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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    Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana
    Hartanto, Margi ; Joosen, Ronny V.L. ; Snoek, Basten L. ; Willems, Leo A.J. ; Sterken, Mark G. ; Ridder, Dick De; Hilhorst, Henk W.M. ; Ligterink, Wilco ; Nijveen, Harm - \ 2020
    G3 : Genes Genomes Genetics 10 (2020)10. - ISSN 2160-1836
    Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTLs in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
    Disentangling the direct and indirect effects of cropland abandonment on soil microbial activity in grassland soil at different depths
    Xu, Hongwei ; Qu, Qing ; Chen, Yanhua ; Wang, Minggang ; Liu, Guobin ; Xue, Sha ; Yang, Xiaomei - \ 2020
    Catena 194 (2020). - ISSN 0341-8162
    Plant-soil interactions - Soil enzyme activity - Soil nutrients - Structural equation models - Vegetation restoration

    Cropland abandonment strongly affects plant-soil interactions. However, knowledge remains limited about how the production and diversity of plants and soil physicochemical parameters drive changes in soil microbial activity (such as microbial biomass, respiration, and enzyme activity) after cropland abandonment. Here, we investigated a grassland restoration chronosequence (0–30 years) to determine the dynamics of soil microbial biomass, respiration, and enzyme activity in the Loess Hilly, Region (China). Overall, cropland abandonment caused an increase in soil microbial activity primarily in the 0–20 cm soil layers. The metabolic quotient in the 0–10 cm layer decreased linearly with time since abandonment (recovery years). Structural equation models showed that recovery years directly and indirectly affected changes to soil microbial activity. Plant species richness, aboveground biomass, and soil organic carbon explained a large proportion of the variability in soil microbial activity in the 0–20 cm layer. However, the variability in soil microbial activity was mostly explained by plant species richness, belowground biomass, and soil total nitrogen in the 20–50 cm layers. Our results indicate that during recovery after cropland abandonment, changes in soil microbial activity are driven by plant characteristics and soil physicochemical parameters, with different drivers at different soil depths.

    Chain conformation and physicochemical properties of polysaccharide (glucuronoxylomannan) from Fruit Bodies of Tremella fuciformis
    Xu, Xiaoqi ; Chen, Aijun ; Ge, Xinyan ; Li, Sha ; Zhang, Tao ; Xu, Hong - \ 2020
    Carbohydrate Polymers 245 (2020). - ISSN 0144-8617
    Chain conformation - Glucuronoxylomannan - Moisture absorption and retention capacity - Rheological properties - Tremella fuciformis - Wormlike cylinder model

    Based on its potential bioactivities and sustainable source, polysaccharide (glucuronoxylomannan) from fruit bodies of Tremella fuciformis (TFP) aroused attention in food, pharmaceutical and cosmetic industry. The present study aimed at revealing its chain conformational and physicochemical properties. By using HPSEC-MALLS-Visc-RI measurement, worm-like cylinder model calculation and AFM observation, we manifested that TFP existed as flexible chains in 0.15 M NaCl (pH 7.4) solution, with the persistence length of 9.20 nm and chain diameter of 0.97 nm. Meanwhile, TFP solution exhibited shear-thinning behavior with C* at 5.3 mg mL−1, owning the feature of entangled polysaccharide. TFP solution changed from liquid-like to solid-like behavior as frequency increases, and the crossover points shifted to lower frequencies with concentration increasing. Besides, the strong moisture retention ability of TFP was evaluated. These characteristics indicated that TFP could be utilized to design microstructure system and applied as stabilizer or moisture holding ingredient in food, pharmaceutical and cosmetic system.

    Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Wageningen University
    GSE145895 - PRJNA608688 - Mus musculus
    Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.

    The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.

