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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    Optimal control of LED light intensity in a plant factory
    Xu, Dan ; Yang, Qichang ; Tong, Yuxing ; Willigenburg, L.G. Van - \ 2020
    In: Proceedings of the 39th Chinese Control Conference, CCC 2020. - IEEE computer society (Chinese Control Conference, CCC ) - ISBN 9781728165233 - p. 1362 - 1367.
    dark time - LED lighting - light intensity - Optimal control - plant factory

    High energy cost of LED lighting is a key factor limiting big-scale plant factory production. In this paper, through optimal control computations, LED light intensity in a plant factory is optimized over time for different electric energy prices and lettuce crop prices. The dynamics of lettuce growth is considered by modifying a greenhouse lettuce growth model. Next, the modified dynamic model is calibrated through the experiment. The dynamic lettuce growth model, like most growth models, does not contain a mechanism that reflects the need for dark periods for proper growth. These are therefore enforced by disabling LED lighting during certain periods at night. Optimal control computations predict the profitability of plant factory production. Moreover, the optimal LED light intensity can be used in the actual production process. The optimal control computations reveal the influence of electric energy price and crop price on the profitability of growing lettuce in a plant factory. This information is highly valuable to growers, legislators, and governments.

    Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences
    Jiang, Yuji ; Luan, Lu ; Hu, Kaijie ; Liu, Manqiang ; Cheng, Ziyun ; Geisen, Stefan ; Chen, Xiaoyun ; Li, Huixin ; Xu, Qinsong ; Bonkowski, Michael ; Sun, Bo - \ 2020
    Microbiome 8 (2020). - ISSN 2049-2618
    Background
    The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fungi (AMF) that provide phosphorous (P) to plants. While plant hosts and abiotic parameters are known to structure AMF communities, it remains largely unknown how higher trophic level organisms, including protists and nematodes, affect AMF abundance and community composition.
    Results
    Here, we explored the connections between AMF, fungivorous protists and nematodes that could partly reflect trophic interactions, and linked those to rhizosphere P dynamics and plant performance in a long-term manure application setting. Our results revealed that manure addition increased AMF biomass and the density of fungivorous nematodes, and tailored the community structures of AMF, fungivorous protists, and nematodes. We detected a higher abundance of AMF digested by the dominant fungivorous nematodes Aphelenchoides and Aphelenchus in high manure treatments compared to no manure and low manure treatments. Structural equation modeling combined with network analysis suggested that predation by fungivorous protists and nematodes stimulated AMF biomass and modified the AMF community composition. The mycorrhizal-fungivore interactions catalyzed AMF colonization and expression levels of the P transporter gene ZMPht1;6 in maize roots, which resulted in enhanced plant productivity.
    Conclusions
    Our study highlights the importance of predation as a key element in shaping the composition and enhancing the biomass of AMF, leading to increased plant performance. As such, we clarify novel biological mechanism of the complex interactions between AMF, fungivorous protists, and nematodes in driving P absorption and plant performance.
    Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe
    Smith, Naomi E. ; Kooijmans, Linda M.J. ; Koren, Gerbrand ; Schaik, Erik van; Woude, Auke M. van der; Wanders, Niko ; Ramonet, Michel ; Xueref-Remy, Irène ; Siebicke, Lukas ; Manca, Giovanni ; Brümmer, Christian ; Baker, Ian T. ; Haynes, Katherine D. ; Luijkx, Ingrid T. ; Peters, Wouter - \ 2020
    Philosophical Transactions of the Royal Society B. Biological sciences 375 (2020)1810. - ISSN 0962-8436 - 1 p.
    CO2 - data assimilation - drought - European carbon balance - remote sensing

    We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO2) by the terrestrial biosphere during the summer of 2018 through observed changes across the Integrated Carbon Observation System (ICOS) network, through biosphere and inverse modelling, and through remote sensing. Highly correlated yet independently-derived reductions in productivity from sun-induced fluorescence, vegetative near-infrared reflectance, and GPP simulated by the Simple Biosphere model version 4 (SiB4) suggest a 130-340 TgC GPP reduction in July-August-September (JAS) of 2018. This occurs over an area of 1.6 × 106 km2 with anomalously low precipitation in northwestern and central Europe. In this drought-affected area, reduced GPP, TER, NEE and soil moisture at ICOS ecosystem sites are reproduced satisfactorily by the SiB4 model. We found that, in contrast to the preceding 5 years, low soil moisture is the main stress factor across the affected area. SiB4's NEE reduction by 57 TgC for JAS coincides with anomalously high atmospheric CO2 observations in 2018, and this is closely matched by the NEE anomaly derived by CarbonTracker Europe (52 to 83 TgC). Increased NEE during the spring (May-June) of 2018 (SiB4 -52 TgC; CTE -46 to -55 TgC) largely offset this loss, as ecosystems took advantage of favourable growth conditions. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

