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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    Metabolomics of Milk Reflects a Negative Energy Balance in Cows
    Xu, Wei ; Knegsel, Ariette Van; Saccenti, Edoardo ; Hoeij, Renny Van; Kemp, Bas ; Vervoort, Jacques - \ 2020
    Journal of Proteome Research 19 (2020)8. - ISSN 1535-3893 - p. 2942 - 2949.
    energy balance - integrated analysis - LC-MS - metabolic status - metabolomics - milk - NMR

    Dairy cows can experience a negative energy balance (NEB) in early lactation when feed intake is too low to meet the energy requirements for body maintenance and milk production. Metabolic changes occur in mammary gland cells of animals experiencing a negative energy balance. We studied these metabolic changes in milk samples from dairy cows in relation to energy balance status using liquid chromatography-mass spectrometry (QQQ-LC-MS) and nuclear magnetic resonance (1H NMR). NMR and LC-MS techniques are complementary techniques that enabled a comprehensive overview of milk metabolites in our study. Energy balance and milk samples were obtained from 87 dairy cows. A total of 55 milk metabolites were reliably detected, of which 15 metabolites were positively correlated to energy balance and 20 were negatively correlated to energy balance. Cows in NEB produced more milk with increased milk fat yield and higher concentrations of citrate, cis-aconitate, creatinine, glycine, phosphocreatine, galactose-1-phosphate, glucose-1-phosphate, UDP-N-acetyl-galactosamine, UDP-N-acetyl-glucosamine, and phosphocholine but lower concentrations of choline, ethanolamine, fucose, N-acetyl-neuraminic acid, N-acetyl-glucosamine, and N-acetyl-galactosamine. During NEB, we observed an increased leakage of cellular content, increased synthesis of nucleic acids and cell membrane phospholipids, an increase in one-carbon metabolic processes, and an increase in lipid-triglyceride anabolism. Overall, both apoptosis combined with cellular renewal is paramount in the mammary gland in cows in NEB.

    Towards a comprehensive and consistent global aquatic land cover characterization framework addressing multiple user needs
    Xu, Panpan ; Herold, Martin ; Tsendbazar, Nandin Erdene ; Clevers, Jan G.P.W. - \ 2020
    Remote Sensing of Environment 250 (2020). - ISSN 0034-4257
    Aquatic land cover monitoring - Characterization framework - Global aquatic land cover dataset - LCCS - User needs

    Aquatic land cover represents the land cover type that is significantly influenced by the presence of water over an extensive part of a year. Monitoring global aquatic land cover types plays an essential role in preserving aquatic ecosystems and maintaining the ecosystem service they provide for humans, while at the same time their accurate and consistent monitoring for multiple purposes (e.g. climate modelling, biodiversity conservation, water resource management) remains challenging. Although a number of global aquatic land cover (GALC) datasets are available for use to monitor aquatic ecosystems, there are prominent variabilities among these datasets, which is primarily caused by the inconsistency between different land versus water-related monitoring approaches and characterization schemes. As aquatic land cover exists in many different forms on Earth (e.g. wetland, open water) and can be mapped by different approaches, it is necessary to consider a much more consistent and comprehensive characterization framework that not only ensures the consistency in the monitoring of aquatic land cover but also serves the needs of multiple users (e.g. climate users, agricultural users) interested in different aspects of aquatic lands. In this study, we addressed this issue by 1) reviewing 33 GALC datasets and user needs identified from the citing papers of current datasets and international conventions, policies and agreements in relation to aquatic ecosystems, 2) proposing a global characterization framework for aquatic land cover based on the Land Cover Classification System (LCCS) classifier principles and the identified user needs, and 3) highlighting the opportunities and challenges provided by remote sensing techniques for the implementation of the proposed framework. Results show that users require or prefer various kinds of information on aquatic types including vegetation type, water persistence, the artificiality of cover (i.e. artificial vs natural), water salinity, and the accessibility to the sea (i.e. coastal vs inland). Datasets with medium to high spatial resolution, intra-annual dynamics and inter-annual changes are needed by many users. However, none of the existing datasets can meet all these requirements and a rigorous quantitative accuracy assessment is lacking to evaluate its quality for most of the GALC datasets. The proposed framework has three levels and users are allowed to derive their aquatic land cover types of interest by combining different levels and classifiers of information. This comprehensive mapping framework can help to bridge the gap between user needs and current GALC datasets as well as the gap between generic and aquatic land cover monitoring. The implementation of the framework can benefit from evolving satellite-data availability, improved computation capability and open-source machine learning algorithms, although at the same time it faces challenges mainly coming from the complexity of aquatic ecosystems. The framework proposed in this study provides insights for future operational aquatic land cover monitoring initiatives and will support better understanding and monitoring of complex aquatic ecosystems.

    Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history
    Schneijderberg, Martinus ; Cheng, Xu ; Franken, Carolien ; Hollander, Mattias de; Velzen, Robin van; Schmitz, Lucas ; Heinen, Robin ; Geurts, Rene ; Putten, Wim H. van der; Bezemer, Martijn T. ; Bisseling, Ton - \ 2020
    ISME Journal (2020). - ISSN 1751-7362

    As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species’ average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

    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.
    Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System
    Wang, Shilei ; Xiong, Wu ; Wang, Yuqiao ; Nie, Yao ; Wu, Qun ; Xu, Yan ; Geisen, Stefan - \ 2020
    mSystems 5 (2020)4. - ISSN 2379-5077
    We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.
    Plant architectural responses in simultaneous maize/soybean strip intercropping do not lead to a yield advantage
    Li, Shuangwei ; Evers, Jochem B. ; Werf, Wopke van der; Wang, Ruili ; Xu, Zhaoli ; Guo, Yan ; Li, Baoguo ; Ma, Yuntao - \ 2020
    Annals of Applied Biology 177 (2020)2. - ISSN 0003-4746 - p. 195 - 210.
    architectural response - border row effect - growth - intercropping - land equivalent ratio

    Maize/soybean strip intercropping is a commonly used system throughout China with high crop yields at reduced nutrient input compared to sole maize. Maize is the taller crop, and due to its dominance in light capture over soybean in the intercrop, maize is expected to outperform maize in sole cropping. Conversely, soybean is the subordinate crop and intercropped soybean plants are expected to perform worse than sole soybean. Crop plants show plastic responses in plant architecture to their growing conditions to forage for light and avoid shading. There is little knowledge on plant architectural responses to growing conditions in simultaneous (non-relay) intercropping and their relationship to species yields. A two-year field experiment with two simultaneous maize/soybean intercropping systems with narrow and wide strips was conducted to characterise architectural traits of maize and soybean plants grown as intercrop and sole crops. Intercropped maize plants, especially those in border rows, had substantially greater leaf area, biomass and yield than maize plants in sole crops. Intercropped soybean plants, especially those in border rows, had lower leaf area, biomass and yield than sole soybean plants. Overall intercrop performance was similar to that of sole crops, with the land equivalent ratio (LER) being only slightly greater than one (1.03–1.08). Soybean displayed typical shade avoidance responses in the intercrop, such as greater internode elongation and changes in specific leaf area, but these responses could not overcome the consequences of the competition with the taller maize plants. Therefore, in contrast to relay intercrop systems, in the studied simultaneous maize/soybean system, plastic responses did not contribute to practically relevant increases in resource capture and yield at whole system (i.e., intercrop) level.

    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.

    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.

    Increasing yield and nitrogen use efficiency of spring maize in Northeast China through ecological intensification management
    Xu, Rui ; Xu, Rui ; Xu, Xin Peng ; Hou, Yun Peng ; Zhang, Jia Jia ; Huang, Shao Hui ; Ding, Wen Cheng ; Liu, Ying Xia ; He, Ping - \ 2020
    Journal of Plant Nutrition and Fertilizers 26 (2020)3. - ISSN 1008-505X - p. 461 - 471.
    Ecological intensive nutrient management - Nitrogen balance - Nitrogen use efficiency - Spring maize

    [Objectives] In view of the problems in ecological environment and sustainable agricultural development caused by excessive and unreasonable fertilizer application in spring maize production in China, the effects of ecological intensive nutrient management on spring maize yield, nitrogen use efficiency and nitrogen balance in Northeast China were studied in order to make full use of resources, increase production efficiency and ensure national food security scientifically and rationally. [Methods] A long-term experiment was conducted from 2009 to 2017 in Gongzhuling City, Jilin Province. Two factors of split plot were designed in the experiment. The main plot was two fertilization managements: the ecological intensive nutrient management (EI) and farmer practice management (FP). The sub-plot was three N application methods, including no N application treatment (N0), N application in two of three years (N2/3) and in three years (N3/3). In EI treatment, P2O575 kg/hm2, K2O 90 kg/hm2, S 30 kg/hm2, Zn 5 kg/hm2and 1/4 of N (180 kg/hm2in 2009-2014, 200 kg/hm2in 2015-2017) applied as basal, 1/2 N top dressed at jointing stage and 1/4 N at tassel stage. In the treatment of FP, N 251 kg/hm2, P2O5145 kg/hm2and K2O 100 kg/hm2were applied once as basal. The yield, N uptake and accumulation of maize and the balance of soil N were investigated. [Results] In N0 treatment, the yield and N uptake showed a downward trend since 2010. In N2/3 treatment, the yield and N uptake decreased in the year without N application, and increased to the level of N3/3 treatment in the case of N application in the following year. In EI treatment, the average yield of N3/3 treatment was 11505 kg/hm2in 9 years, while that of FP treatment was significantly lower, which was 10764 kg/hm2. Compared with FP treatment, EI treatment significantly increased nitrogen agronomic efficiency (AEN), recovery efficiency (REN) and partial factor productivity (PFPN) by 47.4%, 39.6% and 43.8%, respectively. The residual N and apparent loss of N in EI treatment were 49.2% and 63.9% lower than those in FP treatment, respectively. [Conclusions] Ecological intensive nutrient management, including right fertilization rate and time, and suitable cultivar and plant density, is proved to be effective in increasing spring maize yield and N utilization, reducing residue and apparent loss of N in soil. The experiment also confirms that continuous appropriate N fertilizer application is essential for high and stable yield of maize in Northeast China.

    Neighbourhood-dependent root distributions and the consequences on root separation in arid ecosystems
    Chen, Bin J.W. ; Xu, Chi ; Liu, Mao Song ; Huang, Zheng Y.X. ; Zhang, Ming Juan ; Tang, Jian ; Anten, Niels P.R. - \ 2020
    Journal of Ecology 108 (2020)4. - ISSN 0022-0477 - p. 1635 - 1648.
    dryland - growth form - niche partitioning - plant–plant interactions - root competition - root distribution - root separation - species coexistence

    Interspecific root separation is an important example of spatial niche differentiation that drives species coexistence in many ecosystems. Particularly under water-stressed conditions, it is believed to be an inevitable outcome of species interactions. However, evidence for and against this idea has been found. So far, studies aiming at reconciling the debate have mainly focused on abiotic determinants. It remains unclear if and to what extent root separation depends on the type and growth form of interacting plants. We conducted a detailed field study in three adjacently located (with pairwise distances <500 m) arid patchy communities where a common tussock grass species Achnatherum splendens grew in association with either a tree Elaeagnus angustifolia, a shrub Nitraria tangutorum or a perennial forb species Sophora alopecuroides. In each community, roots and soils were sampled along the soil layers from five depths (0–10, 10–30, 30–60, 60–100 and 100–150 cm) in the patches and in the adjacent bare ground outside the patches. Significant vertical interspecific root separation occurred in the species-association patches of tree-grass and forb-grass communities, but not in the shrub-grass community. As the neighbour changed going from trees to shrubs and to forbs, rooting profiles of the grass Achnatherum became progressively deeper, with progressively less roots allocated in the upmost 10 cm soil layer and more in the subsequent two layers. After controlling for the differences in soil water and nutrient conditions among the three communities, the effects of neighbour type on grass rooting profiles remained robust. Synthesis. We found that the root distributions of plants in the dryland strongly depend on the type of neighbour plants, which can, at least partially, determine the extent of interspecific root separation at the community scale. Our work poses new questions about plasticity in root distribution and helps to better understand species interactions and coexistence under stressful conditions.

    Short communication : Prediction of hyperketonemia in dairy cows in early lactation using on-farm cow data and net energy intake by partial least square discriminant analysis
    Xu, Wei ; Saccenti, Edoardo ; Vervoort, Jacques ; Kemp, Bas ; Bruckmaier, Rupert M. ; Knegsel, Ariette T.M. van - \ 2020
    Journal of Dairy Science 103 (2020)7. - ISSN 0022-0302 - p. 6576 - 6582.
    metabolic status - partial least square discriminant analysis - subclinical ketosis

    The objectives of this study were (1) to evaluate if hyperketonemia in dairy cows (defined as plasma β-hydroxybutyrate ≥1.0 mmol/L) can be predicted using on-farm cow data either in current or previous lactation week, and (2) to study if adding individual net energy intake (NEI) can improve the predictive ability of the model. Plasma β-hydroxybutyrate concentration, on-farm cow data (milk yield, percentage of fat, protein and lactose, fat- and protein-corrected milk yield, body weight, body weight change, dry period length, parity, and somatic cell count), and NEI of 424 individual cows were available weekly through lactation wk 1 to 5 postpartum. To predict hyperketonemia in dairy cows, models were first trained by partial least square discriminant analysis, using on-farm cow data in the same or previous lactation week. Second, NEI was included in models to evaluate the improvement of the predictability of the models. Through leave-one trial-out cross-validation, models were evaluated by accuracy (the ratio of the sum of true positive and true negative), sensitivity (68.2% to 84.9%), specificity (61.5% to 98.7%), positive predictive value (57.7% to 98.7%), and negative predictive value (66.2% to 86.1%) to predict hyperketonemia of dairy cows. Through lactation wk 1 to 5, the accuracy to predict hyperketonemia using data in the same week was 64.4% to 85.5% (on-farm cow data only), 66.1% to 87.0% (model including NEI), and using data in the previous week was 58.5% to 82.0% (on-farm cow data only), 59.7% to 85.1% (model including NEI). An improvement of the accuracy of the model due to including NEI ranged among lactation weeks from 1.0% to 4.4% when using data in the same lactation week and 0.2% to 6.6% when using data in the previous lactation week. In conclusion, trained models via partial least square discriminant analysis have potential to predict hyperketonemia in dairy cows not only using data in the current lactation week, but also using data in the previous lactation week. Net energy intake can improve the accuracy of the model, but only to a limited extent. Besides NEI, body weight, body weight change, milk fat, and protein content were important variables to predict hyperketonemia, but their rank of importance differed across lactation weeks.

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

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

    MicroRNA-204-5p modulates mitochondrial biogenesis in C2C12 myotubes and associates with oxidative capacity in humans
    Houzelle, Alexandre ; Dahlmans, Dennis ; Nascimento, Emmani B.M. ; Schaart, Gert ; Jörgensen, Johanna A. ; Moonen-Kornips, Esther ; Kersten, Sander ; Wang, Xu ; Hoeks, Joris - \ 2020
    Journal of Cellular Physiology (2020). - ISSN 0021-9541
    C2C12 - microRNA - mitochondria - mitophagy - skeletal muscle

    Using an unbiased high-throughput microRNA (miRNA)-silencing screen combined with functional readouts for mitochondrial oxidative capacity in C2C12 myocytes, we previously identified 19 miRNAs as putative regulators of skeletal muscle mitochondrial metabolism. In the current study, we highlight miRNA-204-5p, identified from this screen, and further studied its role in the regulation of skeletal muscle mitochondrial function. Following silencing of miRNA-204-5p in C2C12 myotubes, gene and protein expression were assessed using quantitative polymerase chain reaction, microarray analysis, and western blot analysis, while morphological changes were studied by confocal microscopy. In addition, miRNA-204-5p expression was quantified in human skeletal muscle biopsies and associated with in vivo mitochondrial oxidative capacity. Transcript levels of PGC-1α (3.71-fold; p <.01), predicted as an miR-204-5p target, as well as mitochondrial DNA copy number (p <.05) and citrate synthase activity (p =.06) were increased upon miRNA-204-5p silencing in C2C12 myotubes. Silencing of miRNA-204-5p further resulted in morphological changes, induced gene expression of autophagy marker light chain 3 protein b (LC3B; q =.05), and reduced expression of the mitophagy marker FUNDC1 (q =.01). Confocal imaging revealed colocalization between the autophagosome marker LC3B and the mitochondrial marker OxPhos upon miRNA-204-5p silencing. Finally, miRNA-204-5p was differentially expressed in human subjects displaying large variation in oxidative capacity and its expression levels associated with in vivo measures of skeletal muscle mitochondrial function. In summary, silencing of miRNA-204-5p in C2C12 myotubes stimulated mitochondrial biogenesis, impacted on cellular morphology, and altered expression of markers related to autophagy and mitophagy. The association between miRNA-204-5p and in vivo mitochondrial function in human skeletal muscle further identifies miRNA-204-5p as an interesting modulator of skeletal muscle mitochondrial metabolism.

