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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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.

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.

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 - \ 2018
Plant Biotechnology Journal (2018). - ISSN 1467-7644
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.

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.
Governance Options for Addressing Changing Forest-Water Relations
Ellison, David ; Claassen, Marius ; Noordwijk, M. van; Sullivan, Caroline A. ; Vira, Bhaskar ; Xu, Jianchu ; Archer, E. ; Bishop, Kevin ; Gebrehiwot, Solomon Gebreyohannis ; Haywood, Lorren K. ; Robson, James P. - \ 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. 147 - 169.
The burden of cardiovascular diseases among us states, 1990-2016
Roth, Gregory A. ; Johnson, Catherine O. ; Abate, Kalkidan Hassen ; Abd-Allah, Foad ; Ahmed, Muktar ; Alam, Khurshid ; Alam, Tahiya ; Alvis-Guzman, Nelson ; Ansari, Hossein ; Ärnlöv, Johan ; Atey, Tesfay Mehari ; Awasthi, Ashish ; Awoke, Tadesse ; Barac, Aleksandra ; Bärnighausen, Till ; Bedi, Neeraj ; Bennett, Derrick ; Bensenor, Isabela ; Biadgilign, Sibhatu ; Castañeda-Orjuela, Carlos ; Catalá-López, Ferrán ; Davletov, Kairat ; Dharmaratne, Samath ; Ding, Eric L. ; Dubey, Manisha ; Faraon, Emerito Jose Aquino ; Farid, Talha ; Farvid, Maryam S. ; Feigin, Valery ; Fernandes, João ; Frostad, Joseph ; Gebru, Alemseged ; Geleijnse, Johanna M. ; Gona, Philimon Nyakauru ; Griswold, Max ; Hailu, Gessessew Bugssa ; Hankey, Graeme J. ; Hassen, Hamid Yimam ; Havmoeller, Rasmus ; Hay, Simon ; Heckbert, Susan R. ; Irvine, Caleb Mackay Salpeter ; James, Spencer Lewis ; Jara, Dube ; Kasaeian, Amir ; Khan, Abdur Rahman ; Khera, Sahil ; Khoja, Abdullah T. ; Khubchandani, Jagdish ; Kim, Daniel ; Kolte, Dhaval ; Lal, Dharmesh ; Larsson, Anders ; Linn, Shai ; Lotufo, Paulo A. ; Razek, Hassan Magdy Abd El; Mazidi, Mohsen ; Meier, Toni ; Mendoza, Walter ; Mensah, George A. ; Meretoja, Atte ; Mezgebe, Haftay Berhane ; Mirrakhimov, Erkin ; Mohammed, Shafiu ; Moran, Andrew Edward ; Nguyen, Grant ; Nguyen, Minh ; Ong, Kanyin Liane ; Owolabi, Mayowa ; Pletcher, Martin ; Pourmalek, Farshad ; Purcell, Caroline A. ; Qorbani, Mostafa ; Rahman, Mahfuzar ; Rai, Rajesh Kumar ; Ram, Usha ; Reitsma, Marissa Bettay ; Renzaho, Andre M.N. ; Rios-Blancas, Maria Jesus ; Safiri, Saeid ; Salomon, Joshua A. ; Sartorius, Benn ; Sepanlou, Sadaf Ghajarieh ; Shaikh, Masood Ali ; Silva, Diego ; Stranges, Saverio ; Tabarés-Seisdedos, Rafael ; Atnafu, Niguse Tadele ; Thakur, J.S. ; Topor-Madry, Roman ; Truelsen, Thomas ; Tuzcu, E.M. ; Tyrovolas, Stefanos ; Ukwaja, Kingsley Nnanna ; Vasankari, Tommi ; Vlassov, Vasiliy ; Vollset, Stein Emil ; Wakayo, Tolassa ; Weintraub, Robert ; Wolfe, Charles ; Workicho, Abdulhalik ; Xu, Gelin ; Yadgir, Simon ; Yano, Yuichiro ; Yip, Paul ; Yonemoto, Naohiro ; Younis, Mustafa ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Zipkin, Ben ; Afshin, Ashkan ; Gakidou, Emmanuela ; Lim, Stephen S. ; Mokdad, Ali H. ; Naghavi, Mohsen ; Vos, Theo ; Murray, Christopher J.L. - \ 2018
JAMA Cardiology 3 (2018)5. - ISSN 2380-6583 - p. 375 - 389.
Importance: Cardiovascular disease (CVD) is the leading cause of death in the United States, but regional variation within the United States is large. Comparable and consistent state-level measures of total CVD burden and risk factors have not been produced previously. Objective: To quantify and describe levels and trends of lost health due to CVD within the United States from 1990 to 2016 as well as risk factors driving these changes. Design, setting, and participants: Using the Global Burden of Disease methodology, cardiovascular disease mortality, nonfatal health outcomes, and associated risk factors were analyzed by age group, sex, and year from 1990 to 2016 for all residents in the United States using standardized approaches for data processing and statistical modeling. Burden of disease was estimated for 10 groupings of CVD, and comparative risk analysis was performed. Data were analyzed from August 2016 to July 2017. Exposures: Residing in the United States. Main outcomes ans measures: Cardiovascular disease disability-Adjusted life-years (DALYs). Results: Between 1990 and 2016, age-standardized CVD DALYs for all states decreased. Several states had large rises in their relative rank ordering for total CVD DALYs among states, including Arkansas, Oklahoma, Alabama, Kentucky, Missouri, Indiana, Kansas, Alaska, and Iowa. The rate of decline varied widely across states, and CVD burden increased for a small number of states in the most recent years. Cardiovascular disease DALYs remained twice as large among men compared with women. Ischemic heart disease was the leading cause of CVD DALYs in all states, but the second most common varied by state. Trends were driven by 12 groups of risk factors, with the largest attributable CVD burden due to dietary risk exposures followed by high systolic blood pressure, high body mass index, high total cholesterol level, high fasting plasma glucose level, tobacco smoking, and low levels of physical activity. Increases in risk-deleted CVD DALY rates between 2006 and 2016 in 16 states suggest additional unmeasured risks beyond these traditional factors. Conclusions and relevance: Large disparities in total burden of CVD persist between US states despite marked improvements in CVD burden. Differences in CVD burden are largely attributable to modifiable risk exposures.
Spring migration patterns, habitat use, and stopover site protection status for two declining waterfowl species wintering in China as revealed by satellite tracking
Si, Yali ; Xu, Yanjie ; Xu, Fei ; Li, Xueyan ; Zhang, Wenyuan ; Wielstra, Ben ; Wei, Jie ; Liu, Guanhua ; Luo, Hao ; Takekawa, John ; Balachandran, Sivananintha ; Zhang, Tao ; Boer, Willem F. de; Prins, Herbert H.T. ; Gong, Peng - \ 2018
Ecology and Evolution 8 (2018)12. - ISSN 2045-7758 - p. 6280 - 6289.
Anser albifrons - Anser serrirostris - habitat selection - protected area - stopover site

