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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    Acute porcine epidemic diarrhea virus infection reshapes the intestinal microbiota
    Yang, Shanshan ; Li, Yang ; Wang, Bin ; Yang, Ning ; Huang, Xin ; Chen, Qingbo ; Geng, Shuxian ; Zhou, Yawei ; Shi, Han ; Wang, Leyi ; Brugman, Sylvia ; Savelkoul, Huub ; Liu, Guangliang - \ 2020
    Virology 548 (2020). - ISSN 0042-6822 - p. 200 - 212.
    Intestinal microbiota - Pathogenicity - Porcine epidemic diarrhea virus

    The intestinal microbiota is crucial to intestinal homeostasis. Porcine epidemic diarrhea virus (PEDV) is high pathogenic to intestines, causing diarrhea, even death in piglets. To investigate the detailed relationship between PEDV infection and intestinal microbiota, the composition and distribution of intestinal microbiota from pigs were first analyzed using 16S rRNA sequencing technology. The results demonstrated that the composition and distribution of microbes in different intestinal segments were quite similar between 1-week-old and 2-week-old piglets but different from 4-week-old (weaned) piglets. Then piglets at different ages were inoculated with PEDV. The results showed that the 1-week-old piglets exhibited the most severe pathogenicity comparing to the other age groups. Further investigations indicated that Lactobacillus, Escherichia coli, and Lactococcus in the intestinal microbiota of piglets were significantly changed by PEDV infection. These results strengthen our understanding of viruses influencing intestinal microbes and remind us of the potential association between PEDV and intestinal microbes.

    Removing top leaves increases yield and nutrient uptake in maize plants
    Raza, Muhammad Ali ; Werf, Wopke van der; Ahmed, Mukhtar ; Yang, Wenyu - \ 2020
    Nutrient Cycling in Agroecosystems 118 (2020)1. - ISSN 1385-1314 - p. 57 - 73.
    Maize - Nitrogen - Phosphorus - Potassium - Seed filling-phase

    Abstract: Intraspecific competition for light affects nutrient uptake of maize, especially during the seed filling phase (from the blistering-stage to physiological-maturity). Partial leaf removal only affects the top leaves and improves the light-environment, which could then enhance nutrient uptake during the seed filling phase. However, there is a shortage of quantitative information on the yield effects of such a management measure. A 3-year field trial was conducted to evaluate the impact of different leaf removal treatments (no removal of leaves (D0: control), removal of two leaves (D2), removal of four leaves (D4), and removal of six leaves (D6) from maize-canopy) on total dry matter accumulation, and nitrogen, phosphorus, and potassium uptake at the blistering-stage and physiological-maturity, plus seed number per plant, seed weight, and seed yield at physiological maturity. Compared to D0, at physiological-maturity, D2 significantly increased total dry matter accumulation (by 9%), and uptake of nitrogen (by 5%), phosphorus (by 10%), and potassium (by 4%); while excessive leaf removal treatments considerably reduced dry matter accumulation and nutrient uptake. Importantly, during the seed filling phase of maize, treatment D2 significantly enhanced the uptake of nitrogen, phosphorus, and potassium by 76%, 40%, and 65%, respectively, compared to control. Treatment D2 increased seed number per plant (by 6.4%, from 448 under D0 to 477 in D2) and seed weight (by 5.7%). Relative to control, maize in D2 had 12%, 14%, and 11%, higher seed-yields in 2017, 2018, and 2019, respectively, and it also improved the economic profit when taking into account labor costs. Graphic abstract: Graphical representation of changes in light transmittance, photosynthesis, nutrient uptake, carbohydrate, and dry matter accumulation in maize plants as affected by different leaf removal treatments. Treatment codes represent no defoliation (D0: control), removal of two leaves (D2), removal of four leaves (D4), and removal of six leaves (D6) from the top of maize canopy. Yellow and green arrows show the light environment and leaf area of maize plants. The black arrows represent the regulating directions of leaf removal treatments on maize growth and development in this paper. The graphical abstract clearly demonstrates the significant improvement of optimum leaf removal treatment (D2) as compared to control (D0). The red and blue arrows show the relevant increase and decrease of the mentioned components between the optimal leaf removal and control. [Figure not available: see fulltext.]

    Opportunities for fraudsters : When would profitable milk adulterations go unnoticed by common, standardized FTIR measurements?
    Yang, Yuzheng ; Hettinga, Kasper A. ; Erasmus, Sara W. ; Pustjens, Annemieke M. ; Ruth, Saskia M. van - \ 2020
    Food Research International 136 (2020). - ISSN 0963-9969
    Ammonium chloride (PubChem CID: 25517) - Ammonium sulphate (PubChem CID: 6097028) - Dicyandiamide (PubChem CID: 10005) - Formaldehyde (PubChem CID: 712) - Fourier transform infrared - Fructose (PubChem CID: 5984) - Glucose (PubChem CID: 79025) - Hydrogen peroxide (PubChem CID: 784) - Lactose (PubChem CID: 104938) - Maltodextrin (PubChem CID: 68229136) - Melamine (PubChem CID: 7955) - Milk adulteration - Milk composition - Milkoscan measurements - One class classification - Profitability - Sodium bicarbonate (PubChem CID: 516892) - Sodium carbonate (PubChem CID: 10340) - Sodium citrate (PubChem CID: 23666341) - Sodium hydroxide (PubChem CID: 14798) - Starch (PubChem CID: 24836924) - Sucrose (PubChem CID: 5988) - Urea (PubChem CID: 1176)

    Milk is regarded as one of the top food products susceptible to adulteration where its valuable components are specifically identified as high-risk indicators for milk fraud. The current study explores the impact of common milk adulterants on the apparent compositional parameters of milk from the Dutch market as measured by standardized Fourier transform infrared (FTIR) spectroscopy. More precisely, it examines the detectability of these adulterants at various concentration levels using the compositional parameters individually, in a univariate manner, and together in a multivariate approach. In this study we used measured boundaries but also more practical variance-adjusted boundaries to set thresholds for detection of adulteration. The potential economic impact of these adulterations under a milk payment scheme is also evaluated. Twenty-four substances were used to produce various categories of milk adulterations, each at four concentration levels. These substances comprised five protein-rich adulterants, five nitrogen-based adulterants, seven carbohydrate-based adulterants, six preservatives and water, resulting in a set of 360 samples to be analysed. The results showed that the addition of protein-rich adulterants, as well as dicyandiamide and melamine, increased the apparent protein content, while the addition of carbohydrate-based adulterants, whey protein isolate, and skimmed milk powder, increased the apparent lactose content. When considering the compositional parameters univariately, especially protein- and nitrogen-based adulterants did not raise a flag of unusual apparent concentrations at lower concentration levels. Addition of preservatives also went unnoticed. The multivariate approach did not improve the level of detection. Regarding the potential profit of milk adulteration, whey protein and corn starch seem particularly interesting. Combining the artificial inflation of valuable components, the resulting potential profit, and the gaps in detection, it appears that the whey protein isolates deserve particular attention when thinking like a criminal.