    Benthic invertebrate and microbial biodiversity in sub-tropical urban rivers: Correlations with environmental variables and emerging chemicals
    Peng, Feng Jiao ; Pan, Chang Gui ; Zhang, Nai Sheng ; Braak, Cajo J.F. ter; Salvito, Daniel ; Selck, Henriette ; Ying, Guang Guo ; Brink, Paul J. Van den - \ 2020
    Science of the Total Environment 709 (2020). - ISSN 0048-9697
    Benthic bacterial community - Benthic macroinvertebrates - Double constrained ordination - Traits - Urban rivers - WWTP effluents

    Urban rivers often function as sinks for various contaminants potentially placing the benthic communities at risk of exposure. We performed a comprehensive biological survey of the benthic macroinvertebrate and bacterial community compositions in six rivers from the suburb to the central urban area of Guangzhou city (South China), and evaluated their correlations with emerging organic contaminants, heavy metals and nutrients. Overall, the benthic macroinvertebrate community shifted from molluscs to oligochaete from the suburban to the central urban rivers that receive treated and untreated sewage. An exception was the site in the Sha River where chironomids were most abundant. The differences in macroinvertebrate community assemblages were significantly associated with chromium, total phosphorus, galaxolide, triclosan and sand content in the sediment. There was no significant difference in benthic macroinvertebrate composition between the dry and wet season. As assessed by double constrained ordination, sexual reproduction was the only trait of benthic macroinvertebrates that showed a significant correlation with pollution variables, as it was significantly positively correlated with chromium and total phosphorus. This suggests that r-strategist occurs in polluted sampling sites. The benthic bacterial community composition showed a significant difference between seasons and among the Liuxi River, Zhujiang River and central urban rivers. The differences in community composition of the benthic bacteria were significantly correlated with galaxolide, total phosphorus, lead and triclosan. These results suggest that input of treated and untreated sewage significantly altered the benthic macroinvertebrate and bacterial community compositions in urban rivers.

    Revealing the nutrient limitation and cycling for microbes under forest management practices in the Loess Plateau – Ecological stoichiometry
    Zhang, Jiaoyang ; Yang, Xiaomei ; Song, Yahui ; Liu, Hongfei ; Wang, Guoliang ; Xue, Sha ; Liu, Guobin ; Ritsema, Coen J. ; Geissen, Violette - \ 2020
    Geoderma 361 (2020). - ISSN 0016-7061
    Ecological environment - Ecological stoichiometry - Forest management practices - Stoichiometric homeostasis - Threshold elemental ratio

    Forest management practices are commonly used in plantation forestry to obtain renewable energy and harvest biomass, in addition to maintaining the ecological environment, by changing the flow of carbon (C) and nutrients in the food webs of terrestrial ecosystems. To identify which forest management practices, alleviate soil nutrient limitation and impact stoichiometric homeostasis in relation to microbes, we used a Pinus tabuliformis plantation in the Loess Plateau where forest management practices were conducted since 1999. Five forest management practices were implemented: two at the forest level (P. tabuliformis with and without ground litter, CK, LRL) and three of different vegetation restorations after clear-cutting (P. tabuliformis seedlings (SPL), grass land (GL), and shrub land (SL)). Generally, the threshold elemental ratios for carbon:nitrogen (TERC:N; 7.77) and carbon:phosphorus (TERC:P; 44.37) were lower than the ratios influenced by forest management practices. The forest management practices significantly influenced ecoenzymatic activity and the ratios of ecoenzymes; however, the scale of the ecoenzyme activities for acquiring both organic N and organic P to that for acquiring C still follow the global pattern. The regression coefficients of C:N and C:P between the soil and microbial community at 0–20 cm and 20–40 cm depths were also influenced by these practices. Thus, the influence of forest management practices on the soil microbial community was limited by N and P in the Loess Plateau. The soil microbial community changed ecoenzymatic activities and ratios of ecoenzymes and even changed microbial community in order to balance elemental limitations in the soil. Finally, forest management practices have a minimal impact on the stoichiometric homeostasis of the microbial community at our study site.

