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.

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