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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Forest biomass retrieval approaches from earth observation in different biomes
Rodríguez-Veiga, Pedro ; Quegan, Shaun ; Carreiras, Joao ; Persson, Henrik J. ; Fransson, Johan E.S. ; Hoscilo, Agata ; Ziółkowski, Dariusz ; Stereńczak, Krzysztof ; Lohberger, Sandra ; Stängel, Matthias ; Berninger, Anna ; Siegert, Florian ; Avitabile, Valerio ; Herold, Martin ; Mermoz, Stéphane ; Bouvet, Alexandre ; Toan, Thuy Le; Carvalhais, Nuno ; Santoro, Maurizio ; Cartus, Oliver ; Rauste, Yrjö ; Mathieu, Renaud ; Asner, Gregory P. ; Thiel, Christian ; Pathe, Carsten ; Schmullius, Chris ; Seifert, Frank Martin ; Tansey, Kevin ; Balzter, Heiko - \ 2019
International Journal of applied Earth Observation and Geoinformation 77 (2019). - ISSN 0303-2434 - p. 53 - 68.
The amount and spatial distribution of forest aboveground biomass (AGB) were estimated using a range of regionally developed methods using Earth Observation data for Poland, Sweden and regions in Indonesia (Kalimantan), Mexico (Central Mexico and Yucatan peninsula), and South Africa (Eastern provinces) for the year 2010. These regions are representative of numerous forest biomes and biomass levels globally, from South African woodlands and savannas to the humid tropical forest of Kalimantan. AGB retrieval in each region relied on different sources of reference data, including forest inventory plot data and airborne LiDAR observations, and used a range of retrieval algorithms. This is the widest inter-comparison of regional-to-national AGB maps to date in terms of area, forest types, input datasets, and retrieval methods. The accuracy assessment of all regional maps using independent field data or LiDAR AGB maps resulted in an overall root mean square error (RMSE) ranging from 10 t ha−1 to 55 t ha−1 (37% to 67% relative RMSE), and an overall bias ranging from −1 t ha−1 to +5 t ha−1 at pixel level. The regional maps showed better agreement with field data than previously developed and widely used pan-tropical or northern hemisphere datasets. The comparison of accuracy assessments showed commonalities in error structures despite the variety of methods, input data, and forest biomes. All regional retrievals resulted in overestimation (up to 63 t ha−1) in the lower AGB classes, and underestimation (up to 85 t ha−1) in the higher AGB classes. Parametric model-based algorithms present advantages due to their low demand on in situ data compared to non-parametric algorithms, but there is a need for datasets and retrieval methods that can overcome the biases at both ends of the AGB range. The outcomes of this study should be considered when developing algorithms to estimate forest biomass at continental to global scale level.
Combining conventional ground-based and remotely sensed forest measurements
Decuyper, Mathieu - \ 2018
Wageningen University. Promotor(en): Martin Herold; Frans Bongers, co-promotor(en): Jan Clevers. - Wageningen : Wageningen University - ISBN 9789463435246 - 128
Bottom trawl fishing footprints on the world’s continental shelves
Amoroso, Ricardo O. ; Pitcher, C.R. ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Parma, Ana M. ; Suuronen, Petri ; Eigaard, Ole R. ; Bastardie, Francois ; Hintzen, Niels T. ; Althaus, Franziska ; Baird, Susan Jane ; Black, Jenny ; Buhl-Mortensen, Lene ; Campbell, Alexander B. ; Catarino, Rui ; Collie, Jeremy ; Cowan, James H. ; Durholtz, Deon ; Engstrom, Nadia ; Fairweather, Tracey P. ; Fock, Heino O. ; Ford, Richard ; Gálvez, Patricio A. ; Gerritsen, Hans ; Góngora, María Eva ; González, Jessica A. ; Hiddink, Jan G. ; Hughes, Kathryn M. ; Intelmann, Steven S. ; Jenkins, Chris ; Jonsson, Patrik ; Kainge, Paulus ; Kangas, Mervi ; Kathena, Johannes N. ; Kavadas, Stefanos ; Leslie, Rob W. ; Lewis, Steve G. ; Lundy, Mathieu ; Makin, David ; Martin, Julie ; Mazor, Tessa ; Gonzalez-Mirelis, Genoveva ; Newman, Stephen J. ; Papadopoulou, Nadia ; Posen, Paulette E. ; Rochester, Wayne ; Russo, Tommaso ; Sala, Antonello ; Semmens, Jayson M. ; Silva, Cristina - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)43. - ISSN 0027-8424 - p. E10275 - E10282.
Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Overall, 14% of the 7.8 million-km2 study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when highresolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, therewas >95% probability that >90%of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.
Assessing the structural differences between tropical forest types using Terrestrial Laser Scanning
Decuyper, Mathieu ; Mulatu, Kalkidan Ayele ; Brede, Benjamin ; Calders, Kim ; Armston, John ; Rozendaal, Danaë M.A. ; Mora, Brice ; Clevers, Jan G.P.W. ; Kooistra, Lammert ; Herold, Martin ; Bongers, Frans - \ 2018
Forest Ecology and Management 429 (2018). - ISSN 0378-1127 - p. 327 - 335.
Increasing anthropogenic pressure leads to loss of habitat through deforestation and degradation in tropical forests. While deforestation can be monitored relatively easily, forest management practices are often subtle processes, that are difficult to capture with for example satellite monitoring. Conventional measurements are well established and can be useful for management decisions, but it is believed that Terrestrial Laser Scanning (TLS) has a role in quantitative monitoring and continuous improvement of methods. In this study we used a combination of TLS and conventional forest inventory measures to estimate forest structural parameters in four different forest types in a tropical montane cloud forest in Kafa, Ethiopia. Here, the four forest types (intact forest, coffee forest, silvopasture, and plantations) are a result of specific management practices (e.g. clearance of understory in coffee forest), and not different forest communities or tree types. Both conventional and TLS derived parameters confirmed our assumptions that intact forest had the highest biomass, silvopasture had the largest canopy gaps, and plantations had the lowest canopy openness. Contrary to our expectations, coffee forest had higher canopy openness and similar biomass as silvopasture, indicating a significant loss of forest structure. The 3D vegetation structure (PAVD – Plant area vegetation density) was different between the forest types with the highest PAVD in intact forest and plantation canopy. Silvopasture was characterised by a low canopy but high understorey PAVD, indicating regeneration of the vegetation and infrequent fuelwood collection and/or non-intensive grazing. Coffee forest canopy had low PAVD, indicating that many trees had been removed, despite coffee needing canopy shade. These findings may advocate for more tangible criteria such as canopy openness thresholds in sustainable coffee certification schemes. TLS as tool for monitoring forest structure in plots with different forest types shows potential as it can capture the 3D position of the vegetation volume and open spaces at all heights in the forest. To quantify changes in different forest types, consistent monitoring of 3D structure is needed and here TLS is an add-on or an alternative to conventional forest structure monitoring. However, for the tropics, TLS-based automated segmentation of trees to derive DBH and biomass is not widely operational yet, nor is species richness determination in forest monitoring. Integration of data sources is needed to fully understand forest structural diversity and implications of forest management practices on different forest types.
Speciation success of polyploid plants closely relates to the regulation of meiotic recombination
Pelé, Alexandre ; Rousseau-Gueutin, Mathieu ; Chèvre, Anne-Marie - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Crossover - Diploidization - Genome evolution - Meiosis - Polyploidy - Recombination - Unreduced gametes