    Chemical structure predicts the effect of plant‐derived low molecular weight compounds on soil microbiome structure and pathogen suppression
    Gu, Yian ; Wang, Xiaofang ; Yang, Tianjie ; Friman, Ville Petri ; Geisen, Stefan ; Wei, Zhong ; Xu, Yangchun ; Jousset, Alexandre ; Shen, Qirong - \ 2020
    Functional Ecology (2020). - ISSN 0269-8463

    1. Plant‐derived low molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, mout data are case‐specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low molecular weight compounds typically secreted by plant roots – sugars, amino acids, organic acids and phenolic acids – can predictably affect microbiome diversity, composition and functioning in terms of plant disease suppression.

    2. We amended soil with single or mixtures of representative compounds, mimicking carbon deposition by plants. We then assessed how different classes of compounds, or their combinations, affected microbiome composition and the protection of tomato plants from the soil‐borne Ralstonia solanacearum bacterial pathogen.

    3. We found that chemical class predicted well the changes in microbiome composition and diversity. Organic and amino acids generally decreased the microbiome diversity compared to sugars and phenolic acids. These changes were also linked to disease incidence, with amino acids and nitrogen‐containing compound mixtures inducing more severe disease symptoms connected with a reduction in bacterial community diversity.

    4. Together, our results demonstrate that low molecular weight compounds can predictably steer rhizosphere microbiome functioning providing guidelines to engineer microbiomes based on root exudation patterns by specific plant cultivars or crop regimes.
    The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion
    Gu, Yian ; Dong, Ke ; Geisen, Stefan ; Yang, Wei ; Yan, Yaner ; Gu, Dalu ; Liu, Naisen ; Borisjuk, Nikolai ; Luo, Yuming ; Friman, Ville Petri - \ 2020
    Plant and Soil 452 (2020). - ISSN 0032-079X - p. 105 - 117.
    Diversity - Microbial inoculation - Microbial transplants - Plant growth-promotion - Rhizosphere microbiota - Soil functioning

    Aims: Microbial inoculation has been proposed as a potential approach for rhizosphere engineering. However, it is still unclear to what extent successful plant growth-promoting effects are driven by the origin of the microbial inocula and which taxa are responsible for the plant-beneficial effects. Methods: We conducted a microbial transplant experiment by using different microbial inocula (and nutrient controls) isolated from forest, soybean and tomato field soils and determined their effects on tomato plant biomass and nutrient assimilation in sterilized tomato soil. Rhizosphere bacterial communities were compared at the end of the experiment and correlative and machine learning analyses used to identify potential keystone taxa associated with the plant growth-promotion. Results: Microbial inoculants had a clear positive effect on plant growth compared to control nutrient inoculants. Specifically, positive effects on the plant biomass were significantly associated with microbial inoculants from the forest and soybean field soils, while microbial inoculants from the forest and tomato field soils had clear positive effects on the plant nutrient assimilation. Soil nutrients alone had relatively minor effects on rhizosphere bacterial communities. However, the origin of microbial inoculants had clear effects on the structure of bacterial community structure with tomato and soybean inoculants having positive effects on the diversity and abundance of bacterial communities, respectively. Specifically, Streptomyces, Luteimonas and Enterobacter were identified as the potential keystone genera affecting plant growth. Conclusions: The origin of soil microbiome inoculant can predictably influence plant growth and nutrient assimilation and that these effects are associated with certain key bacterial genera.

    Impact of plastic mulch film debris on soil physicochemical and hydrological properties
    Qi, Yueling ; Beriot, Nicolas ; Gort, Gerrit ; Huerta Lwanga, Esperanza ; Gooren, Harm ; Yang, Xiaomei ; Geissen, Violette - \ 2020
    Environmental Pollution 266 (2020). - ISSN 0269-7491
    Agricultural soil - Biodegradable plastic - Microplastics - Plastic pollution - Soil quality

    The plastic mulch films used in agriculture are considered to be a major source of the plastic residues found in soil. Mulching with low-density polyethylene (LDPE) is widely practiced and the resulting macro- and microscopic plastic residues in agricultural soil have aroused concerns for years. Over the past decades, a variety of biodegradable (Bio) plastics have been developed in the hope of reducing plastic contamination of the terrestrial ecosystem. However, the impact of these Bio plastics in agroecosystems have not been sufficiently studied. Therefore, we investigated the impact of macro (around 5 mm) and micro (<1 mm) sized plastic debris from LDPE and one type of starch-based Bio mulch film on soil physicochemical and hydrological properties. We used environmentally relevant concentrations of plastics, ranging from 0 to 2% (w/w), identified by field studies and literature review. We studied the effects of the plastic residue on a sandy soil for one month in a laboratory experiment. The bulk density, porosity, saturated hydraulic conductivity, field capacity and soil water repellency were altered significantly in the presence of the four kinds of plastic debris, while pH, electrical conductivity and aggregate stability were not substantially affected. Overall, our research provides clear experimental evidence that microplastics affect soil properties. The type, size and content of plastic debris as well as the interactions between these three factors played complex roles in the variations of the measured soil parameters. Living in a plastic era, it is crucial to conduct further interdisciplinary studies in order to have a comprehensive understanding of plastic debris in soil and agroecosystems.

    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.