    Future of the human climate niche
    Xu, Chi ; Kohler, Timothy A. ; Lenton, Timothy M. ; Svenning, Jens Christian ; Scheffer, Marten - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)21. - ISSN 0027-8424
    Climate - Migration - Societies

    All species have an environmental niche, and despite technological advances, humans are unlikely to be an exception. Here, we demonstrate that for millennia, human populations have resided in the same narrow part of the climatic envelope available on the globe, characterized by a major mode around ~11 °C to 15 °C mean annual temperature (MAT). Supporting the fundamental nature of this temperature niche, current production of crops and livestock is largely limited to the same conditions, and the same optimum has been found for agricultural and nonagricultural economic output of countries through analyses of year-to-year variation. We show that in a business-as-usual climate change scenario, the geographical position of this temperature niche is projected to shift more over the coming 50 y than it has moved since 6000 BP. Populations will not simply track the shifting climate, as adaptation in situ may address some of the challenges, and many other factors affect decisions to migrate. Nevertheless, in the absence of migration, one third of the global population is projected to experience a MAT >29 °C currently found in only 0.8% of the Earth's land surface, mostly concentrated in the Sahara. As the potentially most affected regions are among the poorest in the world, where adaptive capacity is low, enhancing human development in those areas should be a priority alongside climate mitigation.

    Agriculture green development : A model for China and the world
    Shen, Jianbo ; Zhu, Qichao ; Jiao, Xiaoqiang ; Ying, Hao ; Wang, Hongliang ; Wen, Xin ; Xu, Wen ; Li, Tingyu ; Cong, Wenfeng ; Liu, Xuejun ; Hou, Yong ; Cui, Zhenling ; Oenema, Oene ; Davies, William J. ; Zhang, Fusuo - \ 2020
    Frontiers of Agricultural Science and Engineering 7 (2020)1. - ISSN 2095-7505 - p. 5 - 13.
    Agriculture green development - Food security - Interdisciplinary innovations - Resource use efficiency - Sustainable development - Sustainable intensification - Whole industry chain

    Realizing sustainable development has become a global priority. This holds, in particular, for agriculture. Recently, the United Nations launched the Sustainable Development Goals (SDGs), and the Nineteenth National People's Congress has delivered a national strategy for sustainable development in China-realizing green development. The overall objective of Agriculture Green Development (AGD) is to coordinate "green" with "development" to realize the transformation of current agriculture with high resource consumption and high environmental costs into a green agriculture and countryside with high productivity, high resource use efficiency and low environmental impact. This is a formidable task, requiring joint efforts of government, farmers, industry, educators and researchers. The innovative concept for AGD will focus on reconstructing the whole crop-animal production and food production-consumption system, with the emphasis on high thresholds for environmental standards and food quality as well as enhanced human well-being. This paper addresses the significance, challenges, framework, pathways and potential solutions for realizing AGD in China, and highlights the potential changes that will lead to a more sustainable agriculture in the future. Proposals include interdisciplinary innovations, whole food chain improvement and regional solutions. The implementation of AGD in China will provide important implications for the countries in developmental transition, and contribute to global sustainable development.

    Visual assessment of the impact of agricultural management practices on soil quality
    Alaoui, Abdallah ; Barão, Lúcia ; Ferreira, Carla S.S. ; Schwilch, Gudrun ; Basch, Gottlieb ; Garcia-Orenes, Fuensanta ; Morugan, Alicia ; Mataix-Solera, Jorge ; Kosmas, Costas ; Glavan, Matjaž ; Szabó, Brigitta ; Hermann, Tamás ; Vizitiu, Olga Petrutza ; Lipiec, Jerzy ; Frąc, Magdalena ; Reintam, Endla ; Xu, Minggang ; Di, Jiaying ; Fan, Hongzhu ; Sukkel, Wijnand ; Lemesle, Julie ; Geissen, Violette ; Fleskens, Luuk - \ 2020
    Agronomy Journal 112 (2020)4. - ISSN 0002-1962 - p. 2608 - 2623.

    The intensification of agricultural practices to increase food and feed outputs is a pressing challenge causing deterioration of soil quality and soil functions. Such a challenge demands provision of empirical evidence to provide context-sensitive guidance on agricultural management practices (AMPs) that may enhance soil quality. The objectives of this study are to identify the most promising AMPs (and their combinations) applied by farmers with the most positive effects on soil quality and to evaluate the sensitivity of the soil quality indicators to the applied AMPs. The effect of selected AMPs on soil quality was assessed using a visual soil assessment tool in a total of 138 pairs of plots spread across 14 study site areas in Europe and China covering representative pedo-climatic zones. The inventory and scoring of soil quality were conducted together with landowners. Results show that 104 pairs show a positive effect of AMPs on soil quality. Higher effects of the AMPs were observed in lower fertile soils (i.e., Podzols and Calcisols) as opposed to higher fertile soils (i.e., Luvisols and Fluvisols). For the single use applications, the AMPs with positive effects were crop rotation; manuring, composting, and no-tillage; followed by organic agriculture and residue maintenance. Cluster analysis showed that the most promising combinations of AMPs with the most positive effects on soil quality are composed of crop rotation, mulching, and min-till. The agreement between scientific skills and empirical knowledge in the field identified by the farmers confirm our findings and ensures their applicability.

    Pathogen manipulation of chloroplast function triggers a light-dependent immune recognition
    Gao, Chuyun ; Xu, Huawei ; Huang, Jie ; Sun, Biying ; Zhang, Fan ; Savage, Zachary ; Duggan, Cian ; Yan, Tingxiu ; Wu, Chih Hang ; Wang, Yuanchao ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien ; Bozkurt, Tolga O. ; Dong, Suomeng - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)17. - ISSN 0027-8424 - p. 9613 - 9620.
    Chloroplast - Disease resistance - Light - NLR - Potato blight

    In plants and animals, nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune sensors that recognize and eliminate a wide range of invading pathogens. NLR-mediated immunity is known to be modulated by environmental factors. However, how pathogen recognition by NLRs is influenced by environmental factors such as light remains unclear. Here, we show that the agronomically important NLR Rpi-vnt1.1 requires light to confer disease resistance against races of the Irish potato famine pathogen Phytophthora infestans that secrete the effector protein AVRvnt1. The activation of Rpi-vnt1.1 requires a nuclear-encoded chloroplast protein, glycerate 3-kinase (GLYK), implicated in energy production. The pathogen effector AVRvnt1 binds the full-length chloroplast-targeted GLYK isoform leading to activation of Rpi-vnt1.1. In the dark, Rpi-vnt1.1-mediated resistance is compromised because plants produce a shorter GLYK-lacking the intact chloroplast transit peptide-that is not bound by AVRvnt1. The transition between full-length and shorter plant GLYK transcripts is controlled by a light-dependent alternative promoter selection mechanism. In plants that lack Rpi-vnt1.1, the presence of AVRvnt1 reduces GLYK accumulation in chloroplasts counteracting GLYK contribution to basal immunity. Our findings revealed that pathogen manipulation of chloroplast functions has resulted in a light-dependent immune response.

    Prevalence of coeliac disease in Northwest China: heterogeneity across Northern Silk road ethnic populations
    Zhou, Chunyan ; Gao, Feng ; Gao, Jinyan ; Yuan, Juanli ; Lu, Jiajie ; Sun, Zhenzhu ; Xu, Mengyu ; Engel, J. ; Hui, Wenjia ; Gilissen, L.J.W.J. ; Chen, Hongbing - \ 2020
    Alimentary Pharmacology and Therapeutics 51 (2020)11. - ISSN 0269-2813 - p. 1116 - 1129.
    Background: Epidemiological data of coeliac disease are lacking from the central Asian region. Aims: To verify the occurrence of coeliac disease amongst four major ethnic groups of Xinjiang Uyghur Autonomus Region, China. Methods: 2277 in-patients with gastrointestinal symptoms (1391 Han, 608 Uyghur, 146 Kazakh and 132 Hui; mean age: 54 ± 12.8 years) were included. Total IgA, anti-deamidated gliadin peptide (DGP)-IgG, and anti-tissue transglutaminase (anti-tTG)-IgA were analysed. All antibody-positive subjects were further tested for endomysial (EMA) antibodies and were HLA genotyped. All subjects with antibody positivity were asked to undergo intestinal biopsy. In addition, a subset of antibody-negative subjects were tested for HLA-DQA1and DQB1. Results: Among the 2277 subjects, 29 subjects were defined as coeliac disease au-toimmune (positive results for anti-tTG IgA and EMA-IgA) (1.27%; 95% confidence interval, 0.81%-1.73%), eight of them underwent biopsy and all showed coeliac dis-ease histology (0.35%; 95% Cl, 0.11%-0.59%). The frequency of coeliac disease au-toimmunity was lowest among the Han (0.79%), followed by the Uyghur (1.81%), the Kazakh (2.05%) and the Hui (3.03%). The frequency of the HLA-DQ2 and/or DQ8 haplotype was highest in the Uyghur (52.1%), followed by the Hui (44.4%), the Kazakh (40.0%) and the Han (39.4%). Besides, a three times higher frequency of coeliac dis-ease autoimmunity was found among rural living subjects with significantly higher wheat consumption compared to urban living subjects (3.16% vs 0.97%, P < 0.01). Conclusions: In Xinjiang, coeliac disease does occur, especially in the rural area. The HLA haplotype and environment play key roles in the development of coeliac disease.
    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.
    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.

    Space-time statistical analysis and modelling of nitrogen use efficiency indicators at provincial scale in China
    Liu, Yingxia ; Heuvelink, Gerard B.M. ; Bai, Zhanguo ; He, Ping ; Xu, Xinpeng ; Ma, Jinchuan ; Masiliūnas, Dainius - \ 2020
    European Journal of Agronomy 115 (2020). - ISSN 1161-0301
    Nitrogen use efficiency (NUE) is crucial to establish efficient fertilizer application guidelines that balance crop yield, economic return and environmental sustainability. Although there are quite a few researches about the spatial and temporal variation of NUE, little work has been done on modelling NUE through deriving empirical relationships with explanatory environmental variables and exploring their relative importance quantitatively. The space-time patterns of NUE indicators (i.e., the Partial Factor Productivity of nitrogen, PFPN, and the Partial Nutrient Balance of nitrogen, PNBN) at provincial scale in China were derived and related to environmental covariates using stepwise multiple linear regression. PFPN was higher in east and south China than in central and west China and was smaller than 30 kg kg−1 yr−1 in most provinces, while PNBN was moderate in most provinces (0.41–0.50 kg kg−1 yr−1) and low (< 0.40 kg kg−1 yr−1) in south China. The national PFPN declined slightly from 32 kg kg−1 in 1978 to 27 kg kg−1 in 1995 and went up gradually to reach 38 kg kg−1 in 2015. The national PNBN decreased from 0.53 to 0.36 kg kg−1 from 1978 to 2003, thereafter stabilizing at around 0.40 kg kg−1 yr−1 between 2004 and 2015. The multiple linear regression models explained 74 % of the variance of PFPN and PNBN. The main explanatory variables of PFPN were planting area index of sugar crop (32 % of the R-square), followed by Arenosols (12 %), planting area index of oil crop (8 %), planting area index of vegetables (5 %), silt content (5 %) and total potassium (5 %). For PNBN, the variation was mainly attributed to mean annual daytime surface temperature (28 % of the R-square), planting area index of crops (beans 20 %, orchards 10 % and vegetables 9 %) and wet day frequency (5 %). The results of this study indicate that crop types, temperature and soil properties are important variables that determine NUE. These should be considered by policy makers when agricultural land development decisions are made in order to balance NUE and productivity (i.e., agronomy and environment).
    Critical transitions in Chinese dunes during the past 12,000 years
    Xu, Zhiwei ; Mason, Joseph A. ; Xu, Chi ; Yi, Shuangwen ; Bathiany, Sebastian ; Yizhaq, Hezi ; Zhou, Yali ; Cheng, Jun ; Holmgren, Milena ; Lu, Huayu - \ 2020
    Science Advances 6 (2020)9. - ISSN 2375-2548 - p. eaay8020 - eaay8020.

    Dune systems can have alternative stable states that coexist under certain environmental conditions: a vegetated, stabilized state and a bare active state. This behavior implies the possibility of abrupt transitions from one state to another in response to gradual environmental change. Here, we synthesize stratigraphic records covering 12,000 years of dynamics of this system at 144 localities across three dune fields in northern China. We find side-by-side coexistence of active and stabilized states, and occasional sharp shifts in time between those contrasting states. Those shifts occur asynchronously despite the fact that the entire landscape has been subject to the same gradual changes in monsoon rainfall and other conditions. At larger scale, the spatial heterogeneity in dune dynamics averages out to produce relatively smooth change. However, our results do show different paths of recovery and collapse of vegetation at system-wide scales, implying that hysteretic behavior occurs in spatially extended systems.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    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.]

    Relationship between energy balance and metabolic profiles in plasma and milk of dairy cows in early lactation
    Xu, Wei ; Vervoort, Jacques ; Saccenti, Edoardo ; Kemp, Bas ; Hoeij, Renny J. van; Knegsel, Ariette T.M. van - \ 2020
    Journal of Dairy Science 103 (2020). - ISSN 0022-0302 - p. 4795 - 4805.
    liquid chromatography–mass spectrometry - mammary gland - metabolomics - nuclear magnetic resonance

    Negative energy balance in dairy cows in early lactation is related to alteration of metabolic status. However, the relationships among energy balance, metabolic profile in plasma, and metabolic profile in milk have not been reported. In this study our aims were: (1) to reveal the metabolic profiles of plasma and milk by integrating results from nuclear magnetic resonance (NMR) with data from liquid chromatography triple quadrupole mass spectrometry (LC-MS); and (2) to investigate the relationship between energy balance and the metabolic profiles of plasma and milk. For this study 24 individual dairy cows (parity 2.5 ± 0.5; mean ± standard deviation) were studied in lactation wk 2. Body weight (mean ± standard deviation; 627.4 ± 56.4 kg) and milk yield (28.1 ± 6.7 kg/d; mean ± standard deviation) were monitored daily. Milk composition (fat, protein, and lactose) and net energy balance were calculated. Plasma and milk samples were collected and analyzed using LC-MS and NMR. From all plasma metabolites measured, 27 were correlated with energy balance. These plasma metabolites were related to body reserve mobilization from body fat, muscle, and bone; increased blood flow; and gluconeogenesis. From all milk metabolites measured, 30 were correlated with energy balance. These milk metabolites were related to cell apoptosis and cell proliferation. Nine metabolites detected in both plasma and milk were correlated with each other and with energy balance. These metabolites were mainly related to hyperketonemia; β-oxidation of fatty acids; and one-carbon metabolism. The metabolic profiles of plasma and milk provide an in-depth insight into the physiological pathways of dairy cows in negative energy balance in early lactation. In addition to the classical indicators for energy balance (e.g., β-hydroxybutyrate, acetone, and glucose), the current study presents some new metabolites (e.g., glycine in plasma and milk; kynurenine, panthothenate, or arginine in plasma) in lactating dairy cows that are related to energy balance and may be of interest as new indicators for energy balance.

    Optimizing rates and sources of nutrient input to mitigate nitrogen, phosphorus, and carbon losses from rice paddies
    Ding, Wencheng ; He, Ping ; Zhang, Jiajia ; Liu, Yingxia ; Xu, Xinpeng ; Ullah, Sami ; Cui, Zhenling ; Zhou, Wei - \ 2020
    Journal of Cleaner Production 256 (2020). - ISSN 0959-6526
    Enhanced-efficiency fertilizer - Greenhouse gas - Manure N - N threshold - Nutrient loss - Straw return

    Decreasing nutrient losses from excessive synthetic fertilizer inputs is the direct and valid way to address low nutrient use efficiency and the related environmental consequences. Here, we established a comprehensive database of nitrogen (N), phosphorus (P), and carbon (C) losses from rice paddy fields in China, which we used to evaluate fertilization-induced losses and the impact of environmental factors, and to mitigate losses by adopting alternative fertilization options and setting input thresholds. Our results showed that most N-loss pathways had exponential increases with additional N input. In average, 23.8% of the N applied was lost via NH3 (16.1%), N2O (0.3%), leaching (4.8%), and runoff (2.6%). Total P loss was approximately 2.7% of the input, composed of leaching (1.3%) and runoff (1.4%). C lost as CH4 accounted for 4.9% of the organic C input. A relative importance analysis indicated that climate or soil variation rather than fertilizer rate was the dominant factor driving N and P leaching, and CH4 emissions. Based on the sensitivity of multiple N-loss pathways to N fertilization, we propose upper thresholds for N inputs of 142–191 kg N ha−1 across four rice types, which would avoid dramatic increases in N losses. Compared to conventional chemical fertilization, alternative fertilization options had diverse performances: enhanced-efficiency N fertilizer reduced N loss rate by 7.8 percent points and the global warming potential (GWP, considering N2O and CH4 emissions) by 28.8%; combined manure and chemical N fertilizer reduced N loss rate by 9.0 percent points but increased the GWP by 56.9%; straw return had no effect on total N loss but almost doubled the GWP. Using nutrient sources most appropriate to site-specific conditions is demonstrated as a robust way to decrease nutrient losses. Setting nutrient input thresholds would also contribute to the mitigation of environmental pollution, especially in regions with poor fertilization recommendation systems.