Polyploidization is a widespread phenomenon, especially in flowering plants that have all undergone at least one event of whole genome duplication during their evolutionary history. Consequently, a large range of plants, including many of the world’s crops, combines more than two sets of chromosomes originating from the same (autopolyploids) or related species (allopolyploids). Depending on the polyploid formation pathway, different patterns of recombination will be promoted, conditioning the level of heterozygosity. A polyploid population harboring a high level of heterozygosity will produce more genetically diverse progenies. Some of these individuals may show a better adaptability to different ecological niches, increasing their chance for successful establishment through natural selection. Another condition for young polyploids to survive corresponds to the formation of well-balanced gametes, assuring a sufficient level of fertility. In this review, we discuss the consequences of polyploid formation pathways, meiotic behavior and recombination regulation on the speciation success and maintenance of polyploid species.

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

Arguments for biodiversity conservation : factors influencing their observed effectiveness in European case studies
Tinch, Rob ; Bugter, Rob ; Blicharska, Malgorzata ; Harrison, Paula ; Haslett, John ; Jokinen, Pekka ; Mathieu, Laurence ; Primmer, Eeva - \ 2018
Biodiversity and Conservation 27 (2018). - ISSN 0960-3115 - p. 1763 - 1788.
Argument framing - Arguments for biodiversity conservation - Biodiversity policy - Ecosystem services - Science policy interfaces
Making a strong case for biodiversity protection is central to meeting the biodiversity targets in international agreements such as the CBD and achieving the UN Sustainable Development Goals. Effective arguments are needed to convince diverse actors that protection is worthwhile, and can play a crucial role in closing the implementation gap between biodiversity policy targets and outcomes. Drawing on a database of arguments from 11 European case studies, along with additional interview and case study material from all 13 case studies of the BESAFE project, we analysed relationships between potential and observed effectiveness of arguments. Our results show that strong logic, robustness, and timing of arguments are necessary but not sufficient conditions for arguments to be effective. We find that use of multiple and diverse arguments can enhance effectiveness by broadening the appeal to wider audiences, especially when arguments are repeated and refined through constructive dialogue. We discuss the role of framing, bundling and tailoring arguments to audiences in increasing effectiveness. Our results provide further support for the current shift towards recognition of value pluralism in biodiversity science and decision-making. We hope our results will help to demonstrate more convincingly the value of biodiversity to stakeholders in decision processes and thus build better cases for its conservation.
The antibody response in the bovine mammary gland is influenced by the adjuvant and the site of subcutaneous vaccination
Boerhout, Eveline M. ; Koets, Ad P. ; Mols-Vorstermans, Tanja G.T. ; Nuijten, Piet J.M. ; Hoeijmakers, Mathieu J.H. ; Rutten, Victor P.M.G. ; Bijlsma, Jetta J.E. - \ 2018
Veterinary Research 49 (2018)1. - ISSN 0928-4249
Intramammary infections in cattle resulting in mastitis have detrimental effects on cows' well-being, lifespan and milk production. In the host defense against S. aureus mastitis antibodies are thought to play an important role. To explore potential ways to increase antibody titers in the bovine mammary gland the effects of various adjuvants on the magnitude, isotype, and neutralizing capacity of antibodies produced following subcutaneous vaccine administration at different immunization sites were analyzed. In this study, α-toxoid was used as a model antigen and formulated in three different alum-based adjuvants: Alum-Saponin, Alum-Oil, and Alum-Saponin-Oil. Vaccines were administered near the suspensory ligament of the udder or in the lateral triangular area of the neck. At both immunization sites, immunization with α-toxoid in Alum-Saponin-Oil resulted in higher specific antibody titers in milk and serum as compared with Alum-Oil and Alum-Saponin, without favoring an IgG1, IgG2, or IgA response. Furthermore, the neutralizing capacity of milk serum and serum following immunization near the udder and in the neck was higher when Alum-Saponin-Oil was used as adjuvant compared with Alum-Oil and Alum-Saponin. Prime immunizations near the udder effectively increased both antibody isotype titers and neutralization titers, while prime plus boost immunizations were required to induce similar effects following immunization in the neck. Results indicate that subcutaneous administration of an Alum-Saponin-Oil based vaccine near the udder could be further explored for the development of a one-shot vaccination strategy to efficiently increase intramammary antibody responses.