    A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici
    Steinhauer, Diana ; Salat, Marie ; Frey, Regula ; Mosbach, Andreas ; Luksch, Torsten ; Balmer, Dirk ; Hansen, Rasmus ; Widdison, Stephanie ; Logan, Grace ; Dietrich, Robert A. ; Kema, Gert H.J. ; Bieri, Stephane ; Sierotzki, Helge ; Torriani, Stefano F.F. ; Scalliet, Gabriel - \ 2019
    PLoS Pathogens 15 (2019)12. - ISSN 1553-7366

    Succinate dehydrogenase inhibitor (SDHI) fungicides are widely used for the control of a broad range of fungal diseases. This has been the most rapidly expanding fungicide group in terms of new molecules discovered and introduced for agricultural use over the past fifteen years. A particular pattern of differential sensitivity (resistance) to the stretched heterocycle amide SDHIs (SHA-SDHIs), a subclass of chemically-related SDHIs, was observed in naïve Zymoseptoria tritici populations not previously exposed to these chemicals. Subclassspecific resistance was confirmed at the enzyme level but did not correlate with the genotypes of the succinate dehydrogenase (SDH) encoding genes. Mapping and characterization of the molecular mechanisms responsible for standing SHA-SDHI resistance in natural field isolates identified a gene paralog of SDHC, termed ZtSDHC3, which encodes for an alternative C subunit of succinate dehydrogenase, named alt-SDHC. Using reverse genetics, we showed that alt-SDHC associates with the three other SDH subunits, leading to a fully functional enzyme and that a unique Qp-site residue within the alt-SDHC protein confers SHA-SDHI resistance. Enzymatic assays, computational modelling and docking simulations for the two SQR enzymes (altC-SQR, WT-SQR) enabled us to describe enzymeinhibitor interactions at an atomistic level and to propose rational explanations for differential potency and resistance across SHA-SDHIs. European Z. tritici populations displayed a presence (20-30%) / absence polymorphism of ZtSDHC3, as well as differences in ZtSDHC3 expression levels and splicing efficiency. These polymorphisms have a strong impact on SHA-SDHI resistance phenotypes. Characterization of the ZtSDHC3 promoter in European Z. tritici populations suggests that transposon insertions are associated with the strongest resistance phenotypes. These results establish that a dispensable paralogous gene determines SHA-SDHIs fungicide resistance in natural populations of Z. tritici. This study paves the way to an increased awareness of the role of fungicidal target paralogs in resistance to fungicides and demonstrates the paramount importance of population genomics in fungicide discovery.

    Cadmium uptake in radish (Raphanus sativus L.) and surficial contaminationimplications for food safety and local soil management: implications for food safety and local soil management
    Xu, Genyan ; Zhang, Sha ; Song, Jing ; Brewer, Roger ; Gao, Hui - \ 2019
    Journal of Soils and Sediments 19 (2019)10. - ISSN 1439-0108 - p. 3585 - 3596.
    Bioavailability - Cd - pH - Potentially toxic metals - Soil criteria - Soil extraction tests

    Purpose: Soil management strategies for agricultural lands contaminated with potentially toxic trace elements, especially cadmium (Cd), are still inadequate and require a precise identification of soils that are not s afe for growing crops. Key soil variables need to be identified to connect soil safety with food safety by reliable models. Materials and methods: Soil variables that affect concentrations of metals in different portions of radish, Raphanus sativus L., were examined as part of a greenhouse experiment. 0.01 M di-sodium-di-hydroxy-ethylenediamine-tretra-acetic acid (Na2H2EDTA) solution was used in a strong rinsing experiment. Cd soil-radish relationships were derived by different modeling approaches and were used to develop local risk screening values for Cd in soil. Results and discussion: The current lab washing procedures readily remove surface Cd adherence but are not adequate to remove surface-deposited lead (Pb), thus overestimating bioaccumulation in plants by mean 111%. Shoot and root tissue Cd concentration in fresh weight basis do not present a significant difference and can be precisely predicted by regression models using different Cd pools and soil pH. Preferably a polynomial surface model can be used in developing local rick screening values that yield concentrations of Cd in radish at or below the Chinese food quality standard of 0.1 mg kg−1 (fresh weight). Conclusions: The bioaccumulation of Cd in radish depends on the Cd bioavailability in soil. But for Pb, surficial particle contamination masks the realistic bioaccumulation. We also demonstrated the usefulness of the polynomial surface model to develop local soil protection guidelines that are helpful to local farmers for proper soil management and avoidance of Cd exceedance in food.