    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.

    Resolving humic and fulvic acids in binary systems influenced by adsorptive fractionation to Fe-(hydr)oxide with focus on UV–Vis analysis
    Xu, Yun ; Bai, Yilina ; Hiemstra, Tjisse ; Tan, Wenfeng ; Weng, Liping - \ 2020
    Chemical Engineering Journal 389 (2020). - ISSN 1385-8947
    Acid precipitation - Adsorptive fractionation - Humic Substances - Iron-oxides - Size exclusion chromatography - UV–Vis spectroscopy

    Humic acid (HA) and fulvic acid (FA) are two operationally defined classes of natural organic matter. In the environment, both materials are present simultaneously and bind in a competitive manner to Fe-(hydr)oxides and other minerals, but their quantification in mixtures is a challenge. In this study, an UV–Vis method was developed to quantify concentrations of HA and FA without and after adsorptive fractionation by an iron oxide (goethite, α-FeOOH). In addition, the performance of the UV–Vis method was compared to that of acid precipitation and size exclusion chromatography (SEC). Among the three methodologies (UV–Vis, acid precipitation, SEC), the UV–Vis method is the most successful in quantifying the ratio of HA to FA subject to fractionation. The UV–Vis method is based on distinct differences in the UV–Vis spectra of HA and FA, including fingerprints in both the spectra shape and intensity. Adsorption to goethite decreased the specific light absorbance of HA and FA, but the changes in spectral shape were not significant enough to cover their differences. The acid precipitation method can also quantify the HA to FA ratio. But to minimize the influence of incomplete HA precipitation or co-precipitation of FA, the concentration of both HA and FA needs to be at least ~20 mgC L−1. The SEC method is not suitable to measure HA and FA after adsorption, because preferential adsorption significantly affects the shape of SEC chromatograms.

    Impact of trends in river discharge and ocean tides on water level dynamics in the Pearl River Delta
    Cao, Yu ; Zhang, Wei ; Zhu, Yuliang ; Ji, Xiaomei ; Xu, Yanwen ; Wu, Yao ; Hoitink, A.J.F. - \ 2020
    Coastal Engineering 157 (2020). - ISSN 0378-3839
    Nonstationary harmonic analysis - River discharge - Tidal amplitudes - Tidal forcing - Water levels

    The spectrum of tidal and subtidal water level variations in river deltas responds to river discharge variation, ocean tides, and human activities of many kinds. It remains a contemporary challenge to identify the main sources of changes in tidal dynamics in deltas, because of nonlinear interactions between tides and the river discharge in a changing setting. Understanding the main forcing factors controlling the evolution of mean water levels and the associated amplitudes and phases of tidal constituents can help to understand the causes of floods and the occurrence of low flows hindering navigation. Here, a nonstationary harmonic analysis tool (NS_TIDE) is applied to hydrological data from 14 stations in the Pearl River Delta (PRD) spanning the period 1961–2012. The water levels and main tidal constituent properties are decomposed into contributions of external forcing by river discharges and ocean tides, providing insight into the nonstationary tidal-fluvial processes. Significant temporal trends in mean water levels and tidal properties are observed in the PRD. Results indicate that there is spatial variability in the response of mean water levels and tidal properties to river discharge variation in the delta. The abrupt changes in bathymetry in the delta due to intensive sand excavation are likely responsible for the observed spatial variations in tidal response, which reduce the flood-dominant tidal asymmetry in this area.

    Modelling long-term impacts of fertilization and liming on soil acidification at Rothamsted experimental station
    Xu, Donghao ; Carswell, Alison ; Zhu, Qichao ; Zhang, Fusuo ; Vries, Wim de - \ 2020
    Science of the Total Environment 713 (2020). - ISSN 0048-9697
    Liming - Long-term experiments - Modelling - Soil acidification - VSD+

    Liming is widely used to reduce the impacts of soil acidification and optimize soil pH for agricultural production. Whether models can simulate the effect of liming on soil pH, and base saturation (BS), and thereby guide lime application, is still largely unknown. Long-term experimental data from a grassland (Park Grass, 1965–2012) and arable land (Sawyers Field, 1962–1972) at Rothamsted Research, UK, were thus used to assess the ability of the VSD+ model to simulate the effects of long-term fertilization and liming on soil acidification. The VSD+ model was capable of simulating observed soil pH and BS changes over time in the long-term liming experiments, except for a treatment in which sulphur (S) was added. Normalized Mean Absolute Errors (NMAE) and Normalized Root Mean Square Errors (NRMSE) of simulated and observed pH values, averaged over the observation periods varied between 0.02 and 0.08 (NMAE) and 0.01–0.05 (NRMSE). The acidity budget results for Park Grass suggest that nitrogen (N) transformations contributed most to acidity production, causing predominantly aluminium (Al) exchange in the topsoil (0–23 cm) followed by base cation (BC) release, but in the treatment with S addition, BC uptake had a nearly similar effect on acidity production. However, in Sawyers Field, the acidity budget suggested that BC uptake was the dominant cause of soil acidification, while the impacts of N transformations were limited. Liming was found to sufficiently replenish BC and decrease Al exchange in the topsoil layer. Overall, the VSD+ model can adequately reconstruct the impacts of fertilizer and liming applications on acid neutralizing processes and related soil pH and BC changes at the soil exchange complex.

    Tiara[5]arenes: Synthesis, solid-state conformational studies, host-guest properties and application as nonporous adaptive crystals
    Yang, Weiwei ; Samanta, Kushal ; Wan, Xintong ; Thikekar, Tushar Ulhas ; Chao, Yang ; Li, Shunshun ; Du, Ke ; Xu, Yun ; Gao, Yan ; Zuilhof, H. ; Sue, Andrew C.H. - \ 2020
    Angewandte Chemie 59 (2020)10. - ISSN 0044-8249 - p. 3994 - 3999.
    Tiara[5]arenes (T[5]s), a new class of five‐fold symmetric oligophenolic macrocycles, which are not accessible from the addition of formaldehyde to phenol, were synthesized for the first time. These pillar[5]arene‐derived structures display both unique conformational freedom, differing from that of pillararenes, with a rich blend of solid‐state conformations, and excellent host‐guest interactions in solution. Finally we show how this novel macrocyclic scaffold can be functionalized in a variety of ways and used as functional crystalline materials to distinguish uniquely between benzene and cyclohexane.
    Intercropping maize and soybean increases efficiency of land and fertilizer nitrogen use; A meta-analysis
    Xu, Zhan ; Li, Chunjie ; Zhang, Chaochun ; Yu, Yang ; Werf, Wopke van der; Zhang, Fusuo - \ 2020
    Field Crops Research 246 (2020). - ISSN 0378-4290
    Fertilizer N equivalent ratio (FNER) - Intercropping - Land equivalent ratio (LER) - Maize - Soybean

    Intercropping exploits species complementarities to achieve sustainable intensification by increasing crop outputs per unit land with reduced anthropogenic inputs. Cereal/legume intercropping is a classical case. We carried out a global meta-analysis to assess land and fertilizer N use efficiency in intercropping of maize and soybean as compared to sole crops, based on 47 studies reported in English and 43 studies reported in Chinese. The data were extracted and analyzed with mixed effects models to assess land equivalent ratio (LER) of intercropping and factors affecting LER. The worldwide average LER of maize/soybean intercropping was 1.32 ± 0.02, indicating a substantial land sparing potential of intercropping over sole crops. This advantage increased as the temporal niche differentiation between the two species was increased by sowing or harvesting one crop earlier than the other as in relay intercropping, i.e. with only partial overlap of the growing periods of the two species The mean fertilizer N equivalent ratio (FNER) was 1.44 ± 0.03, indicating that intercrops received substantially less fertilizer N than sole crops for the same product output. These fertilizer savings are mainly due to the high relative maize yield and the lower N input in the intercrop compared to the input in sole maize. This meta-analysis thus shows that exploiting species complementarities by intercropping maize and soybean enables major increases in land productivity with less fertilizer N use. Both LER and FNER increased as the difference in growth duration increased for maize and soybean, but were not affected by fertilizer N rate. LER increased when soil organic matter increased but FNER did not change with soil organic matter.

    Cellular RNA Hubs: Friends and Foes of Plant Viruses
    Xu, Min ; Mazur, Magdalena J. ; Tao, Xiaorong ; Kormelink, Richard - \ 2020
    Molecular Plant-Microbe Interactions 33 (2020)1. - ISSN 0894-0282 - p. 40 - 54.
    RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.
    Negative effects of urbanization on agricultural soil easily oxidizable organic carbon down the profile of the Chengdu Plain, China
    Luo, Youlin ; Li, Qiquan ; Wang, Changquan ; Li, Bing ; Stomph, Tjeerd Jan ; Yang, Juan ; Tao, Qi ; Yuan, Shu ; Tang, Xiaoyan ; Ge, Jinru ; Yu, Xuelian ; Peng, Yueyue ; Xu, Qiang ; Zheng, Gangxun - \ 2020
    Land Degradation and Development 31 (2020)3. - ISSN 1085-3278 - p. 404 - 416.
    easily oxidized organic carbon - impact factors - negative effects - rapid urbanization - soil profile

    Soil easily oxidizable organic carbon (EOC) is directly related to CO2 density; dynamics in subsurface EOC have been observed globally in relation to rapid urbanization. However, in the context of rapid urbanization, the factors related to EOC and the response of the EOC pool to urbanization down the profile remain elusive. The aim of the current paper is to investigate possible changes in the distribution of EOC over the soil profile and the impact of land use, socioeconomic, and natural factors on these. The study used samples from 182 soil profiles (0–100 cm) taken in the peri-urban areas of the megacity Chengdu (a typical megacity with rapid urbanization). Main drivers of changes in soil EOC were analyzed by using spatial and regression analyses. Closer to the centre of the city, soil EOC levels were lower and land-use factors and socioeconomic factors contributed more to explaining variation in EOC levels in the 0–40-cm layer, whereas natural factors were most important at larger distance from the city. The effect of land-use factors and socioeconomic factors on EOC reached down to 60-cm depths. Moreover, an estimated 20% loss of EOC stock was observed close to the city in comparison with the surroundings, suggesting that the rapid process of urbanization was accompanied by a loss of EOC stock down the profile to depths of 60 cm, and the negative effects on EOC stock became more intensive as the distance to the city decreased.

    Environmental impact assessment of water-saving irrigation systems across 60 irrigation construction projects in northern China
    Chen, Xiuzhi ; Thorp, Kelly R. ; Oel, Pieter R. van; Xu, Zhenci ; Zhou, Bo ; Li, Yunkai - \ 2020
    Journal of Cleaner Production 245 (2020). - ISSN 0959-6526
    Carbon footprint - Environmental impact - Irrigation project - Life cycle assessment - Scenario - Water footprint

    With increasing water shortages partly due to increasing demands, water has become a globally relevant issue especially in arid and semi-arid regions. Water-saving irrigation technologies provide new ways for improving the efficiency of water use for agricultural production. Although efficient irrigation management could lead to water savings and increased yields, the water consumption and greenhouse gas emissions during the construction of irrigation projects also puts pressure on environmental health. However, little research has considered the environmental impact of the construction process and materials. To fill this gap, the water footprint (WF) and carbon footprint (CF) of irrigation projects were calculated using life cycle assessment (LCA) methods. The results for sixty typical irrigation projects in northern China showed that the WF accounted for only 0.2–1.5% of the total agricultural WF and 2.3–8.8% of the water saved. When the WF to construct modern irrigation systems is not considered, the water-saving effects of these systems are generally overestimated by 13%. The CF for irrigation projects was 42.0% of all agricultural activities. Due to the difficulty to obtain detailed information for irrigation projects, this paper established the relationship between financial investment or area and CF for three kinds of irrigation projects. It provided a simple quantitative method for assessing its environmental impacts. By comparing environmental impacts and production benefits under different scenarios, using drip irrigation over the long-term could increase crop yield and reduce water footprint, but carbon footprint was increased at the same time. This study suggests that it is necessary to assess the environmental impacts of irrigation construction projects from a life cycle perspective rather focusing only on yield increases and reductions in irrigation amounts.

    A network approach to prioritize conservation efforts for migratory birds
    Xu, Yanjie ; Si, Yali ; Takekawa, John ; Liu, Qiang ; Prins, Herbert H.T. ; Yin, Shenglai ; Prosser, Diann J. ; Gong, Peng ; Boer, Willem F. de - \ 2020
    Conservation Biology 34 (2020)2. - ISSN 0888-8892 - p. 416 - 426.
    bird migration - connectivity - conservation designation - habitat loss - network

    Habitat loss can trigger migration network collapse by isolating migratory bird breeding grounds from nonbreeding grounds. Theoretically, habitat loss can have vastly different impacts depending on the site's importance within the migratory corridor. However, migration-network connectivity and the impacts of site loss are not completely understood. We used GPS tracking data on 4 bird species in the Asian flyways to construct migration networks and proposed a framework for assessing network connectivity for migratory species. We used a node-removal process to identify stopover sites with the highest impact on connectivity. In general, migration networks with fewer stopover sites were more vulnerable to habitat loss. Node removal in order from the highest to lowest degree of habitat loss yielded an increase of network resistance similar to random removal. In contrast, resistance increased more rapidly when removing nodes in order from the highest to lowest betweenness value (quantified by the number of shortest paths passing through the specific node). We quantified the risk of migration network collapse and identified crucial sites by first selecting sites with large contributions to network connectivity and then identifying which of those sites were likely to be removed from the network (i.e., sites with habitat loss). Among these crucial sites, 42% were not designated as protected areas. Setting priorities for site protection should account for a site's position in the migration network, rather than only site-specific characteristics. Our framework for assessing migration-network connectivity enables site prioritization for conservation of migratory species.

    Managing Forests for Both Downstream and Downwind Water
    Creed, Irena F. ; Jones, Julia A. ; Archer, Emma ; Claassen, Marius ; Ellison, David ; Mcnulty, Steven G. ; Noordwijk, Meine Van; Vira, Bhaskar ; Wei, Xiaohua ; Bishop, Kevin ; Blanco, Juan A. ; Gush, Mark ; Gyawali, Dipak ; Jobbágy, Esteban ; Lara, Antonio ; Little, Christian ; Martin-ortega, Julia ; Mukherji, Aditi ; Murdiyarso, Daniel ; Pol, Paola Ovando ; Sullivan, Caroline A. ; Xu, Jianchu - \ 2019
    Frontiers in Forests and Global Change 2 (2019). - ISSN 2624-893X
    Forests and trees are key to solving water availability problems in the face of climate change and to achieving the United Nations Sustainable Development Goals. A recent global assessment of forest and water science posed the question: How do forests matter for water? Here we synthesize science from that assessment, which shows that forests and water are an integrated system. We assert that forests, from the tops of their canopies to the base of the soils in which trees are rooted, must be considered a key component in the complex temporal and spatial dimensions of the hydrologic cycle. While it is clear that forests influence both downstream and downwind water availability, their actual impact depends on where they are located and their processes affected by natural and anthropogenic conditions. A holistic approach is needed to manage the connections between forests, water and people in the face of current governance systems that often ignore these connections. We need policy interventions that will lead to forestation strategies that decrease the dangerous rate of loss in forest cover and that—where appropriate—increase the gain in forest cover. We need collective interventions that will integrate transboundary forest and water management to ensure sustainability of water supplies at local, national and continental scales. The United Nations should continue to show leadership by providing forums in which interventions can be discussed, negotiated and monitored, and national governments must collaborate to sustainably manage forests to ensure secure water supplies and equitable and sustainable outcomes.
    Innovative lateral flow devices for the detection of pesticides harmful to bees
    Xu, Mang ; Hoof, R.A. van; Hamers, A.R.M. ; Rijk, T.C. de; Guo, Yirong ; Bovee, T.F.H. ; Peters, J. - \ 2019
    Conventional instrumental detection of pesticides is complex and time-consuming, and is not realistic at the Point Of Need. In the B-GOOD project, we applied a dual channel lateral flow device (LFD) that is able to detect six out of eight neonicotinoids based on monoclonal antibody interaction and found that these LFDs have strong potential for field application. Additionally, WFSR has developed a LFD prototype that detects fipronil, a pesticide which was responsible for the recent death of hundred-thousands of honey bees in the Netherlands. Other LFDs, for the detection of bee-harming pesticides are also under development. In the near future, B-GOOD is interested in applying the developed LFDs at the point of need.
    对农用地土壤环境质量类别划分的思考:以贵州马铃薯产区Cd风险管控为例
    Song, Jing ; Xu, Genyan ; Luo, Yongming ; Gao, Hui ; Tang, Wei - \ 2019
    Earth Science Frontiers 26 (2019)6. - ISSN 1005-2321 - p. 192 - 198.
    Bioavailable heavy metals - Criteria for safe utilization of soil - DUMIS - Soil-crop synchronized monitoring - Suitability assessment of soil environmental quality standard

    By compilation of data from field sampling, pot experiment and literature, we evaluated the suitability of the existing national standards (GB 15618-2018 and GB/T 36783-2018) for the classification of soil environmental quality in potato producing areas of Guizhou. The results showed that both soil Cd standards were overly stringent as, for example, these for potatoes grown in mining areas were more likely to exceed food standard. Here, we summarized the inadequacy of the existing sampling methods for soil-crop synchronized monitoring and proposed a sampling theory-based Decision Unit-Multi Increment Sampling method (DUMIS) for soil-crop synchronized monitoring and remediation verification. We proposed that the criteria for safe soil utilization should be derived on a site-specific basis using bioavailable fractions. In order to facilitate the evaluation of soil environmental quality and safety for the agricultural production regions of China, we suggested that further research is needed regarding the use of DUMIS in soil-crop synchronized monitoring and bioavailable fractions based criteria for safe utilization of mild to moderately contaminated soils.

