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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Integrated culture of Nile tilapia and Amazon river prawn in stagnant ponds, using nutrient-rich water and substrates
Rodrigues, Caio G. ; Garcia, Baltasar F. ; Verdegem, Marc ; Santos, Michelle R. ; Amorim, Rafael V. ; Valenti, Wagner C. - \ 2019
Aquaculture 503 (2019). - ISSN 0044-8486 - p. 111 - 117.
Amazon river prawn - Integrated aquaculture - Nile tilapia - Nutrient-rich water - Substrates

Monoculture is an inefficient aquaculture system because on average <~20% of the diet supplied is assimilated by the target species. Integrated aquaculture systems are attractive alternatives because they take advantage of the wasted nutrients to produce other marketable species. Substrate addition is known as beneficial management to promote natural food (periphyton) by trapping nutrients. Thus, the aim of this study was to evaluate the technical feasibility of integrating the culture of Nile tilapia, Oreochromis niloticus with the culture of Amazon river prawn, Macrobrachium amazonicum in stagnant ponds supplied with water rich in nitrogen and phosphorus, and investigate if the addition of substrates affects the performance of both species. The target species (tilapia) was fed with commercial diet, while the secondary species (prawn) took advantage directly and indirectly of feed wastes. A completely randomized experimental design comprised of three treatments (culture with geotextile blanket substrates, bamboo substrates, and no substrates) with four replicates per treatment was used. Vertical substrates were installed in each pond, which total area was equivalent to 50% pond bottom area. Twelve 0.01-ha earthen ponds were stocked with Nile tilapia (~30 g) and prawn post-larvae (~0.04 g) together, which were cultured for 140 days. Dissolved oxygen, pH and temperature were measured daily, whereas water samples were collected biweekly to evaluate ammonia-N, nitrite-N and nitrate-N. The water quality remained suitable for production throughout the experimental period and was not affected by the use of substrates. The addition of substrates did not affect the growth, survival, productivity and apparent feed conversion ratio of Nile tilapia. On average, Nile tilapia grew to ~0.5 kg, with a survival close to 90%, resulting in productivity of about 5 t/ha. On the other hand, substrates increased the portion of larger prawns in the harvest, improving market value. A major effect was observed using the geotextile blanket substrate. The proportions of prawn heavier than 3 g were 54.2, 41.9 and 25.6% in ponds using geotextile blanket, bamboo and no substrate, respectively. In conclusion, farming Nile tilapia and Amazon river prawn in integrated systems supplied with nutrient-rich water in stagnant ponds is technically feasible. The addition of substrates does not affect tilapia performance but increase the proportion of large prawns; the effect was more pronounced with geotextile substrates.

Novel haloalkaliphilic methanotrophic bacteria : An attempt for enhancing methane bio-refinery
Cantera, Sara ; Sánchez-Andrea, Irene ; Sadornil, Lidia J. ; García-Encina, Pedro A. ; Stams, Alfons J.M. ; Muñoz, Raúl - \ 2019
Journal of Environmental Management 231 (2019). - ISSN 0301-4797 - p. 1091 - 1099.
Alishewanella - CH bio-refinery - Ectoine - Halomonas - Methane treatment

Methane bioconversion into products with a high market value, such as ectoine or hydroxyectoine, can be optimized via isolation of more efficient novel methanotrophic bacteria. The research here presented focused on the enrichment of methanotrophic consortia able to co-produce different ectoines during CH4 metabolism. Four different enrichments (Cow3, Slu3, Cow6 and Slu6) were carried out in basal media supplemented with 3 and 6% NaCl, and using methane as the sole carbon and energy source. The highest ectoine accumulation (∼20 mg ectoine g biomass−1) was recorded in the two consortia enriched at 6% NaCl (Cow6 and Slu6). Moreover, hydroxyectoine was detected for the first time using methane as a feedstock in Cow6 and Slu6 (∼5 mg g biomass−1). The majority of the haloalkaliphilic bacteria identified by 16S rRNA community profiling in both consortia have not been previously described as methanotrophs. From these enrichments, two novel strains (representing novel species) capable of using methane as the sole carbon and energy source were isolated: Alishewanella sp. strain RM1 and Halomonas sp. strain PGE1. Halomonas sp. strain PGE1 showed higher ectoine yields (70–92 mg ectoine g biomass−1) than those previously described for other methanotrophs under continuous cultivation mode (∼37–70 mg ectoine g biomass−1). The results here obtained highlight the potential of isolating novel methanotrophs in order to boost the competitiveness of industrial CH4-based ectoine production.