Application of the QUENCHER methodology to the food industry
Henrion, Muriel ; Servaes, Mathieu ; Thielecke, Frank ; Fogliano, Vincenzo - \ 2018
Food Chemistry 240 (2018). - ISSN 0308-8146 - p. 951 - 958.
ABTS - Antioxidant capacity - Breakfast cereals - Factory monitoring - Whole grain
The QUENCHER method is a time and cost-saving extraction-free procedure measuring in vitro antioxidant capacity which appears highly relevant from an industrial perspective. However, grinding and exact weighting of material may be considered as critical points and were addressed in the present paper. Increasing sample weight at constant ABTS volume reduced TEAC values up to 50%. Working at higher ABTS radical concentration than recommended furthermore increased the TEAC values by 30%. Both weight and ABTS concentration effect could yet be predicted using a general model built on refined wheat (adjusted R2: 0.9986). Only cryo-milling enabled to reduce granulometry of bran-rich samples in recommended range. Consequent size reduction increased TEAC values up to 90%. Impact of ultrafine jet-milling did however not systemically impact more TEAC values than cryo-milling. The proposed model approach allowed taking the best advantages of QUENCHER and confirmed this method as ideal for industrial applications.
The footprint of bottom trawling in European waters : Distribution, intensity, and seabed integrity
Eigaard, Ole R. ; Bastardie, Francois ; Hintzen, Niels T. ; Buhl-Mortensen, Lene ; Buhl-Mortensen, Pål ; Catarino, Rui ; Dinesen, Grete E. ; Egekvist, Josefine ; Fock, Heino O. ; Geitner, Kerstin ; Gerritsen, Hans D. ; González, Manuel Marín ; Jonsson, Patrik ; Kavadas, Stefanos ; Laffargue, Pascal ; Lundy, Mathieu ; Gonzalez-Mirelis, Genoveva ; Nielsen, J.R. ; Papadopoulou, Nadia ; Posen, Paulette E. ; Pulcinella, Jacopo ; Russo, Tommaso ; Sala, Antonello ; Silva, Cristina ; Smith, Christopher J. ; Vanelslander, Bart ; Rijnsdorp, Adriaan D. - \ 2017
ICES Journal of Marine Science 74 (2017)3. - ISSN 1054-3139 - p. 847 - 865.
benthic impact - bottom trawl - fishing pressure - indicators - Mediterranean Sea - Northeast Atlantic - seabed habitat - seabed integrity - trawling footprint - trawling intensity
Mapping trawling pressure on the benthic habitats is needed as background to support an ecosystem approach to fisheries management. The extent and intensity of bottom trawling on the European continental shelf (0-1000 m) was analysed from logbook statistics and vessel monitoring system data for 2010-2012 at a grid cell resolution of 1 1 min longitude and latitude. Trawling intensity profiles with seabed impact at the surface and subsurface level are presented for 14 management areas in the North-east Atlantic, Baltic Sea and Mediterranean Sea. The footprint of the management areas ranged between 53-99% and 6-94% for the depth zone from 0 to 200 m (Shallow) and from 201 to 1000 m (Deep), respectively. The footprint was estimated as the total area of all grid cells that were trawled fully or partially. Excluding the untrawled proportions reduced the footprint estimates to 28-85% and 2-77%. Largest footprints per unit landings were observed off Portugal and in the Mediterranean Sea. Mean trawling intensity ranged between 0.5 and 8.5 times per year, but was less in the Deep zone with a maximum intensity of 6.4. Highest intensities were recorded in the Skagerrak-Kattegat, Iberian Portuguese area, Tyrrhenian Sea and Adriatic Sea. Bottom trawling was highly aggregated. For the Shallow zone the seabed area where 90% of the effort occurred comprised between 17% and 63% (median 36%) of the management area. Footprints were high over a broad range of soft sediment habitats. Using the longevity distribution of the untrawled infaunal community, the seabed integrity was estimated as the proportion of the biomass of benthic taxa where the trawling interval at the subsurface level exceeds their life span. Seabed integrity was low (>0.1) in large parts of the European continental shelfs, although smaller pockets of seabed with higher integrity values occur. The methods developed here integrate official fishing effort statistics and industry-based gear information to provide high-resolution pressure maps and indicators, which greatly improve the basis for assessing and managing benthic pressure from bottom trawling. Further they provide quantitative estimates of trawling impact on a continuous scale by which managers can steer.
Comparative analysis of spatial genetic structure in an ant-plant symbiosis reveals a tension zone and highlights speciation processes in tropical Africa
Blatrix, Rumsaïs ; Peccoud, Jean ; Born, Céline ; Piatscheck, Finn ; Benoit, Laure ; Sauve, Mathieu ; Djiéto-Lordon, Champlain ; Atteke, Christiane ; Wieringa, Jan J. ; Harris, David J. ; Mckey, Doyle - \ 2017
Journal of Biogeography 44 (2017)8. - ISSN 0305-0270 - p. 1856 - 1868.
Africa - Barteria - Climatic oscillations - Guinea-Congolian rainforest - Incipient speciation - Phylogeography - Pleistocene - Symbiosis - Tension zone - Tetraponera