    Resource scarcity and cooperation : Evidence from a gravity irrigation system in China
    Nie, Zihan ; Yang, Xiaojun ; Tu, Qin - \ 2020
    World Development 135 (2020). - ISSN 0305-750X
    China - Cooperation - Irrigation - Public goods game - Water scarcity

    Resource scarcity has become an increasingly pressing challenge to the world. How scarcity affects people's preferences and behavior has been taken as an important issue for development. This study examines the impact of long-term exposure to resource scarcity on farmers’ cooperation. Specifically, we focus on water scarcity in irrigation agriculture, and examine the effect of water scarcity on cooperation in the context of a gravity irrigation system in western China. A historical irrigation water quota system provides an opportunity to measure exogenous variations of water scarcity within an otherwise homogeneous region. We use the ratio of the arable land area to the irrigation water quota of each village as our measure of water scarcity. Moreover, we use the contributions in a public goods game to measure the farmers’ willingness to cooperate. Combining a household survey and a lab-in-the-field experiment with 312 rural residents in northwestern China, we find that irrigation water scarcity significantly increases farmers’ willingness to cooperate. The results are robust to potential endogeneity concerns and many confounding factors. We also find that water scarcity is positively correlated with irrigation management activities and canal conditions. Our findings provide important policy implications for common pool resource management and collective actions in rural communities.

    The mechanism and application of bidirectional extracellular electron transport in the field of energy and environment
    Xie, Qingqing ; Lu, Yue ; Tang, Lin ; Zeng, Guangming ; Yang, Zhaohui ; Fan, Changzheng ; Wang, Jingjing ; Atashgahi, Siavash - \ 2020
    Critical Reviews in Environmental Science and Technology (2020). - ISSN 1064-3389
    Bioremediation - energy production - extracellular electron transfer

    Bidirectional extracellular electron transfer (EET) is mediated by back and forth electron delivery between microorganisms and extracellular substances. This enables the exchange of biochemical information and energy with the surrounding environments. As a novel bioenergy strategy, bidirectional EET provides low-cost opportunities for the production of clean energy sources and carriers (e.g., hydrogen and methane) as well as the production of value-added chemicals from carbon dioxide. Electrochemically active bacteria (EAB) can also transform pollutants to less toxic or benign substances in contaminated environments, and therefore they have been widely applied in bioremediation studies. Among all the available EAB, Geobacter and Shewanella are well-known for their versatility to accept/donate electrons from/to external environments. In this review, we focus on how these model EAB generate or harvest energy through bidirectional EET, as well as recent advances in the application of EET in bioelectrochemical technology and environmental bioremediation. Finally, the challenges, perspectives and new directions in the bidirectional EET studies are discussed. (Figure presented.).

    Salt stress and fluctuating light have separate effects on photosynthetic acclimation, but interactively affect biomass
    Zhang, Yuqi ; Kaiser, Elias ; Marcelis, Leo F.M. ; Yang, Qichang ; Li, Tao - \ 2020
    Plant, Cell & Environment (2020). - ISSN 0140-7791 - 15 p.
    fluctuating light - light acclimation - photosynthesis - salt stress - stomatal conductance - tomato

    In nature, soil salinity and fluctuating light (FL) often occur concomitantly. However, it is unknown whether salt stress interacts with FL on leaf photosynthesis, architecture, biochemistry, pigmentation, mineral concentrations, as well as whole-plant biomass. To elucidate this, tomato (Solanum lycopersicum) seedlings were grown under constant light (C, 200 μmol m−2 s−1) or FL (5–650 μmol m−2 s−1), in combination with no (0 mM NaCl) or moderate (80 mM NaCl) salinity, for 14 days, at identical photoperiods and daily light integrals. FL and salt stress had separate effects on leaf anatomy, biochemistry and photosynthetic capacity: FL reduced leaf thickness as well as nitrogen, chlorophyll and carotenoid contents per unit leaf area, but rarely affected steady-state and dynamic photosynthetic properties along with abundance of key proteins in the electron transport chain. Salt stress, meanwhile, mainly disorganized chloroplast grana stacking, reduced stomatal density, size and aperture as well as photosynthetic capacity. Plant biomass was affected interactively by light regime and salt stress: FL reduced biomass in salt stressed plants by 17%, but it did not affect biomass of non-stressed plants. Our results stress the importance of considering FL when inferring effects of salt-stress on photosynthesis and productivity under fluctuating light intensities.

    Estimation of nitrogen supply for winter wheat production through a long-term field trial in China
    Huang, Shaohui ; Ding, Wencheng ; Yang, Junfang ; Zhang, Jiajia ; Ullah, Sami ; Xu, Xinpeng ; Liu, Yingxia ; Yang, Yunma ; Liu, Mengchao ; He, Ping ; Jia, Liangliang - \ 2020
    Journal of Environmental Management 270 (2020). - ISSN 0301-4797
    Nitrogen use efficiency - Relative yield - Total nitrogen supply - Winter wheat

    Excessive synthetic nitrogen (N) applications, high mineral N accumulation and low N use efficiency (NUE) are current issues in intensively cultivated winter wheat production system impeding the sustainable development of agriculture in China. To solve these problems, soil accumulated N in the top 1 m of the soil profile before sowing (Nsoil), returned straw-N from the previous maize crop (Nstraw) and fertilizer N application (Nfertilizer) should be comprehensively considered N supply sources in N management. As such, the objective of this research was to determine the optimal total N supply (TNsupply) level needed to meet crop requirements while minimizing environmental impacts. A 9-year on-farm experiment was conducted in accordance with a split-plot design involving two different fertilizer management systems (main treatments) and three N application strategies (sub treatments). Extensive TNsupply levels (ranging from 61 kg ha−1 to 813 kg ha−1) were detected, and relative yield (RY), N input and N output in response to the TNsupply were measured. The relationships between TNsupply and RY, N input, and N output strongly fit linear-plateau, linear, and linear-plateau models, respectively. The minimum TNsupply levels needed to achieve the maximum RY and N output were 325 and 392 kg ha−1, respectively. On the basis of N supply capacity, the TNsupply was removed from the growing system by 61% (N input). As the N input increased past 209 kg ha−1, the NUE declined, at which point the TNsupply reached 433 kg ha−1. Therefore, the suitable TNsupply should range from 325 kg ha−1 (ensuring a total N supply for high yield and N uptake) to 433 kg ha−1 (obtaining a relatively higher NUE and less N loss to the environment). The TNsupply was highlighted to be an indicator for use in N management recommendations. Considering the average high N accumulation in winter wheat production systems, N management should essentially take into account the consumption of Nsoil, the levels of Nstraw and the minimum application of Nfertilizer to obtain high yields while minimizing environmental impacts under suitable TNsupply levels.