    Phosphate speciation on Al-substituted goethite: ATR-FTIR/2D-COS and CD-MUSIC modeling
    Xu, Jinling ; Koopal, Luuk K. ; Wang, Mingxia ; Xiong, Juan ; Hou, Jingtao ; Li, Yan ; Tan, Wenfeng - \ 2019
    Environmental Science: Nano covers the benefits... 6 (2019)12. - ISSN 2051-8153 - p. 3625 - 3637.

    Natural goethite commonly encounters Al substitution for Fe, which alters the surface reactivity of goethite. Whether and how Al substitution affects the surface speciation of phosphate remain poorly understood. Therefore, the phosphate adsorption and speciation of Al-substituted (6 and 9 mol%) goethite were investigated by combining attenuated total reflectance Fourier transform infrared (ATR-FTIR) and CD-MUSIC modeling. Al substitution caused a decrease in the crystal length-To-width ratio of goethite and the ratio of (110)/(021) faces was estimated to be 90/10, 85/10 and 81/19 for goethite with about 0, 6 and 9 mol% Al, respectively. The decreasing (110)/(021) face ratio and increasing surface roughness with increasing Al substitution enhanced the surface charge density and phosphate adsorption capacity of goethite. Two-dimensional correlation spectroscopy (2D-COS) analysis showed that three types of phosphate complexes were formed on both pure and Al-substituted goethites. CD-MUSIC modeling, based on electron microscopy and ATR-FTIR results to arrive at some of the parameters, could describe both the proton and the phosphate adsorption well with optimized remaining parameters. The model parameters indicated that Al substitution in goethite led to larger affinity constants for bidentate phosphate complexes and smaller values for monodentate complexes. Therefore, a larger percentage of bidentate phosphate complexes were formed on Al-substituted goethite than on pure goethite. Monodentate phosphate complexes were hardly formed on the Al sites of Al-substituted goethite. The results improve our insight regarding phosphate binding to Al-substituted goethite and phosphorus availability and mobility in iron-rich soils.

    Designing intercrops for high yield, yield stability and efficient use of resources: Are there principles?
    Stomph, Tjeerd Jan ; Dordas, Christos ; Baranger, Alain ; Rijk, Joshua de; Dong, Bei ; Evers, Jochem ; Gu, Chunfeng ; Li, Long ; Simon, Johan ; Jensen, Erik Steen ; Wang, Qi ; Wang, Yuyun ; Wang, Zishen ; Xu, Huasen ; Zhang, Chaochun ; Zhang, Lizhen ; Zhang, Wei Ping ; Bedoussac, Laurent ; Werf, Wopke van der - \ 2019
    In: Advances in Agronomy Academic Press Inc. (Advances in Agronomy ) - p. 1 - 50.
    Biotic stresses - Cropping system design - Light - Nutrients - Product quality - Resource use efficiency - Water

    Intercropping is the simultaneous cultivation of plant species in the same field for a considerable proportion of their growing periods. Interest in intercropping for sustainable agriculture is on the rise and the number of scientific studies on intercropping is strongly increasing. Here we assess the current status of knowledge on factors that determine yield, yield stability and resource use efficiency of intercropping as compared to sole cropping. Distinguishing resource use into acquisition and conversion shows that intercrops are mainly improving acquisition rather than conversion efficiency. We also make an attempt to quantify the importance of reduced biotic stresses through pests, diseases, and weeds. We particularly focus on blank spots in the knowledge and possible bias in existing literature and ask which research approaches are needed to advance the field and pave the way for a wider usage of intercropping in modern sustainable agriculture.

    Energy balance and metabolic status of dairy cows : a study using metabolomics, proteomics and machine learning approaches
    Xu, Wei - \ 2019
    Wageningen University. Promotor(en): B. Kemp, co-promotor(en): A.T.M. van Knegsel; J.J.M. Vervoort. - Wageningen : Wageningen University - ISBN 9789463951302 - 163

    In early lactation, dairy cows typically experience a negative energy balance (NEB) due to the high energy requirement for milk yield and low energy intake from feed. Negative energy balance has been related to metabolic disorders, compromised health and fertility, and reduced productive lifespan. Estimation of the energy balance and metabolic status is not easy on the farm. Therefore, the aims of this thesis were to estimate energy balance and metabolic status of dairy cows using metabolomics and machine learning techniques, and to investigate the metabolic pathways related to energy metabolism of dairy cows in early lactation using metabolomics and proteomics techniques. In this thesis, on-farm cow data collected from two earlier studies (study I, 168 cows and study II, 127 cows) were used to estimate energy balance and metabolic status of cows with machine learning approach. In addition, milk and blood samples obtained from study II were analysed with metabolomics and proteomics approaches. To estimate energy balance of dairy cows, estimated performance of reduced models with either milk metabolites, or milk production traits or both ranged from 0.53 to 0.78 (adjusted R-square).Milk metabolites important in explaing negative energy balance in cows where glycine, choline and carnitine. . To estimate metabolic status of dairy cows using on-farm cow data, random forest, support vector machine, and partial least square discriminant analysis performed better than other machine learning algorithms. Based on the metabolomics results, plasma and milk metabolites altered during NEB of dairy cows in early lactation reflected the metabolism in the body or the mammary gland of dairy cows. Metabolic processes in the mammary gland during NEB were related to leakage of cell content due to mammary cell apoptosis and, to synthesis of nucleic acids and cell membrane phospholipids, protein glycosylation and an increase in one-carbon metabolic processes. The processes are related to cell renewal and proliferation. Since NEB is highly related to milk production this seem logical. Blood metabolites related to energy balance were mainly reflecting energy metabolism (mobilization of body fat, skeleton muscle, bone) increased blood flow and gluconeogenesis.

    Better understanding of the metabolic pathways through a metabolomics and proteomics approach does not only provide biomarkers for pathways under stress during NEB but may also allow for targeted dietary interventions when glucose and rumen protected choline are interesting candidates.

    In conclusion, the energy balance of dairy cows can be estimated by milk metabolites based on metabolomics study, and metabolic status can be estimated by machine learning algorithms using on-farm cow data. Moreover, energy balance of dairy cows in early lactation was related with milk and plasma metabolites which revealed metabolic pathways that allow more targeted intervention strategies.

    Analytical model captures intratidal variation in salinity in a convergent, well-mixed estuary
    Xu, Yanwen ; Hoitink, Antonius J.F. ; Zheng, Jinhai ; Kästner, Karl ; Zhang, Wei - \ 2019
    Hydrology and Earth System Sciences 23 (2019)10. - ISSN 1027-5606 - p. 4309 - 4322.

    Knowledge of the processes governing salt intrusion in estuaries is important, since it influences the eco-environment of estuaries as well as its water resource potential in many ways. Analytical models of salinity variation offer a simple and efficient method for studying salt intrusion in estuaries. In this paper, an unsteady analytical solution is presented to predict the spatio-temporal variation in salinity in convergent estuaries. It is derived from a one-dimensional advection-diffusion equation for salinity, adopting a constant mixing coefficient and a single-frequency tidal wave, which can directly reflect the influence of the tidal motion and the interaction between the tide and runoff. The deduced analytical solution is illustrated with an application to the Humen estuary of the Pearl River Delta (PRD) and proves to be an efficient and accurate approach for predicting the salt intrusion in convergent estuaries. The unsteady analytical solution is tested against observations from six study sites to validate its capability to predict intratidal variation in salt intrusion. The results show that the proposed unsteady analytical solution can be successfully used to reproduce the spatial distribution and temporal processes governing salinity dynamics in convergent, well-mixed estuaries. The proposed method provides a quick and convenient approach for deciding on water-fetching methods to make good use of water resources.

    Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice
    Zhao, Fan ; Zhou, Guanghong ; Liu, Xinyue ; Song, Shangxin ; Xu, Xinglian ; Hooiveld, Guido ; Müller, Michael ; Liu, Li ; Kristiansen, Karsten ; Li, Chunbao - \ 2019
    Molecular Nutrition & Food Research 63 (2019)23. - ISSN 1613-4125
    Akkermansia muciniphila - chicken protein - oxidative phosphorylation - soy protein

    Scope: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated. Methods and results: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet. Conclusion: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.

    Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking
    Sikdar, Sinjini ; Joehanes, Roby ; Joubert, Bonnie R. ; Xu, Cheng Jian ; Vives-Usano, Marta ; Rezwan, Faisal I. ; Felix, Janine F. ; Ward, James M. ; Guan, Weihua ; Richmond, Rebecca C. ; Brody, Jennifer A. ; Küpers, Leanne K. ; Baïz, Nour ; Håberg, Siri E. ; Smith, Jennifer A. ; Reese, Sarah E. ; Aslibekyan, Stella ; Hoyo, Cathrine ; Dhingra, Radhika ; Markunas, Christina A. ; Xu, Tao ; Reynolds, Lindsay M. ; Just, Allan C. ; Mandaviya, Pooja R. ; Ghantous, Akram ; Bennett, Brian D. ; Wang, Tianyuan ; Consortium, The Bios ; Bakulski, Kelly M. ; Melen, Erik ; Zhao, Shanshan ; Jin, Jianping ; Herceg, Zdenko ; Meurs, Joyce Van; Taylor, Jack A. ; Baccarelli, Andrea A. ; Murphy, Susan K. ; Liu, Yongmei ; Munthe-Kaas, Monica Cheng ; Deary, Ian J. ; Nystad, Wenche ; Waldenberger, Melanie ; Annesi-Maesano, Isabella ; Conneely, Karen ; Jaddoe, Vincent W.V. ; Arnett, Donna ; Snieder, Harold ; Kardia, Sharon L.R. ; Relton, Caroline L. ; Ong, Ken K. ; Ewart, Susan ; Moreno-Macias, Hortensia ; Romieu, Isabelle ; Sotoodehnia, Nona ; Fornage, Myriam ; Motsinger-Reif, Alison ; Koppelman, Gerard H. ; Bustamante, Mariona ; Levy, Daniel ; London, Stephanie J. - \ 2019
    Epigenomics 11 (2019)13. - ISSN 1750-1911 - p. 1487 - 1500.
    cigarette smoking - epigenetics - infant - maternal exposure - methylation

    Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.

    Forest connectivity, host assemblage characteristics of local and neighboring counties, and temperature jointly shape the spatial expansion of lyme disease in United States
    Wang, Yingying X.G. ; Matson, Kevin D. ; Xu, Yanjie ; Prins, Herbert H.T. ; Huang, Zheng Y.X. ; Boer, Willem F. de - \ 2019
    Remote Sensing 11 (2019)20. - ISSN 2072-4292
    Assemblage similarity - Disease spread - Forest cover - Host assemblage composition - Infection intensity

    Understanding risk factors for the spread of infectious diseases over time and across the landscape is critical for managing disease risk. While habitat connectivity and characteristics of local and neighboring animal (i.e., host) assemblages are known to influence the spread of diseases, the interactions among these factors remain poorly understood. In this study, we conducted a county-level analysis to test the effects of forest connectivity, together with the suitability of local assemblage (measured by the similarity of local host assemblage with neighboring assemblages) and the infection intensity of neighboring counties on the spatial expansion of Lyme disease in the United States. Our results suggested that both the similarity of local host assemblage and the infection intensity of neighboring counties were positively correlated with the probability of disease spread. Moreover, we found that increasing forest connectivity could facilitate the positive effect of neighbor infection intensity. In contrast, the effect size of the host assemblage similarity decreased with increasing connectivity, suggesting that host assemblage similarity was less effective in well-connected habitats. Our results thus indicate that habitat connectivity can indirectly influence disease spread by mediating the effects of other risk factors.

    Loss of functional connectivity in migration networks induces population decline in migratory birds
    Xu, Yanjie ; Si, Yali ; Wang, Yingying ; Zhang, Yong ; Prins, Herbert H.T. ; Cao, Lei ; Boer, Willem F. de - \ 2019
    Ecological Applications 29 (2019)7. - ISSN 1051-0761 - p. e01960 - e01960.
    bird migration - habitat loss - life history - network robustness - population dynamics - species traits - wetland

    Migratory birds rely on a habitat network along their migration routes by temporarily occupying stopover sites between breeding and non-breeding grounds. Removal or degradation of stopover sites in a network might impede movement and thereby reduce migration success and survival. The extent to which the breakdown of migration networks, due to changes in land use, impacts the population sizes of migratory birds is poorly understood. We measured the functional connectivity of migration networks of waterfowl species that migrate over the East Asian-Australasian Flyway from 1992 to 2015. We analysed the relationship between changes in non-breeding population sizes and changes in functional connectivity, while taking into account other commonly considered species traits, using a phylogenetic linear mixed model. We found that population sizes significantly declined with a reduction in the functional connectivity of migration networks; no other variables were important. We conclude that the current decrease in functional connectivity, due to habitat loss and degradation in migration networks, can negatively and crucially impact population sizes of migratory birds. Our findings provide new insights into the underlying mechanisms that affect population trends of migratory birds under environmental changes. Establishment of international agreements leading to the creation of systematic conservation networks associated with migratory species' distributions and stopover sites may safeguard migratory bird populations.

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

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

    FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum
    Kong, Xiangjiu ; Zhang, Hao ; Wang, Xiaoliang ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Brankovics, Balázs ; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2019
    Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
    Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH- 1 and 1FgPex3 knock-out strains. The GFP and RFP transformants in the 1FgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The 1FgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid b-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the 1FgPex3 mutant was sensitive to osmotic stressors
    as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of 1FgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
    贵州省白菜种植土壤镉风险管控标准研究
    Xu, Gen Yan ; Song, Jing ; Gao, Hui ; Zhang, Sha - \ 2019
    Journal of Agro-Environment Science 38 (2019)7. - ISSN 1672-2043 - p. 1490 - 1497.
    Cadmium - Risk intervention values - Risk screening values - Soil-crop transfer model

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

    Prediction of metabolic status of dairy cows in early lactation with on-farm cow data and machine learning algorithms
    Xu, Wei ; Knegsel, Ariette T.M. van; Vervoort, Jacques J.M. ; Bruckmaier, Rupert M. ; Hoeij, Renny J. van; Kemp, Bas ; Saccenti, Edoardo - \ 2019
    Journal of Dairy Science 102 (2019)11. - ISSN 0022-0302 - p. 10186 - 10201.
    cattle - cluster analysis - energy metabolism - Random Forest

    Metabolic status of dairy cows in early lactation can be evaluated using the concentrations of plasma β-hydroxybutyrate (BHB), free fatty acids (FFA), glucose, insulin, and insulin-like growth factor 1 (IGF-1). These plasma metabolites and metabolic hormones, however, are difficult to measure on farm. Instead, easily obtained on-farm cow data, such as milk production traits, have the potential to predict metabolic status. Here we aimed (1) to investigate whether metabolic status of individual cows in early lactation could be clustered based on their plasma values and (2) to evaluate machine learning algorithms to predict metabolic status using on-farm cow data. Through lactation wk 1 to 7, plasma metabolites and metabolic hormones of 334 cows were measured weekly and used to cluster each cow into 1 of 3 clusters per week. The cluster with the greatest plasma BHB and FFA and the lowest plasma glucose, insulin, and IGF-1 was defined as poor metabolic status; the cluster with the lowest plasma BHB and FFA and the greatest plasma glucose, insulin, and IGF-1 was defined as good metabolic status; and the intermediate cluster was defined as average metabolic status. Most dairy cows were classified as having average or good metabolic status, and a limited number of cows had poor metabolic status (10–50 cows per lactation week). On-farm cow data, including dry period length, parity, milk production traits, and body weight, were used to predict good or average metabolic status with 8 machine learning algorithms. Random Forest (error rate ranging from 12.4 to 22.6%) and Support Vector Machine (SVM; error rate ranging from 12.4 to 20.9%) were the top 2 best-performing algorithms to predict metabolic status using on-farm cow data. Random Forest had a higher sensitivity (range: 67.8–82.9% during wk 1 to 7) and negative predictive value (range: 89.5–93.8%) but lower specificity (range: 76.7–88.5%) and positive predictive value (range: 58.1–78.4%) than SVM. In Random Forest, milk yield, fat yield, protein percentage, and lactose yield had important roles in prediction, but their rank of importance differed across lactation weeks. In conclusion, dairy cows could be clustered for metabolic status based on plasma metabolites and metabolic hormones. Moreover, on-farm cow data can predict cows in good or average metabolic status, with Random Forest and SVM performing best of all algorithms.