Aim: Pleistocene climatic oscillations induced range fluctuations in African rain forest organisms and may have shaped species diversification through allopatric speciation events. We compared the spatial genetic structure of two forest species that live in obligate symbiosis and thus must have experienced the same range fluctuations, as a means to discriminate incipient speciation from transient differentiation simply resulting from past divergence. Location: Western central Africa. Methods: We genotyped 765 individuals of the tree Barteria fistulosa and 605 colonies of its symbiotic ant Tetraponera aethiops at 12 and 13 microsatellite loci, respectively. We compared the spatial genetic structure of the two symbionts by using Bayesian clustering algorithms, isolation-by-distance analyses and clines of synthetic alleles. We used species niche modelling (climatic and soil variables) to investigate ecological variables associated with genetic discontinuities in tree populations. Results: The trees and the ants showed congruent patterns of spatial genetic structure. However, the trees showed a very steep genetic discontinuity between groups north and south of latitude 1° N, which was much weaker in the ants. There was no evidence for effective gene flow between the two tree lineages in contact at the transition zone, despite the presence of a few hybrids. Niche modelling did not predict the occurrence of northern trees south of this genetic transition, and vice versa. Main conclusions: The genetic discontinuity near latitude 1° N is inferred to be a tension zone resulting from reproductive incompatibilities between previously allopatric tree lineages. This tension zone may have stabilized at a climatic transition (between boreal and austral seasonal regimes), and matches patterns of genetic structure previously observed in other forest plant species. Our results illustrate independent speciation between two species that live in specific and obligate symbiosis and suggest that a tension zone may separate lineages of several central African forest plants near the thermal equator.

