the plant kingdom, directed dispersal (and not just dispersal distance) seems to be of general importance for the ecology of plants.
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.
Data from: Origins of food crops connect countries worldwide
Khoury, C.K. ; Achicanoy, Harold A. ; Bjorkman, Anne D. ; Navarro-Racines, Carlos ; Guarino, Luigi ; Flores-Palacios, Ximena ; Engels, Johannes M.M. ; Wiersema, John H. ; Dempewolf, Hannes ; Sotelo, Steven ; Ramírez-Villegas, Julian ; Castañeda-Álvarez, Nora P. ; Fowler, Cary ; Jarvis, Andy ; Rieseberg, Loren H. ; Struik, P.C. - \ 2016
food security - crop diversity - crop origins - plant genetic resources - crop domestication - crop improvement
Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.
Draft whole-genome sequences of three Lactobacillus plantarum food isolates
Fernandez Ramirez, Monica ; Boekhorst, Jos ; Jong, Anne de; Kuipers, Oscar P. ; Abee, Tjakko ; Nierop Groot, Masja - \ 2016
Genome Announcements 4 (2016)3. - ISSN 2169-8287
Lactobacillus plantarum is a widespread member of the Lactobacillus genus and frequently isolated from spoiled acidified food products. Here, we report the draft genome sequences of three L. plantarum food isolates.
Explanatory note accompanying the database for standardized biomass characterization (and minimal biomass quality requirement for each biomass conversion technology)
Elbersen, H.W. ; Alakangas, E. ; Elbersen, B.S. ; Annevelink, E. ; Ramirez Almeyda, Jacqueline ; Lammens, T.M. - \ 2016
S2Biom - 31 p.
The S2Biom project - Delivery of sustainable supply of non-food biomass to support a
“resource-efficient” Bioeconomy in Europe - supports the sustainable delivery of nonfood
biomass feedstock at local, regional and pan European level through developing
strategies, and roadmaps that will be informed by a “computerized and easy to use”
toolset (and respective databases) with updated harmonized datasets at local,
regional, national and pan European level for EU28, Western Balkans, Moldova,
Turkey and Ukraine.
The genus Amanita should not be split
Tulloss, R.E. ; Kuijper, T.W.M. ; Vellinga, E.C. ; Yang, Z.L. ; Halling, Roy E. ; Geml, J. ; Sanchez-Ramirez, S. ; Goncalves, S.C. ; Hess, J. ; Pringle, A. - \ 2016
Amanitaceae 1 (2016)3. - ISSN 2331-7612 - p. 1 - 16.
Recently the well-known genus Amanita has been split into two genera, Amanita, a genus of putatively
ectomycorrhizal fungi, and Saproamanita, a genus of putatively saprotrophic fungi. We disagree with this generic
split and argue why Amanita should not be split. The proposal to split the genus does not conform to the recently proposed
guidelines for publishing new genera. Concise amended characterizations are provided for the monophyletic
family Amanitaceae and its two monophyletic genera Amanita and Limacella.2 The characterization of Amanita rests
on a single, unique synapomorphy—schizohymenial ontogeny in its agaricoid and secotioid taxa. We propose a minimal
reorganization of Amanita—removal of stirps Hesleri from subsection Vittadiniae. Some open issues in Amanita
systematics are discussed. Amanita is an emblematic genus and the focus of diverse research programs.
Taxonomists and users of taxonomic and systematic products are used to, and rely on, Amanita as a genus with meaningful,
morphologically defined subdivisions, easy to teach and easy to use. Splitting the genus is unnecessary and
would prove costly—degrading our ability to communicate with each other and complicating connections to past literature.
We argue that the current use of next-generation sequencing in studies of fungal ecology does not necessitate
the splitting of Amanita.
Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana
Lozano-Sotomayor, Paulina ; Chávez Montes, Ricardo A. ; Silvestre-Vañó, Marina ; Herrera-Ubaldo, Humberto ; Greco, Raffaella ; Pablo-Villa, Jeanneth ; Galliani, Bianca M. ; Diaz-Ramirez, David ; Weemen, Mieke ; Boutilier, Kim - \ 2016
The Plant Journal 88 (2016)3. - ISSN 0960-7412 - p. 437 - 451.
Arabidopsis thaliana - bZIP transcription factor - bZIP30 - DRINK ME - growth - meristem activity - reproductive development

Here we describe an uncharacterized gene that negatively influences Arabidopsis growth and reproductive development. DRINK ME (DKM; bZIP30) is a member of the bZIP transcription factor family, and is expressed in meristematic tissues such as the inflorescence meristem (IM), floral meristem (FM), and carpel margin meristem (CMM). Altered DKM expression affects meristematic tissues and reproductive organ development, including the gynoecium, which is the female reproductive structure and is determinant for fertility and sexual reproduction. A microarray analysis indicates that DKM overexpression affects the expression of cell cycle, cell wall, organ initiation, cell elongation, hormone homeostasis, and meristem activity genes. Furthermore, DKM can interact in yeast and in planta with proteins involved in shoot apical meristem maintenance such as WUSCHEL, KNAT1/BP, KNAT2 and JAIBA, and with proteins involved in medial tissue development in the gynoecium such as HECATE, BELL1 and NGATHA1. Taken together, our results highlight the relevance of DKM as a negative modulator of Arabidopsis growth and reproductive development.

