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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    Glycation of soy proteins leads to a range of fractions with various supramolecular assemblies and surface activities
    Feng, Jilu ; Berton-Carabin, Claire C. ; Ataç Mogol, Burçe ; Schroën, Karin ; Fogliano, Vincenzo - \ 2020
    Food Chemistry (2020). - ISSN 0308-8146
    Furosine - Interfacial tension - Nε-(carboxymethyl)--lysine (CML) - Protein glycation - Protein oxidation - Protein-carbohydrate conjugates - Soy protein isolate

    Dry and subsequent wet heating were used to glycate soy proteins with dextran or glucose, followed by fractionation based on size and solubility. Dry heating led to protein glycation (formation of furosine, Nε-(carboxymethyl)-L-lysine, Nε-(carboxyethyl)-L-lysine, and protein-bound carbonyls) and aggregation (increased particle size); while subsequent wet heating induced partial unfolding and de-aggregation. The measurable free amino group content of soy proteins changed from 0.77 to 0.14, then to 0.62 mmol/g upon dry and subsequent wet heating; this non-monotonic evolution is probably due to protein structural changes, and shows that this content should be interpreted with caution as a glycation marker. After both heating steps, the smaller-sized water-soluble fractions showed higher surface activity than the larger insoluble ones, and dextran conjugates exhibited a higher surface activity than their glucose counterparts. We thereby achieved a comprehensive understanding of the properties of various fractions in plant protein fractions, which is essential when targeting applications.

    Correction: Roadmap for naming uncultivated Archaea and Bacteria
    Murray, Alison E. ; Freudenstein, John ; Gribaldo, Simonetta ; Hatzenpichler, Roland ; Hugenholtz, Philip ; Kämpfer, Peter ; Konstantinidis, Konstantinos T. ; Lane, Christopher E. ; Papke, R.T. ; Parks, Donovan H. ; Rossello-Mora, Ramon ; Stott, Matthew B. ; Sutcliffe, Iain C. ; Thrash, J.C. ; Venter, Stephanus N. ; Whitman, William B. ; Acinas, Silvia G. ; Amann, Rudolf I. ; Anantharaman, Karthik ; Armengaud, Jean ; Baker, Brett J. ; Barco, Roman A. ; Bode, Helge B. ; Boyd, Eric S. ; Brady, Carrie L. ; Carini, Paul ; Chain, Patrick S.G. ; Colman, Daniel R. ; DeAngelis, Kristen M. ; Rios, Maria Asuncion de los; Estrada-de los Santos, Paulina ; Dunlap, Christopher A. ; Eisen, Jonathan A. ; Emerson, David ; Ettema, Thijs J.G. ; Eveillard, Damien ; Girguis, Peter R. ; Hentschel, Ute ; Hollibaugh, James T. ; Hug, Laura A. ; Inskeep, William P. ; Ivanova, Elena P. ; Klenk, Hans Peter ; Li, Wen Jun ; Lloyd, Karen G. ; Löffler, Frank E. ; Makhalanyane, Thulani P. ; Moser, Duane P. ; Nunoura, Takuro ; Palmer, Marike ; Parro, Victor ; Pedrós-Alió, Carlos ; Probst, Alexander J. ; Smits, Theo H.M. ; Steen, Andrew D. ; Steenkamp, Emma T. ; Spang, Anja ; Stewart, Frank J. ; Tiedje, James M. ; Vandamme, Peter ; Wagner, Michael ; Wang, Feng Ping ; Yarza, Pablo ; Hedlund, Brian P. ; Reysenbach, Anna Louise - \ 2020
    Nature Microbiology (2020). - ISSN 2058-5276