    Assessing long-term spatial movement of wheat area across China
    Fan, Lingling ; Chen, Shi ; Liang, Shefang ; Sun, Xiao ; Chen, Hao ; You, Liangzhi ; Wu, Wenbin ; Sun, Jing ; Yang, Peng - \ 2020
    Agricultural Systems 185 (2020). - ISSN 0308-521X
    China - Climate change - Driving factors - Geographical centroid - Wheat area

    In the context of climate change, assessing spatiotemporal dynamics of crop production is becoming an important component of food security, which is one of the United Nations Sustainable Development Goals. Wheat is a major staple food that is grown worldwide. Although many studies have analyzed wheat production, spatial analyses, particularly geographical centroid (GC) studies, are rare. The GC studies are of important scientific value and policy implications. This study aims to estimate the GC movement of wheat area (including winter and spring wheat) from 1949 to 2014 in China (the largest wheat-producing country). A centroid model was adopted to measure GC movements, and then a regression analysis was conducted to understand the driving factors of wheat area changes (as area changes lead to GC movement). Then multiple scenario analyses were built to study GC movement driven by climatic factors alone. The net GC movements of winter and spring wheat area were estimated at 31 km northwestward and 692 km southwestward from 1949 to 2014, with both displaying a turning point in their movement routes around 1970s (the GC of winter wheat area moved 89 km before 1970s and 66 km after 1970s; while the GC of spring wheat area moved 89 km before 1970s and 799 km after 1970s); furthermore, the major driving factor of winter wheat GC movement is a socioeconomic factor (i.e., expanded irrigation area) while that of spring wheat GC movement is a climatic factor (i.e., temperature) among the factors considered in this study. Our “climate only” scenarios highlighted that the impact of temperature on GC movement of winter wheat is more significant than that of precipitation. We assessed the spatiotemporal movement of wheat area to better understand its production dynamics in response to climate change and human activities. This study provides scientific evidence for policymakers and related stakeholders in China and other countries regarding food production patterns and planting decisions.

    Emulsification and dilatational surface rheology of ultrasonicated milk fat globule membrane (MFGM) materials
    Chen, Min ; Sagis, Leonard M.C. ; Sun, Qingjie - \ 2020
    Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 133 (2020). - ISSN 0023-6438
    Emulsion - Large amplitude oscillatory dilatation (LAOD) - Lecithin - Milk fat globule membrane (MFGM) - Oil/water interface

    Herein milk fat model emulsions (MFMEs) of infant formulas were prepared with ultrasonication-processed milk fat globule membrane (MFGM) materials (as well as MFGM/Lecithin blend and lecithin). The emulsion stability during storage was determined with a turbiscan. The microstructure of MFMEs was examined with confocal laser scanning microscopy (CLSM) at different pH values. Besides, the adsorption kinetics and linear/nonlinear dilatational rheological properties of oil/water interfaces were measured with a droplet tensiometer. After ultrasonication process, the average particle size of MFGM fragments decreased from 800 ± 100 nm to 230 ± 10 nm. The surface tension (at 100 s) of MFGM-stabilized interfaces was 17.4 mN/m (0.5 g/L), 12.9 mN/m (1.0 g/L and 2.0 g/L) and 11.0 mN/m (4.0 g/L), indicating a good emulsifying capacity of ultrasonicated MFGM materials. At neutral and acidic pH, MFMEs stabilized with MFGM dispersions or MFGM/Lecithin (1:1) at a total concentration of 4.0 g/L showed strong resistance against coalescence (CLSM). MFGM dispersions exhibited different surface rheological behaviour from pure phospholipids, proteins or a simple phospholipid/protein mixture, which suggested a heterogeneous structure of MFGM-stabilized interfaces, mainly consisting of MFGM fragment particles, interspersed with free phospholipids and proteins. These findings could provide a better understanding of emulsifying properties of MFGM materials.

    Spatiotemporal dynamics of the northern limit of winter wheat in China using MODIS time series images
    Chen, Shi ; Fan, Lingling ; Liang, Shefang ; Chen, Hao ; Sun, Xiao ; Hu, Yanan ; Liu, Zhenhuan ; Sun, Jing ; Yang, Peng - \ 2020
    Remote Sensing 12 (2020)15. - ISSN 2072-4292
    Crop mapping - MODIS EVI2 - Northern China - Northern limit of winter wheat - Time series classification

    Studying the spatiotemporal changes of the northern limit of winter wheat (NLWW) in China is important to ensure regional food security and deal with the effects of climate change. Previous studies mainly used climate indicators to analyze the variation of the potential NLWW in different historical periods, while little attention has been paid to the actual migrations and changes of the NLWW. The objectives of the present study were three-fold: (i) to map the spatial distribution of winter wheat in northern China in 2001, 2007, 2014 and 2019; (ii) to extract the actual NLWW; and (iii) to quantitatively explore the dynamics of the NLWW. First, we adopted the "combining variations before and after estimated heading dates" method to map the winter wheat in northern China based on time series MODIS EVI2 data. Second, we used the kernel density estimation algorithm to extract the actual NLWW in four historical periods. Finally, the fishnet method was utilized to quantitatively analyze the direction and distance of the spatiotemporal changes of the NLWW. The results demonstrated that the NLWW has exhibited a marked fluctuating trend of migration southward, with a 37-km shift in latitude over the past 20 years. The elevation limit of winter wheat planting was around 1600 m; however, the centroid of winter wheat planting has shifted slowly to lower elevations. There was a gap between the actual NLWW and the potential NLWW. The reason for this gap was that the actual NLWW moved southward under the interacting effects of human activities and climate change, while the potential NLWW moved northward due to climate change. The results of this study are of great scientific value in the formulation of winter wheat planting strategies in climate-sensitive areas to respond to climate change and ensure food security.

