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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    Effect of dietary fiber fermentation on short-chain fatty acid production and microbial composition in vitro
    Bai, Yu ; Zhao, Jin Biao ; Tao, Shi Yu ; Zhou, Xing Jian ; Pi, Yu ; Gerrits, Walter J.J. ; Johnston, Lee J. ; Zhang, Shi Yi ; Yang, Hong Jian ; Liu, Ling ; Zhang, Shuai ; Wang, Jun Jun - \ 2020
    Journal of the Science of Food and Agriculture (2020). - ISSN 0022-5142
    fiber-rich co-products - gas production - in vitro fermentation - microbial community - short chain fatty acid

    BACKGROUND: The efficient utilization of fiber-rich co-products is important for optimizing feed resource utilization and animal health. This study was conducted to evaluate the fermentation characteristics of fiber-rich co-products, which had equal quantities of total dietary fiber (TDF), at different time points using batch in vitro methods. It considered their gas production, short-chain fatty acid (SCFA) production, and microbial composition. RESULTS: The fermentation of wheat bran (WB) and oat bran (OB) showed higher and faster (P < 0.05) gas and SCFA production than corn bran (CB), sugar beet pulp (SBP), and soybean hulls (SH). The α-diversity was higher in the CB, SBP, and SH groups than in the WB and OB groups (P < 0.05). At the phylum level, OB and WB fermentation showed lower (P < 0.05) relative abundance of Actinobacteria than the CB, SBP, and SH groups. At the genus level, OB and WB fermentation increased the Enterococcus population in comparison with the CB, SBP, and SH groups, whereas CB and SBP fermentation improved the relative abundance of the Christensenellaceae R-7 group more than the WB, OB, and SH groups (P < 0.05). CONCLUSION: Overall, WB and OB were rapidly fermented by fecal microbiota, in contrast with SBP, SH, and CB. Fermentation of different fiber-rich co-products with an equal TDF content gives different responses in terms of microbial composition and SCFA production due to variations in their physicochemical properties and molecular structure.

    Correction to: Rewiring of glucose metabolism defines trained immunity induced by oxidized low-density lipoprotein
    Keating, Samuel T. ; Groh, Laszlo ; Thiem, Kathrin ; Bekkering, Siroon ; Li, Yang ; Matzaraki, Vasiliki ; Heijden, Charlotte D.C.C. van der; Puffelen, Jelmer H. van; Lachmandas, Ekta ; Jansen, Trees ; Oosting, Marije ; Bree, L.C.J. de; Koeken, Valerie A.C.M. ; Moorlag, Simone J.C.F.M. ; Mourits, Vera P. ; Diepen, Janna van; Stienstra, Rinke ; Novakovic, Boris ; Stunnenberg, Hendrik G. ; Crevel, Reinout van; Joosten, Leo A.B. ; Netea, Mihai G. ; Riksen, Niels P. - \ 2020
    Journal of Molecular Medicine (2020). - ISSN 0946-2716

    The correct name of the 17th Author is presented in this paper. In the paragraph “Metabolic analysis” of the Method section “an XFp Analyzer” should be changed to “an XFe96 Analyzer”.

    Rewiring of glucose metabolism defines trained immunity induced by oxidized low-density lipoprotein
    Keating, Samuel T. ; Groh, Laszlo ; Thiem, Kathrin ; Bekkering, Siroon ; Li, Yang ; Matzaraki, Vasiliki ; Heijden, Charlotte D.C.C. van der; Puffelen, Jelmer H. van; Lachmandas, Ekta ; Jansen, Trees ; Oosting, Marije ; Bree, L.C.J. de; Koeken, Valerie A.C.M. ; Moorlag, Simone J.C.F.M. ; Mourits, Vera P. ; Diepen, Janna van; Stienstra, Rinke ; Novakovic, Boris ; Stunnenberg, Hendrik G. ; Crevel, Reinout van; Joosten, Leo A.B. ; Netea, Mihai G. ; Riksen, Niels P. - \ 2020
    Journal of Molecular Medicine 98 (2020). - ISSN 0946-2716 - p. 819 - 831.
    Atherosclerosis - Cardiovascular disease - Diabetes complications - Glycolysis - Immunometabolism - Inflammation - Trained immunity