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

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

Discovery of Sabellaria spinulosa reefs in an intensively fished area of the Dutch Continental Shelf, North Sea
Reijden, Karin J. Van Der; Koop, Leo ; O'flynn, Sarah ; Garcia, Silvia ; Bos, Oscar ; Sluis, Christiaan Van; Maaholm, David J. ; Herman, Peter M.J. ; Simons, Dick G. ; Olff, Han ; Ysebaert, Tom ; Snellen, Mirjam ; Govers, Laura L. ; Rijnsdorp, Adriaan D. ; Aguilar, Ricardo - \ 2019
Journal of Sea Research 144 (2019). - ISSN 1385-1101 - p. 85 - 94.
Biogenic Reef - Brown Bank - Ecosystem Engineer - Sabellaria spinulosa - North Sea
The tube-building polychaete Sabellaria spinulosa (Ross worm) can form conspicuous biogenic reefs that stabilize the seabed and increase biodiversity by providing a habitat for a multitude of other species. These reefs, however, are assumed to be vulnerable to human-induced physical disturbances of the seabed. In the Greater North Sea, S. spinulosa reefs are recognized to be under threat and worthy of protection. In August 2017, three S. spinulosa reefs with a minimum extent of 1016m2 were discovered in the Dutch Brown Bank area. This area comprises a large-scale sandbank and adjacent troughs. The reefs were found within the sandbank troughs, which have proven to be subject to high demersal fishing intensities (fished>5 times a year). Detailed bathymetry measurements showed that S. spinulosa reefs were mainly located within valleys of smaller-scaled sand waves, which have a perpendicular orientation compared to the large-scale sandbank structure of the Brown Bank. We hypothesize that the valleys in between sand waves offer suitable substrate for settlement and refuge from abrasion by fishing activities, enabling the S. spinulosa reefs to persist despite high fishing intensities. ROV footage of the reefs showed higher estimates of species abundances on the reefs compared with adjacent habitats, with some species present that are typical for hard substrate (rock gunnel, Pholis gunnellus; edible crab, Cancer pagurus; and velvet swimming crab, Necora puber). The information presented could be used for drafting management policies to protect these reefs, as Contracting Parties of the OSPAR Convention are committed to take measures and protect biodiversity.
Assessment of promising agricultural management practices
Barão, Lúcia ; Alaoui, Abdallah ; Ferreira, Carla ; Basch, Gottlieb ; Schwilch, Gudrun ; Geissen, Violette ; Sukkel, Wijnand ; Lemesle, Julie ; Garcia-Orenes, Fuensanta ; Morugán-Coronado, Alicia ; Mataix-Solera, Jorge ; Kosmas, Costas ; Glavan, Matjaž ; Pintar, Marina ; Tóth, Brigitta ; Hermann, Tamás ; Vizitiu, Olga Petruta ; Lipiec, Jerzy ; Reintam, Endla ; Xu, Minggang ; Di, Jiaying ; Fan, Hongzhu ; Wang, Fei - \ 2019
Science of the Total Environment 649 (2019). - ISSN 0048-9697 - p. 610 - 619.
Environment - Farming systems - Soil threats - Sustainability

iSQAPER project - Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience - aims to develop an app to advise farmers on selecting the best Agriculture Management Practice (AMPs) to improve soil quality. For this purpose, a soil quality index has to be developed to account for the changes in soil quality as impacted by the implementation of the AMPs. Some promising AMPs have been suggested over the time to prevent soil degradation. These practices have been randomly adopted by farmers but which practices are most used by farmers and where they are mostly adopted remains unclear. This study is part of the iSQAPER project with the specific aims: 1) map the current distribution of previously selected 18 promising AMPs in several pedo-climatic regions and farming systems located in ten and four study site areas (SSA) along Europe and China, respectively; and 2) identify the soil threats occurring in those areas. In each SSA, farmers using promising AMP's were identified and questionnaires were used to assess farmer's perception on soil threats significance in the area. 138 plots/farms using 18 promising AMPs, were identified in Europe (112) and China (26).Results show that promising AMPs used in Europe are Crop rotation (15%), Manuring & Composting (15%) and Min-till (14%), whereas in China are Manuring & Composting (18%), Residue maintenance (18%) and Integrated pest and disease management (12%). In Europe, soil erosion is the main threat in agricultural Mediterranean areas while soil-borne pests and diseases is more frequent in the SSAs from France and The Netherlands. In China, soil erosion, SOM decline, compaction and poor soil structure are among the most significant. This work provides important information for policy makers and the development of strategies to support and promote agricultural management practices with benefits for soil quality.