Characterisation of Lactobacillus plantarum single and multi-strain biofilms
Fernández Ramírez, Mónica D. - \ 2016
Wageningen University. Promotor(en): Tjakko Abee; E.J. Smid, co-promotor(en): Masja Nierop Groot. - Wageningen : Wageningen University - ISBN 9789462579217 - 169
lactobacillus plantarum - biofilms - food spoilage - models - environmental factors - lactobacillus plantarum - biofilms - voedselbederf - modellen - milieufactoren

Biofilms consist of microorganisms attached to a surface and embedded in a protective matrix of extracellular polymeric substances. Within a biofilm, micro-organisms are protected from harsh environmental conditions including those resulting from cleaning and disinfecting agents leading to food safety and quality issues after dispersal of life biofilm cells and subsequent contamination of foods. In this thesis, single and multi-strain biofilm formation by Lactobacillus plantarum isolates was characterised including the model strain L. plantarum WCFS1 and food spoilage isolates. Analysis of the L. plantarum single strain biofilm formation showed a role for proteins and/or proteinaceous material in surface colonization and extracellular DNA as components of the biofilm matrix. The relevance of lysis for the build-up of the biofilm matrix with eDNA was demonstrated using L. plantarum WCFS1 mutants affected in the production of cell wall polysaccharides resulting in altered cell surface composition and mutants lacking cell wall lytic enzymes that showed decreased cell lysis. Dual and multi-strain biofilms were studied using quantitative PCR and next generation sequencing based on detection of strain specific alleles in competitive planktonic and surface-attached biofilm growth models. In multi-strain cultures, the performance of individual strains generally correlated with their performance in pure culture, and relative strain abundance in multi-strain static biofilms positively correlated with the relative strain abundance in suspended (planktonic) cultures. Performance of individual strains in dual-strain biofilms was highly influenced by the presence of the secondary strain, and in most cases no correlation between the relative contributions of viable planktonic cells and viable cells in the biofilm was noted. The next generation sequencing approach provided additional insights in the performance of twelve individual L. plantarum strains in static and dynamic flow competitive biofilm models and showed that environmental stresses such as absence of Mn(II) and increased temperature affected not only the relative abundance of each strain both in planktonic and static biofilm growth but also the release of eDNA. The strains dominating the biofilms in static conditions were not the same as those dominating in biofilms developed in dynamic flowing conditions. The genome content of the dominating strains was explored to identify genetic factors that potentially contribute to strain specific competitive-biofilm forming capacity under dynamic flowing conditions, providing leads for further research. All the single, dual and multi-strain biofilms contained a considerable number of viable L. plantarum cells, representing a potential source of contamination. The developed tools and insights obtained in L. plantarum biofilm formation capacity may assist development of strategies to prevent (re)contamination from biofilms in food processing environments.

Variation in stem mortality rates determines patterns of above-ground biomass in Amazonian forests: implications for dynamic global vegetation models
Johnson, Michelle O. ; Galbraith, David ; Gloor, Manuel ; Deurwaerder, Hannes De; Guimberteau, Matthieu ; Rammig, Anja ; Thonicke, Kirsten ; Verbeeck, Hans ; Randow, Celso Von; Monteagudo, Abel ; Phillips, Oliver L. ; Brienen, Roel J.W. ; Feldpausch, Ted R. ; Lopez Gonzalez, Gabriela ; Fauset, Sophie ; Quesada, Carlos A. ; Christoffersen, Bradley ; Ciais, Philippe ; Sampaio, Gilvan ; Kruijt, Bart ; Meir, Patrick ; Moorcroft, Paul ; Zhang, Ke ; Alvarez-Davila, Esteban ; Alves De Oliveira, Atila ; Amaral, Ieda ; Andrade, Ana ; Aragao, Luiz E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmila ; Aymard, Gerardo A. ; Baraloto, Christopher ; Barroso, Jocely ; Bonal, Damien ; Boot, Rene ; Camargo, Jose ; Chave, Jerome ; Cogollo, Alvaro ; Cornejo Valverde, Fernando ; Lola Da Costa, Antonio C. ; Fiore, Anthony Di; Ferreira, Leandro ; Higuchi, Niro ; Honorio, Euridice N. ; Killeen, Tim J. ; Laurance, Susan G. ; Laurance, William F. ; Licona, Juan ; Lovejoy, Thomas ; Malhi, Yadvinder ; Marimon, Bia ; Marimon, Ben Hur ; Matos, Darley C.L. ; Mendoza, Casimiro ; Neill, David A. ; Pardo, Guido ; Peña-Claros, Marielos ; Pitman, Nigel C.A. ; Poorter, Lourens ; Prieto, Adriana ; Ramirez-Angulo, Hirma ; Roopsind, Anand ; Rudas, Agustin ; Salomao, Rafael P. ; Silveira, Marcos ; Stropp, Juliana ; Steege, Hans Ter; Terborgh, John ; Thomas, Raquel ; Toledo, Marisol ; Torres-Lezama, Armando ; Heijden, Geertje M.F. van der; Vasquez, Rodolfo ; Guimarães Vieira, Ima Cèlia ; Vilanova, Emilio ; Vos, Vincent A. ; Baker, Timothy R. - \ 2016
Global Change Biology 22 (2016)12. - ISSN 1354-1013 - p. 3996 - 4013.
Understanding the processes that determine aboveground biomass (AGB) in Amazonian forests is important for predicting the sensitivity of these ecosystems to environmental change and for designing and evaluating dynamic global vegetation models (DGVMs). AGB is determined by inputs from woody productivity (woody NPP) and the rate at which carbon is lost through tree mortality. Here, we test whether two direct metrics of tree mortality (the absolute rate of woody biomass loss and the rate of stem mortality) and/or woody NPP, control variation in AGB among 167 plots in intact forest across Amazonia. We then compare these relationships and the observed variation in AGB and woody NPP with the predictions of four DGVMs. The observations show that stem mortality rates, rather than absolute rates of woody biomass loss, are the most important predictor of AGB, which is consistent with the importance of stand size-structure for determining spatial variation in AGB. The relationship between stem mortality rates and AGB varies among different regions of Amazonia, indicating that variation in wood density and height/diameter relationships also influence AGB. In contrast to previous findings, we find that woody NPP is not correlated with stem mortality rates, and is weakly positively correlated with AGB. Across the four models, basin-wide average AGB is similar to the mean of the observations. However, the models consistently overestimate woody NPP, and poorly represent the spatial patterns of both AGB and woody NPP estimated using plot data. In marked contrast to the observations, DGVMs typically show strong positive relationships between woody NPP and AGB. Resolving these differences will require incorporating forest size structure, mechanistic models of stem mortality and variation in functional composition in DGVMs
Global conservation priorities for crop wild relatives
Castañeda-Álvarez, Nora P. ; Khoury, Colin K. ; Achicanoy, Harold A. ; Bernau, Vivian ; Dempewolf, Hannes ; Eastwood, Ruth J. ; Guarino, Luigi ; Harker, Ruth H. ; Jarvis, Andy ; Maxted, Nigel ; Müller, Jonas V. ; Ramirez-Villegas, Julian ; Sosa, Chrystian C. ; Struik, Paul C. ; Vincent, Holly ; Toll, Jane - \ 2016
Nature Plants 2 (2016)4. - ISSN 2055-026X