    Scaling relationships among functional traits are similar across individuals, species, and communities
    Long, Wenxing ; Zhou, Yadong ; Schamp, Brandon S. ; Zang, Runguo ; Yang, Xiaobo ; Poorter, Lourens ; Xiao, Chuchu ; Xiong, Menghui - \ 2020
    Journal of Vegetation Science 31 (2020)4. - ISSN 1100-9233 - p. 571 - 580.
    bivariate trait relationships - environmental stress - leaf mass per area - plant height - plant strategy - soil phosphorus - tropical forest - wood density

    Question: Bivariate relationships among functional traits reflect how plants adjust to environments through the allocation of limiting resources. Bivariate relationships are well studied across species, but whether the nature of these trait relationships changes across organizational levels (individual, species, community), and whether processes driving these relationships vary across these levels, is seldom explored. Location: The tropical cloud forests of the Bawangling Nature Reserve, Jianfengling Nature Reserve and Limushan Nature Reserve on Hainan Island, Southern China. Methods: We measured leaf mass per area (LMA), plant height (H) and wood density (WD) for 4,748 individual trees, 174 species and 48 communities in three tropical cloud forests, and recorded five soil characteristics that are important for plant growth. We evaluated bivariate relationships between these traits across the three organizational levels, and assessed the effects of soil conditions on these trait relationships. Results: LMA versus H, WD versus H, and LMA versus WD were all positively and disproportionately related, suggesting differential carbon investment between leaves and stem, as well as between stem height and stem density. The slopes of these relationships did not differ significantly across the three levels, suggesting a similar allocation strategy operating at different hierarchical levels. Soil phosphorus had a significant effect on the scaling exponents across all three organizational levels, indicating that phosphorus limitation in cloud forests is a principal driver of resource allocation patterns in trees. conclusions: We conclude that tropical cloud forest trees have relatively consistent scaling relationships between three primary functional traits across the individual, species, and community levels. The coordinated resource allocation strategies in plants are most likely driven by the prevailing environmental constraints.

    Comparisons with wheat reveal root anatomical and histochemical constraints of rice under water-deficit stress
    Ouyang, Wenjing ; Yin, Xinyou ; Yang, Jianchang ; Struik, Paul C. - \ 2020
    Plant and Soil 452 (2020). - ISSN 0032-079X - p. 547 - 568.
    Lignin - Rice - Root anatomy - Root morphology - Suberin - Water deficit - Wheat

    Aims: To face the challenge of decreasing freshwater availability for agriculture, it is important to explore avenues for developing rice genotypes that can be grown like dryland cereals. Roots play a key role in plant adaptation to dry environments. Methods: We examined anatomical and histochemical root traits that affect water acquisition in rice (Oryza sativa) and wheat (Triticum aestivum). These traits and root growth were measured at two developmental stages for three rice and two wheat cultivars that were grown in pots under three water regimes. Results: Wheat roots had larger xylem sizes than rice roots, which potentially led to a higher axial conductance, especially under water-deficit conditions. Suberization, lignification and thickening of the endodermis in rice roots increased with increasing water deficit, resulting in stronger radial barriers for water flow in rice than in wheat, especially near the root apex. In addition, water deficit strongly impeded root growth and lateral root proliferation in rice, but only slightly in wheat, and cultivars within a species differed little in these responses. The stress sensitivity of rice attributes was slightly more prominent at vegetative than at flowering stages. Conclusions: Rice root characteristics, which are essential for growth under inundated conditions, are not conducive to growth under water deficit. Although rice roots show considerable plasticity under different watering regimes, improving root xylem size and reducing the radial barriers would be required if rice is to grow like dryland cereals.

    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 100 (2020)11. - ISSN 0022-5142 - p. 4282 - 4291.
    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 98 (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 11 (2020)7. - ISSN 2041-210X - p. 828 - 838.
    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.

    Optimum strip width increases dry matter, nutrient accumulation, and seed yield of intercrops under the relay intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khan, Imran ; Khan, Ahsin ; Din, Atta Mohi Ud ; Naeem, Muhammd ; Meraj, Tehseen Ahmad ; Hassan, Muhammad Jawad ; Khan, Aaqil ; Lu, Feng Zhi ; Liu, Xin ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2020
    Food and Energy Security 9 (2020)2. - ISSN 2048-3694
    competition ratio - growing space - maize - relay intercropping - soybean

    Strip width management is a critical factor for producing higher crop yields in relay intercropping systems. A 2-year field experiment was carried out during 2012 and 2013 to evaluate the effects of different strip width treatments on dry-matter production, major-nutrient (nitrogen, phosphorus, and potassium) uptake, and competition parameters of soybean and maize in relay intercropping system. The strip width (SW) treatments were 0.40, 0.40, and 0.40 m (SW1); 0.40, 0.40, and 0.50 m (SW2); 0.40, 0.40, and 0.60 m (SW3); and 0.40, 0.40, and 0.70 m (SW4) for soybean row spacing, maize row spacing, and spacing between soybean and maize rows, respectively. As compared to sole maize (SM) and sole soybean (SS), relay-intercropped maize and soybean accumulated lower quantities of nitrogen, phosphorus, and potassium in all treatments. However, maize in SW1 accumulated higher nitrogen, phosphorus, and potassium than SW4 (9%, 9%, and 8% for nitrogen, phosphorus, and potassium, respectively). Soybean in SW3 accumulated 25% higher nitrogen, 33% higher phosphorus, and 24% higher potassium than in SW1. The improved nutrient accumulation in SW3 significantly increased the soybean dry matter by 19%, but slightly decreased the maize dry matter by 6% compared to SW1. Similarly, SW3 increased the competition ratio value of soybean (by 151%), but it reduced the competition ratio value of maize (by 171%) compared to SW1. On average, in SW3, relay-cropped soybean produced 84% of SS seed yield and maize produced 98% of SM seed yield and achieved the land equivalent ratio of 1.8, demonstrating the highest level in the world. Overall, these results suggested that by selecting the appropriate strip width (SW3; 0.40 m for soybean row spacing, 0.40 m maize row spacing, and 0.60 m spacing between soybean and maize rows), we can increase the nutrient uptake (especially nitrogen, phosphorus, and potassium), dry-matter accumulation, and seed yields of relay-intercrop species under relay intercropping systems.