Matching breeding goals with farming systems to enhance the sustainability of fish farming
Besson, Mathieu - \ 2017
University. Promotor(en): Imke de Boer; Hans Komen, co-promotor(en): M. Vandeputte. - Wageningen : Wageningen University - ISBN 9789463430067 - 201
fish culture - sustainability - animal production - farming systems - models - feed conversion - breeding - growth rate - feed conversion efficiency - animal welfare - visteelt - duurzaamheid (sustainability) - dierlijke productie - bedrijfssystemen - modellen - voederconversie - veredelen - groeitempo - voederconversievermogen - dierenwelzijn

Fish farming is growing but is also facing challenges regarding economic viability and environmental sustainability. Selective breeding could enhance the sustainability of fish farming by changing animal performances. Thus, our aim was to develop sustainable breeding goals by using economic (EV) or environmental values (ENV) to weigh the traits to improve. EV and ENV represent the economic and environmental impacts of improving a trait. They were calculated using a bioeconomic model combined with a life cycle assessment. We showed that the EV and ENV of traits change with the factor constraining the production of the farm. It suggests that breeding goals should be finely tuned according to the limiting factor to maximize economic or environmental responses. In addition, we showed that improving feed conversion ratio is a major trait to improve because it always increases profit and decreases environmental impacts. We conclude that it is possible to develop breeding programs enhancing the sustainability of fish farming by improving the right trait in the right production system.

The frankincense tree Boswellia neglecta reveals high potential for restoration of woodlands in the Horn of Africa
Mokria, Mulugeta ; Tolera, Motuma ; Sterck, Frank J. ; Gebrekirstos, Aster ; Bongers, Frans ; Decuyper, Mathieu ; Sass-Klaassen, Ute - \ 2017
Forest Ecology and Management 385 (2017). - ISSN 0378-1127 - p. 16 - 24.
Boswellia neglecta S. Moore is a frankincense-producing tree species dominantly found in the dry woodlands of southeastern Ethiopia. Currently, the population of this socio-economically and ecologically important species is threatened by complex anthropogenic and climate change related factors. Evaluation of tree age and its radial growth dynamics in relation to climate variables helps to understand the response of the species to climate change. It is also crucial for sustainable forest resource management and utilization. Dendrochronological and remote-sensing techniques were used to study periodicity of wood formation and leaf phenology and to assess the growth dynamics of B. neglecta. The results show that B. neglecta forms two growth rings per year in the study area. The growth ring structure is characterized by larger vessels at the beginning of each growing season and smaller vessels formed later in the growing season, suggesting adaptation to decreasing soil moisture deficits at the end of the growing season. Seasonality in cambial activity matches with a bimodal leaf phenological pattern. The mean annual radial growth rate of B. neglecta trees is 2.5 mm. Tree age varied between 16 and 28 years, with an average age of 22 years. The young age of these trees indicates recent colonization of B. neglecta in the study region. The growth rate and seasonal canopy greenness (expressed by Normalized Difference Vegetation Index – NDVI) were positively correlated with rainfall, suggesting that rainfall is the main climatic factor controlling growth of B. neglecta. The observed temporal changes in leaf phenology and vessel size across the growth rings indicate that the species is drought tolerant. Therefore, it can be regarded as a key tree species for restoration of moisture-related limited areas across the Horn of Africa.
Temperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana
Posé, D. ; Verhage, D.S.L. ; Yant, L. ; Mathieu, J. ; Angenent, G.C. ; Immink, G.H. ; Schmid, M. - \ 2016
Arabidopsis thaliana - GSE48082 - PRJNA208886
How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-β and FLM-δ, which compete for interaction with the floral repressor SVP. The SVP/FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-δ complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change. Overall design ChIP-seq A. thaliana FLM (3 replicates for gFLM and 2 replicates for FLM splice variants)
Trends in soil solution dissolved organic carbon (DOC) concentrations across European forests
Camino-Serrano, Marta ; Graf Pannatier, Elisabeth ; Vicca, Sara ; Luyssaert, Sebastiaan ; Jonard, Mathieu ; Ciais, Philippe ; Guenet, Bertrand ; Gielen, Bert ; Peñuelas, Josep ; Sardans, Jordi ; Waldner, Peter ; Sawicka, Kasia - \ 2016
Biogeosciences 13 (2016)19. - ISSN 1726-4170 - p. 5567 - 5585.