The wild relatives of domesticated crops possess genetic diversity useful for developing more productive, nutritious and resilient crop varieties. However, their conservation status and availability for utilization are a concern, and have not been quantified globally. Here, we model the global distribution of 1,076 taxa related to 81 crops, using occurrence information collected from biodiversity, herbarium and gene bank databases. We compare the potential geographic and ecological diversity encompassed in these distributions with that currently accessible in gene banks, as a means to estimate the comprehensiveness of the conservation of genetic diversity. Our results indicate that the diversity of crop wild relatives is poorly represented in gene banks. For 313 (29.1% of total) taxa associated with 63 crops, no germplasm accessions exist, and a further 257 (23.9%) are represented by fewer than ten accessions. Over 70% of taxa are identified as high priority for further collecting in order to improve their representation in gene banks, and over 95% are insufficiently represented in regard to the full range of geographic and ecological variation in their native distributions. The most critical collecting gaps occur in the Mediterranean and the Near East, western and southern Europe, Southeast and East Asia, and South America. We conclude that a systematic effort is needed to improve the conservation and availability of crop wild relatives for use in plant breeding.

3D-liquid chromatography as a complex mixture characterization tool for knowledge-based downstream process development.
Hanke, A.T. ; Tsintavi, E. ; Pilar Ramirez Vazquez, M. Del; Wielen, L.A.M. van der; Verhaert, P.D.E.M. ; Sandt, E.J.A.X. van de; Eppink, M.H.M. ; Ottens, M. - \ 2016
Biotechnology Progress 32 (2016)5. - ISSN 8756-7938 - p. 1283 - 1291.
Knowledge-based development of chromatographic separation processes requires efficient techniques to determine the physicochemical properties of the product and the impurities to be removed. These characterization techniques are usually divided into approaches that determine molecular properties, such as charge, hydrophobicity and size, or molecular interactions with auxiliary materials, commonly in the form of adsorption isotherms. In this study we demonstrate the application of a three-dimensional liquid chromatography approach to a clarified cell homogenate containing a therapeutic enzyme. Each separation dimension determines a molecular property relevant to the chromatographic behaviour of each component. Matching of the peaks across the different separation dimensions and against a high-resolution reference chromatogram allows to assign the determined parameters to pseudo-components, allowing to determine the most promising technique for the removal of each impurity. More detailed process design using mechanistic models requires isotherm parameters. For this purpose, the second dimension consists of multiple linear gradient separations on columns in a high-throughput screening compatible format, that allow regression of isotherm parameters with an average standard error of 8%. This article is protected by copyright. All rights reserved.
Origins of food crops connect countries worldwide
Khoury, Colin K. ; Achicanoy, Harold A. ; Bjorkman, Anne D. ; Navarro-Racines, Carlos ; Guarino, Luigi ; Flores-Palacios, Ximena ; Engels, Johannes M.M. ; Wiersema, John H. ; Dempewolf, Hannes ; Sotelo, Steven ; Ramírez-Villegas, Julian ; Castañeda-Álvarez, Nora P. ; Fowler, Cary ; Jarvis, Andy ; Rieseberg, Loren H. ; Struik, Paul C. - \ 2016
Proceedings of the Royal Society. B: Biological Sciences 283 (2016)1832. - ISSN 0962-8452 - 9 p.
Crop diversity - Crop domestication - Crop improvement - Crop origins - Food security - Plant genetic resources

Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins ('primary regions of diversity') of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own ('foreign crops'), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.

Conceptual design of sustainable integrated microalgae biorefineries: Parametric analysis of energy use, greenhouse gas emissions and techno-economics
Posada, John ; Brentner, Laura ; Ramirez, Andrea ; Patel, Martin - \ 2016
Algal Research 17 (2016). - ISSN 2211-9264 - p. 113 - 131.
This study covers four main aspects of the conceptual design of sustainable integrated microalgae-based biorefineries using flue gas from CO2-intensive industries (i.e. 100% CO2): i) screening of technologies (4 options for cultivation, 3 for culture dewatering, 3 for cell disruption, 4 for lipids extraction & purification, and 4 for fractions upgrading); ii) analysis of processing variables (parametric study of the main cultivation conditions affecting the global performance of the biorefinery systems); iii) combination of final products (10 biorefinery configurations are generated from the combination of 9 final products); and iv) assessment of sustainability criteria (i.e., non-renewable energy use (NREU), greenhouse gas (GHG) emissions and economics). The used approach compares processing options and operation conditions to identify those combinations of production processes that minimize NREU and GHG emissions. In a second step, 10 integrated biorefinery concepts are selected and compared with respect to their environmental and economic performances. The impacts of choosing different microalgae species, locations, and nutrient sources were also studied as part of the scenario analysis. The results showed that the biorefinery systems with the best economic and environmental performances are those where microalgae oil-free cake is used as nutrient for substitution of animal feed and where lipids are used for substitution of vegetable oils. The worst economic and environmental performances of biorefineries were obtained when microalgae oil-free cake is anaerobically digested to biogas and lipids are converted to either biodiesel or green diesel. Regarding the cultivation technologies for the biorefinery systems with the best performance, favorable environmental results were obtained for flat panel photobioreactors (FPPBRs), followed by open ponds (OPs), vertical photobioreactors (VPBRs) and horizontal photobioreactors (HPBRs). In contrast, the best economic results were found for FPPBRs followed by VPBRs, HPBRs and OPs.
Global soil biodiversity atlas
Orgiazzi, A. ; Bardgett, R.D. ; Barrios, E. ; Behan-Pelletier, V. ; Briones, M.J.I. ; Chotte, J.L. ; Deyn, G.B. de; Eggleton, P. ; Fierer, N. ; Fraser, T. ; Hedlund, K. ; Jeffery, S. ; Johnson, N.C. ; Jones, A. ; Kandeler, E. ; Kaneko, N. ; Lavelle, P. ; Lemanceau, P. ; Miko, L. ; Montanarella, L. ; Moreira, F.M.S. ; Ramirez, K.S. ; Scheu, S. ; Singh, B.K. ; Six, J. ; Putten, W.H. van der; Wall, D.H. - \ 2016
Luxembourg : European Union (EUR ) - ISBN 9789279481697 - 176 p.
The IsoButanol Rotterdam Platform Project
Dijkstra, J.W.H. ; Straathof, A.J.J. ; Lopez Contreras, A.M. ; Zirkzee, H. ; Wermink, W. ; Ramirez-Ramirez, A. ; Hal, J.W. van - \ 2016
A resource efficiency assessment of the industrial mushroom production chain : The influence of data variability
Zisopoulos, Filippos K. ; Becerra Ramírez, Henry A. ; Goot, Atze Jan van der; Boom, Remko M. - \ 2016
Journal of Cleaner Production 126 (2016). - ISSN 0959-6526 - p. 394 - 408.
Exergy analysis - Food industry - Recycling - Sustainability