    Effect of CMC degree of substitution and gliadin/CMC ratio on surface rheology and foaming behavior of gliadin/CMC nanoparticles
    Peng, Dengfeng ; Jin, Weiping ; Arts, Miriam ; Yang, Jack ; Li, Bin ; Sagis, Leonard M.C. - \ 2020
    Food Hydrocolloids 107 (2020). - ISSN 0268-005X
    Degree of substitution - Foam - Nanoparticle - Ratio - Structure - Surface behavior

    To understand the influence of the degree of substitution (DS) of sodium carboxymethyl cellulose (CMC) and gliadin:CMC ratio on the surface and foaming behaviors of gliadin-CMC nanoparticles (G-CMC NPs) at pH 3, three DS (0.7–1.2) and four ratios (G:CMC~1:0.5–1:2) were investigated. Gliadin NPs with a pH of 3 were utilized as a control. Results showed that G-CMC NPs at all investigated DS and ratios possessed higher foamability and foam stability when compared to the control. This indicated that adding CMC to gliadin NP suspensions could greatly improve their foaming properties. G-CMC NPs with a DS of 0.7 and 0.9, had lower surface charge than G-CMC1.2 NPs, resulting in a weaker electrostatic repulsion, thus leading to faster adsorption kinetics and higher foamability. By increasing the G:CMC ratio from 1:0.5 to 1:2, the particle size gradually rose, and the zeta potential remained unchanged. At a ratio of 1:2, the highest foam stability was observed. This might be ascribed to the high continuous phase viscosity at this ratio, which could slow down the drainage rate and protect the bubbles against coalescence and disproportionation. It was worth mentioning that G-CMC NPs at all ratios exhibited impressive foamability (~220%) even at a very low concentration of G-CMC NPs (gliadin was fixed at 1 mg/mL). This implies that G-CMC NPs could act as a new efficient foaming agent, and based on its simple preparation, have the potential to be widely applied in foamed food.

    Assessing the impacts of recent-past climatic constraints on potential wheat yield and adaptation options under Mediterranean climate in southern Portugal
    Yang, Chenyao ; Fraga, Helder ; Ieperen, Wim van; Santos, João A. - \ 2020
    Agricultural Systems 182 (2020). - ISSN 0308-521X
    Adaptation strategy - Regional crop modelling - STICS - Terminal abiotic stress - Winter wheat - Yield gap

    Wheat yield potentials under rainfed Mediterranean conditions have been long limited by late-in-season occurrence of enhanced water deficits and high temperatures, coinciding with sensitive reproductive stages. Present study aims to quantify and separate the impacts of two main abiotic stresses (drought & heat) on potentially attainable wheat yields, in a typical Mediterranean environment of southern Portugal (Alentejo) over 1986—2015. We also evaluate how possible adaptation options could mitigate potential yield losses (reduce the gap between actual and potential yield). Previously calibrated STICS soil-crop model is used for these purposes, which has been satisfactorily evaluated herein for yield simulations using additional field data before running at regional level. By coupling with high-resolution gridded soil and climate datasets, STICS simulations reliably reproduce the inter-annual variability of 30-year regional yield statistics, together with reasonable estimations of experimental potential yields. Therefore, the model is useful to explore the source of yield gap in the region. The quantified impacts, though with some uncertainties, identify the prolonged terminal drought stress as the major cause of yield gap, causing 40–70% mean potential yield losses. In contrast, a short-duration of crop heat stress (≥38 °C) during late grain-filling phase only results in small-to-moderate reductions (up to 20%). Supplemental Irrigation (SI) during reproductive stages provides good adaptive gains to recover potential yield losses by 15–30%, while the proposed early-flowering cultivar is more useful in escaping the terminal heat stress (5–15% adaptive gains) than avoiding prolonged drought stress. In addition, advancing sowing date generally favours wheat production with a robust spatial-temporal pattern. Therefore, combined options based on application of SI, using balanced early-flowering cultivar and early sowing date, may contribute to considerably reduce local yield gap, where current yields can account for 60% of potential yields (26–32% without adaptation). Regional impact assessment and adaptation modelling studies are essential to support agricultural policy development under climate change and variability. The recommended combined adaptation may also represent a promising adaptation strategy for rainfed wheat cropping system in other regions with similar Mediterranean conditions. However, the existing spatial-temporal variability of adaptation response highlights the need to address adaptation strategies at a more detailed local scale with better flexible design.

    Border-row proportion determines strength of interspecific interactions and crop yields in maize/peanut strip intercropping
    Wang, Ruonan ; Sun, Zhanxiang ; Zhang, Lizhen ; Yang, Ning ; Feng, Liangshan ; Bai, Wei ; Zhang, Dongsheng ; Wang, Qi ; Evers, Jochem B. ; Liu, Yang ; Ren, Jianhong ; Zhang, Yue ; Werf, Wopke van der - \ 2020
    Field Crops Research 253 (2020). - ISSN 0378-4290
    border-row effect - relative yield total - row configuration - strip cropping - yield components

    Strip intercropping enables increases in yields and ecological services in agriculture. Crop yields of species grown in strip intercropping are often related to the yield responses (increases or decreases) in the outer rows of the strips: the border rows. This suggests that the yield response can be modulated by changing the proportion of border rows in the field. Here we studied the relationship between component species yields and proportion of border rows in strip intercrops of maize (Zea mays L.) and peanut (Arachis hypogaea Linn.). We tested four different intercrops with equal proportions of maize and peanut but a different number of rows per strip: M2P2 (2 rows maize intercropped with 2 rows peanut), M4P4, M6P6, M8P8, and sole maize (SM) and sole peanut (SP). The border-row proportions were 1, 0.5, 0.33 and 0.25 for the intercropping M2P2 to M8P8, respectively, and 0 for the pure stands. Yield responded positively to the proportion of border rows for maize, but negatively for peanut, confirming the dominance of maize in this system. Kernel number per ear of maize and pod number per plant of peanut were the main yield components that responded to the border-row proportion. Across three years, relative maize yield (yield in intercropping divided by yield in monoculture), varied from 0.76 in M2P2 to 0.56 in M8P8, while relative peanut yield varied from 0.19 in M2P2 to 0.39 in M8P8. Relative yield total was not significantly different from one in any of the mixtures. Yield of intercropped maize in border rows was 48% higher than in inner rows and the sole crop, in part due to a significantly higher kernel number per ear (13%). Yield of intercropped peanut in border rows was on average 29% lower than in inner rows and 48% lower than in sole peanut. Yield responses in border rows were independent from the border-row proportion. The results show that relative crop yields responded strongly to variation in border-row proportion resulting from variation in strip width from 1 to 4 m. Strip width thus provides a mechanism to control the strength of interspecific plant interactions and relative yields in strip intercropping.