    From present to future development pathways in fragile mountain landscapes
    Karpouzoglou, Timos ; Dewulf, Art ; Perez, Katya ; Gurung, Praju ; Regmi, Santosh ; Isaeva, Aiganysh ; Foggin, Marc ; Bastiaensen, Johan ; Hecken, Gert Van; Zulkafli, Zed ; Mao, Feng ; Clark, Julian ; Hannah, David M. ; Chapagain, Prem Sagar ; Buytaert, Wouter ; Cieslik, Katarzyna - \ 2020
    Environmental Science & Policy 114 (2020). - ISSN 1462-9011 - p. 606 - 613.
    Development pathway - Kyrgyzstan - Landscapes - Mountains - Nepal - Peru - Power - Social-ecological systems - Water

    Mountains are dynamic landscapes that are home to rich natural and human heritage. However, climatic variability, globalisation and increasing ecomomic integration are making these landscapes more fragile with implications for present and future development. Using a pathways lens, we examine development trajectories in mountains and relate these to environmental and social-economic change currently taking place. We analyse and compare pathways in three case studies in Peru (Andes); Nepal (Himalayas); and Kyrgyzstan (Tien Shan). The paper highlights that development pathways in fragile mountain regions may be shifting in new directions, but because they emerge out of complex socio-environmental and historical contexts, there are also social risks associated with the articulation of future pathways, particularly in terms of social equity and sustainability. Building on different pathway approaches with their various strengths and weaknesses, this study examines the role of human agency and power, the role of historical and present context and feedbacks between social and ecological features in shaping future development pathways of mountain landscapes.

    Plant community composition steers grassland vegetation via soil legacy effects
    Heinen, Robin ; Hannula, S.E. ; Long, Jonathan R. De; Huberty, Martine ; Jongen, Renske ; Kielak, Anna ; Steinauer, Katja ; Zhu, Feng ; Bezemer, T.M. - \ 2020
    Ecology Letters 23 (2020)6. - ISSN 1461-023X - p. 973 - 982.
    Field experiment - grassland - pathogens - plant-soil feedback - soil bacteria - soil fungi - soil legacy effects - soil microbiome

    Soil legacy effects are commonly highlighted as drivers of plant community dynamics and species co-existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots using six different plant communities with different ratios of grasses and forbs and for different durations. Soil microbial legacies were evident for soil fungi, but not for soil bacteria, while soil abiotic parameters did not significantly change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities with different ratios of grasses and forbs left soil legacies that negatively affected succeeding plants of the same functional type. We conclude that fungal-mediated soil legacy effects play a significant role in vegetation assembly of natural plant communities.