We compare the exergetic performance of a conventional industrial mushroom production chain with a mushroom production chain where part of the compost waste is recycled and reused as raw material. The critical exergy loss points (CEPs) identified are the cooking-out process of the spent mushroom substrate, and the phase I composting process which are related to chemical and physical exergy losses, respectively. The total exergy input requirements for the conventional chain are higher (24 GJ per three flushes of mushrooms) than for the alternative chain (17 GJ per three flushes of mushrooms) since more raw materials are required. The largest exergy losses are due to unclosed material balances, i.e. chemical exergy losses, which represent 69% of the total exergy losses for the conventional chain, and 56% for the alternative production chain. Therefore, it only makes sense to reduce any avoidable physical exergy losses after utilizing all mass streams maximally that translate into chemical exergy flows. Further comparison of exergetic indicators (e.g. specific exergy losses, and exergetic cost) shows that recycling material streams would improve the resource efficiency of the industrial mushroom production chain considerably. The variations in the assumed electricity consumption values for the ventilation in phase I composting and for the ammonia scrubbing process affect greatly the exergetic indicators and the number of critical exergy loss points indicating that any further improvement on the exergetic performance of the mushroom production chain should focus on these two process variables. This study shows that variability in data can influence both quantitatively and qualitatively the outcome of exergetic analyses of food production chains since it can lead to the calculation of different values for the selected indicators as well as to the identification of completely different critical exergy loss points.

QTL mapping and breeding value estimation through pedigree-based analysis of fruit size and weight in four diverse peach breeding programs
Fresnedo-Ramírez, Jonathan ; Frett, Terrence J. ; Sandefur, Paul J. ; Bink, Marco C.A.M. ; Weg, Eric van de - \ 2016
Tree Genetics and Genomes 12 (2016)2. - ISSN 1614-2942
Breeding germplasm diversity - Complex traits - Dominance - Prunus persica (L.) Batsch - “Orange Cling”

The narrow genetic base of peach (Prunus persica L. Batsch) challenges efforts to accurately dissect the genetic architecture of complex traits. Standardized phenotypic assessment of pedigree-linked breeding germplasm and new molecular strategies and analytical approaches developed and conducted during the RosBREED project for enabling marker-assisted breeding (MAB) in Rosaceae crops has overcome several aspects of this challenge. The genetic underpinnings of fruit size (fruit equatorial diameter (FD)) and weight (fresh weight (FW)), two most important components of yield, were investigated using the pedigree-based analysis (PBA) approach under a Bayesian framework which has emerged as an alternative strategy to study the genetics of quantitative traits within diverse breeding germplasm across breeding programs. In this study, a complex pedigree with the common founder “Orange Cling” was identified and FD and FW data from 2011 and 2012 analyzed. A genetic model including genetic additive and dominance effects was considered, and its robustness was evaluated by using various prior and initial values in the Markov chain Monte Carlo procedure. Five QTLs were identified which accounted for up to 29 and 17 % of the phenotypic variation for FD and FW, respectively. Additionally, genomic breeding values were obtained for both traits, with accuracies >85 %. This approach serves as a model study for performing PBA across diverse pedigrees. By incorporating multiple breeding programs, the method and results presented support and highlight the ability of this strategy to identify genomic resources as targets for DNA marker development and subsequent MAB within each program.

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.

CCoAOMT down-regulation activates anthocyanin biosynthesis in petunia
Shaipulah, N.F.M. ; Muhlemann, Joëlle K. ; Woodworth, Benjamin D. ; Moerkercke, Alex Van; Verdonk, J.C. ; Ramirez, A.A. ; Haring, Michel A. ; Dudareva, Natalia ; Schuurink, Robert C. - \ 2016
Plant Physiology 170 (2016)2. - ISSN 0032-0889 - p. 717 - 731.

Anthocyanins and volatile phenylpropenes (isoeugenol and eugenol) in petunia (Petunia hybrida) flowers have the precursor 4-coumaryl coenzyme A (CoA) in common. These phenolics are produced at different stages during flower development. Anthocyanins are synthesized during early stages of flower development and sequestered in vacuoles during the lifespan of the flowers. The production of isoeugenol and eugenol starts when flowers open and peaks after anthesis. To elucidate additional biochemical steps toward (iso)eugenol production, we cloned and characterized a caffeoyl-coenzyme A O-methyltransferase (PhCCoAOMT1) from the petals of the fragrant petunia ‘Mitchell’. Recombinant PhCCoAOMT1 indeed catalyzed the methylation of caffeoyl-CoA to produce feruloyl CoA. Silencing of PhCCoAOMT1 resulted in a reduction of eugenol production but not of isoeugenol. Unexpectedly, the transgenic plants had purple-colored leaves and pink flowers, despite the fact that cv Mitchell lacks the functional R2R3-MYB master regulator ANTHOCYANIN2 and has normally white flowers. Our results indicate that down-regulation of PhCCoAOMT1 activated the anthocyanin pathway through the R2R3-MYBs PURPLE HAZE (PHZ) and DEEP PURPLE, with predominantly petunidin accumulating. Feeding cv Mitchell flowers with caffeic acid induced PHZ expression, suggesting that the metabolic perturbation of the phenylpropanoid pathway underlies the activation of the anthocyanin pathway. Our results demonstrate a role for PhCCoAOMT1 in phenylpropene production and reveal a link between PhCCoAOMT1 and anthocyanin production.