    Dynamic balancing of intestinal short-chain fatty acids: the crucial role of bacterial metabolism
    Xu, Youqiang ; Zhu, Yang ; Li, Xiuting ; Sun, Baoguo - \ 2020
    Trends in Food Science and Technology 100 (2020). - ISSN 0924-2244 - p. 118 - 130.
    Background: Short-chain fatty acids (SCFAs) play important physiological roles in human health. Adverse effects on health are known with a low or excessive concentration of SCFAs although the optimal level of SCFAs in the body is unknown yet. The level of endogenous SCFAs is affected by many factors of which gut bacteria are the most important one. However, how gut bacteria and a dietary intervention affect SCFA balance in the gut still needs to be clarified.
    Scope and approach: In addition to addressing the importance of a dynamic balance of SCFAs for health, we discuss the factors affecting the dynamic balance of SCFAs, especially the gut SCFA-producing bacteria, including the classification of the bacteria, their response to diet, the SCFAs metabolic pathways and the catalytic mechanisms of the main rate-limiting enzymes.
    Key findings and conclusions: SCFAs levels can be regulated endogenously and exogenously. Exogenous regulation delivers SCFAs to gut by esterification with dietary fibres. Endogenous regulation like diet, directly or indirectly affect gut microbiota, including their abundance, fitness and SCFAs production. Until now, 74 bacterial species are reported to produce SCFAs, the metabolic pathways are classified into 4 categories, and the 4 rate-limiting enzymes in the metabolic pathways are summarized. We also propose methods for long-lasting endogenous SCFAs balancing, including identifying the minimum sets of SCFA-producing bacterial group, and possible dietary intervention to form a minimum group of gut microbiota for SCFAs synthesis. An integrated approach will help realize the rational regulation of balanced SCFAs levels to benefit human health.
    Valuation of Wetland Ecosystem Services in National Nature Reserves in China’s Coastal Zones
    Li, Xiaowei ; Yu, Xiubo ; Hou, Xiyong ; Liu, Yubin ; Li, Hui ; Zhou, Yangming ; Xia, Shaoxia ; Liu, Yu ; Duan, Houlang ; Wang, Yuyu ; Dou, Yuehan ; Yang, Meng ; Zhang, Li - \ 2020
    Sustainability 12 (2020)8. - ISSN 2071-1050
    Wetlands provide ecosystem services for regional development, and, thus, have considerable economic value. In this study, a combination of evaluation methods was carried out to evaluate the wetland ecosystem services provided by national nature reserves in 11 coastal provinces/municipalities in China. We constructed a literature database containing 808observations (over 170 papers) on field-scale research for wetlands in China’s coastal zones. Using this literature database, as well as land use (LU) data, net primary productivity (NPP), and statistical data, and digital elevation model (DEM) data, we established a valuation framework and database for nine important ecosystem services of the 13 wetland types in the study area. After the large-scale academic literature review, the ordinary kriging offered by Geostatistical Analyst tools was used to interpolate the physical dimensions of the unmeasured locations. The results showed that: 1) the wetland ecosystem services in 35 national nature reserves have a total value of 33.168billion USD/year; 2) the values of wetland ecosystem services revealed considerable spatial variability along China’s coastal zones; and 3) assessments provide additional insights into the trade-offs between different ecosystem services and wetland types. The valuation framework and database established in this study can contribute to the mapping of wetland ecosystem services in coastal zones.
    Modeling of industrial-scale anaerobic solid-state fermentation for Chinese liquor production
    Jin, Guangyuan ; Uhl, Philipp ; Zhu, Yang ; Wijffels, René H. ; Xu, Yan ; Rinzema, Arjen - \ 2020
    Chemical Engineering Journal 394 (2020). - ISSN 1385-8947
    Chinese liquor - Heat transfer - Mathematical modeling - Product inhibition - Solid-state fermentation - Temperature modeling

    Traditional solid-state fermentation processes can give fluctuating product quality and quantity due to difficulties in control and scale up. This paper describes an engineering study of an industrial-scale anaerobic solid-state fermentation process for Chinese liquor (Baijiu) production, aimed at better understanding of the traditional process, as an initial step for future optimization. This mixed-culture fermentation is done in 0.44-m3 vessels embedded in the soil. At this scale, the fermentation is limited by product inhibition. We developed mathematical models based on the Han-Levenspiel equation for product inhibition, with parameters derived from measured data. The models accurately predicted the concentrations of starch and dry matter. A model with radial conduction into a small soil volume around the fermenter and consecutive vertical conduction into the underlying soil accurately predicted the pit temperature in the heating and cooling phases. This model is very sensitive to the values used for the enthalpies of combustion, meaning that direct measurement of the heat production rate would be preferable. In the industry practice, the fermenter volume can be from around 0.20 to 15.00 m3. The model predicts that overheating will occur not only in larger fermenters, but also in the 0.44-m3 fermenters when the soil temperature is high in summer. Our model predictions are consistent with observed behavior in the industry. Our findings can be used to improve this traditional process, as well as similar systems.

    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    Partial purification and characterization of a broad-spectrum bacteriocin produced by a Lactobacillus plantarum zrx03 isolated from infant's feces
    Lei, Shuang ; Zhao, Ruixiang ; Sun, Junliang ; Ran, Junjian ; Ruan, Xiaoli ; Zhu, Yang - \ 2020
    Food Science and Nutrition 8 (2020)5. - ISSN 2048-7177 - p. 2214 - 2222.
    antimicrobial stability - bacteriocin - Lactobacillus plantarum zrx03 - purification