    Improving Forecast Skill of Lowland Hydrological Models Using Ensemble Kalman Filter and Unscented Kalman Filter
    Sun, Y. ; Bao, W. ; Valk, K. ; Brauer, C.C. ; Sumihar, J. ; Weerts, A.H. - \ 2020
    Water Resources Research 56 (2020)8. - ISSN 0043-1397
    Kalman filters - lowland hydrology - state updating - streamflow - verification

    For operational water management in lowlands and polders (for instance, in the Netherlands), lowland hydrological models are used for flow prediction, often as an input for a real-time control system to steer water with pumps and weirs to keep water levels within acceptable bounds. Therefore, proper initialization of these models is essential. The ensemble Kalman filter (EnKF) has been widely used due to its relative simplicity and robustness, while the unscented Kalman filter (UKF) has received little attention in the operational context. Here, we test both UKF and EnKF using a lowland lumped hydrological model. The results of a reforecast experiment in an operational context using an hourly time step show that when using nine ensemble members, both filters can improve the accuracy of the forecast by updating the state of a lumped hydrological model (Wageningen Lowland Runoff Simulator, WALRUS) based on the observed discharge, while UKF has achieved better performance than EnKF. Additionally, we show that an increase in the ensemble members does not necessarily mean a significant increase in performance. WALRUS model with either UKF or EnKF could be considered for hydrological forecasting for supporting water management of polders and lowlands, with UKF being the computationally leaner option.

    Towards standardized processing of eddy covariance flux measurements of carbonyl sulfide
    Kohonen, Kukka Maaria ; Kolari, Pasi ; Kooijmans, Linda M.J. ; Chen, Huilin ; Seibt, Ulli ; Sun, Wu ; Mammarella, Ivan - \ 2020
    Atmospheric Measurement Techniques 13 (2020)7. - ISSN 1867-1381 - p. 3957 - 3975.

    Carbonyl sulfide (COS) flux measurements with the eddy covariance (EC) technique are becoming popular for estimating gross primary productivity. To compare COS flux measurements across sites, we need standardized protocols for data processing. In this study, we analyze how various data processing steps affect the calculated COS flux and how they differ from carbon dioxide (CO2) flux processing steps, and we provide a method for gap-filling COS fluxes. Different methods for determining the time lag between COS mixing ratio and the vertical wind velocity (w) resulted in a maximum of 15.9% difference in the median COS flux over the whole measurement period. Due to limited COS measurement precision, small COS fluxes (below approximately 3 pmolm-2 s-1) could not be detected when the time lag was determined from maximizing the covariance between COS and w. The difference between two highfrequency spectral corrections was 2.7% in COS flux calculations, whereas omitting the high-frequency spectral correction resulted in a 14.2% lower median flux, and different detrending methods caused a spread of 6.2 %. Relative total uncertainty was more than 5 times higher for low COS fluxes (lower than3 pmolm-2 s-1) than for low CO2 fluxes (lower than1:5 molm-2 s-1), indicating a low signal-tonoise ratio of COS fluxes. Due to similarities in ecosystem COS and CO2 exchange, we recommend applying storage change flux correction and friction velocity filtering as usual in EC flux processing, but due to the low signal-to-noise ratio of COS fluxes, we recommend using CO2 data for time lag and high-frequency corrections of COS fluxes due to the higher signal-to-noise ratio of CO2 measurements.