Gender Systems and Women’s Labor Force Participation in the Salmon Industry in Chiloé, Chile
Ramirez, Eduardo ; Ruben, R. - \ 2015
World Development 73 (2015). - ISSN 0305-750X - p. 96 - 104.
This paper, which follows the emergence of the salmon industry in the 1990s in Chiloé, Chile, demonstrates that factors restricting women’s participation in labor force and wage differences between women and men are related to the gender systems operating in Chiloe. Results indicate that these systems reflect the territory’s demographic and agrarian history and that local gender systems have a positive influence on women’s participation in the labor market, though this is not accompanied by decreased salary discrimination in the salmon industry. The implication is that territory-specific and gender factors must be considered in national employment policies.
A survey of preharvest conditions affecting the regulation of water loss during vase life
Fanourakis, D. ; Velez-Ramirez, A.I. ; In, B.C. ; Barendse, H. ; Meeteren, U. van; Woltering, E.J. - \ 2015
In: Acta Horticulturae International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462610552 - p. 195 - 204.
Air humidity - Air velocity - Continuous light - Cut rose - Preharvest - Stomatal responsiveness - Vase life evaluation

Vase life (VL) tests on cut roses obtained from commercial sources were conducted at FloraHolland. Water stress symptoms were the most important criterion terminating VL in 46 out of 50 assessed cultivars. These symptoms appear when water loss exceeds water uptake. Inadequate control of water loss during postharvest period, therefore, limits VL. Here we review the link between preharvest conditions and the control of water loss in the postharvest phase, and discuss how the VL evaluation protocol may affect the outcome. Key cultivation-related environmental factors affecting the stomatal functionality are a low evaporative demand, as a result of either high air humidity or low air velocity, and continuous light (CL). Low evaporative demand weakens stomatal functionality considerably more than CL; the combination of both factors is detrimental. Reduced foliar abscisic acid concentration underlies the attenuated stomatal responsiveness following cultivation under either condition. For a given batch of roses the incidence of water stress symptoms during the VL may be either accelerated or delayed depending on the evaluation protocol. For instance, assessing the effect of high humidity during growth by using long stems with several leaves leads to short VL, but when e.g., short stem roses are evaluated VL may not be affected. This resulting shift in both the phenotype and the relationship between phenotype and preharvest conditions highlights the necessity for common standards in VL analysis. Although our understanding of how preharvest conditions induce adverse water relations during VL has developed significantly, the gap between phenotype and genotype remains particularly large.

Arabidopsis BIRD zinc finger proteins jointly stabilize tissue boundaries by confining the cell fate regulator SHORT-ROOT and contributing to fate specification
Long, Yuchen ; Smet, Wouter ; Cruz-Ramírez, Alfredo ; Sanchez Perez, Gabino ; Scheres, Ben ; Blilou, Ikram - \ 2015
The Plant Cell 27 (2015)4. - ISSN 1040-4651 - p. 1185 - 1199.

Plant cells cannot rearrange their positions; therefore, sharp tissue boundaries must be accurately programmed. Movement of the cell fate regulator SHORT-ROOT from the stele to the ground tissue has been associated with transferring positional information across tissue boundaries. The zinc finger BIRD protein JACKDAW has been shown to constrain SHORT-ROOT movement to a single layer, and other BIRD family proteins were postulated to counteract JACKDAWs role in restricting SHORT-ROOT action range. Here, we report that regulation of SHORT-ROOT movement requires additional BIRD proteins whose action is critical for the establishment and maintenance of the boundary between stele and ground tissue. We show that BIRD proteins act in concert and not in opposition. The exploitation of asymmetric redundancies allows the separation of two BIRD functions: constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6. Our data indicate that BIRD proteins promote formative divisions and tissue specification in the Arabidopsis thaliana root meristem ground tissue by tethering and regulating transcriptional competence of SHORT-ROOT complexes. As a result, a tissue boundary is not “locked in” after initial patterning like in many animal systems, but possesses considerable developmental plasticity due to continuous reliance on mobile transcription factors.