Dissolved organic carbon (DOC) in surface waters is connected to DOC in soil solution through hydrological pathways. Therefore, it is expected that long-term dynamics of DOC in surface waters reflect DOC trends in soil solution. However, a multitude of site studies have failed so far to establish consistent trends in soil solution DOC, whereas increasing concentrations in European surface waters over the past decades appear to be the norm, possibly as a result of recovery from acidification. The objectives of this study were therefore to understand the long-term trends of soil solution DOC from a large number of European forests (ICP Forests Level II plots) and determine their main physicochemical and biological controls. We applied trend analysis at two levels: (1) to the entire European dataset and (2) to the individual time series and related trends with plot characteristics, i.e., soil and vegetation properties, soil solution chemistry and atmospheric deposition loads. Analyses of the entire dataset showed an overall increasing trend in DOC concentrations in the organic layers, but, at individual plots and depths, there was no clear overall trend in soil solution DOC. The rate change in soil solution DOC ranged between-16.8 and +23%yr-1 (median=+0.4%yr-1 across Europe. The non-significant trends (40 %) outnumbered the increasing (35 %) and decreasing trends (25 %) across the 97 ICP Forests Level II sites. By means of multivariate statistics, we found increasing trends in DOC concentrations with increasing mean nitrate (NO3 -) deposition and increasing trends in DOC concentrations with decreasing mean sulfate (SO2- 4) deposition, with the magnitude of these relationships depending on plot deposition history. While the attribution of increasing trends in DOC to the reduction of SO2- 4 deposition could be confirmed in low to medium N deposition areas, in agreement with observations in surface waters, this was not the case in high N deposition areas. In conclusion, longterm trends of soil solution DOC reflected the interactions between controls acting at local (soil and vegetation properties) and regional (atmospheric deposition of SO2- 4 and inorganic N) scales.

Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway
Hanemian, Mathieu ; Barlet, Xavier ; Sorin, Céline ; Thomma, Bart P.H.J. - \ 2016
New Phytologist 211 (2016)2. - ISSN 0028-646X - p. 502 - 515.
Affymetrix gene Chip - Arabidopsis thaliana - Bacterial wilt disease - CLAVATA - MiR169 - NF-YA - Plant susceptibility

Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module.

Multi-step control over self-assembled hydrogels of peptide-derived building blocks and a polymeric cross-linker
Nguyen, Duc ; Pal, Asish ; Snijkers, Frank ; Colomb-Delsuc, Mathieu ; Leonetti, Giulia ; Otto, Sijbren ; Gucht, Jasper Van Der - \ 2016
Soft Matter 12 (2016)2. - ISSN 1744-683X - p. 432 - 440.