    CloudRoots: integration of advanced instrumental techniques and process modelling of sub-hourly and sub-kilometre land–atmosphere interactions
    Vilà-Guerau de Arellano, Jordi ; Ney, Patrizia ; Hartogensis, Oscar ; Boer, Hugo De; Diepen, Kevin Van; Emin, Dzhaner ; Groot, Geiske De; Klosterhalfen, Anne ; Langensiepen, Matthias ; Matveeva, Maria ; Miranda-García, Gabriela ; Moene, Arnold F. ; Rascher, Uwe ; Röckmann, Thomas ; Adnew, Getachew ; Brüggemann, Nicolas ; Rothfuss, Youri ; Graf, Alexander - \ 2020
    Biogeosciences 17 (2020)17. - ISSN 1726-4170 - p. 4375 - 4404.
    The CloudRoots field experiment was designed to obtain a comprehensive observational dataset that includes soil, plant, and atmospheric variables to investigate the interaction between a heterogeneous land surface and its overlying atmospheric boundary layer at the sub-hourly and sub-kilometre scale. Our findings demonstrate the need to include measurements at leaf level to better understand the relations between stomatal aperture and evapotranspiration (ET) during the growing season at the diurnal scale. Based on these observations, we obtain accurate parameters for the mechanistic representation of photosynthesis and stomatal aperture. Once the new parameters are implemented, the model reproduces the stomatal leaf conductance and the leaf-level photosynthesis satisfactorily. At the canopy scale, we find a consistent diurnal pattern on the contributions of plant transpiration and soil evaporation using different measurement techniques. From highly resolved vertical profile measurements of carbon dioxide (CO2) and other state variables, we infer a profile of the CO2 assimilation in the canopy with non-linear variations with height. Observations taken with a laser scintillometer allow us to quantify the non-steadiness of the surface turbulent fluxes during the rapid changes driven by perturbation of photosynthetically active radiation by cloud flecks. More specifically, we find 2 min delays between the cloud radiation perturbation and ET. To study the relevance of advection and surface heterogeneity for the land–atmosphere interaction, we employ a coupled surface–atmospheric conceptual model that integrates the surface and upper-air observations made at different scales from leaf to the landscape. At the landscape scale, we calculate a composite sensible heat flux by weighting measured fluxes with two different land use categories, which is consistent with the diurnal evolution of the boundary layer depth. Using sun-induced fluorescence measurements, we also quantify the spatial variability of ET and find large variations at the sub-kilometre scale around the CloudRoots site. Our study shows that throughout the entire growing season, the wide variations in stomatal opening and photosynthesis lead to large diurnal variations of plant transpiration at the leaf, plant, canopy, and landscape scales. Integrating different advanced instrumental techniques with modelling also enables us to determine variations of ET that depend on the scale where the measurement were taken and on the plant growing stage
    Intercomparison of Large-Eddy Simulations of the Antarctic Boundary Layer for Very Stable Stratification
    Couvreux, Fleur ; Bazile, Eric ; Rodier, Quentin ; Maronga, Björn ; Matheou, Georgios ; Chinita, Maria J. ; Edwards, John ; Stratum, Bart J.H. van; Heerwaarden, Chiel C. van; Huang, Jing ; Moene, Arnold F. ; Cheng, Anning ; Fuka, Vladimir ; Basu, Sukanta ; Bou-Zeid, Elie ; Canut, Guylaine ; Vignon, Etienne - \ 2020
    Boundary-Layer Meteorology 176 (2020)3. - ISSN 0006-8314 - p. 369 - 400.
    Antarctica - Dome C - Large-eddy simulation - Parametrization - Stable boundary layer - Subgrid turbulence parametrization

    In polar regions, where the boundary layer is often stably stratified, atmospheric models produce large biases depending on the boundary-layer parametrizations and the parametrization of the exchange of energy at the surface. This model intercomparison focuses on the very stable stratification encountered over the Antarctic Plateau in 2009. Here, we analyze results from 10 large-eddy-simulation (LES) codes for different spatial resolutions over 24 consecutive hours, and compare them with observations acquired at the Concordia Research Station during summer. This is a challenging exercise for such simulations since they need to reproduce both the 300-m-deep convective boundary layer and the very thin stable boundary layer characterized by a strong vertical temperature gradient (10 K difference over the lowest 20 m) when the sun is low over the horizon. A large variability in surface fluxes among the different models is highlighted. The LES models correctly reproduce the convective boundary layer in terms of mean profiles and turbulent characteristics but display more spread during stable conditions, which is largely reduced by increasing the horizontal and vertical resolutions in additional simulations focusing only on the stable period. This highlights the fact that very fine resolution is needed to represent such conditions. Complementary sensitivity studies are conducted regarding the roughness length, the subgrid-scale turbulence closure as well as the resolution and domain size. While we find little dependence on the surface-flux parametrization, the results indicate a pronounced sensitivity to both the roughness length and the turbulence closure.

    Pathologists and entomologists must join forces against forest pest and pathogen invasions
    Jactel, Hervé ; Desprez-Loustau, Marie Laure ; Battisti, Andrea ; Brockerhoff, Eckehard ; Santini, Alberto ; Stenlid, Jan ; Björkman, Christer ; Branco, Manuela ; Dehnen-Schmutz, Katharina ; Douma, Jacob C. ; Drakulic, Jassy ; Drizou, Fryni ; Eschen, René ; Franco, José Carlos ; Gossner, Martin M. ; Green, Samantha ; Kenis, Marc ; Klapwijk, Maartje J. ; Liebhold, Andrew M. ; Orazio, Christophe ; Prospero, Simone ; Robinet, Christelle ; Schroeder, Martin ; Slippers, Bernard ; Stoev, Pavel ; Sun, Jianghua ; Dool, Robbert van den; Wingfield, Michael J. ; Zalucki, Myron P. - \ 2020
    NeoBiota 58 (2020). - ISSN 1619-0033 - p. 107 - 127.
    Capacity building - Detection - Disease - Exotic - Forest health - Fungi - Identification - Insects - Interdisciplinarity - Management