    Abstract: Stimulation of monocytes with microbial and non-microbial products, including oxidized low-density lipoprotein (oxLDL), induces a protracted pro-inflammatory, atherogenic phenotype sustained by metabolic and epigenetic reprogramming via a process called trained immunity. We investigated the intracellular metabolic mechanisms driving oxLDL-induced trained immunity in human primary monocytes and observed concomitant upregulation of glycolytic activity and oxygen consumption. In two separate cohorts of healthy volunteers, we assessed the impact of genetic variation in glycolytic genes on the training capacity of monocytes and found that variants mapped to glycolytic enzymes PFKFB3 and PFKP influenced trained immunity by oxLDL. Subsequent functional validation with inhibitors of glycolytic metabolism revealed dose-dependent inhibition of trained immunity in vitro. Furthermore, in vivo administration of the glucose metabolism modulator metformin abrogated the ability for human monocytes to mount a trained response to oxLDL. These findings underscore the importance of cellular metabolism for oxLDL-induced trained immunity and highlight potential immunomodulatory strategies for clinical management of atherosclerosis. Key messages: Brief stimulation of monocytes to oxLDL induces a prolonged inflammatory phenotype.This is due to upregulation of glycolytic metabolism.Genetic variation in glycolytic genes modulates oxLDL-induced trained immunity.Pharmacological inhibition of glycolysis prevents trained immunity.

    Mitochondrial genomes as phylogenetic backbone
    Brankovics, Balázs ; Yang, Meixin ; Waalwijk, Cees ; Lee, Theo van der; Diepeningen, Anne van - \ 2020
    Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum
    Yang, Meixin ; Zhang, Hao ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Feng, Jie ; Brankovics, Balázs ; Chen, Wanquan - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    Fusarium asiaticum is one of the pivotal members of the Fusarium graminearum species complex (FGSC) causing Fusarium head blight (FHB) on wheat, barley and rice in large parts of Asia. Besides resulting in yield losses, FHB also causes the accumulation of mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON). The aim of this study was to conduct population studies on F. asiaticum from Southern China through mitochondrial genome analyses. All strains were isolated from wheat or rice from several geographic areas in seven provinces in Southern China. Based on geographic location and host, 210 isolates were selected for next generation sequencing, and their mitogenomes were assembled by GRAbB and annotated to explore the mitochondrial genome variability of F. asiaticum. The F. asiaticum mitogenome proves extremely conserved and variation is mainly caused by absence/presence of introns harboring homing endonuclease genes. These variations could be utilized to develop molecular markers for track and trace of migrations within and between populations. This study illustrates how mitochondrial introns can be used as markers for population genetic analysis. SNP analysis demonstrate the occurrence of mitochondrial recombination in F. asiaticum as was previously found for F. oxysporum and implied for F. graminearum. Furthermore, varying degrees of genetic diversity and recombination showed a high association with different geographic regions as well as with cropping systems. The mitogenome of F. graminearum showed a much higher SNP diversity while the interspecies intron variation showed no evidence of gene flow between the two closely related and sexual compatible species
    Field performance of different maize varieties in growth cores at natural and reduced mycorrhizal colonization : yield gains and possible fertilizer savings in relation to phosphorus application
    Wang, Xin Xin ; Werf, Wopke van der; Yu, Yang ; Hoffland, Ellis ; Feng, Gu ; Kuyper, Thomas W. - \ 2020
    Plant and Soil 450 (2020)1-2. - ISSN 0032-079X - p. 613 - 624.
    Crop - Genetic variation - In-growth cores - Landrace - Maize - Mycorrhizal colonization - Phosphorus

    Aims: The benefits of arbuscular mycorrhizal fungi (AMF) on yield and phosphorus (P) uptake of crops have commonly been studied by inoculating a single mycorrhizal fungal species in pot experiments. Yet, how the native AMF community affects the performance of different maize varieties under field conditions remains obscure. Methods: In-growth cores with and without rotation were used in three soils that differed in P application to assess shoot biomass, P uptake, and mycorrhizal colonization of three maize varietal groups, encompassing four inbred lines, 12 hybrids, and four landraces. Results: Rotating cores drastically reduced mycorrhizal colonization, biomass and P uptake for each varietal group at every P level. Performance of plants at natural mycorrhizal colonization at 30 kg P ha−1 was equal to that of reduced-mycorrhizal plants at 60 kg P ha−1, suggesting the potential for adequate mycorrhizal management to save P fertilizer. Conclusion: There were no significant differences between varietal groups for mycorrhizal responsiveness, confirming that the ability to associate with and benefit from AMF has been maintained in modern breeding. Mycorrhizal plants both exhibited higher P acquisition efficiency and higher P use efficiency than reduced-mycorrhizal plants. Disadvantages of in-growth cores should be duly considered.