Climate regimes override micro-site effects on the summer temperature signal of scots pine at its northern distribution limits
Lange, Jelena ; Buras, Allan ; Cruz-García, Roberto ; Gurskaya, Marina ; Jalkanen, Risto ; Kukarskih, Vladimir ; Seo, Jeong Wook ; Wilmking, Martin - \ 2018
Advances in Intelligent Systems and Computing 871 (2018). - ISSN 2194-5357
Boreal forest - Climate change - Climate regime - Maximum latewood density - Micro-site - Pinus sylvestris - Tree-ring width - Treeline

Tree growth at northern boreal treelines is generally limited by summer temperature, hence tree rings serve as natural archives of past climatic conditions. However, there is increasing evidence that a changing summer climate as well as certain micro-site conditions can lead to a weakening or loss of the summer temperature signal in trees growing in treeline environments. This phenomenon poses a challenge to all applications relying on stable temperature-growth relationships such as temperature reconstructions and dynamic vegetation models. We tested the effect of differing ecological and climatological conditions on the summer temperature signal of Scots pine at its northern distribution limits by analyzing twelve sites distributed along a 2200 km gradient from Finland to Western Siberia (Russia). Two frequently used proxies in dendroclimatology, ring width and maximum latewood density, were correlated with summer temperature for the period 1901–2013 separately for (i) dry vs. wet micro-sites and (ii) years with dry/warm vs. wet/cold climate regimes prevailing during the growing season. Differing climate regimes significantly affected the temperature signal of Scots pine at about half of our sites: While correlations were stronger in wet/cold than in dry/warm years at most sites located in Russia, differing climate regimes had only little effect at Finnish sites. Both tree-ring proxies were affected in a similar way. Interestingly, micro-site differences significantly affected absolute tree growth, but had only minor effects on the climatic signal at our sites. We conclude that, despite the treeline-proximal location, growth-limiting conditions seem to be exceeded in dry/warm years at most Russian sites, leading to a weakening or loss of the summer temperature signal in Scots pine here. With projected temperature increase, unstable summer temperature signals in Scots pine tree rings might become more frequent, possibly affecting dendroclimatological applications and related fields.