The re-organization of belowground microbial communities under range shifting plant species
Ramirez, K.S. ; Snoek, L.B. ; Bloem, J. ; Putten, W.H. van der - \ 2015
Range expanding plant species establishing in the new range: are the effects on native plant communities determined by soil biota?
Koorem, K. ; Kostenko, O. ; Snoek, L.B. ; Geisen, S. ; Ramirez, K.S. ; Wilschut, R.A. ; Manrubia Freixa, M. ; Putten, W.H. van der - \ 2015
In: Proceedings of 58th Annual Symposium of the International Association for Vegetation Science. - - p. 201 - 201.
Current climate warming has brought about range expansion of plants, animals, and microor-ganisms to higher altitudes and latitudes. Range shifts of plant species are well documented, but we still know little about the ecological consequences, for example how the establishment of range-expanding plant species influences native plant communities. Plants are living in close association with aboveground and belowground higher trophic level organisms. Research has shown that soil organisms can have major impact on plant community dynamics, but relatively little is known about their role in community organization following plant range expansion. As plants disperse faster than soil organisms, range-expanding plants may in their new range be released from their natural enemies, but also from symbionts and decomposer organisms. How-ever, with time soil organisms may also disperse over long distances and expand their ranges but so far, no studies have investigated how this may influence plant community dynamics in the new range. We established a greenhouse experiment to examine (i) how the addition of range-expanding plant species affects the performance of native plant species and (ii) how range expansion of soil organisms influences plant community composition in the new range. Eight plant individuals, consisting of plants from distinctive ecological strategies (range-expand-ing plants, native plant species, and their combination), were grown in 7l mesocosms, which were inoculated with different soil communities (sterile soil, soil community from the original range, new range or a mixture of the original and new range). After 14 weeks of growth, plants were harvested, dried and weighed. Our results show that the addition of range-expanding plant species increases the productivity of plant communities in the new range. However, the effect of range-expanding plant species depends on their relativeness to the native plant community: range-expanders that have no closely related plant species in native plant communities sup-press the growth of native plants, whereas range-expanders with closely related species in the native plant community have no negative effect. Interestingly, the effect of soil communities differed also between these two types of range-expanding plants and also between individual species. We will discuss more specific responses in the presentation.
Plants are expanding their range: does this affect their association with arbuscular mycorrhizal fungi?
Koorem, K. ; Kostenko, O. ; Snoek, L.B. ; Geisen, S. ; Ramirez, K.S. ; Wilschut, R.A. ; Manrubia Freixa, M. ; Putten, W.H. van der - \ 2015
In: Proceedings of 8th International Conference on Mycorrhiza. - - p. 96 - 96.
Current climate warming has brought about range expansion of plants, animals, and microorganisms to higher altitudes and latitudes. Range shifts of plant species are well documented, but we know little about the ecological consequences of this expansion. As plants disperse faster than soil organisms, range-expanding plants may in their new range be released from their natural enemies, but also from symbionts and decomposer organisms. To test this expectation, we characterized fungal communities (targeting the ITS region) associated to range expanding plant species (Centaurea stoebe, Solanum nigrum, Rorippa sylvestris) in their original and new range. We detected differences in fungal community composition associated to these plants in the two ranges. Fungal community dynamics, focusing on arbuscular mycorrhizal fungi, will be discussed in the presentation. With time, soil organisms may also disperse over long distances and expand their ranges but the effects of this possible event has never been tested. We established a greenhouse experiment to examine how range expansion of soil organisms influences the establishment of range expanding plants in the new range. Eight plant individuals, consisting of plants from distinctive ecological strategies (range-expanding plants, native plant species, and their combination), were grown in mesocosms, which were inoculated with different soil communities (sterile soil, soil community from original range, new range, or a mixture of original and new range). Our results show that the range-expanding plant species, which do not have closely related plant species in native plant communities, suppress the growth of native plants, whereas range-expanders with closely related species in the native plant community have no negative effect. Interestingly, the effect of soil communities differed also between these two types of range-expanding plants, being clearly distinctive between plants that commonly form arbuscular mycorrhizas and plants that do not.
Closely related and novel range expanders influence native plant communities by changing soil communities
Koorem, K. ; Ramirez, K.S. ; Crowther, T.W. ; Snoek, L.B. ; Kostenko, O. ; Bloem, J. ; Weser, C. ; Hooven, F. ten; Geisen, S. ; Manrubia Freixa, M. ; Raaij, D.R. van; Wilschut, R.A. ; Putten, W.H. van der - \ 2015
Policy Brief - Where our Food Crops Come from: A New Estimation of Countries’ Interdependence in Plant Genetic Resources
Khoury, C.K. ; Achicanoy, H.A. ; Bjorkman, A.D. ; Navarro-Racines, C. ; Guarino, L. ; Flores-Palacios, X. ; Engels, J.M.M. ; Wiersema, J.H. ; Dempewolf, H. ; Ramirez-Villegas, J. ; Castaneda-Alvarez, N.P. ; Fowler, C. ; Jarvis, A. ; Rieseberg, L.H. ; Struik, P.C. - \ 2015
CIAT International Center for Tropical Agriculture
Key messages: • Access to plant genetic resources used in crop improvement is essential for achieving food and nutrition security. • All countries utilize crops whose genetic diversity originates outside their borders and therefore benefi t from international collaboration to access plant genetic resources. • Countries are highly interdependent in regard to these resources, as 68.7% of their diets and 69.3% of their national agricultural production systems depend on crops whose genetic diversity originates largely outside their borders, on average across countries worldwide. • Countries’ dependence on crops that originated in other regions has increased over the past 50 years in concert with economic and agricultural development and the globalization of food systems. Increased utilization of these “foreign” crops is correlated with greater dietary diversity and higher GDP. • Global interdependence in plant genetic resources provides a strong rationale for proactively conserving and facilitating access to this diversity worldwide. We recommend more comprehensive participation of countries in the Multilateral System of Access and Benefi t Sharing of the ITPGRFA, and for widening international cooperation and a multilateral approach to the exchange of plant genetic diversity in order to consider all crops of present and future international importance.
Estimation of countries’ interdependence in plant genetic resources provisioning national food supplies and production systems