    Antimethanogenic effects of nitrate supplementation in cattle : A meta-analysis
    Feng, X.Y. ; Dijkstra, J. ; Bannink, A. ; Gastelen, S. van; France, J. ; Kebreab, E. - \ 2020
    Journal of Dairy Science 103 (2020)12. - ISSN 0022-0302 - p. 11375 - 11385.
    beef - dairy - meta-analysis - methane - nitrate
    Supplementing a diet with nitrate is regarded as an effective and promising methane (CH4) mitigation strategy by competing with methanogens for available hydrogen through its reduction of ammonia in the rumen. Studies have shown major reductions in CH4 emissions with nitrate supplementation, but with large variation in response. The objective of this study was to quantitatively investigate the effect of dietary nitrate on enteric CH4 production and yield and evaluate the variables with high potential to explain the heterogeneity of between-study variability using meta-analytical models. A data set containing 56 treatments from 24 studies was developed to conduct a meta-analysis. Dry matter (DM) intake, nitrate dose (g/kg of DM), animal body weight, roughage proportion of diet, dietary crude protein and neutral detergent fiber content, CH4 measurement technique, and type of cattle (beef or dairy) were considered as explanatory variables. Average DM intake and CH4 production for dairy cows (16.2 ± 2.93 kg/d; 311 ± 58.8 g/d) were much higher than for beef cattle (8.1 ± 1.57 kg/d; 146 ± 50.9 g/d). Therefore, a relative mean difference was calculated and used to conduct random-effect and mixed-effect model analysis to eliminate the large variations between types of animal due to intake. The final mixed-effect model for CH4 production (g of CH4/d) had 3 explanatory variables and included nitrate dose, type of cattle, and DM intake. The final mixed-effect model for CH4 yield (g of CH4/kg of DM intake) had 2 explanatory variables and included nitrate dose and type of cattle. Nitrate effect sizes on CH4 production (dairy: −20.4 ± 1.89%; beef: −10.1 ± 1.52%) and yield (dairy: −15.5 ± 1.15%; beef: −8.95 ± 1.764%) were significantly different between the 2 types of cattle. When data from slow-release nitrate sources were removed from the analysis, there was no significant difference in type of cattle anymore for CH4 production and yield. Nitrate dose enhanced the mitigating effect of nitrate on CH4 production and yield by 0.911 ± 0.1407% and 0.728 ± 0.2034%, respectively, for every 1 g/kg of DM increase from its mean dietary inclusion (16.7 g/kg of DM). An increase of 1 kg of DM/d in DM intake from its mean dietary intake (11.1 kg of DM/d) decreased the effect of nitrate on CH4 production by 0.691 ± 0.2944%. Overall, this meta-analysis demonstrated that nitrate supplementation reduces CH4 production and yield in a dose-dependent manner, and that elevated DM intake decreases the effect of nitrate supplementation on CH4 production. Furthermore, the stronger antimethanogenic effect on CH4 production and yield in dairy cows than in beef steers could be related to use of slow-release nitrate in beef cattle.
    COSTE: Complexity-based OverSampling TEchnique to alleviate the class imbalance problem in software defect prediction
    Feng, Shuo ; Keung, Jacky ; Yu, Xiao ; Xiao, Yan ; Bennin, Kwabena Ebo ; Kabir, Md Alamgir ; Zhang, Miao - \ 2020
    Information and Software Technology 129 (2020). - ISSN 0950-5849
    Class imbalance - Effort-aware defect prediction - MAHAKIL - Oversampling - SMOTE - Software defect prediction
    Context: Generally, there are more non-defective instances than defective instances in the datasets used for software defect prediction (SDP), which is referred to as the class imbalance problem. Oversampling techniques are frequently adopted to alleviate the problem by generating new synthetic defective instances. Existing techniques generate either near-duplicated instances which result in overgeneralization (high probability of false alarm, pf) or overly diverse instances which hurt the prediction model's ability to find defects (resulting in low probability of detection, pd). Furthermore, when existing oversampling techniques are applied in SDP, the effort needed to inspect the instances with different complexity is not taken into consideration. Objective: In this study, we introduce Complexity-based OverSampling TEchnique (COSTE), a novel oversampling technique that can achieve low pf and high pd simultaneously. Meanwhile, COSTE also performs better in terms of Norm(popt) and ACC, two effort-aware measures that consider the testing effort. Method: COSTE combines pairs of defective instances with similar complexity to generate synthetic instances, which improves the diversity within the data, maintains the ability of prediction models to find defects, and takes the different testing effort needed for different instances into consideration. We conduct experiments to compare COSTE with Synthetic Minority Oversampling TEchnique, Borderline-SMOTE, Majority Weighted Minority Oversampling TEchnique and MAHAKIL. Results: The experimental results on 23 releases of 10 projects show that COSTE greatly improves the diversity of the synthetic instances without compromising the ability of prediction models to find defects. In addition, COSTE outperforms the other oversampling techniques under the same testing effort. The statistical analysis indicates that COSTE's ability to outperform the other oversampling techniques is significant under the statistical Wilcoxon rank sum test and Cliff's effect size. Conclusion: COSTE is recommended as an efficient alternative to address the class imbalance problem in SDP.
    Double constrained ordination for assessing biological trait responses to multiple stressors : A case study with benthic macroinvertebrate communities
    Peng, Feng Jiao ; Braak, Cajo J.F. ter; Rico, Andreu ; Brink, Paul J. Van den - \ 2020
    Science of the Total Environment 754 (2020). - ISSN 0048-9697
    Benthic macroinvertebrates - Biomonitoring - Double constrained correspondence analysis - Multiple stressors - RLQ - Trait-environment relationships