    Propolis modulates the gut microbiota and improves the intestinal mucosal barrier function in diabetic rats
    Xue, Meilan ; Liu, Ying ; Xu, Hongwei ; Zhou, Zhitong ; Ma, Yan ; Sun, Ting ; Liu, Man ; Zhang, Huaqi ; Liang, Hui - \ 2019
    Biomedicine and Pharmacotherapy 118 (2019). - ISSN 0753-3322
    16S rDNA high-throughput sequencing - Diabetes - Gut microbiota - Propolis - Short chain fatty acid

    Objective: Diabetes mellitus is associated with gut microbiota disturbance and intestinal mucosal injuries. This study investigated the influence of propolis on the gut microbiota and intestinal mucosa in rats with diabetes. Methods: Sprague-Dawley (SD) rats were randomly assigned to the control group, model group, and three propolis groups (supplemented with 80, 160, and 240 mg/kg·bw propolis, respectively). A high-fat diet combined with a streptozotocin (STZ) abdominal injection were used to induce diabetes in the rats. After 4 weeks, the intestinal histopathological analysis of the ileum was observed by transmission electron microscopy. The fasting blood glucose (FBG), plasma insulin, glucose tolerance (OGTT) and glycosylated hemoglobin (HbA1c) levels were measured. The expression of tight junction (TJ) proteins in the ileum was measured using western blotting. The molecular ecology of the fecal gut microbiota was analyzed by 16S rDNA high-throughput sequencing. The contents of the short-chain fatty acids (SCFAs) in feces were measured using high-performance liquid chromatography (HPLC). Results: After propolis treatment, compared to the model group, FBG and HbA1c levels declined, while the glucose tolerance and insulin sensitivity index (ISI) increased. The levels of TJ proteins in the ileum increased in the propolis groups. The tight junctions and gap junctions of the intestinal epithelium were also improved in the propolis groups. The contents of the feces acetic acid, propionic acid and butyrate were increased in the propolis groups. 16S rDNA high-throughput sequencing revealed that the composition of the gut microbiota of rats in the propolis supplement group was significantly improved. Conclusions: Compared to the model group, propolis exerted hypoglycemic effects in diabetic rats, and it repaired intestinal mucosal damage, benefited the communities of the gut microbiota and increased SCFA levels in diabetic rats.

    Colletotrichum species associated with anthracnose of Pyrus spp. in China
    Fu, M. ; Crous, P.W. ; Bai, Q. ; Zhang, P.F. ; Xiang, J. ; Guo, Y.S. ; Zhao, F.F. ; Yang, M.M. ; Hong, N. ; Xu, W.X. ; Wang, G.P. - \ 2019
    Persoonia 42 (2019). - ISSN 0031-5850 - p. 1 - 35.
    Colletotrichum - Multi-gene phylogeny - Pathogenicity - Pyrus

    Colletotrichum species are plant pathogens, saprobes, and endophytes on a range of economically important hosts. However, the species occurring on pear remain largely unresolved. To determine the morphology, phylogeny and biology of Colletotrichum species associated with Pyrus plants, a total of 295 samples were collected from cultivated pear species (including P. pyrifolia, P. bretschneideri, and P. communis) from seven major pear-cultivation provinces in China. The pear leaves and fruits affected by anthracnose were sampled and subjected to fungus isolation, resulting in a total of 488 Colletotrichum isolates. Phylogenetic analyses based on six loci (ACT, TUB2, CAL, CHS-1, GAPDH, and ITS) coupled with morphology of 90 representative isolates revealed that they belong to 10 known Colletotrichum species, including C. aenigma, C. citricola, C. conoides, C. fioriniae, C. fructicola, C. gloeosporioides, C. karstii, C. plurivorum, C. siamense, C. wuxiense, and two novel species, described here as C. jinshuiense and C. pyrifoliae. Of these, C. fructicola was the most dominant, occurring on P. pyrifolia and P. bretschneideri in all surveyed provinces except in Shandong, where C. siamense was dominant. In contrast, only C. siamense and C. fioriniae were isolated from P. communis, with the former being dominant. In order to prove Koch’s postulates, pathogenicity tests on pear leaves and fruits revealed a broad diversity in pathogenicity and aggressiveness among the species and isolates, of which C. citricola, C. jinshuiense, C. pyrifoliae, and C. conoides appeared to be organ-specific on either leaves or fruits. This study also represents the first reports of C. citricola, C. conoides, C. karstii, C. plurivorum, C. siamense, and C. wuxiense causing anthracnose on pear.

    Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology (2019). - ISSN 1087-0156

    In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

    Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations
    Deng, Yale ; Ruan, Yunjie ; Ma, Bin ; Timmons, Michael B. ; Lu, Huifeng ; Xu, Xiangyang ; Zhao, Heping ; Yin, Xuwang - \ 2019
    Environment International 132 (2019). - ISSN 0160-4120
    Denitrification - Microbial aggregation - Multi-omics - Network - Niche difference

    Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.

    Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
    Contribution of methylation regulation of MpDREB2A promoter to drought resistance of Mauls prunifolia
    Li, Xuewei ; Xie, Yinpeng ; Lu, Liyuan ; Yan, Mingjia ; Fang, Nan ; Xu, Jidi ; Wang, Liping ; Yan, Yan ; Zhao, Tao ; Nocker, Steve van; Ma, Fengwang ; Liang, Dong ; Guan, Qingmei - \ 2019
    Plant and Soil 441 (2019)1-2. - ISSN 0032-079X - p. 15 - 32.
    ChIP-seq - DNA methylation - DREB2A - Drought resistance - Gene expression - Malus

    Background and aims: Malus prunifolia (Chinese name: Fu Ping Qiu Zi), a wild relative of cultivated apple (Malus x domestica Borkh), is extremely resistant to drought compared with domesticated cultivars, such as ‘Golden Delicious’. However, the molecular mechanisms underlying drought resistance of M. prunifolia have not been characterized. This study investigates a new regulatory mechanism to improve apple drought resistance. Methods: M. prunifolia and ‘Golden Delicious’ were each grafted on M. hupehensis for gene expression analysis. The methylation level of the DREB2A promoter was determined by bisulfite sequencing and ChIP-qPCR. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify target genes of MpDREB2A in apple. Results: The exposure to drought stress stimulated the expression level of DREB2A gene more than 100-fold in M. prunifolia, but only 16-fold in ‘Golden Delicious’. This difference in gene expression could not be explained in terms of difference in leaf relative water content. Correspondingly, the methylation level of M. prunifolia DREB2A (MpDREB2A) promoter region was significantly reduced. Additionally, MpDREB2A conferred enhanced drought resistance when ectopically expressed in Arabidopsis. Over 2800 potential downstream target genes of MpDREB2A were identified by ChIP-seq and these downstream genes have diverse potential functions related to stress resistance. Conclusions: Methylation regulation in promoter of MpDREB2A may contribute to the drought resistance of M. prunifolia.

    Twenty-three unsolved problems in hydrology (UPH)–a community perspective
    Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
    Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
    hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

    This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

    Data from: Horizontal and vertical diversity jointly shape food web stability against small and large perturbations
    Zhao, Qinghua ; Brink, P.J. van den; Carpentier, Camille ; Wang, Yingying ; Rodríguez Sánchez, P. ; Xu, Chi ; Vollbrecht, Silke ; Gillissen, F. ; Vollebregt, M.E. ; Wang, Shaopeng ; Laender, Frederik De - \ 2019
    Wageningen University & Research
    The biodiversity of food webs is composed of horizontal (i.e. within trophic levels) and vertical diversity (i.e. the number of trophic levels). Understanding their joint effect on stability is a key challenge. Theory mostly considers their individual effects and focuses on small perturbations near equilibrium in hypothetical food webs. Here, we study the joint effects of horizontal and vertical diversity on the stability of hypothetical (modelled) and empirical food webs. In modelled food webs, horizontal and vertical diversity increased and decreased stability, respectively, with a stronger positive effect of producer diversity on stability at higher consumer diversity. Experiments with an empirical plankton food-web, where we manipulated horizontal and vertical diversity and measured stability from species interactions and from resilience against large perturbations, confirmed these predictions. Taken together, our findings highlight the need to conserve horizontal biodiversity at different trophic levels to ensure stability.
    Patterns of nitrogen-fixing tree abundance in forests across Asia and America
    Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
    Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
    forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

    Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

    Impact hotspots of reduced nutrient discharge shift across the globe with population and dietary changes
    Wang, Xu ; Daigger, Glen ; Vries, Wim de; Kroeze, Carolien ; Yang, Min ; Ren, Nan Qi ; Liu, Junxin ; Butler, David - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723

    Reducing nutrient discharge from wastewater is essential to mitigating aquatic eutrophication; however, energy- and chemicals-intensive nutrient removal processes, accompanied with the emissions of airborne contaminants, can create other, unexpected, environmental consequences. Implementing mitigation strategies requires a complete understanding of the effects of nutrient control practices, given spatial and temporal variations. Here we simulate the environmental impacts of reducing nutrient discharge from domestic wastewater in 173 countries during 1990–2050. We find that improvements in wastewater infrastructure achieve a large-scale decline in nutrient input to surface waters, but this is causing detrimental effects on the atmosphere and the broader environment. Population size and dietary protein intake have the most significant effects over all the impacts arising from reduction of wastewater nutrients. Wastewater-related impact hotspots are also shifting from Asia to Africa, suggesting a need for interventions in such countries, mostly with growing populations, rising dietary intake, rapid urbanisation, and inadequate sanitation.

    Exploring the treasure of plant molecules with integrated biorefineries
    Torres, Andres F. ; Xu, Xuan ; Nikiforidis, Constantinos V. ; Bitter, Johannes H. ; Trindade, Luisa M. - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    Biobased economy - Biomass deconstruction - Biorefinery - Cross-disciplinary - Plant breeding - Plant compounds - Process technology

    Despite significant progress toward the commercialization of biobased products, today’s biorefineries are far from achieving their intended goal of total biomass valorization and effective product diversification. The problem is conceptual. Modern biorefineries were built around well-optimized, cost-effective chemical synthesis routes, like those used in petroleum refineries for the synthesis of fuels, plastics, and solvents. However, these were designed for the conversion of fossil resources and are far from optimal for the processing of biomass, which has unique chemical characteristics. Accordingly, existing biomass commodities were never intended for modern biorefineries as they were bred to meet the needs of conventional agriculture. In this perspective paper, we propose a new path toward the design of efficient biorefineries, which capitalizes on a cross-disciplinary synergy between plant, physical, and catalysis science. In our view, the best opportunity to advance profitable and sustainable biorefineries requires the parallel development of novel feedstocks, conversion protocols and synthesis routes specifically tailored for total biomass valorization. Above all, we believe that plant biologists and process technologists can jointly explore the natural diversity of plants to synchronously develop both, biobased crops with designer chemistries and compatible conversion protocols that enable maximal biomass valorization with minimum input utilization. By building biorefineries from the bottom-up (i.e., starting with the crop), the envisioned partnership promises to develop cost-effective, biomass-dedicated routes which can be effectively scaled-up to deliver profitable and resource-use efficient biorefineries.

    Impact of low-molecular weight organic acids on selenite immobilization by goethite: Understanding a competitive-synergistic coupling effect and speciation transformation
    Fang, Dun ; Wei, Shiyong ; Xu, Yun ; Xiong, Juan ; Tan, Wenfeng - \ 2019
    Science of the Total Environment 684 (2019). - ISSN 0048-9697 - p. 694 - 704.
    Adsorption - Ferric selenite - Organic acids - Reduction - Selenium - Speciation transformation
    © 2019 Elsevier B.V. The interactions between low-molecular weight organic acids (LMWOAs)and selenium (Se)on mineral/water interfaces affect the release, immobilization and bioavailability of Se in nature. Herein, the effects of three environmentally relevant LMWOAs (i.e., oxalic (Oxa), succinic (Suc)and citric (Cit)acids)on Se(IV)adsorption to goethite under oxic conditions were investigated using batch experiments, speciation fractionation, and ATR-FTIR and XPS analyses. The LMWOAs exhibited a competitive-synergistic coupling effect on Se(IV)adsorption to goethite, which inhibited the adsorption rate of Se(IV)by 14.1, 13.3 and 8.0 times. However, immobilization of Se(IV)was simultaneously enhanced by 39.1%, 34.6% and 14.1% in the following order Oxa > Suc > Cit. The results obtained by fractionation of the adsorbed Se(IV)revealed that the enhancement was due to surface binding as well as speciation transformation from ligand-exchangeable Se(IV)into residual fractions, which increased by approximately 18% in the presence of the LMWOAs. The dissolution of goethite significantly improved due to the LMWOAs and decreased to different degrees as the concentration of Se(IV)increased. The monodentate mononuclear complexes (58.2%)and Lewis base sites bonded Se (41.8%)were the predominant surface species of Se(IV)in goethite-Se(IV)system. The ATR-FTIR and high-resolution XPS analyses demonstrated that the formation of ≡FeO(SeO)O-CO surface complexes (22.8–27.0%)occurred in the presence of LMWOAs, which could be closely correlated with the interface-mediated reduction of Se(IV). In addition, the predominant mechanism for the formation of residual Se is LMWOA specific, in which ferric selenite-like precipitation was dominant for Suc (10.6%)and Cit (11.6%)and reduction was dominant for Oxa (17.5%). Overall, LMWOAs play an important role in Se(IV)immobilization and speciation transformation and may facilitate understanding the Se bioavailability in rhizosphere soils under oxic conditions.
    Horizontal and vertical diversity jointly shape food web stability against small and large perturbations
    Zhao, Qinghua ; Brink, Paul J. Van den; Carpentier, Camille ; Wang, Yingying X.G. ; Rodríguez-Sánchez, Pablo ; Xu, Chi ; Vollbrecht, Silke ; Gillissen, Frits ; Vollebregt, Marlies ; Wang, Shaopeng ; Laender, Frederik De - \ 2019
    Ecology Letters 22 (2019)7. - ISSN 1461-023X - p. 1152 - 1162.
    Equilibrium - horizontal diversity - large perturbations - small perturbations - stability - vertical diversity

    The biodiversity of food webs is composed of horizontal (i.e. within trophic levels) and vertical diversity (i.e. the number of trophic levels). Understanding their joint effect on stability is a key challenge. Theory mostly considers their individual effects and focuses on small perturbations near equilibrium in hypothetical food webs. Here, we study the joint effects of horizontal and vertical diversity on the stability of hypothetical (modelled) and empirical food webs. In modelled food webs, horizontal and vertical diversity increased and decreased stability, respectively, with a stronger positive effect of producer diversity on stability at higher consumer diversity. Experiments with an empirical plankton food web, where we manipulated horizontal and vertical diversity and measured stability from species interactions and from resilience against large perturbations, confirmed these predictions. Taken together, our findings highlight the need to conserve horizontal biodiversity at different trophic levels to ensure stability.

    Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds
    Huang, Zheng Y.X. ; Xu, Chi ; Langevelde, Frank van; Ma, Yuying ; Langendoen, Tom ; Mundkur, Taej ; Si, Yali ; Tian, Huaiyu ; Kraus, Robert H.S. ; Gilbert, Marius ; Han, Guan Zhu ; Ji, Xiang ; Prins, Herbert H.T. ; Boer, Willem F. de - \ 2019
    Journal of Animal Ecology 88 (2019)7. - ISSN 0021-8790 - p. 1044 - 1053.
    avian influenza - community composition - dilution effect - diversity–disease relationship - phylogenetic distance - waterfowl

    Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long-distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related. Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental-scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity. Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence. Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.

    Inter-provincial electricity transmissions’ co-benefit of national water savings in China
    Liao, Xiawei ; Chai, Li ; Jiang, Yu ; Ji, Junping ; Zhao, Xu - \ 2019
    Journal of Cleaner Production 229 (2019). - ISSN 0959-6526 - p. 350 - 357.
    Co-benefit - Electricity transmission - Water conservation - Water-energy nexus

    Interprovincial electricity transmissions have been utilised in China to overcome the country's imbalanced social-economic development and resource endowments. A bottom-up technology-based model is adopted to estimate water uses in electricity-exporting provinces to produce the transmitted electricity as well as opportunistic water savings in the receiving provinces. The results highlight that, in 2014, on a national scale, electricity transmissions generated co-benefit of saving 20.1 billion m³ of water nationally due to the electric power sector's water productivity differences in the exporting and importing provinces. Taking regional water stresses into account, 10.98 billion m³ of national scarce water saving is realized through electricity transmissions. Moreover, electricity transmissions by China's proposed 12 future transmission lines are expected to use additional 3.22 billion m³ of water in the electricity-exporting provinces. As more water-intensive technologies, e.g. open-loop cooling, are more commonly utilised in the electricity-receiving provinces, a total amount of 16.97 billion m³ of water use will be avoided nationally. Water-use efficiency for power production should be improved in all regions. Transmitted power imports should still be encouraged in water-scarce regions to alleviate their water stresses while power exports should be shifted away from water-stressed regions to water-abundant ones. Energy transformation by utilising gas-fired capacity and hydropower in water-abundant Southern China could be advanced.

    Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
    Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723

    Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.

    Pyrethric acid of natural pyrethrin insecticide: complete pathway elucidation and reconstitution in Nicotiana benthamiana
    Xu, H. ; Li, Wei ; Schilmiller, Anthony L. ; Eekelen, H.D.L.M. van; Vos, C.H. de; Jongsma, M.A. ; Pichersky, E. - \ 2019
    New Phytologist 223 (2019)2. - ISSN 0028-646X - p. 751 - 765.
    In the natural pesticides known as pyrethrins, which are esters produced in flowers of Tanacetum cinerariifolium (Asteraceae), the monoterpenoid acyl moiety is pyrethric acid or chrysanthemic acid.
    We show here that pyrethric acid is produced from chrysanthemol in six steps catalyzed by four enzymes, the first five steps occurring in the trichomes covering the ovaries and the last one occurring inside the ovary tissues.
    Three steps involve the successive oxidation of carbon 10 (C10) to a carboxylic group by TcCHH, a cytochrome P450 oxidoreductase. Two other steps involve the successive oxidation of the hydroxylated carbon 1 to give a carboxylic group by TcADH2 and TcALDH1, the same enzymes that catalyze these reactions in the formation of chrysanthemic acid. The ultimate result of the actions of these three enzymes is the formation of 10‐carboxychrysanthemic acid in the trichomes. Finally, the carboxyl group at C10 is methylated by TcCCMT, a member of the SABATH methyltransferase family, to give pyrethric acid. This reaction occurs mostly in the ovaries.
    Expression in N. benthamiana plants of all four genes encoding aforementioned enzymes, together with TcCDS, a gene that encodes an enzyme that catalyzes the formation of chrysanthemol, led to the production of pyrethric acid.
    Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota
    Deng, Yale ; Xu, Xiangyang ; Yin, Xuwang ; Lu, Huifeng ; Chen, Guangshuo ; Yu, Jianhai ; Ruan, Yunjie - \ 2019
    Applied Microbiology and Biotechnology 103 (2019)10. - ISSN 0175-7598 - p. 4241 - 4252.
    Biofloc technology - Gut microbiota - Microbial community - Shrimp - Stock density

    Biofloc technology is an efficient approach for intensive shrimp culture. However, the extent to which this process can influence the composition of intestinal microbial community is still unknown. Here, we surveyed the shrimp intestinal bacteria as well as the floc water from three biofloc systems with different stock densities. Our study revealed a similar variation trend in phylum taxonomy level between floc bacteria and gut microbiota. Microbial community varied notably in floc water from different stock densities, while a core genus with dominating relative abundance was detected in gut samples. Extensive variation was discovered in gut microbiota, but still clustered into groups according to stock density. Our results indicated that shrimp intestinal microbiota as well as bacteria aggregated in flocs assembled into distinct communities from different stock densities, and the intestinal communities were more similar with the surrounding environment as the increase of stock density and resulting high floc biomass. The high stock density changed the core gut microbiota by reducing the relative abundance of Paracoccus and increasing that of Nocardioides, which may negatively influence shrimp performance. Therefore, this study helps us to understand further bacteria and host interactions in biofloc system.

    Livestock Herbivory Shapes Fire Regimes and Vegetation Structure Across the Global Tropics
    Bernardi, Rafael E. ; Staal, Arie ; Xu, Chi ; Scheffer, Marten ; Holmgren, Milena - \ 2019
    Ecosystems 22 (2019)7. - ISSN 1432-9840 - p. 1457 - 1465.
    Africa - Australia - savannas - shrub encroachment - South America - subtropical - tree cover - woody plants

    Livestock grazing is the most extensive human land use and one of the key drivers of the conversion of tropical forests into grasslands. Livestock effects on vegetation structure are complex, as they can prevent tree recruitment and growth through browsing and trampling, but they can also affect vegetation indirectly through fire interactions. However, a systematic analysis of the overall effects of livestock across the global tropics is lacking. We analyzed remote sensing data on vegetation height and cover, climate, and fire as well as ground data on livestock density. We used generalized linear models and structural equation models to analyze the effects of livestock on fire regimes and vegetation structure. Across the global tropics, higher livestock densities are associated to lower fire frequency and a higher cover of shrubs and dwarf trees. This pattern occurs across continents, and is particularly pronounced at intermediate precipitation levels (1000–1500 mm y −1 ) where fire frequency is highest. In those regions, fire frequency is on average 49% lower in areas with high versus low livestock densities. South America has much higher livestock density and lower fire frequency than Africa and Asia–Australia across the whole precipitation gradient. Our findings suggest that livestock grazing reduces fire incidence through grass consumption and favors shrubs and a sparse cover of trees in regions where forests could potentially exist. Livestock can thus be a strong modifier of the climatic effect on vegetation structure, and livestock management changes can impact the structure and functioning of savannas and grasslands throughout the global tropics.

    iSQAPER task WP 3.3 soil quality indicators : Influence of soil type and land management on chemical, physical and biological soil parameters assessed visually and analytically
    Hoek, J. ; Berg, W. van den; Wesselink, M. ; Sukkel, W. ; Mäder, P. ; Bünemann, E. ; Bongiorno, G. ; Goede, R. de; Brussaard, L. ; Bai, Z. ; Haagsma, W. ; Verstegen, H. ; Glavan, M. ; Ferreira, C.S. ; Garcia Orenes, F. ; Toth, Z. ; Zhang, W. ; Fan, H. ; Fu, H. ; Gao, H. ; Xu, M. - \ 2019
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Wageningen Plant Research Report 783) - 114
    Transcriptional profiling of PPARα-/- and CREB3L3-/- livers reveals disparate regulation of hepatoproliferative and metabolic functions of PPARα
    Ruppert, P.M.M. ; Park, Jong-Gil ; Xu, Xu ; Hur, Kyu Yeon ; Kersten, A.H. ; Lee, Ann-Hwee - \ 2019
    Wageningen University
    GSE121096 - Mus musculus - PRJNA495632
    Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The aim of the present study was to characterize the interrelationship between PPARα and CREB3L3 in regulating hepatic gene expression. Male wildtype, PPARα-/-, CREB3L3-/- and combined PPARα/CREB3L3-/- mice were subjected to a 16-hour fast or 4 days of ketogenic diet. Whole genome expression analysis was performed on liver samples. Under conditions of overnight fasting, the effects of PPARα ablation and CREB3L3 ablation on plasma triglyceride, plasma β-hydroxybutyrate, and hepatic gene expression were largely disparate, and showed only limited interdependence. Gene and pathway analysis underscored the importance of CREB3L3 in regulating (apo)lipoprotein metabolism, and of PPARα as master regulator of intracellular lipid metabolism. A small number of genes, including Fgf21 and Mfsd2a, were under dual control of PPARα and CREB3L3. By contrast, a strong interaction between PPARα and CREB3L3 ablation was observed during ketogenic diet feeding. Specifically, the pronounced effects of CREB3L3 ablation on liver damage and hepatic gene expression during ketogenic diet were almost completely abolished by the simultaneous ablation of PPARα. Loss of CREB3L3 influenced PPARα signalling in two major ways. Firstly, it reduced expression of PPARα and its target genes involved in fatty acid oxidation and ketogenesis. In stark contrast, the hepatoproliferative function of PPARα was markedly activated by loss of CREB3L3. These data indicate that CREB3L3 ablation uncouples the hepatoproliferative and lipid metabolic effects of PPARα. Overall, except for the shared regulation of a very limited number of genes, the roles of PPARα and CREB3L3 in hepatic lipid metabolism are clearly distinct and are highly dependent on dietary status.
    Transcriptional profiling of PPARα−/− and CREB3L3−/− livers reveals disparate regulation of hepatoproliferative and metabolic functions of PPARα
    Ruppert, Philip M.M. ; Park, Jong-Gil ; Xu, Xu ; Hur, Kyu Yeon ; Lee, Ann-Hwee ; Kersten, Sander - \ 2019
    BMC Genomics 20 (2019). - ISSN 1471-2164
    Background: Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The aim of the present study was to characterize the interrelationship between PPARα and CREB3L3 in regulating hepatic gene expression. Male wild-type, PPARα−/−, CREB3L3−/− and combined PPARα/CREB3L3−/− mice were subjected to a 16-h fast or 4 days of ketogenic diet. Whole genome expression analysis was performed on liver samples. Results: Under conditions of overnight fasting, the effects of PPARα ablation and CREB3L3 ablation on plasma triglyceride, plasma β-hydroxybutyrate, and hepatic gene expression were largely disparate, and showed only limited interdependence. Gene and pathway analysis underscored the importance of CREB3L3 in regulating (apo)lipoprotein metabolism, and of PPARα as master regulator of intracellular lipid metabolism. A small number of genes, including Fgf21 and Mfsd2a, were under dual control of PPARα and CREB3L3. By contrast, a strong interaction between PPARα and CREB3L3 ablation was observed during ketogenic diet feeding. Specifically, the pronounced effects of CREB3L3 ablation on liver damage and hepatic gene expression during ketogenic diet were almost completely abolished by the simultaneous ablation of PPARα. Loss of CREB3L3 influenced PPARα signalling in two major ways. Firstly, it reduced expression of PPARα and its target genes involved in fatty acid oxidation and ketogenesis. In stark contrast, the hepatoproliferative function of PPARα was markedly activated by loss of CREB3L3. Conclusions: These data indicate that CREB3L3 ablation uncouples the hepatoproliferative and lipid metabolic effects of PPARα. Overall, except for the shared regulation of a very limited number of genes, the roles of PPARα and CREB3L3 in hepatic lipid metabolism are clearly distinct and are highly dependent on dietary status.
    The frost wave hypothesis : How the environment drives autumn departure of migratory waterfowl
    Xu, Fei ; Si, Yali - \ 2019
    Ecological Indicators 101 (2019). - ISSN 1470-160X - p. 1018 - 1025.
    Autumn migration - Food deterioration - Migration phenology - Temperature - Wind selectivity

    Migration phenology plays a critical role in shaping bird life histories. While the spring migration phenology of birds has been widely studied, our understanding about the mechanisms underlying autumn migration is limited. Frost is an indicator of cold weather, food scarcity, and water unavailability, but how frost drives the autumn departure of migratory birds has not yet been quantified. In this study we propose the ‘frost wave hypothesis’, which posits that the autumn departure of waterfowl is driven by a successive wave of the onset of frost. Using bird satellite tracking data and generalized linear mixed models, we analyze how the departure probability of two waterfowl species during autumn migration is affected by frost, accumulated temperature, food, snow, ice, short-term weather conditions (i.e., wind, temperature and precipitation), remaining migration distances, relative stopover duration, and flight distances between stopover sites. We find that bird autumn departure probability sharply increases after the first frost spell when the accumulated temperature reaches 0 °C, facilitated by surface meridional wind and longer remaining migration distances. We underline the dominant effect of frost on autumn departure, as birds tend to leave even under head wind if the time lag since the onset of frost is large. Time constraints that trigger southward departure are likely to be stronger when migrating birds are still far from their wintering site. By riding the frost wave, birds manage to maximize stopover site utilization while escaping harsh environmental conditions. Our findings improve the understanding of annual avian migration and help quantify the impact of global climate change on migratory waterfowl.

    Correction to: In Vitro Seeding Activity of Glycoform-Deficient Prions from Variably Protease-Sensitive Prionopathy and Familial CJD Associated with PrPV180I Mutation
    Wang, Zerui ; Yuan, Jue ; Shen, Pingping ; Abskharon, Romany ; Lang, Yue ; Dang, Johnny ; Adornato, Alise ; Xu, Ling ; Chen, Jiafeng ; Feng, Jiachun ; Moudjou, Mohammed ; Kitamoto, Tetsuyuki ; Langeveld, Jan ; Appleby, Brian ; Ma, Jiyan ; Kong, Qingzhong ; Petersen, Robert B. ; Zou, Wen Quan ; Cui, Li - \ 2019
    Molecular Neurobiology 56 (2019)8. - ISSN 0893-7648 - p. 5470 - 5470.

    The original version of this article unfortunately contained a mistake. The email address Dr. Wen-Quan Zou, one of the corresponding authors should be written as “wxz6@case.edu” instead of “wxz@case.edu”.

    Species-dependent effects of habitat degradation in relation to seasonal distribution of migratory waterfowl in the East Asian–Australasian Flyway
    Xu, Yanjie ; Si, Yali ; Yin, Shenglai ; Zhang, Wenyuan ; Grishchenko, Mikhail ; Prins, Herbert H.T. ; Gong, Peng ; Boer, Willem F. de - \ 2019
    Landscape Ecology 34 (2019)2. - ISSN 0921-2973 - p. 243 - 257.
    East Asian–Australasian Flyway - Fragmentation - Habitat loss - Isolation - Migratory connectivity - Migratory waterfowl - Seasonal distribution - Species trait - Wetland
    Context: Migratory species’ resilience to landscape changes depends on spatial patterns of habitat degradation in relation to their migratory movements, such as the distance between breeding and non-breeding areas, and the location and width of migration corridors. Objectives: We investigated to what extent the impact of habitat degradation depended on the seasonal distributions of migratory waterfowl. Methods: Using logistic regression, we selected wetland sites for eight waterfowl species in the East Asian–Australasian Flyway (EAAF) by calculating the probabilities of species occurrence per wetland site in relation to environmental factors. We quantified landscape metrics related to habitat degradation within these wetland sites. We used general linear models to test for differences in the effects of habitat degradation on waterfowl species with different migration extents and at different latitudes. Results: The patterns of habitat degradation differed spatially across the EAAF and affected species to a different degree. Species with shorter and broader migration corridors (Anser cygnoid and A. anser) could benefit from improved habitat conditions in the west of the EAAF. Species with longer and narrower migration corridors (Cygnus columbianus, A. fabalis, A. albifrons, A. erythropus, Anas crecca, and Anas acuta) were under higher risk of habitat degradation in the coastal regions of China and Japan. Conclusions: Migratory species with longer and narrower migration corridors are more affected by habitat degradation, because they might have fewer alternative stopover sites at similar latitude. Our findings improve the understanding of species-specific effects of environmental changes on migratory species, and defines critical and endangered wetland sites, and vulnerable species.
    Homoeostatic maintenance of nonstructural carbohydrates during the 2015–2016 El Niño drought across a tropical forest precipitation gradient
    Dickman, Lee Turin ; McDowell, Nate G. ; Grossiord, Charlotte ; Collins, Adam D. ; Wolfe, Brett T. ; Detto, Matteo ; Wright, S.J. ; Medina-Vega, José A. ; Goodsman, Devin ; Rogers, Alistair ; Serbin, Shawn P. ; Wu, Jin ; Ely, Kim S. ; Michaletz, Sean T. ; Xu, Chonggang ; Kueppers, Lara ; Chambers, Jeffrey Q. - \ 2019
    Plant, Cell & Environment 42 (2019)5. - ISSN 0140-7791 - p. 1705 - 1714.
    climate - ENSO - NSC - Panama - storage - sugars - tropics - vegetation

    Nonstructural carbohydrates (NSCs) are essential for maintenance of plant metabolism and may be sensitive to short- and long-term climatic variation. NSC variation in moist tropical forests has rarely been studied, so regulation of NSCs in these systems is poorly understood. We measured foliar and branch NSC content in 23 tree species at three sites located across a large precipitation gradient in Panama during the 2015–2016 El Niño to examine how short- and long-term climatic variation impact carbohydrate dynamics. There was no significant difference in total NSCs as the drought progressed (leaf P = 0.32, branch P = 0.30) nor across the rainfall gradient (leaf P = 0.91, branch P = 0.96). Foliar soluble sugars decreased while starch increased over the duration of the dry period, suggesting greater partitioning of NSCs to storage than metabolism or transport as drought progressed. There was a large variation across species at all sites, but total foliar NSCs were positively correlated with leaf mass per area, whereas branch sugars were positively related to leaf temperature and negatively correlated with daily photosynthesis and wood density. The NSC homoeostasis across a wide range of conditions suggests that NSCs are an allocation priority in moist tropical forests.