High Output LED in hybride belichting : monitoring praktijkproef bij Alstroemeria
García Victoria, Nieves ; Weerheim, Kees ; Kempkes, Frank ; Steenhuizen, Johan ; Vreugdenhil, Arend ; Groot, Marco de - \ 2018
Bleiswijk : Stichting Wageningen Research, Wageningen Plant Research, Business unit Glastuinbouw (Rapport WPR 806) - 50
In order to increase the intensity of the artificial light with the least possible electricity costs, an Alstroemeria production company experiments with a Hybrid light installation. The Hybrid lighting was created by complementing the existing 61 μmol/m2 HPS lamps with 21 μmol/m2s Philips High Output (HO) LED lamps to a total intensity of 81 μmol/m2s. The performance of this hybrid lighting was investigated between January 2017 and May 2019 and compared with the existing HPS installation (62 μmol/m2s) and with Regular Output (RO) LED at an intensity of 79 μmol/m2s. The light sum in the Hybrid lighting was 288 Mol/m2 higher than in the HPS reference (4%) thanks to the 33% higher light level and the 442 more burning hours of the HO LED, and yielded 8% more production (longer, heavier stems). The light sum in the LED treatment was 215 Mol light (3%) higher than the reference, due to 33% higher intensity but was used as many hours as the HPS lamps, and increased production by 6% (more branches). Of the three systems, the Full LED option is the most energy-efficient and
the Hybrid lighting had the lowest EUE (electricity use efficiency). The research was funded by the program “ Greenhouse as Source of Energy” of the Dutch Ministry of Agriculture and LTO Glaskracht, the Knowledge Cooperative Alstroemeria, Philips Lighting and Fa. Vreugdenhil.
High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities
Olmos, A. ; Boonham, N. ; Candresse, T. ; Gentit, P. ; Giovani, B. ; Kutnjak, D. ; Liefting, L. ; Maree, H.J. ; Minafra, A. ; Moreira, A. ; Nakhla, M.K. ; Petter, F. ; Ravnikar, M. ; Rodoni, B.C. ; Roenhorst, J.W. ; Rott, M. ; Ruiz-Garcia, A.B. ; Santala, J. ; Stancanelli, G. ; Vlugt, R.A.A. van der; Varveri, C. ; Westenberg, M. ; Wetzel, T. ; Ziebell, H. ; Massart, S. - \ 2018
EPPO Bulletin 48 (2018)2. - ISSN 0250-8052 - p. 219 - 224.
High‐throughput sequencing (HTS) technologies have revolutionized plant pest research and are now raising interest for plant pest diagnostics, with plant virus diagnostics at the forefront of development. However, the application of HTS in plant pest diagnostics raises important challenges that plant health regulators will have to address. Adapted infrastructures, technical guidelines and training are pivotal for further use and adoption of the HTS technologies in the phytosanitary framework.
Exploring cooperative place-based approaches to restorative agriculture
Swagemakers, Paul ; Domínguez García, M.D. ; Milone, Pierluigi ; Ventura, Flaminia ; Wiskerke, Johannes S.C. - \ 2018
Journal of Rural Studies (2018). - ISSN 0743-0167
Agriculture - Governance - Place-based development - Stewardship - Sustainability transition

The modernisation of agriculture has been, and continues to be, the cause of an increasing disconnection between farming, nature, and society. This has given rise to a series of social, economic, and ecological crises in the food chain. Some farmers are responding to this by adjusting their land-use and farming practices so as to make their farms more sustainable. But such changes need to be aligned with the specificities of the local bio-physical environment and the logic of the political economic environment. This article highlights how cooperative approaches allow public and private regulatory systems to support ecological transitions. Through a theoretical lens on place-based and restorative farming practices it analyses and interprets three complementary cooperative approaches as possible starting points for the transition towards a more sustainable agri-food system. The case studies show how farmers cooperatives can be either linked to the environment and to public policies (and thus extrinsic product quality), or to the market (and intrinsic product quality), or a combination of both. These links provide competitive advantages to farmers, and enable them to increase income from farming. We then discuss the effectiveness of these forms of self-governance, and how cooperative approaches, if well organised and implemented and appropriately embedded, can empower farmers to further change and adapt their farming practices so as to restore and improve their endogenous resource base. The analysis shows that while they are place-specific they are far from locally/regionally-bounded and that their success (or failure) critically depends on their alignment with national, supra-national and global actants.

Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice
Fernández Calleja, J.M.S. ; Konstanti, Prokopis ; Swarts, J.J.M. ; Bouwman, L.M.S. ; Garcia-Campayo, Vicenta ; Billecke, Nils ; Oosting, Annemarie ; Smidt, H. ; Keijer, J. ; Schothorst, E.M. van - \ 2018
PRJEB23475 - ERP105229
The gut microbiome interacts continuously with the host and its diet. Studying these interactions and their evolution in vivo as soon as they happen have been impossible. Here we develop a method to study microbiota-host-diet interactions continuously, non-invasively, and in real time, by measuring hydrogen (H2) and methane (CH4) production in mice housed in indirect calorimetry chambers.
Area of habitation strongly influences faecal microbial composition of wild lemurs
Umanets, A. ; Winter, I.I. de; IJdema, F. ; Ramiro Garcia, J. ; Hooft, W.F. van; Heitkönig, I.M.A. ; Prins, H.H.T. ; Smidt, H. - \ 2018
PRJEB20007 - ERP022109
The microbiota of the mammalian gut is a complex ecosystem, the composition of which is greatly influenced by host genetics and environmental factors. The goal of this comparative study was to investigate the influence of area of habitation, species, age and sex on intestinal microbiota composition of the three lemur species Eulemur fulvus, E. rubriventer, and E. rufifrons.MethodsFecal samples were collected from wild lemurs across Madagascar, and microbial composition was determined using next generation sequencing of PCR-amplified 16S ribosomal RNA gene fragments. Results Fecal microbiota of all three lemur species was dominated by members of the phyla Firmicutes, Bacteroidetes, Proteobacteria and Cyanobacteria. Consistent with reports from other primate species, the most predominant phyla were Firmicutes (43±6.4% [s.d.]) and Bacteroidetes (30.3±5.3%). The microbial composition was strongly associated with geographical area of habitation, with up to 19.9% of the total variation in microbial composition being explained by this factor in the E. fulvus population distributed across three sampling locations. In turn, differences observed in fecal microbiota of sympatric lemur species were less pronounced, as was the impact of the factors sex and age. Conclusions Our findings showed that among the studied factors the geographical region of habitation had the strongest influence on intestinal microbiota of congeneric lemur species. This suggests adaptation of microbiota to natural differences in forest composition, climate variations, and corresponding differences in the available diet in different geographical locations of Madagascar.
Cascading spatial and trophic impacts of oak decline on the soil food web
Domínguez-Begines, Jara ; Deyn, Gerlinde B. De; García, Luis V. ; Eisenhauer, Nico ; Gómez-Aparicio, Lorena - \ 2018
Journal of Ecology (2018). - ISSN 0022-0477
bioindicators - neighbourhood models - Phytophthora cinnamomi - plant–soil interactions - Quercus suber - soil food web - soil nematodes - soil-borne pathogens - spatial patterns - tree mortality

Tree defoliation and mortality have considerably increased world-wide during the last decades due to global change drivers such as increasing drought or invasive pests and pathogens. However, the effects of this tree decline on soil food webs are poorly understood. In this study, we evaluated the impacts of Quercus suber decline on soil food webs of Mediterranean mixed forests invaded by the exotic oomycete pathogen Phytophthora cinnamomi, using soil nematodes as bioindicator taxa. We used a spatially explicit neighbourhood approach to predict the characteristics of the nematode community (diversity, trophic structure, and several indices indicative of soil food web conditions) as a function of the characteristics of the tree and shrub community (species composition, size, and health status). Our results indicate that the process of defoliation and mortality of Q. suber caused significant alterations in the nematode trophic structure increasing the abundance of lower trophic levels (bacterivores, fungivores, and herbivores) and decreasing the abundance of higher levels (predators and omnivores). Furthermore, Q. suber decline altered the functional composition of soil communities, producing a setback of the ecological succession in the soil food web to an earlier stage (decrease in the maturity index and increase in the plant parasitic index), simplified soil food webs (decrease in the structure index), and shifts in the predominant decomposition channel (increase in the fungivores/bacterivores ratio). We also detected contrasting characteristics of the nematode community in neighbourhoods dominated by coexisting woody species, which suggests potential for long-term indirect effects on soil food webs due to the substitution of Q. suber by non-declining species. Synthesis. Our study provides novel results that show the major impacts that ongoing health deterioration of dominant tree species can have on the structure and composition of soil food webs in forest systems invaded by exotic pathogens, with cascading consequences for soil biogeochemical processes in both the short- and long term.