    Benthic macroinvertebrate communities are used as indicators for anthropogenic stress in freshwater ecosystems. To better understand the relationship between anthropogenic stress and changes in macroinvertebrate community composition, it is important to understand how different stressors and species traits are associated, and how these associations influence variation in species occurrence and abundances. Here, we show the capacity of the multivariate technique of double constrained correspondence analysis (dc-CA) to analyse trait-environment relationships, and we compare it with the redundancy analysis method on community weighted mean values of traits (CWM-RDA), which is frequently used for this type of analysis. The analyses were based on available biomonitoring data for macroinvertebrate communities from the Danube River. Results from forward selection of traits and environmental variables using dc-CA analyses showed that aquatic stages, reproduction techniques, dispersal tactics, locomotion and substrate relations, altitude, longitudinal and transversal distribution, and substrate preferendum were significantly related to habitat characteristics, hydromorphological alterations and water quality measurements such as physico-chemical parameters, heavy metals, pesticides and pharmaceuticals. Environmental variables significantly associated with traits using the CWM-RDA method were generally consistent with those found in dc-CA analysis. However, the CWM-RDA does neither test nor explicitly select traits, while dc-CA tests and selects both traits and environmental variables. Moreover, the dc-CA analysis revealed that the set of environmental variables was much better in explaining the community data than the available trait set, a kind of information that can neither be obtained from CWM-RDA nor from RLQ (Environment, Link and Trait data), which is a close cousin of dc-CA but not regression-based. Our results suggest that trait-based analysis based on dc-CA may be useful to assess mechanistic links between multiple anthropogenic stressors and ecosystem health, but more data sets should be analysed in the same manner.

    Arbuscular mycorrhizal symbiosis increases phosphorus uptake and productivity of mixtures of maize varieties compared to monocultures
    Wang, Xin Xin ; Hoffland, Ellis ; Feng, Gu ; Kuyper, Thomas W. - \ 2020
    Journal of Applied Ecology (2020). - ISSN 0021-8901
    complementarity effects - maize varieties - mixtures - monocultures - mycorrhizal networks - overyielding - phosphorus - relative yield total

    Ecological intensification seeks to achieve crop yield increases by intensifying complementary or facilitative interactions between plant species or varieties. Different species of arbuscular mycorrhizal fungi (AMF) exhibit niche differentiation and show selectivity towards certain plants, which can further enhance complementarity. It is not clear whether in the presence of one AMF species, where mycelial networks connect crop species, opportunities for complementarity effects may be reduced. We grew monocultures and mixtures of maize varieties in a greenhouse with one species of AMF, Funneliformis mosseae, during two consecutive years to investigate whether under such conditions the mycorrhizal symbiosis would affect complementarity and overyielding compared to non-mycorrhizal plants. Variety mixtures showed increased phosphatase activity and mycorrhizal colonization, enhanced phosphorus uptake and overyielding when plants were mycorrhizal. There was no overyielding when plants were non-mycorrhizal. The increase in relative yield total was due to complementarity effects. Synthesis and applications. Our study implies that appropriate agricultural management that enhances mycorrhizal fungal contribution to ecosystem services may result in overyielding in terms of yield or phosphorus uptake through mixing varieties within one crop species.