    Xu, Gen Yan ; Song, Jing ; Gao, Hui ; Zhang, Sha - \ 2019
    Journal of Agro-Environment Science 38 (2019)7. - ISSN 1672-2043 - p. 1490 - 1497.
    Cadmium - Risk intervention values - Risk screening values - Soil-crop transfer model

    The objective of this study was to derive regional soil Cd criteria for cultivated land. Six representative soils were collected from Guizhou plateau and were spiked with Cd(NO3)2 in a pot experiment using Chinese cabbage. Two widely utilized extractants, 0.43 mol·L-1 HNO3 and 0.01 mol·L-1 CaCl2, were also included to evaluate the phytoavailability of Cd and were correlated to Cd concentrations in cabbage by either linear regression or multi-linear regression(log transformed). Soil Cd risk screening values(RSVs)and risk intervention values(RIVs)were back calculated based on food quality standards. The results indicated that total Cd and available Cd could be used to establish a highly significant regression model or multiple regression model for the Cd content in the edible parts of Chinese cabbage. Within the pH range(5.5≤pH≤8.0), the calculated soil Cd RSVs50(0.8~1.7 mg·kg-1)and RIVs95(2.8~8.4 mg·kg-1)were higher than the existing national standard(GB 15618—2018). The 0.43 mol·L-1 HNO3-Cd based soil Cd criteria increased with increasing soil pH. The 0.01 mol·L-1 CaCl2-Cd based soil Cd criteria was independent of soil pH. RSVs95, RSVs50, and RIVs95 were 0.02, 0.078 mg·kg-1, and 0.09 mg·kg-1, respectively. Standard suitability assessment using field and literature data showed that the existing national soil Cd standard was rather conservative. The RSVs50 based on total Cd and two available Cd proposed in this study showed a high rate of correctness(>80%). The present study confirmed that for better risk management of agricultural land, the establishment of regional soil environmental standards based on available concentration and specific crops is required.

    Interactive effects of microplastics and glyphosate on the dynamics of soil dissolved organic matter in a Chinese loess soil
    Liu, Hongfei ; Yang, Xiaomei ; Liang, Chutao ; Li, Yuanze ; Qiao, Leilei ; Ai, Z. ; Xue, Sha ; Liu, Guobin - \ 2019
    Catena 182 (2019). - ISSN 0341-8162
    Dissolved organic carbon (DOC) - Dissolved organic nitrogen (DON) - Dissolved organic phosphorus (DOP) - Excitation-emission matrix (EEM) - Glyphosate

    The increased use of plastic films and pesticides on agricultural soil leads to the accumulation of plastic debris and pesticide residues in soil. This accumulation has become a serious environmental issue, as it threatens life of earthworms, inhibits the enzyme activities and microbial diversity, and contributes to the loss of soil microbial carbon and nitrogen. However, little information is available regarding the effects of pesticides on soil dissolved organic matter (DOM). It is also unknown how plastic debris, especially small-sized particles called microplastics, influences the effects of pesticides on soil DOM. In this study, we performed a 30-day soil incubation experiment. Three levels of the common herbicide glyphosate were applied to soil: 0 (control, CK), 3.6 kg ha 1 (G1) and 7.2 kg ha 1 (G2). We also tested four levels of glyphosate and microplastics (homopolymer polypropylene powder) co-addition: 3.6 kg ha 1 + 7% (w/w) (M1G1), 3.6 kg ha 1 + 28% (w/w) (M2G1), 7.2 kg ha 1 + 7% (w/w) (M1G2), and 7.2 kg ha 1 + 28% (w/w) (M2G2). Glyphosate addition slightly increased soil fluorescein diacetate hydrolase (FDAse) and phenol oxidase (PO) activities. Although the glyphosate addition significantly promoted the accumulation of dissolved organic phosphorus (DOP) within the first 14 days, the M2 treatment decreased DOP at day 30. M2G1 and M2G2 increased soil FDAse activity and promoted the accumulation of DOC and DOP relative to G1 and G2 respectively while M1G1 and M1G2 benefited DON accumulation. Our results highlighted that the interaction between glyphosate and low microplastics content negatively affected DOC and DOP dynamics, leading to the loss of bioavailable C and P loss. The interaction between glyphosate and high content microplastics negatively affected DON compared with glyphosate addition, possibly decreasing DON.