Role for Arabidopsis PLC7 in Stomatal Movement, Seed Mucilage Attachment, and Leaf Serration
Wijk, Ringo van; Zhang, Qianqian ; Zarza, Xavier ; Lamers, M. ; Reyes Marquez, F.C. ; Guardia, Aisha ; Scuffi, Denise ; García-Mata, Carlos ; Ligterink, W. ; Haring, M.A. ; Laxalt, A.M. ; Munnik, Teun - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Phospholipase C (PLC) has been suggested to play important roles in plant stress and development. To increase our understanding of PLC signaling in plants, we have started to analyze knock-out (KO), knock-down (KD) and overexpression mutants of Arabidopsis thaliana, which contains nine PLCs. Earlier, we characterized PLC2, PLC3 and PLC5. Here, the role of PLC7 is functionally addressed. Promoter-GUS analyses revealed that PLC7 is specifically expressed in the phloem of roots, leaves and flowers, and is also present in trichomes and hydathodes. Two T-DNA insertion mutants were obtained, i.e., plc7-3 being a KO- and plc7-4 a KD line. In contrast to earlier characterized phloem-expressed PLC mutants, i.e., plc3 and plc5, no defects in primary- or lateral root development were found for plc7 mutants. Like plc3 mutants, they were less sensitive to ABA during stomatal closure. Double-knockout plc3 plc7 lines were lethal, but plc5 plc7 (plc5/7) double mutants were viable, and revealed several new phenotypes, not observed earlier in the single mutants. These include a defect in seed mucilage, enhanced leaf serration, and an increased tolerance to drought. Overexpression of PLC7 enhanced drought tolerance too, similar to what was earlier found for PLC3-and PLC5 overexpression. In vivo 32Pi-labeling of seedlings and treatment with sorbitol to mimic drought stress, revealed stronger PIP2 responses in both drought-tolerant plc5/7 and PLC7-OE mutants. Together, these results show novel functions for PLC in plant stress and development. Potential molecular mechanisms are discussed.
A CUDA approach to compute perishable inventory control policies using value iteration
Ortega, G. ; Hendrix, E.M.T. ; García, I. - \ 2018
Journal of Supercomputing (2018). - ISSN 0920-8542 - 14 p.
CUDA - GPU - Inventory control - Value iteration

Dynamic programming (DP) approaches, in particular value iteration, is often seen as a method to derive optimal policies in inventory management. The challenge in this approach is to deal with an increasing state space when handling realistic problems. As a large part of world food production is thrown out due to its perishable character, a motivation exists to have a good look at order policies in retail. Recently, investigation has been introduced to consider substitution of one product by another, when one is out of stock. Taking this tendency into account in a policy requires an increasing state space. Therefore, we investigate the potential of using GPU platforms in order to derive optimal policies when the number of products taken into account simultaneously is increasing. First results show the potential of the GPU approach to accelerate computation in value iteration for DP.

The mystery of Tetrodotoxinen shellfish in the Netherlands manage the non-understood
Poelman, M. ; Gerssen, A. ; Heuvel-Greve, M.J. van den; Blanco Garcia, A. ; Klijnstra, M.D. ; Murk, A.J. - \ 2018
Soil properties maps in hydrological modelling with SWAT
Rivas, David A. ; Miguel Garcia, A. de; Willaarts, Bárbara ; Zegianini, Silvana ; Tarquis, Ana M. - \ 2018
Geophysical Research Abstracts 20 (2018). - ISSN 1029-7006 - 1 p.
Simulation of flow processes in hyperregulated Mediterranean watersheds is critical to attend general water demand and established ecological flows of River Basin Management Plans. Soil and Water Assessment Tool (SWAT) is a widespread tool that involves complex processes of water cycle at basin scale, providing information about water dynamics related with land use as a fundamental characteristic for water balance calculation. Therefore, soil properties map constitute an important aspect to take into account and in many cases the available data is incomplete and sparse. The objective of this study is to assess watershed outlet flow with SWAT model including detailed soil properties, land uses and management practices to quantify agricultural water demand in the Cega-Eresma-Adaja (CEA) watershed, an area of 8.000 km2, for the period (2004-2014). Based on 407 soil samples of the area, an optimized process through self-organizing maps (SOM) were applied to create soil units. As a result, 16 clusters were identified as the most suitable number of clusters including the standard deviation for each soil property as a measure of the variability. The SWAT model was calibrated and run using a soil map derived from SOM using the soil sample data rasterized in the whole area and optimized to reduce the number of clusters. The study reveals that aspects as crop rotation, soil management and their associated measures in Mediterranean basins are a key fact for water resources management facing climate change. ACKNOWLEDGEMENTS This research was funded partially by Spanish Ministerio de Ciencia e Innovación (MICINN) through project no. PCIN-2014-080, project no. MTM2015-63914-P.
Water shortages worsened by reservoir effects
Baldassarre, Giuliano Di; Wanders, Niko ; AghaKouchak, Amir ; Kuil, Linda ; Rangecroft, Sally ; Veldkamp, Ted I.E. ; Garcia, Margaret ; Oel, Pieter R. van; Breinl, Korbinian ; Loon, Anne F. van - \ 2018
Nature Sustainability 1 (2018)11. - ISSN 2398-9629 - p. 617 - 622.