    In Vitro Seeding Activity of Glycoform-Deficient Prions from Variably Protease-Sensitive Prionopathy and Familial CJD Associated with PrPV180I Mutation
    Wang, Zerui ; Yuan, Jue ; Shen, Pingping ; Abskharon, Romany ; Lang, Yue ; Dang, Johnny ; Adornato, Alise ; Xu, Ling ; Chen, Jiafeng ; Feng, Jiachun ; Moudjou, Mohammed ; Kitamoto, Tetsuyuki ; Langeveld, Jan ; Appleby, Brian ; Ma, Jiyan ; Kong, Qingzhong ; Petersen, Robert B. ; Zou, Wen Quan ; Cui, Li - \ 2019
    Molecular Neurobiology 56 (2019)8. - ISSN 0893-7648 - p. 5456 - 5469.
    Humanized transgenic mice - Polymorphism - Prion - Prion disease - Real-time quaking-induced conversion (RT-QuIC) - Serial protein misfolding cyclic amplification (sPMCA) - Variably protease-sensitive prionopathy (VPSPr)

    Both sporadic variably protease-sensitive prionopathy (VPSPr) and familial Creutzfeldt-Jakob disease linked to the prion protein (PrP) V180I mutation (fCJDV180I) have been found to share a unique pathological prion protein (PrPSc) that lacks the protease-resistant PrPSc glycosylated at residue 181 because two of four PrP glycoforms are apparently not converted into the PrPSc from their cellular PrP (PrPC). To investigate the seeding activity of these unique PrPSc molecules, we conducted in vitro prion conversion experiments using serial protein misfolding cyclic amplification (sPMCA) and real-time quaking-induced conversion (RT-QuIC) assays with different PrPC substrates. We observed that the seeding of PrPSc from VPSPr or fCJDV180I in the sPMCA reaction containing normal human or humanized transgenic (Tg) mouse brain homogenates generated PrPSc molecules that unexpectedly exhibited a dominant diglycosylated PrP isoform along with PrP monoglycosylated at residue 181. The efficiency of PrPSc amplification was significantly higher in non-CJDMM than in non-CJDVV human brain homogenate, whereas it was higher in normal TgVV than in TgMM mouse brain homogenate. PrPC from the mixture of normal TgMM and Tg mouse brain expressing PrPV180I mutation (Tg180) but not TgV180I alone was converted into PrPSc by seeding with the VPSPr or fCJDV180I. The RT-QuIC seeding activity of PrPSc from VPSPr and fCJDV180I was significantly lower than that of sCJD. Our results suggest that the formation of glycoform-selective prions may be associated with an unidentified factor in the affected brain and the glycoform-deficiency of PrPSc does not affect the glycoforms of in vitro newly amplified PrPSc.

    Double closed-loop optimal control of greenhouse cultivation
    Xu, Dan ; Du, Shangfeng ; Willigenburg, Gerard van - \ 2019
    Control Engineering Practice 85 (2019). - ISSN 0967-0661 - p. 90 - 99.
    Double closed-loop - Greenhouse cultivation - LED lighting - Optimal control - Time-scale decomposition

    Two time-scale receding horizon optimal control (TTRHOC) of greenhouse cultivation is investigated. Recent developments enable closure of the outer-loop of this control system because they facilitate on-line recomputation of the optimal control of the slow dynamics on a daily basis. This paper quantifies the benefits obtained from having an outer closed-loop that counteracts errors and changes concerning predictions of crop growth, long-term weather, revenues obtained from selling crops and costs to control greenhouse climate. As a special, important case LED lighting is considered which increases both crop growth and profit. Having an outer closed-loop is especially beneficial in this case.

    Water dynamics during solid-state fermentation by Aspergillus oryzae YH6
    Jin, Guangyuan ; Zhu, Yang ; Rinzema, Arjen ; Wijffels, René H. ; Ge, Xiangyang ; Xu, Yan - \ 2019
    Bioresource Technology 277 (2019). - ISSN 0960-8524 - p. 68 - 76.
    Aspergillus oryzae - Nuclear magnetic resonance (NMR) - Solid-state fermentation - Water activity - Water dynamics

    Water is crucial for microbial growth, heat transfer and substrate hydrolysis, and dynamically changes with time in solid-state fermentation. However, water dynamics in the solid substrate is difficult to define and measure. Here, nuclear magnetic resonance was used to monitor water dynamics during the pure culture of Aspergillus oryzae YH6 on wheat in a model system to mimic solid starter (Qu or Koji) preparation. During fermentation, overall water content gradually decreased from 0.84 to 0.36 g/g, and water activity decreased from 0.99 to 0.93. Water content in different state (bound, immobilized and free) changed differently and all moved to more “bound” direction. The internal water distribution over the substrate matrix also showed a faster reduction inward both in the radical and axial direction. Our findings provide the prerequisites for optimal processes where water dynamics in solid-state fermentation can be monitored and controlled.

    Water footprint of the energy sector in China's two megalopolises
    Liao, Xiawei ; Zhao, Xu ; Jiang, Yu ; Liu, Yu ; Yi, Yujun ; Tillotson, Martin R. - \ 2019
    Ecological Modelling 391 (2019). - ISSN 0304-3800 - p. 9 - 15.
    Jing-Jin-Ji - Urban - Water footprint - Water-for-energy nexus - Yangtze Delta

    Using a consumption-based Multi-Regional Input-Output (MRIO) model, we investigate the distinctive characteristics, self-efficiency or external dependency, of energy demand's water footprint in China's two biggest and fastest developing megalopolises. We find that energy demand water footprint in the Jing-Jin-Ji and the Yangtze Delta amounted to 2.41 and 9.59 billion m³of water withdrawal respectively in 2010, of which 848.06 and 973.91 million m³was consumed. Among all energy products, electricity contributed the largest share to the energy sector's water footprint in both regions. The sectoral distribution of water footprint in the upstream supply chain differed by region. Most significantly, the agricultural sector accounted for more than 30% of water consumption footprint. In addition to water used locally, final energy demands in these two regions induced external water footprint beyond their administrative boundaries. The Jing-Jin-Ji region's energy sector had a smaller water footprint compared to the water-abundant Yangtze Delta region. However, external water footprint occupied a larger proportion in the former. Such divergence can be attributed to the distinctive water endowments and water-using technologies utilized in their respective energy sectors. Bespoke urban governance and policies tailored to local resource and technology portfolios are recommended for different urban agglomeration energy and water flows.

    Drivers of tree carbon storage in subtropical forests
    Li, Yin ; Bao, Weikai ; Bongers, Frans ; Chen, Bin ; Chen, Guoke ; Guo, Ke ; Jiang, Mingxi ; Lai, Jiangshan ; Lin, Dunmei ; Liu, Chunjiang ; Liu, Xiaojuan ; Liu, Yi ; Mi, Xiangcheng ; Tian, Xingjun ; Wang, Xihua ; Xu, Wubing ; Yan, Junhua ; Yang, Bo ; Zheng, Yuanrun ; Ma, Keping - \ 2019
    Science of the Total Environment 654 (2019). - ISSN 0048-9697 - p. 684 - 693.
    Biodiversity-ecosystem function - Environmental conditions - Mass-ratio effect - Niche complementarity - Stand age - Stand structure

    Tropical and subtropical forest ecosystems play an important role in the global carbon regulation. Despite increasing evidence for effects of biodiversity (species diversity, functional diversity and functional dominance), stand structural attributes, stand age and environmental conditions (climate and topography) on tree carbon storage, the relative importance of these drivers at large scale is poorly understood. It is also still unclear whether biodiversity effects on tree carbon storage work through niche complementarity (i.e. increased tree carbon storage due to interspecific resource partitioning) or through the mass-ratio effect (tree carbon storage regulated by dominant traits within communities). Here we analyze tree carbon storage and its drivers using data of 480 plots sampled across subtropical forests in China. We use multiple regression models to test the relative effects of biodiversity, stand structural attributes, stand age and environmental conditions on tree carbon storage, and use a partial least squares path model to test how these variables directly and/or indirectly affect tree carbon storage. Our results show that tree carbon storage is most strongly affected by stand age, followed by climate, biodiversity and stand structural attributes. Stand age and climate had both direct and indirect (through species diversity, functional dominance and stand structural attributes) effects. We find that tree carbon storage correlates with both species diversity and functional dominance after stand age and environmental drivers are accounted for. Our results suggest that niche complementarity and the mass-ratio effect, not necessarily mutually exclusive, both play a role in maintaining ecosystem functioning. Our results further indicate that biodiversity conservation might be an effective way for enhancing tree carbon storage in natural, species-rich forest ecosystems.

    Water resource potential for large-scale sweet sorghum production as bioenergy feedstock in Northern China
    Fu, Hai Mei ; Chen, Yan Hua ; Yang, Xiao Mei ; Di, Jia Ying ; Xu, Ming Gang ; Zhang, Bao Gui - \ 2019
    Science of the Total Environment 653 (2019). - ISSN 0048-9697 - p. 758 - 764.
    Arid and semi-arid conditions - Bioenergy - Marginal lands - Sweet sorghum - Water resource potential

    This study investigated the water resource potential for bioenergy production from sweet sorghum (Sorghum bicolor (L.)) in Northern China according to the distribution of water resources, climate conditions and the total water consumption of bioenergy based on sweet sorghum, which consisted of blue water, green water and grey water. At a case study site in Inner Mongolia, simulation with a plant phenological model was used to determine whether sweet sorghum could reach the harvestable stage for sugar juice production. The blue water in the agricultural phase was estimated according to the potential crop evapotranspiration (ETc), the drought sensitivity of sweet sorghum in different stages and the precipitation during the growing season. The results showed that the irrigation water was significantly different among the districts, ranging from 730 to 5500 m3/ha and 2060 to 6680 m3/ha for early-maturing and late-maturing varieties, respectively. To avoid the water pressure level to be exacerbated and the severe reallocation of water resources resulting in negative effects on other sectors, the maximal annual water withdrawal was set to not surpass the upper threshold of water stress level of 40%. That makes the maximum area for the production of sweet sorghum cannot exceed 1.95 × 104 ha, representing only 0.24% of the total marginal land area in Inner Mongolia. However, the economic benefits of bioenergy production from sweet sorghum would be negative due to the high labour input. Therefore, not only the availability of marginal land, the climate conditions and local water resources but also the improvement of mechanisation and agricultural production techniques should be considered to attain the sustainable development of bioenergy production and address global energy and environmental crises.

    Use of biological agents in fruit tree disease management
    Köhl, J. - \ 2019
    In: Integrated management of insect pests and diseases of tree fruit / Xu, X., Fountain, M., Burleigh Dodds Science Publishing Limited - ISBN 9781786762566
    MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells
    Dahlmans, Dennis ; Houzelle, Alexandre ; Andreux, Pénélope ; Wang, Xu ; Jörgensen, Johanna A. ; Moullan, Norman ; Daemen, Sabine ; Kersten, Sander ; Auwerx, Johan ; Hoeks, Joris - \ 2019
    Journal of Cellular Physiology 234 (2019)5. - ISSN 0021-9541 - p. 6601 - 6610.
    microRNA - mitochondria - protein stress - skeletal muscle

    Proper mitochondrial function plays a central role in cellular metabolism. Various diseases as well as aging are associated with diminished mitochondrial function. Previously, we identified 19 miRNAs putatively involved in the regulation of mitochondrial metabolism in skeletal muscle, a highly metabolically active tissue. In the current study, these 19 miRNAs were individually silenced in C2C12 myotubes using antisense oligonucleotides, followed by measurement of the expression of 27 genes known to play a major role in regulating mitochondrial metabolism. Based on the outcomes, we then focused on miR-382-5p and identified pathways affected by its silencing using microarrays, investigated protein expression, and studied cellular respiration. Silencing of miRNA-382-5p significantly increased the expression of several genes involved in mitochondrial dynamics and biogenesis. Conventional microarray analysis in C2C12 myotubes silenced for miRNA-382-5p revealed a collective downregulation of mitochondrial ribosomal proteins and respiratory chain proteins. This effect was accompanied by an imbalance between mitochondrial proteins encoded by the nuclear and mitochondrial DNA (1.35-fold, p < 0.01) and an induction of HSP60 protein (1.31-fold, p < 0.05), indicating activation of the mitochondrial unfolded protein response (mtUPR). Furthermore, silencing of miR-382-5p reduced basal oxygen consumption rate by 14% (p < 0.05) without affecting mitochondrial content, pointing towards a more efficient mitochondrial function as a result of improved mitochondrial quality control. Taken together, silencing of miR-382-5p induces a mitonuclear protein imbalance and activates the mtUPR in skeletal muscle, a phenomenon that was previously associated with improved longevity.

    Tracking disease resistance deployment in potato breeding by enrichment sequencing
    Armstrong, Miles R. ; Vossen, Jack ; Lim, Tze Yin ; Hutten, Ronald C.B. ; Xu, Jianfei ; Strachan, Shona M. ; Harrower, Brian ; Champouret, Nicolas ; Gilroy, Eleanor M. ; Hein, Ingo - \ 2019
    Plant Biotechnology Journal 17 (2019)2. - ISSN 1467-7644 - p. 540 - 549.
    breeding - crops - disease resistance genes - dRenSeq - potato - tracking of NLRs

    Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans) gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.

    Quantitative proteomics reveals the crucial role of YbgC for Salmonella enterica serovar Enteritidis survival in egg white
    Qin, Xiaojie ; He, Shoukui ; Zhou, Xiujuan ; Cheng, Xu ; Huang, Xiaozhen ; Wang, Yanyan ; Wang, Siyun ; Cui, Yan ; Shi, Chunlei ; Shi, Xianming - \ 2019
    International Journal of Food Microbiology 289 (2019). - ISSN 0168-1605 - p. 115 - 126.
    Chicken egg white - iTRAQ - Salmonella - Survival mechanisms - YbgC

    Salmonella enterica serovar Enteritidis (S. Enteritidis) is a food-borne bacterial pathogen that can cause human salmonellosis predominately by contamination of eggs and egg products. However, its survival mechanisms in egg white are not fully understood, especially from a proteomic point of view. In this study, the proteomic profiles of S. Enteritidis in Luria-Bertani (LB) broth containing 50% and 80% egg white, and in whole egg white were compared with the profile in LB broth using iTRAQ technology to identify key proteins that were involved in S. Enteritidis survival in egg white. It was found that there were 303, 284 and 273 differentially expressed proteins in S. Enteritidis after 6 h exposure to whole, 80% and 50% egg white, respectively. Most of up-regulated proteins were primarily associated with iron acquisition, cofactor and amino acid biosynthesis, transporter, regulation and stress responses, whereas down-regulated proteins were mainly involved in energy metabolism, virulence as well as motility and chemotaxis. Three stress response-related proteins (YbgC, TolQ, TolA) of the tol-pal system responsible for maintaining cell membrane stability of Gram-negative bacteria were up-regulated in S. Enteritidis in response to whole egg white. Interestingly, deletion of ybgC resulted in a decreased resistance of S. Enteritidis to egg white. Compared with the wild type and complementary strains, a 3-log population reduction was observed in △ybgC mutant strain after incubation in whole egg white for 24 h. Cellular morphology of △ybgC mutant strain was altered from rods to spheres along with cell lysis in whole egg white. Furthermore, deletion of ybgC decreased the expression of tol-pal system-related genes (tolR, tolA). Collectively, these proteomic and mutagenic analysis reveal that YbgC is essential for S. Enteritidis survival in egg white.

    Assessment of promising agricultural management practices
    Barão, Lúcia ; Alaoui, Abdallah ; Ferreira, Carla ; Basch, Gottlieb ; Schwilch, Gudrun ; Geissen, Violette ; Sukkel, Wijnand ; Lemesle, Julie ; Garcia-Orenes, Fuensanta ; Morugán-Coronado, Alicia ; Mataix-Solera, Jorge ; Kosmas, Costas ; Glavan, Matjaž ; Pintar, Marina ; Tóth, Brigitta ; Hermann, Tamás ; Vizitiu, Olga Petruta ; Lipiec, Jerzy ; Reintam, Endla ; Xu, Minggang ; Di, Jiaying ; Fan, Hongzhu ; Wang, Fei - \ 2019
    Science of the Total Environment 649 (2019). - ISSN 0048-9697 - p. 610 - 619.
    Environment - Farming systems - Soil threats - Sustainability

    iSQAPER project - Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience - aims to develop an app to advise farmers on selecting the best Agriculture Management Practice (AMPs) to improve soil quality. For this purpose, a soil quality index has to be developed to account for the changes in soil quality as impacted by the implementation of the AMPs. Some promising AMPs have been suggested over the time to prevent soil degradation. These practices have been randomly adopted by farmers but which practices are most used by farmers and where they are mostly adopted remains unclear. This study is part of the iSQAPER project with the specific aims: 1) map the current distribution of previously selected 18 promising AMPs in several pedo-climatic regions and farming systems located in ten and four study site areas (SSA) along Europe and China, respectively; and 2) identify the soil threats occurring in those areas. In each SSA, farmers using promising AMP's were identified and questionnaires were used to assess farmer's perception on soil threats significance in the area. 138 plots/farms using 18 promising AMPs, were identified in Europe (112) and China (26).Results show that promising AMPs used in Europe are Crop rotation (15%), Manuring & Composting (15%) and Min-till (14%), whereas in China are Manuring & Composting (18%), Residue maintenance (18%) and Integrated pest and disease management (12%). In Europe, soil erosion is the main threat in agricultural Mediterranean areas while soil-borne pests and diseases is more frequent in the SSAs from France and The Netherlands. In China, soil erosion, SOM decline, compaction and poor soil structure are among the most significant. This work provides important information for policy makers and the development of strategies to support and promote agricultural management practices with benefits for soil quality.