    The world's forests have never been more threatened by invasions of exotic pests and pathogens, whose causes and impacts are reinforced by global change. However, forest entomologists and pathologists have, for too long, worked independently, used different concepts and proposed specific management methods without recognising parallels and synergies between their respective fields. Instead, we advocate increased collaboration between these two scientific communities to improve the long-term health of forests. Our arguments are that the pathways of entry of exotic pests and pathogens are often the same and that insects and fungi often coexist in the same affected trees. Innovative methods for preventing invasions, early detection and identification of non-native species, modelling of their impact and spread and prevention of damage by increasing the resistance of ecosystems can be shared for the management of both pests and diseases. We, therefore, make recommendations to foster this convergence, proposing in particular the development of interdisciplinary research programmes, the development of generic tools or methods for pest and pathogen management and capacity building for the education and training of students, managers, decision-makers and citizens concerned with forest health.

    Configuration of active site segments in lytic polysaccharide monooxygenases steers oxidative xyloglucan degradation
    Sun, Peicheng ; Laurent, Christophe V.F.P. ; Scheiblbrandner, Stefan ; Frommhagen, Matthias ; Kouzounis, Dimitrios ; Sanders, Mark G. ; Berkel, Willem J.H. van; Ludwig, Roland ; Kabel, Mirjam A. - \ 2020
    Biotechnology for Biofuels 13 (2020)1. - ISSN 1754-6834 - 19 p.
    AA9 LPMO - Active site segments - Biomass - Biorefinery - Hemicellulose - Lignocellulose - Neurospora crassa - Phylogenetic tree - Plant cell wall - Xyloglucan

    Background: Lytic polysaccharide monooxygenases (LPMOs) are powerful enzymes that oxidatively cleave plant cell wall polysaccharides. LPMOs classified as fungal Auxiliary Activities family 9 (AA9) have been mainly studied for their activity towards cellulose; however, various members of this AA9 family have been also shown to oxidatively cleave hemicelluloses, in particularly xyloglucan (XG). So far, it has not been studied in detail how various AA9 LPMOs act in XG degradation, and in particular, how the mode-of-action relates to the structural configuration of these LPMOs. Results: Two Neurospora crassa (Nc) LPMOs were found to represent different mode-of-action towards XG. Interestingly, the configuration of active site segments of these LPMOs differed as well, with a shorter Segment 1 (Seg1) and a longer Segment 2 (+Seg2) present in NcLPMO9C and the opposite for NcLPMO9M (+Seg1Seg2). We confirmed that NcLPMO9C cleaved the non-reducing end of unbranched glucosyl residues within XG via the oxidation of the C4-carbon. In contrast, we found that the oxidative cleavage of the XG backbone by NcLPMO9M occurred next to both unbranched and substituted glucosyl residues. The latter are decorated with xylosyl, xylosyl-galactosyl and xylosyl-galactosyl-fucosyl units. The relationship between active site segments and the mode-of-action of these NcLPMOs was rationalized by a structure-based phylogenetic analysis of fungal AA9 LPMOs. LPMOs with a Seg1+Seg2 configuration clustered together and appear to have a similar XG substitution-intolerant cleavage pattern. LPMOs with the +Seg1Seg2 configuration also clustered together and are reported to display a XG substitution-tolerant cleavage pattern. A third cluster contained LPMOs with a Seg1Seg2 configuration and no oxidative XG activity. Conclusions: The detailed characterization of XG degradation products released by LPMOs reveal a correlation between the configuration of active site segments and mode-of-action of LPMOs. In particular, oxidative XG-active LPMOs, which are tolerant and intolerant to XG substitutions are structurally and phylogenetically distinguished from XG-inactive LPMOs. This study contributes to a better understanding of the structure-function relationship of AA9 LPMOs.