    Intercropping enables a sustainable intensification of agriculture
    Werf, Wopke van der; Li, Chunjie ; Cong, Wen Feng ; Zhang, Fusuo - \ 2020
    Frontiers of Agricultural Science and Engineering 7 (2020)3. - ISSN 2095-7505 - p. 254 - 256.
    Yield components, reproductive allometry and the tradeoff between grain yield and yield stability in dryland spring wheat
    Du, Yan Lei ; Xi, Yue ; Cui, Ting ; Anten, Niels P.R. ; Weiner, Jacob ; Li, Xinmao ; Turner, Neil C. ; Zhao, Yi Min ; Li, Feng Min - \ 2020
    Field Crops Research 257 (2020). - ISSN 0378-4290
    Risk reduction - Smallholder farms - Variety screening - Wheat breeding - Yield stability

    Yield improvement for smallholder farmers in developing countries via crop breeding has been slow, in part because breeders have focused primarily on higher yields rather than stability of yield across environments. We investigated the relationships between (i) grain yield and yield-component traits, (ii) grain yield and yield stability, and (iii) reproductive (R) and vegetative (V) biomass in a field experiment with 18 spring wheat genotypes varying from landraces to recently-released breeding lines in a semiarid region under three different levels of precipitation. Genotypic differences in grain yield varied with the environment. The relationship between grain yield and yield components was also dependent on the environment, making it difficult to identify early-screening parameters for use in breeding programs. A genotype main effects and genotype by environment interaction effect analysis (GGE) showed a negative relationship between mean grain yield and yield stability across environments. There were significant differences among genotypes in the allometric exponent of the R-V relationship (slope of the log R – log V relationship). For the three highest yielding but less stable genotypes, this slope value was > 1, while the five lowest yielding, but more stable genotypes, it was < 1. We hypothesize that the tradeoff between grain yield and yield stability reported here is biologically constrained and cannot be eliminated through breeding. Therefore, a balance between yield stability and high yield should be considered in future wheat breeding programs for smallholder farmers, rather than attempting to improve both.

    Applications of anodized TiO2 nanotube arrays on the removal of aqueous contaminants of emerging concern: A review
    Feng, Yanyue ; Rijnaarts, Huub H.M. ; Yntema, Doekle ; Gong, Zhengjun ; Dionysiou, Dionysios D. ; Cao, Zhourong ; Miao, Shiyu ; Chen, Yanlong ; Ye, Yin ; Wang, Yuheng - \ 2020
    Water Research 186 (2020). - ISSN 0043-1354
    Contaminants of emerging concern - Photocatalysis - Photoelectrocatalysis - TiO nanotube arrays - Water treatment

    The presence of contaminants of emerging concern (CECs) in various water bodies and the associated threats to eco-system and human society have raised increasing concerns. To fight against such a problem, TiO2 photocatalysis is considered to be a powerful tool. In recent decades, TiO2 nanotube array (TNA) fabricated by electrochemical anodization emerged as a viable immobilized catalyst and its applications on CECs removal have gained a considerable amount of research interest. We herein present a critical review on the development of TNA and its applications on the removal of aqueous CECs. In this work, the CECs removal in different TNA based processes, the CECs removal mechanisms, the role of TNA properties, the role of operational parameters, and the role of water matrices are discussed. Moreover, perspectives on the current research progress are presented and recommendations on future research are elaborated.

    Pantothenic acid requirement of male White Pekin ducks from hatch to 21 days of age
    Tang, J. ; Zhang, B. ; Xue, M. ; Shi, W.B. ; Wu, Y.B. ; Feng, Y.L. ; Huang, W. ; Zhou, Z.K. ; Xie, M. ; Hou, S.S. - \ 2020
    Animal Feed Science and Technology 269 (2020). - ISSN 0377-8401
    Duck - Growth performance - Pantothenic acid - Requirement