The expansion of reservoirs to cope with droughts and water shortages is hotly debated in many places around the world. We argue that there are two counterintuitive dynamics that should be considered in this debate: supply–demand cycles and reservoir effects. Supply–demand cycles describe instances where increasing water supply enables higher water demand, which can quickly offset the initial benefits of reservoirs. Reservoir effects refer to cases where over-reliance on reservoirs increases vulnerability, and therefore increases the potential damage caused by droughts. Here we illustrate these counterintuitive dynamics with global and local examples, and discuss policy and research implications.

Carbon storage potential in degraded forests of Kalimantan, Indonesia
Ferraz, António ; Saatchi, Sassan ; Xu, Liang ; Hagen, Stephen ; Chave, Jerome ; Yu, Yifan ; Meyer, Victoria ; Garcia, Mariano ; Silva, Carlos ; Roswintiart, Orbita ; Samboko, Ari ; Sist, Plinio ; Walker, Sarah ; Pearson, Timothy R.H. ; Wijaya, Arief ; Sullivan, Franklin B. ; Rutishauser, Ervan ; Hoekman, Dirk ; Ganguly, Sangram - \ 2018
Environmental Research Letters 13 (2018)9. - ISSN 1748-9318
aboveground biomass mapping - airborne lidar - carbon - forest degradation - Indonesia - Kalimantan - peat swamp forests

The forests of Kalimantan are under severe pressure from extensive land use activities dominated by logging, palm oil plantations, and peatland fires. To implement the forest moratorium for mitigating greenhouse gas emissions, Indonesia's government requires information on the carbon stored in forests, including intact, degraded, secondary, and peat swamp forests. We developed a hybrid approach of producing a wall-to-wall map of the aboveground biomass (AGB) of intact and degraded forests of Kalimantan at 1 ha grid cells by combining field inventory plots, airborne lidar samples, and satellite radar and optical imagery. More than 110 000 ha of lidar data were acquired to systematically capture variations of forest structure and more than 104 field plots to develop lidar-biomass models. The lidar measurements were converted into biomass using models developed for 66 439 ha of drylands and 44 250 ha of wetland forests. By combining the AGB map with the national land cover map, we found that 22.3 Mha (106 ha) of forest remain on drylands ranging in biomass from 357.2 ±12.3 Mgha-1 in relatively intact forests to 134.2 ±6.1 Mgha-1 in severely degraded forests. The remaining peat swamp forests are heterogeneous in coverage and degradation level, extending over 3.62 Mha and having an average AGB of 211.8 ±12.7 Mgha-1. Emission factors calculated from aboveground biomass only suggest that the carbon storage potential of more than 15 Mha of degraded and secondary dryland forests will be about 1.1 PgC.

A SIX1 homolog in Fusarium oxysporum f.sp. Cubense tropical race 4 contributes to virulence towards Cavendish banana
Widinugraheni, S. ; Niño-Sánchez, J. ; Does, H.C. van der; Dam, P. van; García-Bastidas, F.A. ; Subandiyah, S. ; Meijer, H.J.G. ; Kistler, H.C. ; Kema, G.H.J. ; Rep, M. - \ 2018
PLoS One 13 (2018)10. - ISSN 1932-6203

The fungus Fusarium oxysporum f.sp. cubense (Focub) causes Fusarium wilt of banana. Focub strains are divided into races according to their host specificity, but which virulence factors underlie these interactions is currently unknown. In the F. oxysporum f.sp. lycopersici (Fol)-tomato system, small secreted fungal proteins, called Six proteins, were identified in the xylem sap of infected plants. The Fol Six1 protein contributes to virulence and has an avirulence function by activating the I-3 immune receptor of tomato. The Focub tropical race 4 (TR4) genome harbors three SIX1 homologs: SIX1a, b and c. In this study, the role of Focub-SIX1a in pathogenicity was evaluated since this homolog is present in not only TR4 but also in other races. A deletion mutant of the SIX1a gene from Focub TR4 strain II5 was generated (FocubΔSIX1a) and tested in planta. Mutants were found to be severely compromised in their virulence. Ectopic integration of the Focub-SIX1a gene in the FocubΔSIX1a strain restored virulence to wild type levels. We conclude that Focub-SIX1a is required for full virulence of Focub TR4 towards Cavendish banana.

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research (2018). - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
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