    Biogenic transport of glyphosate in the presence of LDPE microplastics : A mesocosm experiment
    Yang, Xiaomei ; Lwanga, Esperanza Huerta ; Bemani, Akram ; Gertsen, Hennie ; Salanki, Tamas ; Guo, Xuetao ; Fu, Haimei ; Xue, Sha ; Ritsema, Coen ; Geissen, Violette - \ 2019
    Environmental Pollution 245 (2019). - ISSN 0269-7491 - p. 829 - 835.
    Earthworm burrows - Glyphosate transport - Microplastics - Soil ecosystem

    The accumulation of plastic debris and herbicide residues has become a huge challenge and poses many potential risks to environmental health and soil quality. In the present study, we investigated the transport of glyphosate and its main metabolite, aminomethylphosphonic acid (AMPA) via earthworms in the presence of different concentrations of light density polyethylene microplastics in the litter layer during a 14-day mesocosm experiment. The results showed earthworm gallery weight was negatively affected by the combination of glyphosate and microplastics. Glyphosate and AMPA concentrated in the first centimetre of the top soil layer and the downward transport of glyphosate and AMPA was only detected in the earthworm burrows, ranging from 0.04 to 4.25 μg g−1 for glyphosate and from 0.01 (less than limit of detection) to 0.76 μg g−1 for AMPA. The transport rate of glyphosate (including AMPA) from the litter layer into earthworm burrows ranged from 6.6 ± 4.6% to 18.3 ± 2.4%, depending on synergetic effects of microplastics and glyphosate application. The findings imply that earthworm activities strongly influence pollutant movement into the soil, which potentially affects soil ecosystems. Further studies focused on the fate of pollutants in the microenvironment of earthworm burrows are needed. Glyphosate was mainly transported into deeper soil layers via earthworm galleries which were influenced by synergetic effects of microplastics and glyphosate application.

    Are the G20 economies making enough progress to meet their NDC targets?
    Elzen, Michel den; Kuramochi, Takeshi ; Höhne, Niklas ; Cantzler, Jasmin ; Esmeijer, Kendall ; Fekete, Hanna ; Fransen, Taryn ; Keramidas, Kimon ; Roelfsema, Mark ; Sha, Fu ; Soest, Heleen van; Vandyck, Toon - \ 2019
    Energy Policy 126 (2019). - ISSN 0301-4215 - p. 238 - 250.
    China - G20 economies - National climate and energy policies - NDCs - Paris Agreement

    Under the Paris Agreement, countries committed to a variety of climate actions, including post-2020 greenhouse gas (GHG) emissions reduction targets. This study compares projected GHG emissions in the G20 economies under current climate policies to those under the GHG targets outlined in the nationally determined contributions (NDCs). It is based on an assessment of official governmental estimates and independent national and global studies. The study concludes that six G20 members (China, India, Indonesia, Japan, Russia and Turkey) are projected to meet their unconditional NDC targets with current policies. Eight members (Argentina, Australia, Canada, the European Union, Republic of Korea, South Africa and the United States) require further action to achieve their targets. Insufficient information is available for Saudi Arabia, and emission projections for Brazil and Mexico are subject to considerable uncertainty. The study also presents high-level decarbonisation indicators to better understand the current progress towards meeting the NDCs – Saudi Arabia and South Africa were found to continue increasing both emission intensity per unit GDP and emissions per capita under current policies by 2030 from 2015 levels.

    Environmental tuning of the genetic control of seed performance : a systems genetics approach
    Serin, Elise Anna Renée - \ 2018
    Wageningen University. Promotor(en): R.G.H. Immink, co-promotor(en): H.W.M. Hilhorst; J.W. Ligterink. - Wageningen : Wageningen University - ISBN 9789463433341 - 214