    Causal relationship in the interaction between land cover change and underlying surface climate in the grassland ecosystems in China
    Li, Zhouyuan ; Wang, Zezhong ; Liu, Xuehua ; Fath, Brian D. ; Liu, Xiaofei ; Xu, Yanjie ; Hutjes, Ronald ; Kroeze, Carolien - \ 2019
    Science of the Total Environment 647 (2019). - ISSN 0048-9697 - p. 1080 - 1087.
    Cause-effect - Correlation analysis - Eco-climatology - Grassland - Land-climate - Remote sensing

    Land-climate interactions are driven by causal relations that are difficult to ascertain given the complexity and high dimensionality of the systems. Many methods of statistical and mechanistic models exist to identify and quantify the causality in such highly-interacting systems. Recent advances in remote sensing development allowed people to investigate the land-climate interaction with spatially and temporally continuous data. In this study, we present a new approach to measure how climatic factors interact with each other under land cover change. The quantification method is based on the correlation analysis of the different order derivatives, with the canonical mathematical definitions developed from the theories of system dynamics and practices of the macroscopic observations. We examined the causal relationship between the interacting variables on both spatial and temporal dimensions based on macroscopic observations of land cover change and surface climatic factors through a comparative study in the different grassland ecosystems of China. The results suggested that the interaction of land-climate could be used to explain the temporal lag effect in the comparison of the three grassland ecosystems. Significant spatial correlations between the vegetation and the climatic factors confirmed feedback mechanisms described in the theories of eco-climatology, while the uncertain temporal synchronicity reflects the causality among the key indicators. This has been rarely addressed before. Our research show that spatial correlations and the temporal synchronicity among key indicators of the land surface and climatic factors can be explained by a novel method of causality quantification using derivative analysis.

    Discovering novel hydrolases from hot environments
    Wohlgemuth, Roland ; Littlechild, Jennifer ; Monti, Daniela ; Schnorr, Kirk ; Rossum, Teunke van; Siebers, Bettina ; Menzel, Peter ; Kublanov, Ilya V. ; Rike, Anne Gunn ; Skretas, Georgios ; Szabo, Zalan ; Peng, Xu ; Young, Mark J. - \ 2018
    Biotechnology Advances 36 (2018)8. - ISSN 0734-9750 - p. 2077 - 2100.
    Biocatalysis - Enrichment - Enzyme characterization - Enzyme screening - Gene expression - Genomics - Hydrolases - Metagenomics - Sequencing - Thermophiles

    Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.

    Latitudinal adaptation and genetic insights into the origins of cannabis sativa L.
    Zhang, Qingying ; Chen, Xuan ; Guo, Hongyan ; Trindade, Luisa M. ; Salentijn, Elma M.J. ; Guo, Rong ; Guo, Mengbi ; Xu, Yanping ; Yang, Ming - \ 2018
    Frontiers in Plant Science 871 (2018). - ISSN 1664-462X
    Cannabaceae - CpDNA - Genetic diversity - Industrial hemp - Phylogeography

    Cannabis is one of the most important industrial crops distributed worldwide. However, the phylogeographic structure and domestication knowledge of this crop remains poorly understood. In this study, sequence variations of five chloroplast DNA (cpDNA) regions were investigated to address these questions. For the 645 individuals from 52 Cannabis accessions sampled (25 wild populations and 27 domesticated populations or cultivars), three haplogroups (Haplogroup H, M, L) were identified and these lineages exhibited distinct high-middle-low latitudinal gradients distribution pattern. This pattern can most likely be explained as a consequence of climatic heterogeneity and geographical isolation. Therefore, we examined the correlations between genetic distances and geographical distances, and tested whether the climatic factors are correlated with the cpDNA haplogroup frequencies of populations. The “isolation-by-distance” models were detected for the phylogeographic structure, and the day-length was found to be the most important factor (among 20 BioClim factors) that influenced the population structures. Considering the distinctive phylogeographic structures and no reproductive isolation among members of these lineages, we recommend that Cannabis be recognized as a monotypic genus typified by Cannabis sativa L., containing three subspecies: subsp. sativa, subsp. Indica, and subsp. ruderalis. Within each haplogroup which possesses a relatively independent distribution region, the wild and domesticated populations shared the most common haplotypes, indicating that there are multiregional origins for the domesticated crop. Contrast to the prevalent Central-Asia-Origin hypothesis of C. saltiva, molecular evidence reveals for the first time that the low latitude haplogroup (Haplogroup L) is the earliest divergent lineage, implying that Cannabis is probably originated in low latitude region.

    Eighty Years of Mycopathologia: A Retrospective Analysis of Progress Made in Understanding Human and Animal Fungal Pathogens
    Chaturvedi, Vishnu ; Bouchara, Jean Philippe ; Hagen, Ferry ; Alastruey-Izquierdo, Ana ; Badali, Hamid ; Bocca, Anamelia Lorenzetti ; Cano-Lira, Jose F. ; Cao, Cunwei ; Chaturvedi, Sudha ; Chotirmall, Sanjay H. ; Diepeningen, Anne D. Van; Gangneux, Jean Pierre ; Guinea, Jesus ; Hoog, Sybren De; Ilkit, Macit ; Kano, Rui ; Liu, Weida ; Martinez-Rossi, Nilce M. ; Souza Carvalho Melhem, Marcia De; Ono, Mario Augusto ; Ran, Yuping ; Ranque, Stephane ; Almeida Soares, Celia Maria De; Sugita, Takashi ; Thomas, Philip A. ; Vecchiarelli, Anna ; Wengenack, Nancy L. ; Woo, Patrick C.Y. ; Xu, Jianping ; Zancope-Oliveira, Rosely M. - \ 2018
    Mycopathologia 183 (2018)6. - ISSN 0301-486X - p. 859 - 877.
    Mycopathologia was founded in 1938 to ‘diffuse the understanding of fungal diseases in man and animals among mycologists.’ This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5–5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of ‘classic papers’ since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host–pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that emerging and re-emerging fungal pathogens will continue to cause significant health burden in the coming decades. It remains vital that scientists and physicians continue to collaborate by learning each other’s language for the study of fungal diseases, and Mycopathologia will strive to be their partner in this increasingly important endeavor to its 100th anniversary in 2038 and beyond.
    MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells
    Hoeks, Joris ; Schrauwen, P. ; Houzelle, Alexandre ; Dahlmans, Dennis ; Andreux, Pénélope ; Wang, Xu ; Jörgensen, Johanna A. ; Moullan, Norman ; Daemen, Sabine ; Kersten, A.H. ; Auwerx, Johan - \ 2018
    Wageningen University
    GSE116786 - PRJNA480248 - Mus musculus
    Proper mitochondrial function plays a central role in cellular metabolism. Various diseases as well as aging are associated with diminished mitochondrial function. Previously, we identified 19 miRNAs putatively involved in the regulation of mitochondrial metabolism in skeletal muscle, a highly metabolically active tissue. In the present study, these 19 miRNAs were individually silenced in C2C12 myotubes using antisense oligonucleotides, followed by measurement of the expression of 27 genes known to play a major role in regulating mitochondrial metabolism. Based on the outcomes, we then focused on miR-382-5p and identified pathways affected by its silencing using microarrays, investigated protein expression and studied cellular respiration. Silencing of miRNA-382-5p significantly increased the expression of several genes involved in mitochondrial dynamics and -biogenesis. Microarray analysis of C2C12 myotubes silenced for miRNA-382-5p revealed a collective downregulation of mitochondrial ribosomal proteins and respiratory chain proteins. This effect was accompanied by an imbalance between mitochondrial proteins encoded by the nuclear and mitochondrial DNA (1.35-fold, p<0.01) and an induction of HSP60 protein (1.31-fold, p<0.05), indicating activation of the mitochondrial unfolded protein response (mtUPR). Furthermore, silencing of miR-382-5p reduced basal oxygen consumption rate by 14% (p<0.05) without affecting mitochondrial content, pointing towards a more efficient mitochondrial function as a result of improved mitochondrial quality control. Taken together, silencing of miR-382-5p induces a mitonuclear protein imbalance and activates the mtUPR in skeletal muscle, a phenomenon that was previously associated with improved longevity.
    Carbon storage potential in degraded forests of Kalimantan, Indonesia
    Ferraz, António ; Saatchi, Sassan ; Xu, Liang ; Hagen, Stephen ; Chave, Jerome ; Yu, Yifan ; Meyer, Victoria ; Garcia, Mariano ; Silva, Carlos ; Roswintiart, Orbita ; Samboko, Ari ; Sist, Plinio ; Walker, Sarah ; Pearson, Timothy R.H. ; Wijaya, Arief ; Sullivan, Franklin B. ; Rutishauser, Ervan ; Hoekman, Dirk ; Ganguly, Sangram - \ 2018
    Environmental Research Letters 13 (2018)9. - ISSN 1748-9318
    aboveground biomass mapping - airborne lidar - carbon - forest degradation - Indonesia - Kalimantan - peat swamp forests

    The forests of Kalimantan are under severe pressure from extensive land use activities dominated by logging, palm oil plantations, and peatland fires. To implement the forest moratorium for mitigating greenhouse gas emissions, Indonesia's government requires information on the carbon stored in forests, including intact, degraded, secondary, and peat swamp forests. We developed a hybrid approach of producing a wall-to-wall map of the aboveground biomass (AGB) of intact and degraded forests of Kalimantan at 1 ha grid cells by combining field inventory plots, airborne lidar samples, and satellite radar and optical imagery. More than 110 000 ha of lidar data were acquired to systematically capture variations of forest structure and more than 104 field plots to develop lidar-biomass models. The lidar measurements were converted into biomass using models developed for 66 439 ha of drylands and 44 250 ha of wetland forests. By combining the AGB map with the national land cover map, we found that 22.3 Mha (106 ha) of forest remain on drylands ranging in biomass from 357.2 ±12.3 Mgha-1 in relatively intact forests to 134.2 ±6.1 Mgha-1 in severely degraded forests. The remaining peat swamp forests are heterogeneous in coverage and degradation level, extending over 3.62 Mha and having an average AGB of 211.8 ±12.7 Mgha-1. Emission factors calculated from aboveground biomass only suggest that the carbon storage potential of more than 15 Mha of degraded and secondary dryland forests will be about 1.1 PgC.

    Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation
    Xu, Wei ; Vervoort, Jacques ; Saccenti, Edoardo ; Hoeij, Renny van; Kemp, Bas ; Knegsel, Ariette van - \ 2018
    Scientific Reports 8 (2018). - ISSN 2045-2322

    In early lactation, dairy cows typically have a negative energy balance which has been related to metabolic disorders, compromised health and fertility, and reduced productive lifespan. Assessment of the energy balance, however, is not easy on the farm. Our aims were to investigate the milk metabolic profiles of dairy cows in early lactation, and to obtain models to estimate energy balance from milk metabolomics data and milk production traits. Milk samples were collected in week 2 and 7 after calving from 31 dairy cows. For each cow, the energy balance was calculated from energy intake, milk production traits and body weight. A total of 52 milk metabolites were detected using LC-QQQ-MS. Data from different lactation weeks was analysed by partial least squares analysis, the top 15 most relevant variables from the metabolomics data related to energy balance were used to develop reduced linear models to estimate energy balance by forward selection regression. Milk fat yield, glycine, choline and carnitine were important variables to estimate energy balance (adjusted R2: 0.53 to 0.87, depending on the model). The relationship of these milk metabolites with energy balance is proposed to be related to their roles in cell renewal.

    Resilience of tropical tree cover : The roles of climate, fire, and herbivory
    Staal, Arie ; Nes, Egbert H. van; Hantson, Stijn ; Holmgren, Milena ; Dekker, Stefan C. ; Pueyo, Salvador ; Xu, Chi ; Scheffer, Marten - \ 2018
    Global Change Biology 24 (2018)11. - ISSN 1354-1013 - p. 5096 - 5109.
    alternative stable states - bistability - forest - grasslands - livestock - model - regime shifts - remote sensing - tipping points - wildfire

    Fires and herbivores shape tropical vegetation structure, but their effects on the stability of tree cover in different climates remain elusive. Here, we integrate empirical and theoretical approaches to determine the effects of climate on fire- and herbivore-driven forest-savanna shifts. We analyzed time series of remotely sensed tree cover and fire observations with estimates of herbivore pressure across the tropics to quantify the fire–tree cover and herbivore–tree cover feedbacks along climatic gradients. From these empirical results, we developed a spatially explicit, stochastic fire-vegetation model that accounts for herbivore pressure. We find emergent alternative stable states in tree cover with hysteresis across rainfall conditions. Whereas the herbivore–tree cover feedback can maintain low tree cover below 1,100 mm mean annual rainfall, the fire–tree cover feedback can maintain low tree cover at higher rainfall levels. Interestingly, the rainfall range where fire-driven alternative vegetation states can be found depends strongly on rainfall variability. Both higher seasonal and interannual variability in rainfall increase fire frequency, but only seasonality expands the distribution of fire-maintained savannas into wetter climates. The strength of the fire–tree cover feedback depends on the spatial configuration of tree cover: Landscapes with clustered low tree-cover areas are more susceptible to cross a tipping point of fire-driven forest loss than landscapes with scattered deforested patches. Our study shows how feedbacks involving fire, herbivores, and the spatial structure of tree cover explain the resilience of tree cover across climates.

    Climate-Forest-Water-People Relations: : Seven System Delineations
    Noordwijk, M. van; Creed, Irena F. ; Jones, Julia A. ; Wei, Xiaohua ; Gush, Mark ; Blanco, Juan A. ; Sullivan, Caroline A. ; Bishop, Kevin ; Murdiyarso, Daniel ; Xu, Jianchu ; Claassen, Marius ; McNulty, Steven ; Bruijnzeel, L.A. ; Harper, Richard J. ; Mwangi, Hosea ; Hacket-Pain, Andrew ; Orland, Chloé - \ 2018
    In: Forest and Water on a Changing Planet: Vulnerability, Adaptation and Governance Opportunities / Creed, Irena F., van Noordwijk, Meine, International Union of Forest Research Organizations (IUFRO) (IUFRO World Series ) - ISBN 9783902762955 - p. 27 - 58.
    Determinants of the Forest-Water Relationship
    McNulty, Steven ; Archer, E. ; Gush, Mark ; Noordwijk, M. van; Ellison, David ; Blanco, Juan A. ; Xu, Jianchu ; Bishop, Kevin ; Wei, Xiaohua ; Vira, Bhaskar ; Creed, Irena F. ; Mukherji, A. ; Baca, Aurelia ; Serran, Jacqueline ; Harper, Richard J. ; Aldred, David ; Sullivan, Caroline A. - \ 2018
    In: Forest and Water on a Changing Planet: Vulnerability, Adaptation and Governance Opportunities / Creed, Irena F., van Noordwijk, Meine, International Union of Forest Research Organizations (IUFRO) (IUFRO World Series ) - ISBN 9783902762955 - p. 61 - 78.
    Forest Landscape Hydrology in a ‘New Normal’ Era of Climate and Land Use Change
    Jones, Julia A. ; Wei, Xiaohua ; Noordwijk, M. van; Creed, Irena F. ; Gush, Mark ; Ellison, David ; Blanco, Juan A. ; Bishop, Kevin ; McNulty, Steven ; BarguésTobella, Aida ; Archer, E. ; Bruijnzeel, L.A. ; Duinker, P. ; Foster, David ; Gebrekirstos, Aster ; Giles-Hansen, Krysta ; Hacket-Pain, Andrew ; Harper, Richard J. ; Ilstedt, Ulrik ; Li, Qiang ; Liao, Yingchun ; Malmer, Anders ; Mwangi, Hosea ; Orland, Chloé ; Steenberg, James ; Wang, Yi ; Worthy, Fiona ; Xu, Jianchu ; Zhang, Mingfang - \ 2018
    In: Forest and Water on a Changing Planet: Vulnerability, Adaptation and Governance Opportunities / Creed, Irena F., van Noordwijk, Meine, International Union of Forest Research Organizations (IUFRO) (IUFRO World Series ) - ISBN 9783902762955 - p. 81 - 99.
    Management Options for Dealing with Changing Forest-Water Relations
    Vira, Bhaskar ; Ellison, David ; McNulty, Steven ; Archer, E. ; Bishop, Kevin ; Claassen, Marius ; Creed, Irena F. ; Gush, Mark ; Gyawali, Dipak ; Martin-Ortega, Julia ; Mukherji, A. ; Murdiyarso, Daniel ; Ovando Pol, Paola ; Sullivan, Caroline A. ; Noordwijk, M. van; Wei, Xiaohua ; Xu, Jianchu ; Reed, Maureen G. ; Wilson, Sarah J. - \ 2018
    In: Forest and Water on a Changing Planet: Vulnerability, Adaptation and Governance Opportunities / Creed, Irena F., van Noordwijk, Meine, International Union of Forest Research Organizations (IUFRO) (IUFRO World Series ) - ISBN 9783902762955 - p. 122 - 141.
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