    An experiment was conducted to determine the effects of dietary pantothenic acid levels on growth performance, carcass traits, and pantothenic acid status of male White Pekin ducks from hatch to 21 days of age, and to evaluate the requirement of this B-vitamin for starter ducks. Different levels pantothenic acid (0, 2, 4, 6, 8, 10, and 20 mg/kg) were supplemented to corn-soy isolate protein basal diet to produce 7 dietary treatments with different analyzed total pantothenic acid levels (4.65, 6.80, 8.39, 9.98, 12.04, 13.70, and 22.50 mg/kg). A total of 448 one-day-old male White Pekin ducks were allotted to 7 dietary treatments with 8 replicate pens of 8 birds per pen. At 21 days of age, body weight, average daily weight gain (ADG), average daily feed intake (ADFI), gain to feed ratio (G/F), liver pantothenic acid content, as well as percentage yield of breast meat, leg meat, and abdominal fat were examined. The growth depression, exudate on eyelids, dermatosis, poor feathering, and 100 % of mortality were observed in the ducks fed the basal diet without pantothenic acid supplementation, and these adverse effects were ameliorated by pantothenic acid supplementation. The starter ducks on the diet containing 6.80 mg/kg of pantothenic acid had a lower parameter profile of body weight, ADG, ADFI, G/F, breast meat yield, abdominal fat yield, and liver pantothenic acid content compared to the birds fed the diets with higher levels of pantothenic acid (P < 0.05). And these criteria showed a linear or quadratic response to increasing dietary pantothenic acid levels (P < 0.05). The pantothenic acid requirements (based on dietary total pantothenic acid) of starter male White Pekin ducks for body weight, ADG, ADFI, G/F, and liver pantothenic acid content were 8.95, 8.95, 8.59, 9.56, and 10.22 mg/kg based on broken-line regression, while were 10.04, 10.05, 9.18, 11.01, and 11.24 mg/kg based on quadratic broken-line regression, respectively.

    Rural household migration in China – the roles of actual and perceived tenure security
    Ren, Guangcheng ; Zhu, Xueqin ; Heerink, Nico ; Feng, Shuyi - \ 2020
    China Economic Review 63 (2020). - ISSN 1043-951X
    China - Household perceptions - Land rental market - Land tenure security - Migration

    Migration can make an important contribution to rural poverty reduction and overall productivity growth, but it may be limited by prevailing rural land tenure arrangements. Since 1998, the Chinese government has implemented a number of land tenure reforms with the aim of improving the tenure security and the transferability of land. Although these reforms enhanced legal tenure security, it is not clear to what extent they remove existing land tenure bottlenecks in migration. Both actual tenure security, i.e. local implementation of laws that warrant tenure security, and household perceptions of tenure security are likely to play a role. In this paper we examine the impacts of actual and perceived tenure security on rural household migration in China, taking into account the degree of development of land rental markets. We argue that actual and perceived tenure security can have both positive and negative effects on migration decisions and that the presence of land rental markets may modify these effects. A two-step control function approach that controls for endogeneity of tenure security perceptions is applied to household and village-level data collected in Jiangsu, Jiangxi, Liaoning provinces and Chongqing municipality. We find that both actual and perceived tenure security affect migration, but the impact of perceived tenure security measured by land reallocation expectations is much stronger and is positive, whereas the independent impact of actual tenure security is negative. Households perceiving a lower risk of losing land when one or more members migrate are more inclined to migrate, independent of the availability of land rental markets in their villages. Actual tenure security, as measured by absence of land reallocations and possession of land certificates, has an independent negative effect on migration only in villages with underdeveloped land rental markets.