    The environmental conditions under which plants grow affect the quality of seeds produced in a genotype-dependent manner. In nature, genotype-by-environment interactions are often observed however little is known about the underlying mechanisms. The combined use of genetic tools and omics data can help to explore the influence of the environment on the genetic control of seed performance. The research presented in this thesis explores genotype-by-environment interaction at the phenotypic with an effort to connect phenotypic changes to changes observed at the metabolome and transcriptome in a systems genetics approach. For this purpose, an Arabidopsis thaliana recombinant inbred lines population derived from the cross between the parental lines Bay-0 and Sha was grown under different conditions, namely standard, high light, high temperature and low phosphate conditions from flowering until seed harvest. The germination properties of the seeds produced under the different environments were investigated and the seed germination QTLs identified displayed large QTL-by-environment interaction. Quantitative changes in primary metabolites in response to the maternal environment were investigated by GC-TOF-MS. Further, mQTLs under the different environments were identified. RNA-seq of the same lines enabled to explore changes in gene expression across genotypes and environments as well as differences in the eQTL landscape under the different maternal environment. The findings of this research show that seed quality is largely influenced by genotype-by-environment interactions which result in large changes at the molecular level. The data generated provide many opportunities to further study.

    Influence of microplastic addition on glyphosate decay and soil microbial activities in Chinese loess soil
    Yang, Xiaomei ; Bento, Célia P.M. ; Chen, Hao ; Zhang, Hongming ; Xue, Sha ; Lwanga, Esperanza H. ; Zomer, Paul ; Ritsema, Coen J. ; Geissen, Violette - \ 2018
    Environmental Pollution 242 (2018). - ISSN 0269-7491 - p. 338 - 347.
    Glyphosate - Microplastic - Pesticide decay - Soil microbial activities - Soil quality

    The intensive use of pesticide and plastic mulches has considerably enhanced crop growth and yield. Pesticide residues and plastic debris, however, have caused serious environmental problems. This study investigated the effects of the commonly used herbicide glyphosate and micrometre-sized plastic debris, referred as microplastics, on glyphosate decay and soil microbial activities in Chinese loess soil by a microcosm experiment over 30 days incubation. Results showed that glyphosate decay was gradual and followed a single first-order decay kinetics model. In different treatments (with/without microplastic addition), glyphosate showed similar half-lives (32.8 days). The soil content of aminomethylphosphonic acid (AMPA), the main metabolite of glyphosate, steadily increased without reaching plateau and declining phases throughout the experiment. Soil microbial respiration significantly changed throughout the entirety of the experiment, particularly in the treatments with higher microplastic addition. The dynamics of soil β-glucosidase, urease and phosphatase varied, especially in the treatments with high microplastic addition. Particles that were considerably smaller than the initially added microplastic particles were observed after 30 days incubation. This result thus implied that microplastic would hardly affect glyphosate decay but smaller plastic particles accumulated in soils which potentially threaten soil quality would be further concerned especially in the regions with intensive plastic mulching application. Microplastic hardly affected herbicide glyphosate decay in soil but soil microbial activities which, in turn, would indirectly influence pesticide behaviour in soil ecosystem.