    Lactobacillus plantarum zrx03 was a bacteriocin-producing strain isolated from infant's feces. The fermentation supernatant produced by this strain could strongly inhibit Escherichia coli JM109 ATCC 67387, Staphylococcus aureus ATCC 25923, and Listeria monocytogenes CICC 21633, in which the diameter of inhibition zone was 12.83 ± 0.62 mm, 15.08 ± 0.31 mm, 6.75 ± 0.20 mm, respectively, compared with lactic acid bacteria N1, N2, M13, M21, M31, and M37. According to amplification of 16S rRNA gene and identification of phylogenetic tree, this strain had a 1,450 bp sequence and 100% identity to the L. plantarum strain. Based on the influence of different protease treatments, such as pepsin, trypsin, papain, and proteinase K on the antimicrobial activity, this antimicrobial substance was considered to be a natural protein. Using bacteriocin produced by this strain as study object of this experiment, it had been extracted from ammonium sulfate precipitation and different organic solvents. The results showed that ethyl acetate was selected as the optimal solution to crude extraction of bacteriocin after comparing ammonium sulfate precipitation method and organic solvent extraction method, such as n-butanol, n-hexane, dichloromethane, trichloromethane, in which the diameter of the inhibition zones was above 28 mm. Results also showed the inhibition spectrum of the obtained bacteriocin had a broad spectrum of inhibition which could inhibit Gram-positive, Gram-negative, yeast. Especially, it could effectively inhibit S. aureus ATCC 25923, Bacillus subtilis CICC 10002, Bacillus anthracis CICC 20443, E. coli JM109 ATCC 67387, and Salmonella CMCC 541, and the zone diameter of inhibition has reached more than 28 mm. Moreover, it had a good thermal stability which antibacterial activity was retained 70.58% after treatment at 121°C for 30 min, and pH-stability was between pH 2.0–9.0. These results suggested bacteriocin produced by L. plantarum zrx03 had potential application prospects in food preservation.

    Rhizosphere protists are key determinants of plant health
    Xiong, Wu ; Song, Yuqi ; Yang, Keming ; Gu, Yian ; Wei, Zhong ; Kowalchuk, George A. ; Xu, Yangchun ; Jousset, Alexandre ; Shen, Qirong ; Geisen, Stefan - \ 2020
    Microbiome 8 (2020)1. - ISSN 2049-2618
    Pathogen of Ralstonia solanacearum - Plant health - Predator-prey interactions - Protists - Rhizosphere - Secondary metabolite genes

    Background: Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators - protists - are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. Results: We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. Conclusions: We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance. [MediaObject not available: see fulltext.]

    The Chinese milk supply chain: A fraud perspective
    Yang, Yuzheng ; Huisman, Wim ; Hettinga, Kasper A. ; Zhang, Liebing ; Ruth, Saskia M. van - \ 2020
    Food Control 113 (2020). - ISSN 0956-7135
    China - Dairy farmer - Economically motivated adulteration - Fraud vulnerability assessment - Milk processor - Milk supply chain

    Food fraud has become a serious concern all over the world and especially in China. The melamine contaminated infant formula in 2008 has brought food fraud in the spotlights. This incident had grave consequences for the Chinese citizens as well as the Chinese milk industry. Fraud vulnerability assessments are the first step towards food fraud prevention and mitigation. To combat food fraud, one has to think like a criminal. In the current study, we determined the most vulnerable points in the Chinese milk supply chain, and examined the underlying causes. The fraud vulnerability perceived by 90 Chinese dairy farmers and 14 milk processors was evaluated with the SSAFE food fraud vulnerability assessment tool. Overall, actors perceived the milk supply chain as low to medium vulnerable to food fraud. Farmers appeared significantly more vulnerable than processors due to enhanced opportunities and motivations, and less adequate controls. Both geographical location of the farms and their size affected their perceived fraud vulnerability significantly.

    Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite
    Qi, Wanhe ; Taherzadeh, Mohammad J. ; Ruan, Yunjie ; Deng, Yale ; Chen, Ji Shuang ; Lu, Hui Feng ; Xu, Xiang Yang - \ 2020
    Bioresource Technology 305 (2020). - ISSN 0960-8524
    Bacterial community - Fungal community - PBS/Bamboo composite - RAS effluent treatment - Solid-phase denitrification

    This study explored the denitrification performance of solid-phase denitrification (SPD) systems packed with poly (butylene succinate)/bamboo powder composite to treat synthetic aquaculture wastewater under different salinity conditions (0‰ Vs. 25‰). The results showed composite could achieve the maximum denitrification rates of 0.22 kg (salinity, 0‰) and 0.34 kg NO3 -N m−3 d−1 (salinity, 25‰) over 200-day operation. No significant nitrite accumulation and less dissolved organic carbon (DOC) release (<15 mg/L) were found. The morphological and spectroscopic analyses demonstrated the mixture composites degradation. Microbial community analysis showed that Acidovorax, Simplicispira, Denitromonas, SM1A02, Marinicella and Formosa were the dominant genera for denitrifying bacteria, while Aspergillus was the major genus for denitrifying fungus. The co-network analysis also indicated the interactions between bacterial and fungal community played an important role in composite degradation and denitrification. The outcomes provided a potential strategy of DOC control and cost reduction for aquaculture nitrate removal by SPD.

    Synthesis and evaluation of historical meridional heat transport from midlatitudes towards the Arctic
    Liu, Yang ; Attema, Jisk ; Moat, Ben ; Hazeleger, Wilco - \ 2020
    Earth System dynamics 11 (2020)1. - ISSN 2190-4979 - p. 77 - 96.

    Meridional energy transport (MET), both in the atmosphere (AMET) and ocean (OMET), has significant impact on the climate in the Arctic. In this study, we quantify AMET and OMET at subpolar latitudes from six reanalysis data sets. We investigate the differences between the data sets and we check the coherence between MET and the Arctic climate variability at interannual timescales. The results indicate that, although the mean transport in all data sets agrees well, the spatial distributions and temporal variations of AMET and OMET differ substantially among the reanalysis data sets. For the ocean, only after 2007, the low-frequency signals in all reanalysis products agree well. A further comparison with observed heat transport at 26.5° N and the subpolar Atlantic, and a high-resolution ocean model hindcast confirms that the OMET estimated from the reanalysis data sets are consistent with the observations. For the atmosphere, the differences between ERA-Interim and the Japanese 55-year Reanalysis (JRA-55) are small, while the Modern-Era Retrospective analysis for Research and Applications version 2 (MERRA-2) differs from them. An extended analysis of linkages between Arctic climate variability and AMET shows that atmospheric reanalyses differ substantially from each other. Among the chosen atmospheric products, ERA-Interim and JRA-55 results are most consistent with those from coupled climate models. For the ocean, the Ocean Reanalysis System 4 (ORAS4) and Simple Ocean Data Assimilation version 3 (SODA3) agree well on the relation between OMET and sea ice concentration (SIC), while the GLobal Ocean reanalyses and Simulations version 3 (GLORYS2V3) deviates from those data sets. The regressions of multiple fields in the Arctic on both AMET and OMET suggest that the Arctic climate is sensitive to changes of meridional energy transport at subpolar latitudes in winter. Given the good agreement on the diagnostics among assessed reanalysis products, our study suggests that the reanalysis products are useful for the evaluation of energy transport. However, assessments of products with the AMET and OMET estimated from reanalysis data sets beyond interannual timescales should be conducted with great care and the robustness of results should be evaluated through intercomparison, especially when studying variability and interactions between the Arctic and midlatitudes.