    A soil colour map of China
    Liu, Feng ; Rossiter, David G. ; Zhang, Gan-Lin ; Li, De-Cheng - \ 2020
    Geoderma 379 (2020). - ISSN 0016-7061
    Colour space - Digital soil mapping - Predictive soil mapping

    Soil colour can indicate soil physical, chemical and biological properties and processes, and is an important indicator for soil classification, soil quality evaluation and soil management. It varies in both horizontal and vertical dimensions, and thus regional maps of soil colour can reveal spatial patterns of these properties, processes, and indicators. However, although soil regions are sometimes named for their dominant soil colour, it is directly measured only at “point” support, i.e., during soil profile description, whereas it is desirable to know soil colour over the entire soilscape. To achieve this for China we used predictive soil mapping methods to produce soil colour maps (dry and moist colours) at 1 km2 grid cell size and over multiple depths from a consistent dataset of approximately 4 600 full profile descriptions taken as part of a national survey to define soil series in Chinese Soil Taxonomy, and a set of environmental covariates covering the national territory. The covariates characterized soil forming factors including climate, parent materials, terrain, vegetation, land surface water and thermal conditions. Soil colour descriptions in the Munsell system were extracted from the genetic horizon descriptions at the selected depths and converted to the sRGB and L*a*b* colour spaces. Dry and moist colour separates were not well-correlated in either space (r<0.76). Random forest models were constructed in both spaces, for dry and moist colours separately. Models in sRGB space were moderately successful (R2≈0.43,RMSE≈26/255) at 5 cm, with success decreasing with depth. Models smoothed the colour space and thus did not predict the more extreme values or chromas, nor the rarer hues. Models in L*a*b* space were less successful. The fitted sRGB models were used to produce predictive maps over all of China. Regional patterns as well as local detail are clearly shown. Solar radiation, wind exposure, regolith thickness, and Landsat TM bands 7 and 5 contributed most to the predictions, followed by elevation, mean annual precipitation, terrain wetness index, air temperature seasonality, precipitation standard deviation and standard deviation of NDVI. These suggest pedological processes acting on the development of soil colours, including weathering of parent materials, oxidation-reduction chemistry and biochemistry of the decomposing of organic matter. This study shows that predictive methods from points using suitable covariates are an alternative to spatial predictions over map units from their representative profiles.

    Resistance to Fusarium head blight and mycotoxin accumulation among 129 wheat cultivars from different ecological regions in China
    Yan, Z. ; Zhang, H. ; Lee, T.A.J. Van Der; Waalwijk, C. ; Diepeningen, A.D. Van; Deng, Y. ; Feng, J. ; Liu, T. ; Chen, W. - \ 2020
    World Mycotoxin Journal 13 (2020)2. - ISSN 1875-0710 - p. 189 - 199.
    Disease index - Fusarium head blight - Resistance - Toxin - Wheat

    A total of 129 wheat cultivars collected from local breeders in four ecological regions in China was evaluated for Fusarium head blight resistance after natural infection under epidemic conditions. The disease index was scored and seven toxins concentrations were determined by UPLC-MS/MS. The disease index ranged from 6.3 to 80.9% and a strong correlation was found between the regions from which the cultivars originate and disease index. The middle and lower reaches of Yangtze River Region showed the highest disease resistance, followed by the upper reaches of the Yangtze River Region. FHB resistance of cultivars from northern and southern Huanghuai Region was lowest and all cultivars in these regions are highly or moderately susceptible. Disease index was significantly correlated with toxin accumulation on nation scale, but no clear correlation was found within most ecological regions. The toxin accumulation was also not well correlated with resistant levels. As the incidence of FHB has increased dramatically over the last decade, improved FHB resistance in cultivars is urgently needed. We recommend that besides scoring for disease index also mycotoxin accumulation in cultivars is incorporated in breeding procedures and the evaluation of cultivars.