    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.

    Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs
    Yang, Bin ; Cui, Leilei ; Perez-Enciso, Miguel ; Traspov, Aleksei ; Crooijmans, Richard P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Archibald, Alan ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, Martien A.M. ; Huang, Lusheng ; Megens, Hendrik Jan - \ 2020
    Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X - 1 p.

    An amendment to this paper has been published and can be accessed via the original article.

    Institutional preferences, social preferences and cooperation : Evidence from a lab-in-the-field experiment in rural China
    Yang, Xiaojun ; Nie, Zihan ; Qiu, Jianying ; Tu, Qin - \ 2020
    Journal of Behavioral and Experimental Economics 87 (2020). - ISSN 2214-8043
    Cooperation - Institutional preferences - Punishment - Reward - Social preferences

    We examine institutional preferences, social preferences, contribution in public goods games, and their relationships by conducting a lab-in-the-field experiment in rural China. Specifically, we examine whether people contribute differently depending on whether they are facing their preferred enforcement institution (punishment versus reward); that is, whether there is an institutional match or mismatch effect on cooperation. We also examine what factors are behind their institutional preferences. We find that most subjects prefer reward over punishment. However, institutional (mis)match does not have significant impacts on contributions in the public goods game. Moreover, subjects who prefer punishment tend to be free-riders. We further find that there is a robust relationship between the preference for punishment and certain efficiency-reducing social preference profiles, such as anti-social preferences, which may help understand the institutional preferences.

    Genome-wide identification of small G protein ROPs and their potential roles in Solanaceous family
    Yang, Shuqing ; Yan, Ningning ; Bouwmeester, Klaas ; Na, Ren ; Zhang, Zhiwei ; Zhao, Jun - \ 2020
    Gene 753 (2020). - ISSN 0378-1119
    Genome-wide screening - Phylogenetic analysis - Plant growth and development - Plant immunity - Small GTPase ROPs - Solanaceous family

    Small GTPases function as molecular switches to active or inactive signaling cascades via binding or hydrolyzing GTP. A type of plant specific small GTPases, the ROPs are known to be involved in plant growth, development and immunity. We determined whether ROPs are conserved in Solanaceous species and whether they are involved in plant growth, development and resistance against Phytophthora capsisi. In genome-wide screening, a total of 66 ROPs in six Solanaceous species (SolROPs) were identified, including 16 ROPs in Solanum tuberosum L. (potato), 9 in Solanum lycopersicum L. (tomato), 5 in Solanum melongena L. (eggplant), 9 in Capsicum annuum L. (pepper), 13 in Nicotiana benthamiana Domin and 14 in Nicotiana tabacum L. (tobacco). Phylogenetic analysis revealed that 11 AtROPs and 66 SolROPs fall into five distinct clades (I-V) and hence a novel and systematic gene nomenclature was proposed. In addition, a comprehensive expression analysis was performed by making use of an online database. This revealed that ROP genes are differentially expressed during plant growth and development. Moreover, gene expression of SlROP-II.1 in S. lycopersicum could be significantly induced by P. capsici. Subsequently, SlROP-II.1 and its homologues in N. benthamiana and C. annuum (NbROP-II.1 and CaROP-II.1) were selected for functional analysis using virus-induced gene silencing. Infection assays with P. capsici on silenced plants revealed that SlROP-II.1, NbROP-II.1 and CaROP-II.1 play a role in P. capsici resistance, suggesting conserved function of ROP-II clade across different Solanaceous species. In addition, NbROP-II.1 is also involved in regulating plant growth and development. This study signified the diversity of Solanaceous ROPs and their potential roles in plant growth, development and immunity.