    Global environmental costs of China's thirst for milk
    Bai, Zhaohai ; Lee, Michael R.F. ; Ma, Lin ; Ledgard, Stewart ; Velthof, Gerard L. ; Ma, Wenqi ; Guo, Mengchu ; Zhao, Zhanqing ; Wei, Sha ; Li, Shengli ; Liu, Xia ; Havlík, Petr ; Luo, Jiafa ; Hu, Chunsheng ; Zhang, Fusuo - \ 2018
    Global Change Biology 24 (2018)5. - ISSN 1354-1013 - p. 2198 - 2211.
    Cattle feed - Greenhouse gas - Land use, nitrogen losses - Milk trade - Shared socio-economic pathways scenarios
    China has an ever-increasing thirst for milk, with a predicted 3.2-fold increase in demand by 2050 compared to the production level in 2010. What are the environmental implications of meeting this demand, and what is the preferred pathway? We addressed these questions by using a nexus approach, to examine the interdependencies of increasing milk consumption in China by 2050 and its global impacts, under different scenarios of domestic milk production and importation. Meeting China's milk demand in a business as usual scenario will increase global dairy-related (China and the leading milk exporting regions) greenhouse gas (GHG) emissions by 35% (from 565 to 764 Tg CO 2eq ) and land use for dairy feed production by 32% (from 84 to 111 million ha) compared to 2010, while reactive nitrogen losses from the dairy sector will increase by 48% (from 3.6 to 5.4 Tg nitrogen). Producing all additional milk in China with current technology will greatly increase animal feed import; from 1.9 to 8.5 Tg for concentrates and from 1.0 to 6.2 Tg for forage (alfalfa). In addition, it will increase domestic dairy related GHG emissions by 2.2 times compared to 2010 levels. Importing the extra milk will transfer the environmental burden from China to milk exporting countries; current dairy exporting countries may be unable to produce all additional milk due to physical limitations or environmental preferences/legislation. For example, the farmland area for cattle-feed production in New Zealand would have to increase by more than 57% (1.3 million ha) and that in Europe by more than 39% (15 million ha), while GHG emissions and nitrogen losses would increase roughly proportionally with the increase of farmland in both regions. We propose that a more sustainable dairy future will rely on high milk demanding regions (such as China) improving their domestic milk and feed production efficiencies up to the level of leading milk producing countries. This will decrease the global dairy related GHG emissions and land use by 12% (90 Tg CO 2eq reduction) and 30% (34 million ha land reduction) compared to the business as usual scenario, respectively. However, this still represents an increase in total GHG emissions of 19% whereas land use will decrease by 8% when compared with 2010 levels, respectively.
    Response of soil dissolved organic matter to microplastic addition in Chinese loess soil
    Liu, Hongfei ; Yang, Xiaomei ; Liu, Guobin ; Liang, Chutao ; Xue, Sha ; Chen, Hao ; Ritsema, Coen J. ; Geissen, Violette - \ 2017
    Chemosphere 185 (2017). - ISSN 0045-6535 - p. 907 - 917.
    Dissolved organic carbon (DOC) - Dissolved organic nitrogen (DON) - Dissolved organic phosphorus (DOP) - Excitation-emission matrix (EEM) - Microplastic
    Plastic debris is accumulating in agricultural land due to the increased use of plastic mulches, which is causing serious environmental problems, especially for biochemical and physical properties of the soil. Dissolved organic matter (DOM) plays a central role in driving soil biogeochemistry, but little information is available on the effects of plastic residues, especially microplastic, on soil DOM. We conducted a soil-incubation experiment in a climate-controlled chamber with three levels of microplastic added to loess soil collected from the Loess Plateau in China: 0% (control, CK), 7% (M1) and 28% (M2) (w/w). We analysed the soil contents of dissolved organic carbon (DOC), dissolved organic nitrogen (DON), NH4 +, NO3 −, dissolved organic phosphorus (DOP), and PO4 3− and the activities of fluorescein diacetate hydrolase (FDAse) and phenol oxidase. The higher level of microplastic addition significantly increased the nutrient contents of the DOM solution. The lower level of addition had no significant effect on the DOM solution during the first seven days, but the rate of DOM decomposition decreased in M1 between days 7 and 30, which increased the nutrient contents. The microplastic facilitated the accumulation of high-molecular-weight humic-like material between days 7 and 30. The DOM solutions were mainly comprised of high-molecular-weight humic-like material in CK and M1 and of high-molecular-weight humic-like material and tyrosine-like material in M2. The Microplastic stimulated the activities of both enzymes. Microplastic addition thus stimulated enzymatic activity, activated pools of organic C, N, and P, and was beneficial for the accumulation of dissolved organic C, N and P.
    Modeling farm nutrient flows in the North China Plain to reduce nutrient losses
    Zhao, Zhanqing ; Bai, Zhaohai ; Wei, Sha ; Ma, Wenqi ; Wang, Mengru ; Kroeze, Carolien ; Ma, Lin - \ 2017
    Nutrient Cycling in Agroecosystems 108 (2017)2. - ISSN 1385-1314 - p. 231 - 244.
    Farm system - Losses - Nitrogen - North China Plain - NUFER-farm model - Phosphorus - Use efficiency
    Years of poor nutrient management practices in the agriculture industry in the North China Plain have led to large losses of nutrients to the environment, causing severe ecological consequences. Analyzing farm nutrient flows is urgently needed in order to reduce nutrient losses. A farm-level nutrient flow model was developed in this study based on the NUFER (NUtrient flows in Food chains, Environment and Resources use) model, and was used to analyze nitrogen (N) and phosphorus (P) flows, use efficiencies, and losses for nine representative farm types in the North China Plain. Data from 401 farms were evaluated for the years 2012–2015. The analysis showed that mixed farms were more efficient in nutrient utilization than crop-based or landless livestock farms. The efficiencies of N and P used in crop production were highest for mixed dairy farms, reaching 67% for N and 68% for P. Consistently, mixed dairy farms had the lowest N and P surpluses and losses in crop production. Mixed swine farms were 5 and 9% higher in N and P efficiency in livestock production than landless swine farms, respectively. Losses of N and P from the animal manure management chain were 20–42% lower for mixed swine and 69–78% lower for mixed poultry farms than for landless farms of the same animal type. This is at least partially due to more frequent manure removal. Integrated crop-livestock production using livestock wastes as crop fertilizer was shown to be the most sustainable model in nutrient use for the agriculture industry in the North China Plain.
    Effects of elevated CO2 and drought on the microbial biomass and enzymatic activities in the rhizospheres of two grass species in Chinese loess soil
    Xue, Sha ; Yang, Xiaomei ; Liu, Guobin ; Gai, Lingtong ; Zhang, Changsheng ; Ritsema, Coen J. ; Geissen, Violette - \ 2017
    Geoderma 286 (2017). - ISSN 0016-7061 - p. 25 - 34.
    Drought stress - Elevated atmospheric CO - Enzymatic activities - Interactive effect - Microbial biomass - Rhizospheric soil