    Roadmap for naming uncultivated Archaea and Bacteria
    Murray, Alison E. ; Freudenstein, John ; Gribaldo, Simonetta ; Hatzenpichler, Roland ; Hugenholtz, Philip ; Kämpfer, Peter ; Konstantinidis, Konstantinos T. ; Lane, Christopher E. ; Papke, R.T. ; Parks, Donovan H. ; Rossello-Mora, Ramon ; Stott, Matthew B. ; Sutcliffe, Iain C. ; Thrash, J.C. ; Venter, Stephanus N. ; Whitman, William B. ; Acinas, Silvia G. ; Amann, Rudolf I. ; Anantharaman, Karthik ; Armengaud, Jean ; Baker, Brett J. ; Barco, Roman A. ; Bode, Helge B. ; Boyd, Eric S. ; Brady, Carrie L. ; Carini, Paul ; Chain, Patrick S.G. ; Colman, Daniel R. ; DeAngelis, Kristen M. ; Rios, Maria Asuncion de los; Estrada-de los Santos, Paulina ; Dunlap, Christopher A. ; Eisen, Jonathan A. ; Emerson, David ; Ettema, Thijs J.G. ; Eveillard, Damien ; Girguis, Peter R. ; Hentschel, Ute ; Hollibaugh, James T. ; Hug, Laura A. ; Inskeep, William P. ; Ivanova, Elena P. ; Klenk, Hans Peter ; Li, Wen Jun ; Lloyd, Karen G. ; Löffler, Frank E. ; Makhalanyane, Thulani P. ; Moser, Duane P. ; Nunoura, Takuro ; Palmer, Marike ; Parro, Victor ; Pedrós-Alió, Carlos ; Probst, Alexander J. ; Smits, Theo H.M. ; Steen, Andrew D. ; Steenkamp, Emma T. ; Spang, Anja ; Stewart, Frank J. ; Tiedje, James M. ; Vandamme, Peter ; Wagner, Michael ; Wang, Feng Ping ; Hedlund, Brian P. ; Reysenbach, Anna Louise - \ 2020
    Nature Microbiology 5 (2020). - ISSN 2058-5276 - p. 987 - 994.

    The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

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

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

    Can pedotransfer functions based on environmental variables improve soil total nutrient mapping at a regional scale?
    Song, Xiao Dong ; Rossiter, David G. ; Liu, Feng ; Wu, Hua Yong ; Zhao, Xiao Rui ; Cao, Qi ; Zhang, Gan Lin - \ 2020
    Soil & Tillage Research 202 (2020). - ISSN 0167-1987
    Digital soil mapping - Random forest - Regression analysis - Total nitrogen - Total phosphorus - Total potassium

    Numerous pedotransfer functions (PTFs) have been developed to predict the soil properties of interest from other soil properties and, less commonly, from environmental variables. However, only a few PTFs have been developed to predict soil nutrients using environmental variables and to extrapolate them to characterize spatial soil variations at a regional scale. In this study, we attempted to develop PTFs for the total nitrogen (TN), total phosphorus (TP) and total potassium (TK) concentrations in three typical pedo-climatic areas of China (Fujian Province, Jiangsu Province and Qilian Mountains) with diverse climate, terrain and soil types. A series of linear PTFs were developed to quantify the effect of terrain and climate on the predictive relations between the soil nutrients and other measured soil properties and environmental variables. In addition, digital soil mapping (DSM) based on the random forest (RF) technique was performed to test the hypothesis that the best-fit PTFs could be extrapolated, based on soil maps and environmental variables, to describe regional soil variations in the soil nutrients. The root mean square errors (RMSEs) of the best-fit PTFs for TN, TP and TK ranged from 0.21 to 0.79 g kg−1, 0.20 to 0.58 g kg−1, and 3.68 to 5.00 g kg−1, respectively. Different RMSEs were produced by DSM, namely 0.37-1.89 g kg−1, 0.19−0.56 g kg−1 and 3.79-4.83 g kg−1 for TN, TP and TK, respectively. PTFs provided a sound basis for database compilation if the soil properties were highly correlated. However, the extrapolation of best-fit PTFs to regional scales yielded greater errors than those produced by DSM. The comparison results reveal the limitations of PTFs and suggest that their performance could be improved by using environmental covariates or by fitting data in areas with relatively homogeneous soil landscapes. The DSM techniques may provide satisfactory alternatives to predict soil data at both regional and plot scales.

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

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

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