    Improvement in municipal wastewater treatment alters lake nitrogen to phosphorus ratios in populated regions
    Tong, Yindong ; Wang, Mengzhu ; Peñuelas, Josep ; Liu, Xueyan ; Paerl, Hans W. ; Elser, James J. ; Sardans, Jordi ; Couture, Raoul Marie ; Larssen, Thorjørn ; Hu, Hongying ; Dong, Xin ; He, Wei ; Zhang, Wei ; Wang, Xuejun ; Zhang, Yang ; Liu, Yi ; Zeng, Siyu ; Kong, Xiangzhen ; Janssen, Annette B.G. ; Lin, Yan - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Anthropogenic source - Aquatic ecosystem - Nutrient balance - Wastewater treatment - Water quality change

    Large-scale and rapid improvement in wastewater treatment is common practice in developing countries, yet this influence on nutrient regimes in receiving waterbodies is rarely examined at broad spatial and temporal scales. Here, we present a study linking decadal nutrient monitoring data in lakes with the corresponding estimates of five major anthropogenic nutrient discharges in their surrounding watersheds over time. Within a continuous monitoring dataset covering the period 2008 to 2017, we find that due to different rates of change in TN and TP concentrations, 24 of 46 lakes, mostly located in China's populated regions, showed increasing TN/TP mass ratios; only 3 lakes showed a decrease. Quantitative relationships between in-lake nutrient concentrations (and their ratios) and anthropogenic nutrient discharges in the surrounding watersheds indicate that increase of lake TN/TP ratios is associated with the rapid improvement in municipal wastewater treatment. Due to the higher removal efficiency of TP compared with TN, TN/TP mass ratios in total municipal wastewater discharge have continued to increase from a median of 10.7 (95% confidence interval, 7.6 to 15.1) in 2008 to 17.7 (95% confidence interval, 13.2 to 27.2) in 2017. Improving municipal wastewater collection and treatment worldwide is an important target within the 17 sustainable development goals set by the United Nations. Given potential ecological impacts on biodiversity and ecosystem function of altered nutrient ratios in wastewater discharge, our results suggest that long-term strategies for domestic wastewater management should not merely focus on total reductions of nutrient discharges but also consider their stoichiometric balance.

    Prevalence of milk fraud in the Chinese market and its relationship with fraud vulnerabilities in the chain
    Yang, Yuzheng ; Zhang, Liebing ; Hettinga, Kasper A. ; Erasmus, Sara W. ; Ruth, Saskia M. Van - \ 2020
    Foods 9 (2020)6. - ISSN 2304-8158
    China - Fourier transform-infrared spectroscopy - Fraud vulnerability - Milk adulteration - Milk composition - One-class classifications

    This study aimed to assess the prevalence of ultra-high-temperature (UHT) processed milk samples suspected of being adulterated on the Chinese market and, subsequently, relate their geographical origin to the earlier determined fraud vulnerability. A total of 52 UHT milk samples purchased from the Chinese market were measured to detect possible anomalies. The milk compositional features were determined by standardized Fourier transform-infrared spectroscopy, and the detection limits for common milk adulterations were investigated. The results showed that twelve of the analysed milk samples (23%) were suspected of having quality or fraud-related issues, while one sample of these was highly suspected of being adulterated (diluted with water). Proportionally, more suspected samples were determined among milks produced in the Central- Northern and Eastern areas of China than in those from the North-Western and North-Eastern areas, while those from the South were in between. Combining the earlier collected results on fraud vulnerability in the Chinese milk chains, it appears that increased fraud prevalence relates to poorer business relationships and lack of adequate managerial controls. Since very few opportunities and motivations differ consistently across high and low-prevalence areas, primarily the improvement of control measures can help to mitigate food fraud in the Chinese milk supply chains.

    Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix
    Yang, Shuo ; Diem, Matthias ; Liu, Jakob D.H. ; Wesseling, Sebastiaan ; Vervoort, Jacques ; Oostenbrink, Chris ; Rietjens, Ivonne M.C.M. - \ 2020
    Archives of Toxicology 94 (2020)4. - ISSN 0340-5761 - p. 1349 - 1365.
    DNA adduct - DNA repair efficiency - Estragole - Molecular modeling and simulation

    Estragole, naturally occurring in a variety of herbs and spices, can form DNA adducts after bioactivation. Estragole DNA adduct formation and repair was studied in in vitro liver cell models, and a molecular dynamics simulation was used to investigate the conformation dependent (in)efficiency of N2-(trans-isoestragol-3′-yl)-2′-deoxyguanosine (E-3′-N2-dG) DNA adduct repair. HepG2, HepaRG cells, primary rat hepatocytes and CHO cells (including CHO wild-type and three NER-deficient mutants) were exposed to 50 μM estragole or 1′-hydroxyestragole and DNA adduct formation was quantified by LC–MS immediately following exposure and after a period of repair. Results obtained from CHO cell lines indicated that NER plays a role in repair of E-3′-N2-dG adducts, however, with limited efficiency since in the CHO wt cells 80% DNA adducts remained upon 24 h repair. Inefficiency of DNA repair was also found in HepaRG cells and primary rat hepatocytes. Changes in DNA structure resulting from E-3′-N2-dG adduct formation were investigated by molecular dynamics simulations. Results from molecular dynamics simulations revealed that conformational changes in double-stranded DNA by E-3′-N2-dG adduct formation are small, providing a possible explanation for the restrained repair, which may require larger distortions in the DNA structure. NER-mediated enzymatic repair of E-3′-N2-dG DNA adducts upon exposure to estragole will be limited, providing opportunities for accumulation of damage upon repeated daily exposure. The inability of this enzymatic repair is likely due to a limited distortion of the DNA double-stranded helix resulting in inefficient activation of nucleotide excision repair.

    Syndromes of production in intercropping impact yield gains
    Li, Chunjie ; Hoffland, Ellis ; Kuyper, Thomas W. ; Yu, Yang ; Zhang, Chaochun ; Li, Haigang ; Zhang, Fusuo ; Werf, Wopke van der - \ 2020
    Nature Plants 6 (2020)6. - ISSN 2055-026X
    Intercropping, the simultaneous production of multiple crops on the same field, provides opportunities for the sustainable intensification of agriculture if it can provide a greater yield per unit land and fertilizer than sole crops. The worldwide absolute yield gain of intercropping as compared with sole crops has not been analysed. We therefore performed a global meta-analysis to quantify the effect of intercropping on the yield gain, exploring the effects of crop species combinations, temporal and spatial arrangements, and fertilizer input. We found that the absolute yield gains, compared with monocultures, were the greatest for mixtures of maize with short-grain cereals or legumes that had substantial temporal niche differentiation from maize, when grown with high nutrient inputs, and using multirow strips of each species. This approach, commonly practised in China, provided yield gains that were (in an absolute sense) about four times as large as those in another, low-input intercropping strategy, commonly practised outside China. The alternative intercropping strategy consisted of growing mixtures of short-stature crop species, often as full mixtures, with the same growing period and with low to moderate nutrient inputs. Both the low- and high-yield intercropping strategies saved 16–29% of the land and 19–36% of the fertilizer compared with monocultures grown under the same management as the intercrop. The two syndromes of production in intercropping uncovered by this meta-analysis show that intercropping offers opportunities for the sustainable intensification of both high- and low-input agriculture.
    Computer-assisted terrain sketch mapping that considers the geomorphological features in a loess landform
    Cheng, Yihan ; Yang, Xin ; Liu, Hailong ; Li, Min ; Rossiter, David G. ; Xiong, Liyang ; Tang, Guoan - \ 2020
    Geomorphology 364 (2020). - ISSN 0169-555X
    DEM - Loess landform - Terrain sketch map - Visual hierarchy division - Visual outline generalisation

    In geography, a terrain sketch map is necessary to understand the features and internal structures of a landscape due to its ability to depict key information in a geographical scene using as few lines as possible. Previous computer-drawn sketch maps have focused on the artistic effect rather than on depicting terrain features and landform structures, and thus, they differ considerably from hand-drawn sketch maps by geographers or geologists. This study develops a DEM-based method for terrain sketch mapping that considers the typical feature descriptions of a loess landform and the visual hierarchy expression in line with the law of visual perspective. The method was tested with experiments on two landforms of Chinese Loess Plateau, based on digital elevation models (DEM) with a horizontal resolution of 5 m. In the developed method, first, typical terrain features, including the visual outline, shoulder line, gully and flow lines, are extracted from the DEM. Second, the map is divided into three visual levels in accordance with the data extension and viewing point. Then, terrain feature lines are assigned to different visual levels. Finally, the visual outlines in the distant view are generalized following the law of visual perspective. Results are assessed through a questionnaire with specialists (experts) and students (non-experts). The sketch map was able to characterise loess landforms, and is somewhat similar to traditional hand-drawn maps. The generalisation method realises the near and distant view characteristics of a sketch map, which are detailed and simplified, respectively. The results of the questionnaire also showed that our method presents terrain morphology and geographical scene more accurately and reliably than a hand-drawn sketch map.