    Elevated CO2 and drought are key consequences of climate change and affect soil processes and plant growth. This study investigated the effects of elevated CO2 and drought on the microbial biomass and enzymatic activities in the rhizospheres of Bothriochloa ischaemum and Medicago sativa in loess soil. Drought exerted significant species-specific negative effects on root and shoot biomass and microbial properties except for the soil basal respiration in the rhizospheres of B. ischaemum and M. sativa. Increased CO2 exerted weak effects on plant biomass and enzymatic activities but demonstrated significant effects on the amounts of carbon and nitrogen in soil microbial biomass, basal respiration, substrate-induced respiration, and the metabolic quotients in the rhizospheres of M. sativa and B. ischaemum. The rhizosphere soil microbial index was a good aggregative indicator of the general state of the microbial properties of the rhizospheres. The interactive effects of elevated CO2 and drought on plant growth and microbial properties significantly differed, indicating that elevated CO2 significantly alleviated the effects of drought stress on the microbial properties of the rhizosphere. In addition, the effects of elevated CO2 and drought on microbial biomass and enzymatic activities considerably varied between the two selected species. M. sativa generally experienced a better ameliorative effect than B. ischaemum.

    Paris Agreement climate proposals need a boost to keep warming well below 2 °c
    Rogelj, Joeri ; Elzen, Michel Den; Höhne, Niklas ; Fransen, Taryn ; Fekete, Hanna ; Winkler, Harald ; Schaeffer, Roberto ; Sha, Fu ; Riahi, Keywan ; Meinshausen, Malte - \ 2016
    Nature 534 (2016)7609. - ISSN 0028-0836 - p. 631 - 639.

    The Paris climate agreement aims at holding global warming to well below 2 degrees Celsius and to "pursue efforts" to limit it to 1.5 degrees Celsius. To accomplish this, countries have submitted Intended Nationally Determined Contributions (INDCs) outlining their post-2020 climate action. Here we assess the effect of current INDCs on reducing aggregate greenhouse gas emissions, its implications for achieving the temperature objective of the Paris climate agreement, and potential options for overachievement. The INDCs collectively lower greenhouse gas emissions compared to where current policies stand, but still imply a median warming of 2.6-3.1 degrees Celsius by 2100. More can be achieved, because the agreement stipulates that targets for reducing greenhouse gas emissions are strengthened over time, both in ambition and scope. Substantial enhancement or over-delivery on current INDCs by additional national, sub-national and non-state actions is required to maintain a reasonable chance of meeting the target of keeping warming well below 2 degrees Celsius.

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