    A systems analysis of microplastic pollution in Laizhou Bay, China
    Teng, Jia ; Zhao, Jianmin ; Zhang, C. ; Cheng, Bo ; Koelmans, A.A. ; Wu, Di ; Gao, Meng ; Sun, Xiyan ; Wang, Qing - \ 2020
    Science of the Total Environment 745 (2020). - ISSN 0048-9697
    Microplastic contamination is attracting increasing attention worldwide. In this study, the patterns of microplastic contamination in surface water and sediment from 58 sites, and living fish from 31 sites were investigated in a semi-closed bay (Laizhou Bay, China). Microplastics in Laizhou Bay were pervasively distributed, particularly in the form of fibers. Microplastic abundance exhibited no significant differences among regions in either surface waters or sediments, indicating multiple sources of microplastics pollution in the bay. Spatial hotspot (Getis-Ord Gi*) analysis demonstrated that microplastic pollution was mainly concentrated in the Laizhou-Weifang area, which in turn was mainly affected by ocean current dynamics. Although the spatial distribution of microplastics in sediments was different from surface water, it was also affected by geology, hydrogeology, and anthropogenic activities. The most common polymer in the surface waters was polyethylene terephthalate (PET), while cellophane (CP) was the most frequently observed polymer in sediment, suggesting different sinking behaviors of these microplastics. The proportion of low-density microplastics (PE and PP) in surface water was approximately 19.9%, but these microplastics accounted for only approximately 1.7% in the sediment, suggesting that low-density microplastic particles preferentially migrate to open sea. There were significant differences in shape, size and polymer type of the microplastics among surface water, sediment and biota (p < 0.05). Cluster analysis suggested that the Gudong, Yellow River Estuary and Laizhou-Weifang regions are three sources of microplastics, which might originate from river input, plastic recycling and marine raft aquaculture. Furthermore, microplastic particle diversity was greater in sediment at offshore sites, suggesting that these sites receive microplastics from multiple sources. Our results characterize the microplastic pollution pattern, clarify the possible transfer mechanisms between different environmental media, and will provide important information for risk evaluation and pollution control in this area.
    Transferability of a soil variogram for sampling design : A case study of three grasslands in Ireland
    Sun, Xiao Lin ; Brus, Dick J. - \ 2020
    European Journal of Soil Science (2020). - ISSN 1351-0754
    grid spacing - mapping - MCMC - precision agriculture - sample size

    It is commonly accepted that an estimated soil variogram can be transferred to another similar area for deriving the tolerable spacing of a sampling grid or, more generally, the sample size, given a requirement on the quality of the soil property map of the recipient area. The quality of the derived tolerable grid spacing depends on how similar the population variograms of the donor area and recipient area are. In practice we are uncertain about the variograms of both areas due to sampling errors. Ideally, the uncertainty about the variogram of the donor area is accounted for in deriving the tolerable grid spacing. To assess the transferability, we should also account for uncertainty in the estimated variogram of the recipient area. In this study the transferability of variograms of soil pH, P, Mg and K is analysed for three grassland fields in Ireland, which are similar in soil-forming factors. One field served as donor area, the other two as recipient area. For all three fields and for each soil property, 500 variograms were sampled from the posterior distribution of the variogram parameters. Results showed that the estimated variogram parameters of the recipient fields differed largely from those of the transferred variograms. The ranges of estimated mean kriging variance values for the various grid spacings, as obtained with the two sets of variograms (one set of the donor field, one set of the recipient field), did not overlap. Even after scaling the transferred variogram with an estimate of the variance of the recipient field, the transferred variogram was of no use for determining the tolerable grid spacing. The difference in the variograms can possibly be explained by the difference in historical land use. Highlights: Transferability of variograms to derive tolerable grid spacing for mapping grassland fields is assessed Transferability should be based on the uncertainty distributions of the tolerable grid spacings Due to difference in historical land use, local and transferred variograms differed largely Transferability of a variogram is very poor, even after scaling the transferred variogram.

    Long-term response of groundcover components to organic and conventional weed control in shaded and open-sun coffee in Nicaragua
    Staver, Charles ; Juventia, Stella Dimitri ; Navarrete, Elvin ; Correo, Ledis N. ; Sepulveda, Norvin ; Barrios, Mirna - \ 2020
    Crop Protection 133 (2020). - ISSN 0261-2194
    The weed-free period is employed to evaluate the effectiveness of practices to reduce crop loss to weeds. To orient sustainable cropping system approaches in perennial crops such as coffee which are often grown with trees, orchard floor or groundcover management has been proposed to address not only crop loss, but also soil protection, plant nutrition, habitat for beneficial organisms and labor and input costs. The results of a long-term experiment in Masatepe, Nicaragua, comparing two intensities of organic and conventional coffee management under four combinations of deciduous and evergreen trees either leguminous (Inga laurina and Samanea saman) and non-leguminous (Simarouba glauca and Tabebuia rosea) and full sun concluded that with selective weed management under trees, soil is protected with both low-growing, shallow-rooted cover vegetation and tree leaf litter without yield loss, while also reducing herbicide and labor use. Over 11 years, treatments with trees compared to full sun coffee showed near absence of bare soil (P < .001) and increasing presence of leaf litter (P < .001) and cover vegetation (P < .001), especially in the first 8 years. Selective control, either herbicide or manual, resulted in minimal bare soil, a declining area covered by weeds and increased area, from 40 to 70%, under cover vegetation. Selective control with herbicides had less weedy vegetation than manual selective control. Trees compared to full sun showed increased accumulation of whole leaf and fractionated leaf layers measured in the dry season with treatments including Inga laurina greater than other tree treatments. Labor and herbicide costs declined with increasing time under trees (P < .001), while selective control reduced herbicide use with higher labor costs. A regression of groundcover components on coffee berry yields explained less than 10% of variability. Two research priorities are identified to increase the contribution of groundcover components to sustainable coffee systems – 1) cover vegetation species and management in water conservation and use and 2) the role of tree species and their litter on water, soil biology dynamics and O horizon formation.
    Fatty acids in the de novo lipogenesis pathway and incidence of type 2 diabetes : A pooled analysis of prospective cohort studies
    Imamura, Fumiaki ; Fretts, Amanda M. ; Marklund, Matti ; Ardisson Korat, Andres V. ; Yang, Wei Sin ; Lankinen, Maria ; Qureshi, Waqas ; Helmer, Catherine ; Chen, Tzu An ; Virtanen, Jyrki K. ; Wong, Kerry ; Bassett, Julie K. ; Murphy, Rachel ; Tintle, Nathan ; Yu, Chaoyu Ian ; Brouwer, Ingeborg A. ; Chien, Kuo Liong ; Chen, Yun Yu ; Wood, Alexis C. ; Gobbo, Liana C. Del; Djousse, Luc ; Geleijnse, Johanna M. ; Giles, Graham G. ; Goede, Janette de; Gudnason, Vilmundur ; Harris, William S. ; Hodge, Allison ; Hu, Frank ; Koulman, Albert ; Laakso, Markku ; Lind, Lars ; Lin, Hung Ju ; McKnight, Barbara ; Rajaobelina, Kalina ; Riserus, Ulf ; Robinson, Jennifer G. ; Samieri, Cecilia ; Senn, Mackenzie ; Siscovick, David S. ; Soedamah-Muthu, Sabita S. ; Sotoodehnia, Nona ; Sun, Qi ; Tsai, Michael Y. ; Tuomainen, Tomi Pekka ; Uusitupa, Matti ; Wagenknecht, Lynne E. ; Wareham, Nick J. ; Wu, Jason H.Y. ; Micha, Renata ; Lemaitre, Rozenn N. - \ 2020
    PLOS Medicine 17 (2020)6. - ISSN 1549-1676 - p. e1003102 - e1003102.