We present a detailed study of self-assembled hydrogels of bundled and cross-linked networks consisting of positively charged amyloid-like nanofibers and a triblock copolymer with negatively charged end blocks as a cross-linker. In a first step small oligopeptides self-assemble into macrocycles which are held together by reversible disulfide bonds. Interactions between the peptides cause the macrocycles to assemble into nanofibers, which form a reversible hydrogel. The physical properties of the hydrogel are tuned using various methods such as control over the fibre length, addition of a cross-linking copolymer, and addition of salt. We establish a relationship between the bulk mechanical properties, the properties of the individual fibers and the hydrogel morphology using characterization techniques operating at different length scales such as rheology, atomic force microscopy (AFM) and cryo transmission electron microscopy (Cryo-TEM). This allows for a precise control of the elastic behaviour of these networks.

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Willing, Eva Maria ; Rawat, Vimal ; Mandáková, Terezie ; Maumus, Florian ; James, Geo Velikkakam ; Nordström, Karl J.V. ; Becker, Claude ; Warthmann, Norman ; Chica, Claudia ; Szarzynska, Bogna ; Zytnicki, Matthias ; Albani, Maria C. ; Kiefer, Christiane ; Bergonzi, Sara ; Castaings, Loren ; Mateos, Julieta L. ; Berns, Markus C. ; Bujdoso, Nora ; Piofczyk, Thomas ; Lorenzo, Laura De; Barrero-Sicilia, Cristina ; Mateos, Isabel ; Piednoël, Mathieu ; Hagmann, Jörg ; Chen-Min-Tao, Romy ; Iglesias-Fernández, Raquel ; Schuster, Stephan C. ; Alonso-Blanco, Carlos ; Roudier, François ; Carbonero, Pilar ; Paz-Ares, Javier ; Davis, Seth J. ; Pecinka, Ales ; Quesneville, Hadi ; Colot, Vincent ; Lysak, Martin A. ; Weigel, Detlef ; Coupland, George ; Schneeberger, Korbinian - \ 2015
Nature Plants 1 (2015). - ISSN 2055-026X - 7 p.
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 .Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
Soil Compaction
Schjonning, Per ; Akker, J.J.H. van den; Keller, T. ; Greve, M. ; Lamandé, Mathieu ; Simojoki, Asko ; Stettler, M. ; Arvidsson, Johan ; Breuning-Madsen, Henrik - \ 2015
In: Soil in Europe - threats, functions and ecosystem services Bioforsk - p. 80 - 93.
Driver-Pressure-State-Impact-Response (DPSIR) analysis and risk assessment for soil compaction-A European perspective
Schjønning, Per ; Akker, J.J.H. van den; Keller, Thomas ; Greve, M.H. ; Lamandé, Mathieu ; Simojoki, Asko ; Stettler, Matthias ; Arvidsson, Johan ; Breuning-Madsen, Henrik - \ 2015
In: Advances in Agronomy Apple Academic Press Inc (Advances in Agronomy ) - ISBN 9780128030523 - p. 183 - 237.

Compaction of subsoil is a hidden but persistent damage that impairs a range of soil functions and ecosystem services. We analyzed the soil compaction issue in the Driver-Pressure-State-Impact-Response (DPSIR) context. The driving force (DPSIR-D) is the farmers' efforts to sustain economic viability. This entails a steady increase in the size and weight of the agricultural machinery (DPSIR-P) exerting the specific pressures on the soil system. Simulations using historical data for agricultural machinery show significant increases in the mechanical stresses exerted on the soil profile during the last five decades. Surveys and comparative measurements (DPSIR-S) in the literature indicate that much of the European subsoil is compacted to critical levels for cropping. This calls for changes in agricultural management (DPSIR-R). Mechanical stresses impact the soil (DPSIR-I) by reducing the volume, dimensions, and interconnections of soil pores. Subsequent impacts on ecosystem services (subtle DPSIR-I aspects) include a decrease in crop production, an impaired soil filtering of pollutants, and the risk of higher greenhouse gas emissions. The natural ability of compacted subsoil to recover is poor. We highlight the need to expand the DPSIR concept to include a risk assessment methodology to identify sustainable management systems. Risk assessment involves the evaluation of the mechanistic causeeeffect chain of the compaction process. Measured data as well as modeling indicate that contemporary tires are not able to carry the loads frequently inflicted on wet soil without exerting critical stresses on deep subsoil layers. We suggest the use of online modeling tools that combine existing knowledge. Such tools may also create maps of vulnerable areas from the field to the continent scale. Groups of stakeholders including researchers, farmers and their consultants, and policy-makers need to identify sustainable traffic systems that secure both presently focused ecosystem services as well as nonuse soil values (the bequest for future generations).

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