    Belowground soil water response in the afforestation-cropland interface under semi-arid conditions
    Huang, Ze ; Yang, Wen Jin ; Liu, Yu ; Shen, Weibo ; López-Vicente, Manuel ; Wu, Gao Lin - \ 2020
    Catena 193 (2020). - ISSN 0341-8162
    Agroforestry system interface - Semi-arid area - Soil water deficit degree - Soil water storage

    Agroforestry is an effective measure to control soil erosion and maintain or increase productivity in semi-arid areas. However, the belowground soil water responses in the afforestation-cropland interface (ACI) is not well known. This study analyzed the variability of soil water storage (SWS) and deficit in three ACIs taking into account the distance between the forest and cropland. The variations of soil water content up to 4 m depth and at five distances from the interface (−5 m (in forest), 0 m (interface), 1 m, 3 m and 5 m (in cropland)) were estimated in three artificial forests (Salix matsudana, Sophora japonica, and Populus cathayana) and their adjacent croplands (maize). The results showed that soil water at the interfaces was significantly affected by forest. This effect was effective up to 160–170 cm of soil depth, and the ACI of S. matsudana had the greatest impact on the farmland soil water. There was no significant relative soil water deficit between 1 and 3 m length, and the ACI of P. cathayana showed the lowest changes in the lateral direction. The SWS of S. japonica in the ACI was clearly higher than the other two artificial forests (P < 0.05). Our findings indicated that S. japonica was the most suitable forest species for agriculture sustainability in the study area. The tree species and the distance between cropland and forest should be considered during the establishment of agroforestry systems. This study provided insights for water conservation and effective management of ACIs in semi-arid areas.

    Methodology matters for comparing coarse wood and bark decay rates across tree species
    Chang, Chenhui ; Logtestijn, Richard S.P. van; Goudzwaard, Leo ; Hal, Jurgen van; Zuo, Juan ; Hefting, Mariet ; Sass-Klaassen, Ute ; Yang, Shanshan ; Sterck, Frank J. ; Poorter, Lourens ; Cornelissen, Johannes H.C. - \ 2020
    Methods in Ecology and Evolution (2020). - ISSN 2041-210X
    asynchronous - dead wood - decomposition - ecological methodology - fragment loss - inner bark thickness - interspecific variation - volume loss

    The importance of wood decay for global carbon and nutrient cycles is widely recognized. However, relatively little is known about bark decay dynamics, even though bark represents up to 25% of stem dry mass. Moreover, bark presence versus absence can significantly alter wood decay rates. Therefore, it really matters for the fate of carbon whether variation in bark and wood decay rates is coordinated across tree species. Answering this question requires advances in methodology to measure both bark and wood mass loss accurately. Decay rates of large logs in the field are often quantified as loss in tissue density, in which case volume depletions of bark and wood can yield large underestimations. To quantify the real decay rates, we assessed bark mass loss per stem surface area and wood mass loss based on volume-corrected density loss. We further defined the range of actual bark mass loss by considering bark cover loss. Then, we tested the correlation between bark and wood mass loss across 20 temperate tree species during 4 years of decomposition. The area-based method generally showed more than 3-fold higher bark mass loss than the density-based method (even higher if considering bark cover loss), and volume-corrected wood mass losses were 1.08–1.12 times higher than density-based mass loss. The deviation of bark mass loss between the two methods was higher for tree species with thicker inner bark. Bark generally decomposed twice as fast as wood across species, and faster decaying bark came with faster decaying wood (R2 = 0.26, p = 0.006). We strongly suggest using corrected volume when assessing wood mass loss especially for the species with faster decomposable sapwood and all the wood at advanced decay stages. Further studies of coarse stem decomposition should consider trait ‘afterlife’ effects of inner bark and estimate fraction of stem bark cover to obtain more accurate decay rates. Our new method should benefit our understanding of the in situ dynamics of woody debris decay and monitoring research in different forest ecosystems world-wide, and should aid meta-analyses across diverse studies.

