Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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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.
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