Khoury, C.K. ; Achicanoy, H.A. ; Bjorkman, A.D. ; Navarro-Racines, C. ; Guarino, L. ; Flores-Palacios, X. ; Engels, J.M.M. ; Wiersema, J.H. ; Dempewolf, H. ; Ramirez-Villegas, J. ; Castaneda-Alvarez, N.P. ; Fowler, C. ; Jarvis, A. ; Rieseberg, L.H. ; Struik, P.C. - \ 2015
The International Treaty on Plant Genetic Resources for Food and Agriculture (Research study 8) - 26 p.
The Contracting Parties of the International Treaty recognize that plant genetic resources for food and agriculture are a common concern of all countries, in that all countries depend largely on plant genetic resources for food and agriculture that originated elsewhere. Nearly 20 years ago, an initial research on interdependence mong countries on crop diversity provided information helpful for countries to establish the Treaty, and in particular its Multilateral System of Access and Benefit-sharing. Through Resolution 2/2013, the Governing established an intergovernmental process to enhance the functioning of the Multilateral System requested all available information be taken into account as a basis for supporting the work of the Ad Hoc Open-Ended Working Group to Enhance the Functioning of the Multilateral System. The Secretariat of the International Treaty published a notification encouraging international organizations to make available information relevant to the work of the Working Group. In response to such call, the International Center for Tropical Agriculture (CIAT) in collaboration with a wide range of research partners, have prepared a fully updated estimation of interdependence among countries, with enhancements in regard to the breadth and depth of the analysis for more than 150 countries. The research confirms the results of the initial research, and provides major enhancements in regard to the breadth and depth of the analyses, using powerful visualization tools to display the results. While the initial research focused only on calories, the new analyses include all available measures of national food supplies (calories, protein, fat, and food weight) and three pertinent measures of national production systems (production quantity, harvested area, and production value), and reveal change over the past 50 years.
Toward a global platform for linking soil biodiversity data
Ramirez, K.S. ; Döring, M. ; Eisenhauer, N. ; Gardi, C. ; Ladau, J. ; Leff, J.W. ; Lentendu, G. ; Lindo, Z. ; Rillig, M.C. ; Russell, D. ; Scheu, S. ; John, M. ; Vries, F.T. de; Wubet, T. ; Putten, W.H. van der; Wall, D.H. - \ 2015
Frontiers in Ecology and Evolution 3 (2015). - ISSN 2296-701X - 7 p.
Soil biodiversity is immense, with an estimated 10–100 million organisms belonging to over 5000 taxa in a handful of soil. In spite of the importance of soil biodiversity for ecosystem functions and services, information on soil species, from taxonomy to biogeographical patterns, is incomplete and there is no infrastructure to connect pre-existing or future data. Here, we propose a global platform to allow for greater access to soil biodiversity information by linking databases and repositories through a single open portal. The proposed platform would for the first time, link data on soil organisms from different global sites and biomes, and will be inclusive of all data types, from molecular sequences to morphology measurements and other supporting information. Access to soil biodiversity species records and information will be instrumental to progressing scientific research and education. Further, as demonstrated by previous biodiversity synthesis efforts, data availability is key for adapting to, and creating mitigation plans in response to global changes. With the rapid influx of soil biodiversity data, now is the time to take the first steps forward in establishing a global soil biodiversity information platform.
QTL mapping of pomological traits in peach and related species breeding germplasm
Fresnedo-Ramírez, J. ; Bink, M.C.A.M. ; Weg, W.E. van de; Famula, T.R. ; Crisosto, C.H. ; Frett, T. ; Gasic, K. ; Peace, C.P. ; Gradziel, T.M. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 19 p.
persica l. batsch - prunus-persica - linkage disequilibrium - fruit size - population-structure - candidate genes - genome database - sweet cherry - almond - cultivars
Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in marker-assisted breeding.
Characterisation of biofilms formed by Lactobacillus plantarum WCFS1 and food spoilage isolates
Fernández Ramírez, M.D. ; Smid, E.J. ; Abee, T. ; Nierop Groot, M.N. - \ 2015
International Journal of Food Microbiology 207 (2015). - ISSN 0168-1605 - p. 23 - 29.
lactic-acid bacteria - enterococcal surface protein - listeria-monocytogenes - pseudomonas-putida - bacillus-subtilis - starter cultures - genetic-analysis - rhamnosus gg - resistance - industry
Lactobacillus plantarum has been associated with food spoilage in a wide range of products and the biofilm growth mode has been implicated as a possible source of contamination. In this study we analysed the biofilm forming capacity of L. plantarum WCFS1 and six food spoilage isolates. Biofilm formation as quantified by crystal violet staining and colony forming units was largely affected by the medium composition, growth temperature and maturation time and by strain specific features. All strains showed highest biofilm formation in Brain Heart Infusion medium supplemented with manganese and glucose. For L. plantarum biofilms the crystal violet (CV) assay, that is routinely used to quantify total biofilm formation, correlates poorly with the number of culturable cells in the biofilm. This can in part be explained by cell death and lysis resulting in CV stainable material, conceivably extracellular DNA (eDNA), contributing to the extracellular matrix. The strain to strain variation may in part be explained by differences in levels of eDNA, likely as result of differences in lysis behaviour. In line with this, biofilms of all strains tested, except for one spoilage isolate, were sensitive to DNase treatment. In addition, biofilms were highly sensitive to treatment with Proteinase K suggesting a role for proteins and/or proteinaceous material in surface colonisation. This study shows the impact of a range of environmental factors and enzyme treatments on biofilm formation capacity for selected L. plantarum isolates associated with food spoilage, and may provide clues for disinfection strategies in food industry.
Large-scale evolutionary analysis of genes and supergene clusters from terpenoid modular pathways provides insights into metabolic diversification in flowering plants.
Hofberger, J.A. ; Ramirez, A.M. ; Bergh, E. van den; Zhu, X. ; Bouwmeester, H.J. ; Schuurink, R.C. ; Schranz, M.E. - \ 2015
PLoS ONE 10 (2015)6. - ISSN 1932-6203 - 37 p.
isopentenyl diphosphate isomerases - disease resistance genes - arabidopsis-thaliana - genome sequence - whole-genome - protein families - draft genome - isoprenoid biosynthesis - secondary metabolism - oxidosqualene cyclase
An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species.
Bedrijven financieren weinig promotieonderzoek : dossier universiteit en bedrijf
Sikkema, A. ; Winkel, G.L. van; Velez Ramirez, A.I. - \ 2015
Resource: nieuwssite voor studenten en medewerkers van Wageningen UR 9 (2015)18. - ISSN 1389-7756 - p. 12 - 15.
universitair onderzoek - financieren - publiek-private samenwerking - universiteiten - dissertaties - university research - financing - public-private cooperation - universities - theses