    Compound in basil, fennel and aniseed harms DNA
    Yang, Shuo - \ 2020
    UVA radiation promotes tomato growth through morphological adaptation leading to increased light interception
    Zhang, Yating ; Kaiser, Elias ; Zhang, Yuqi ; Zou, Jie ; Bian, Zhonghua ; Yang, Qichang ; Li, Tao - \ 2020
    Environmental and Experimental Botany 176 (2020). - ISSN 0098-8472
    Blue light - Leaf photosynthesis - Phenolics - Photomorphogenesis - Red light syndrome - UVA radiation

    UVA radiation (315−400 nm) is the main component of solar UV radiation. Although it shares photoreceptors (i.e. cryptochromes and phototropins) with blue light (400−500 nm), its function in plant biology is unclear to a large extent. This study aimed at exploring how UVA radiation affects plant morphology and physiology, and at distinguishing to what extent these effects differ from those of blue light. Tomato plants were grown under monochromatic red (R), dichromatic red and blue (R/B = 7:1), as well as red and two different levels of UVA radiation (R/UVA = 7:1 and 15:1, respectively), with identical photon flux density (250 μmol⋅m−2⋅s−1). Peak intensities of UVA, B and R were 370, 450 and 660 nm, respectively. We showed that replacing blue by UVA (in a background of red light) induced plant morphological modifications, as reflected by larger leaf area, steeper leaf angles, flatter leaves and longer stems. UVA had reduced effects on leaf secondary metabolism compared to blue light, resulting in significantly lower total phenolics and flavonoid contents, as well as concentrations of UV-absorbing compounds. In addition, UVA had a similar function as blue light in shaping the development of the photosynthetic apparatus, as both wavebands alleviated the ‘red light syndrome’ (i.e. low photosynthetic capacity, reduced photosynthetic electron transport, and unresponsive stomata). We conclude that: 1) UVA promotes tomato growth through morphological adaptation leading to increased light interception; 2) UVA affects leaf secondary metabolite accumulation less strongly than blue light; 3) UVA functions similarly to blue light in maintaining leaf photosynthetic functioning. Thus, unlike previously suggested, UVA cannot be unequivocally considered as an abiotic stress factor. This research adds to the understanding of plant processes in response to UVA radiation and provides a basis for future recipes for growing plants with artificial light.

    Effects of nitrogen addition on soil methane uptake in global forest biomes
    Xia, Nan ; Du, Enzai ; Wu, Xinhui ; Tang, Yang ; Wang, Yang ; Vries, Wim de - \ 2020
    Environmental Pollution 264 (2020). - ISSN 0269-7491
    Forest - Nitrogen addition - Nitrogen deposition - Soil methane uptake

    Nitrogen (N) deposition has been conventionally thought to decrease forest soil methane (CH4) uptake, while the biome specific and dose dependent effect is poorly understood. Based on a meta-analysis of 63 N addition trials from 7 boreal forests, 8 temperate forests, 13 subtropical and 4 tropical forests, we evaluated the effects of N addition on soil CH4 uptake fluxes across global forest biomes. When combining all N addition levels, soil CH4 uptake was insignificantly decreased by 7% in boreal forests, while N addition significantly decreased soil CH4 uptake by 39% in temperate forests and by 21% in subtropical and tropical forests, respectively. Meta-regression analyses, however, indicated a shift from a positive to a negative effect on soil CH4 uptake with increasing N additions both in boreal forests (threshold = 48 kg N ha−1 yr−1) and temperate forests (threshold = 27 kg N ha−1 yr−1), while no such shift was found in subtropical and tropical forests. Considering that current N deposition to most boreal and temperate forests is below the abovementioned thresholds, N deposition likely exerts a positive to neutral effect on soil CH4 uptake in both forest biomes. Our results provide new insights on the biome specific and dose dependent effect of N addition on soil CH4 sink in global forests and suggest that the current understanding that N deposition decreases forest soil CH4 uptake is flawed by high levels of experimental N addition.

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