    Eleven grand challenges in single-cell data science
    Lähnemann, David ; Köster, Johannes ; Szczurek, Ewa ; McCarthy, Davis J. ; Hicks, Stephanie C. ; Robinson, Mark D. ; Vallejos, Catalina A. ; Campbell, Kieran R. ; Beerenwinkel, Niko ; Mahfouz, Ahmed ; Pinello, Luca ; Skums, Pavel ; Stamatakis, Alexandros ; Attolini, Camille Stephan Otto ; Aparicio, Samuel ; Baaijens, Jasmijn ; Balvert, Marleen ; Barbanson, Buys de; Cappuccio, Antonio ; Corleone, Giacomo ; Dutilh, Bas E. ; Florescu, Maria ; Guryev, Victor ; Holmer, Rens ; Jahn, Katharina ; Lobo, Thamar Jessurun ; Keizer, Emma M. ; Khatri, Indu ; Kielbasa, Szymon M. ; Korbel, Jan O. ; Kozlov, Alexey M. ; Kuo, Tzu Hao ; Lelieveldt, Boudewijn P.F. ; Mandoiu, Ion I. ; Marioni, John C. ; Marschall, Tobias ; Mölder, Felix ; Niknejad, Amir ; Raczkowski, Lukasz ; Reinders, Marcel ; Ridder, Jeroen de; Saliba, Antoine Emmanuel ; Somarakis, Antonios ; Stegle, Oliver ; Theis, Fabian J. ; Yang, Huan ; Zelikovsky, Alex ; McHardy, Alice C. ; Raphael, Benjamin J. ; Shah, Sohrab P. ; Schönhuth, Alexander - \ 2020
    Genome Biology 21 (2020)1. - ISSN 1474-7596

    The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands - or even millions - of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.

    Mycotoxin exposure assessments in a multi-center European validation study by 24-hour dietary recall and biological fluid sampling
    Ruyck, Karl De; Huybrechts, Inge ; Yang, Shupeng ; Arcella, Davide ; Claeys, Liesel ; Abbeddou, Souheila ; Keyzer, Willem De; Vries, Jeanne De; Ocke, Marga ; Ruprich, Jiri ; Boevre, Marthe De; Saeger, Sarah De - \ 2020
    Environment International 137 (2020). - ISSN 0160-4120
    Aflatoxins - Deoxynivalenol - Europe - Exposure - Mycotoxins - Risk

    The European Food Consumption Validation (EFCOVAL) project includes 600 men and women from Belgium, the Czech Republic, France, the Netherlands, and Norway, who had given serum and 24-hour urine samples, and completed 24-hour dietary recall (24-HDR) interviews. Consumption, according to 24-HDR, was matched against the European Food Safety Authority (EFSA) databases of mycotoxin contaminations, via the FoodEx1 standard classifications, producing an indirect external estimate of dietary mycotoxin exposure. Direct, internal measurements of dietary mycotoxin exposure were made in serum and urine by ultra-performance liquid chromatography coupled to tandem mass spectrometry. For the first time, mycotoxin exposures were thoroughly compared between two 24-HDRs, and two 24-hour urine samples collected during the same days covered by the 24-HDRs. These measurements were compared to a single-time point serum measurement to investigate evidence of chronic mycotoxin exposure. According to 24-HDR data, all 600 individuals were exposed to between 4 and 34 mycotoxins, whereof 10 found to exceed the tolerable daily intake. Correlations were observed between two time points, and significant correlations were observed between concentrations in serum and urine. However, only acetyldeoxynivalenol, ochratoxin A, and sterigmatocystin were found to have significant positive correlations between 24-HDR exposures and serum, while aflatoxin G1 and G2, HT-2 toxin, and deoxynivalenol were associated between concurrent 24-HDR and 24-hour urine. Substantial agreements on quantitative levels between serum and urine were observed for the groups Type B Trichothecenes and Zearalenone. Further research is required to bridge the interpretation of external and internal exposure estimates of the individual on a time scale of hours. Additionally, metabolomic profiling of dietary mycotoxin exposures could help with a comprehensive assessment of single time-point exposures, but also with the identification of chronic exposure biomarkers. Such detailed characterization informs population exposure assessments, and aids in the interpretation of epidemiological health outcomes related to multi-mycotoxin exposure.

    DIX Domain Polymerization Drives Assembly of Plant Cell Polarity Complexes
    Dop, Maritza van; Fiedler, Marc ; Mutte, Sumanth ; Keijzer, Jeroen de; Olijslager, Lisa ; Albrecht, Catherine ; Liao, Che Yang ; Janson, Marcel E. ; Bienz, Mariann ; Weijers, Dolf - \ 2020
    Cell 180 (2020)3. - ISSN 0092-8674 - p. 427 - 439.e12.
    cell polarity - dishevelled - DIX domain - plant development - protein oligomerization - signalosome - SOSEKI

    The identities of cell polarity determinants are not conserved between animals and plants; however, characterization of a DIX-domain containing protein in land plants reveals that the physical principles of polar complex assembly are preserved across eukaryotes.

    Dairy farming system markers: The correlation of forage and milk fatty acid profiles from organic, pasture and conventional systems in the Netherlands
    Liu, Ningjing ; Pustjens, Annemieke M. ; Erasmus, Sara W. ; Yang, Yuzheng ; Hettinga, Kasper ; Ruth, Saskia M. van - \ 2020
    Food Chemistry 314 (2020). - ISSN 0308-8146
    Classification - Correlation analysis - Fatty acids - Forage - Milk - Organic

    The relationships between the fatty acid (FA) composition in forage and milk (F&M) from different dairy systems were investigated. Eighty milk samples and 91 forage samples were collected from 40 farms (19 organic, 11 pasture and 10 conventional) in the Netherlands, during winter and summer. The FA profiles of F&M samples were measured with gas chromatography. The results showed that the F&M of organic farms were significantly differentiated from the F&M of other farms, both in summer and winter. The differences are likely due to the different grazing strategies in summer and different forage composition in winter. The Pearson's correlation results showed the specific relationship between individual FAs in forages and related milk. A PLS-DA model was applied to classify all milks samples, resulting in 87.5% and 83.3% correct classifications of training set and validation set.

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