    BACKGROUND: De novo lipogenesis (DNL) is the primary metabolic pathway synthesizing fatty acids from carbohydrates, protein, or alcohol. Our aim was to examine associations of in vivo levels of selected fatty acids (16:0, 16:1n7, 18:0, 18:1n9) in DNL with incidence of type 2 diabetes (T2D). METHODS AND FINDINGS: Seventeen cohorts from 12 countries (7 from Europe, 7 from the United States, 1 from Australia, 1 from Taiwan; baseline years = 1970-1973 to 2006-2010) conducted harmonized individual-level analyses of associations of DNL-related fatty acids with incident T2D. In total, we evaluated 65,225 participants (mean ages = 52.3-75.5 years; % women = 20.4%-62.3% in 12 cohorts recruiting both sexes) and 15,383 incident cases of T2D over the 9-year follow-up on average. Cohort-specific association of each of 16:0, 16:1n7, 18:0, and 18:1n9 with incident T2D was estimated, adjusted for demographic factors, socioeconomic characteristics, alcohol, smoking, physical activity, dyslipidemia, hypertension, menopausal status, and adiposity. Cohort-specific associations were meta-analyzed with an inverse-variance-weighted approach. Each of the 4 fatty acids positively related to incident T2D. Relative risks (RRs) per cohort-specific range between midpoints of the top and bottom quintiles of fatty acid concentrations were 1.53 (1.41-1.66; p < 0.001) for 16:0, 1.40 (1.33-1.48; p < 0.001) for 16:1n-7, 1.14 (1.05-1.22; p = 0.001) for 18:0, and 1.16 (1.07-1.25; p < 0.001) for 18:1n9. Heterogeneity was seen across cohorts (I2 = 51.1%-73.1% for each fatty acid) but not explained by lipid fractions and global geographical regions. Further adjusted for triglycerides (and 16:0 when appropriate) to evaluate associations independent of overall DNL, the associations remained significant for 16:0, 16:1n7, and 18:0 but were attenuated for 18:1n9 (RR = 1.03, 95% confidence interval (CI) = 0.94-1.13). These findings had limitations in potential reverse causation and residual confounding by imprecisely measured or unmeasured factors. CONCLUSIONS: Concentrations of fatty acids in the DNL were positively associated with T2D incidence. Our findings support further work to investigate a possible role of DNL and individual fatty acids in the development of T2D.

    Reproducible molecular networking of untargeted mass spectrometry data using GNPS
    Aron, Allegra T. ; Gentry, Emily C. ; McPhail, Kerry L. ; Nothias, Louis Félix ; Nothias-Esposito, Mélissa ; Bouslimani, Amina ; Petras, Daniel ; Gauglitz, Julia M. ; Sikora, Nicole ; Vargas, Fernando ; Hooft, Justin J.J. van der; Ernst, Madeleine ; Kang, Kyo Bin ; Aceves, Christine M. ; Caraballo-Rodríguez, Andrés Mauricio ; Koester, Irina ; Weldon, Kelly C. ; Bertrand, Samuel ; Roullier, Catherine ; Sun, Kunyang ; Tehan, Richard M. ; Boya P, Cristopher A. ; Christian, Martin H. ; Gutiérrez, Marcelino ; Ulloa, Aldo Moreno ; Tejeda Mora, Javier Andres ; Mojica-Flores, Randy ; Lakey-Beitia, Johant ; Vásquez-Chaves, Victor ; Zhang, Yilue ; Calderón, Angela I. ; Tayler, Nicole ; Keyzers, Robert A. ; Tugizimana, Fidele ; Ndlovu, Nombuso ; Aksenov, Alexander A. ; Jarmusch, Alan K. ; Schmid, Robin ; Truman, Andrew W. ; Bandeira, Nuno ; Wang, Mingxun ; Dorrestein, Pieter C. - \ 2020
    Nature protocols 15 (2020). - ISSN 1754-2189 - p. 1954 - 1991.

    Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking—one of the main analysis tools used within the GNPS platform—creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

    Assessment of the quality of tropomi high-spatial-resolution no2 data products in the greater toronto area
    Zhao, Xiaoyi ; Griffin, Debora ; Fioletov, Vitali ; McLinden, Chris ; Cede, Alexander ; Tiefengraber, Martin ; Müller, Moritz ; Bognar, Kristof ; Strong, Kimberly ; Boersma, Folkert ; Eskes, Henk ; Davies, Jonathan ; Ogyu, Akira ; Chi Lee, Sum - \ 2020
    Atmospheric Measurement Techniques 13 (2020)4. - ISSN 1867-1381 - p. 2131 - 2159.

    The TROPOspheric Monitoring Instrument (TROPOMI) aboard the Sentinel-5 Precursor satellite (launched on 13 October 2017) is a nadir-viewing spectrometer measuring reflected sunlight in the ultraviolet, visible, near-infrared, and shortwave infrared spectral ranges. The measured spectra are used to retrieve total columns of trace gases, including nitrogen dioxide (NO2). For ground validation of these satellite measurements, Pandora spectrometers, which retrieve high-quality NO2 total columns via direct-sun measurements, are widely used. In this study, Pandora NO2 measurements made at three sites located in or north of the Greater Toronto Area (GTA) are used to evaluate the TROPOMI NO2 data products, including a standard Royal Netherlands Meteorological Institute (KNMI) tropospheric and stratospheric NO2 data product and a TROPOMI research data product developed by Environment and Climate Change Canada (ECCC) using a high-resolution regional air quality forecast model (in the air mass factor calculation). It is found that these current TROPOMI tropospheric NO2 data products (standard and ECCC) met the TROPOMI design bias requirement (< 10 %). Using the statistical uncertainty estimation method, the estimated TROPOMI upper-limit precision falls below the design requirement at a rural site but above in the other two urban and suburban sites. The Pandora instruments are found to have sufficient precision (< 0.02 DU) to perform TROPOMI validation work. In addition to the traditional satellite validation method (i.e., pairing ground-based measurements with satellite measurements closest in time and space), we analyzed TROPOMI pixels located upwind and downwind from the Pandora site. This makes it possible to improve the statistics and better interpret the high-spatial-resolution measurements made by TROPOMI. By using this wind-based validation technique, the number of coincident measurements can be increased by about a factor of 5. With this larger number of coincident measurements, this work shows that both TROPOMI and Pandora instruments can reveal detailed spatial patterns (i.e., horizontal distributions) of local and transported NO2 emissions, which can be used to evaluate regional air quality changes. The TROPOMI ECCC NO2 research data product shows improved agreement with Pandora measurements compared to the TROPOMI standard tropospheric NO2 data product (e.g., lower multiplicative bias at the suburban and urban sites by about 10 %), demonstrating benefits from the high-resolution regional air quality forecast model.

    Sun cream for trees?
    Sluis, Bart van der - \ 2020
    Arabidopsis in the wild—the effect of seasons on seed performance
    Souza Vidigal, Deborah de; He, Hanzi ; Hilhorst, Henk W.M. ; Willems, Leo A.J. ; Bentsink, Leónie - \ 2020
    Plants 9 (2020)5. - ISSN 2223-7747
    Arabidopsis - Environmental effects - Field conditions - Seed dormancy - Seed longevity

    Climate changes play a central role in the adaptive life histories of organisms all over the world. In higher plants, these changes may impact seed performance, both during seed development and after dispersal. To examine the plasticity of seed performance as a response to environmental fluctuations, eight genotypes known to be affected in seed dormancy and longevity were grown in the field in all seasons of two years. Soil and air temperature, day length, precipitation, and sun hours per day were monitored. We show that seed performance depends on the season. Seeds produced by plants grown in the summer, when the days began to shorten and the temperature started to decrease, were smaller with deeper dormancy and lower seed longevity compared to the other seasons when seeds were matured at higher temperature over longer days. The performance of seeds developed in the different seasons was compared to seeds produced in controlled conditions. This revealed that plants grown in a controlled environment produced larger seeds with lower dormancy than those grown in the field. All together the results show that the effect of the environment largely overrules the genetic effects, and especially, differences in seed dormancy caused by the different seasons were larger than the differences between the genotypes.

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