Steeds meer onderzoek van Wageningen Universiteit wordt betaald en bepaald door externe financiers. Dat roept vragen op – wie stuurt het Wageningse onderzoek? Resource dook eens grondig in het promotieonderzoek, het leeuwendeel van de wetenschappelijke productie op de universiteit. De belangrijkste financiers zijn niet bedrijven. De EU en andere publieke financiers zijn veel belangrijker.
Crop wild relatives of pigeonpea [Cajanus cajan (L.) Millsp.]: Distributions, ex situ conservation status, and potential genetic resources for abiotic stress tolerance
Khoury, C.K. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Bernau, V. ; Kassa, M.T. ; Norton, S.L. ; Maesen, L. ; Upadhyaya, H.D. ; Ramirez-Villegas, J. ; Jarvis, A. ; Struik, P.C. - \ 2015
Biological Conservation 184 (2015). - ISSN 0006-3207 - p. 259 - 270.
species distribution models - global food security - male-sterility - climate-change - osmotic adjustment - diversity - bias - biodiversity - adaptation - accessions
Pigeonpea [Cajanus cajan (L.) Millsp.] is a versatile, stress-tolerant, and nutritious grain legume, possessing traits of value for enhancing the sustainability of dry sub-tropical and tropical agricultural systems. The use of crop wild relatives (CWR) in pigeonpea breeding has been successful in providing important resistance, quality, and breeding efficiency traits to the crop. Current breeding objectives for pigeonpea include increasing its tolerance to abiotic stresses, including heat, cold, drought, and waterlogging. Here we assess the potential for pigeonpea CWR to be further employed in crop improvement by compiling wild species occurrence and ex situ conservation information, producing geographic distribution models for the species, identifying gaps in the omprehensiveness of current germplasm collections, and using ecogeographic information to identify CWR populations with the potential to contribute agronomic traits of priority to breeders. The fifteen prioritized relatives of pigeonpea generally occur in South and Southeast Asia to Australia, with the highest concentrations of species in southern India and northern Australia. These taxa differ considerably among themselves and in comparison to the crop in their adaptations to temperature, precipitation and edaphic conditions. We find that these wild genetic resources are broadly under-represented in ex situ conservation systems, with 80% of species assessed as high priority for further collecting, thus their availability to plant breeders is insufficient. We identify species and highlight geographic locations for further collecting in order to improve the completeness of pigeonpea CWR germplasm collections, with particular emphasis on potential traits for abiotic stress tolerance.
Continuous-light tolerance in tomato is graft-transferable
Vélez Ramírez, A.I. ; Ieperen, W. van; Vreugdenhil, D. ; Millenaar, F.F. - \ 2015
Planta 241 (2015)1. - ISSN 0032-0935 - p. 285 - 290.
lycopersicon-esculentum - plants - temperature - photosynthesis - rootstock - increase - growth - injury - xylem - fruit
Continuous light induces a potentially lethal injury in domesticated tomato (Solanum lycopersicum) plants. Recently, continuous-light tolerance was reported in several wild tomato species, yet the molecular mechanisms underpinning tolerance/sensitivity are still elusive. Here, we investigated from which part of the plant continuous-light tolerance originates and whether this trait acts systemically within the plant. By exposing grafted plants bearing both tolerant and sensitive shoots, the trait was functionally located in the shoot rather than the roots. Additionally, an increase in continuous-light tolerance was observed in sensitive plants when a continuous-light-tolerant shoot was grafted on it. Cultivation of greenhouse tomatoes under continuous light promises high yield increases. Our results show that to pursuit this, the trait should be bred into scion rather than rootstock lines. In addition, identifying the nature of the signal/molecule(s) and/or the mechanism of graft-induced, continuous-light tolerance can potentially result in a better understanding of important physiological processes like long-distance signaling.
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.
Nieuw tomaat groeit dag en nacht
Ieperen, W. van; Vélez Ramírez, A.I. - \ 2014
WageningenWorld 3 (2014). - ISSN 2210-7908 - p. 5 - 5.
Gen laat tomatenplant 24 uur per dag groeien
Ieperen, W. van; Vélez Ramírez, A.I. - \ 2014
Groenten en Fruit Actueel 17 (2014). - ISSN 0925-9694 - p. 23 - 23.
Biofilm formation by Lactobacillus plantarum WCFS1 under static and dynamic conditions
Fernandez Ramirez, M.D. ; Nierop Groot, M.N. ; Smid, E.J. ; Abee, T. - \ 2014
In: Book of abstracts 11th International Symposium on Lactic Acid Bacteria. - - p. B028 - B028.
Irreversible fate commitment in the Arabidopsis stomatal lineage requires a Fama and Retinoblastoma-related module
Matos, J.L. ; Lau, O.S. ; Hachez, C. ; Cruz-Ramirez, A. ; Scheres, B. ; Bergmann, D.C. - \ 2014
eLife 3 (2014). - ISSN 2050-084X
asymmetric cell divisions - gateway binary vectors - transcription factor - secretory peptide - guard-cells - differentiation - expression - genes - transformation - termination
The presumed totipotency of plant cells leads to questions about how specific stem cell lineages and terminal fates could be established. In the Arabidopsis stomatal lineage, a transient self-renewing phase creates precursors that differentiate into one of two epidermal cell types, guard cells or pavement cells. We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. Disrupting physical interactions between FAMA and RBR preferentially reveals the role of RBR in enforcing fate commitment over its role in cell-cycle control in this developmental context. Analysis of the phenotypes linked to the modulation of FAMA and RBR sheds new light on the way iterative divisions and terminal differentiation are coordinately regulated in a plant stem-cell lineage. - See more at: http://elifesciences.org/content/3/e03271#sthash.f3srCCrx.dpuf
The tomato phosphatidylinositol-phospholipase C2 (SlPLC2) is required for defense gene induction by the fungal elicitor xylanase
Gonorazky, G. ; Ramirez, L. ; Abd-El-Haliem, A. ; Vossen, J.H. ; Lamattina, L. ; Have, A. ten; Joosten, M.H.A.J. ; Laxalt, A.M. - \ 2014
Journal of Plant Physiology 171 (2014)11. - ISSN 0176-1617 - p. 959 - 965.
phosphatidic-acid accumulation - cultured rice cells - nitric-oxide - disease resistance - c/diacylglycerol kinase - arabidopsis-thaliana - signaling pathways - activation - responses - plants
The tomato [Solanum lycopersicum (Sl)] phosphatidylinositol-phospholipase C (PI-PLC) gene family is composed of six members, named SlPLC1 to SlPLC6, differentially regulated upon pathogen attack. We have previously shown that the fungal elicitor xylanase rapidly induces nitric oxide (NO), which is required for PI-PLCs activity and downstream defense responses in tomato cell suspensions. Here, we show that all six SlPLC genes are expressed in tomato cell suspensions. Treatment of the cells with xylanase induces an early increase in SlPLC5 transcript levels, followed by a raise of the amount of SlPLC2 transcripts. The production of NO is required to augment SlPLC5 transcript levels in xylanase-treated tomato cells. Xylanase also induces SlPLC2 and SlPLC5 transcript levels in planta. We knocked-down the expression of SlPLC2 and SlPLC5 by virus-induced gene silencing. We found that SlPLC2 is required for xylanase-induced expression of the defense-related genes PR1 and HSR203J.
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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