East Asian migratory waterfowl have greatly declined since the 1950s, especially the populations that winter in China. Conservation is severely hampered by the lack of primary information about migration patterns and stopover sites. This study utilizes satellite tracking techniques and advanced spatial analyses to investigate spring migration of the greater white-fronted goose (Anser albifrons) and tundra bean goose (Anser serrirostris) wintering along the Yangtze River Floodplain. Based on 24 tracks obtained from 21 individuals during the spring of 2015 and 2016, we found that the Northeast China Plain is far-out the most intensively used stopover site during migration, with geese staying for over 1 month. This region has also been intensely developed for agriculture, suggesting a causal link to the decline in East Asian waterfowl wintering in China. The protection of waterbodies used as roosting area, especially those surrounded by intensive foraging land, is critical for waterfowl survival. Over 90% of the core area used during spring migration is not protected. We suggest that future ground surveys should target these areas to confirm their relevance for migratory waterfowl at the population level, and core roosting area at critical spring-staging sites should be integrated in the network of protected areas along the flyway. Moreover, the potential bird–human conflict in core stopover area needs to be further studied. Our study illustrates how satellite tracking combined with spatial analyses can provide crucial insights necessary to improve the conservation of declining Migratory species.

Unravelling the causes of tidal asymmetry in deltas
Zhang, Wei ; Cao, Yu ; Zhu, Yuliang ; Zheng, Jinhai ; Ji, Xiaomei ; Xu, Yanwen ; Wu, Yao ; Hoitink, A.J.F. - \ 2018
Journal of Hydrology 564 (2018). - ISSN 0022-1694 - p. 588 - 604.
Deltas - Nonstationary tides - River flow - Tidal asymmetry

Tidal asymmetry in deltas is caused by both the intrinsic asymmetry, resulting from the combination of astronomical tides, and by nonlinear tidal interactions that occur in shallow water. The relative importance of these sources of tidal asymmetry in delta channel networks have remained poorly studied, partly due to the limitations of classical harmonic analysis (HA) in hindcasting nonstationary tides. The Pearl River Delta (PRD) is a multichannel system with rapidly changing bathymetry, subject to severe human interventions. This work applies a nonstationary harmonic model (NS_TIDE) to hydrological data from 15 stations in the PRD spanning the period 1961–2012. The spatiotemporal variation of multiple sources of tidal asymmetry is quantified by a skewness metric, revealing how similar or dissimilar the development of alternative sources of tidal asymmetry develop in the delta subject to study. A relative sensitivity coefficient (RSC) is introduced to decompose the contribution of tidal amplitude variations to multiple tidal asymmetries. Analytical results show the development of tides becoming gradually more asymmetric as they propagate into delta channel networks, and how this depends on the river flow. Variation in the orientation of tidal asymmetries induced by different combinations of tidal constituents leads to a complex pattern of the overall tidal asymmetry in the PRD. Our results show that tidal asymmetry in deltas can be significantly dependent on the river flow.

The Fusarium graminearum Histone Acetyltransferases Are Important for Morphogenesis, DON Biosynthesis, and Pathogenicity
Kong, Xiangjiu ; Diepeningen, A.D. van; Lee, T.A.J. van der; Waalwijk, C. ; Xu, Jingsheng ; Xu, Jin ; Zhang, Hao ; Chen, Wanquan ; Feng, Jie - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
Post-translational modifications of chromatin structure by histone acetyltransferase (HATs) play a central role in the regulation of gene expression and various biological processes in eukaryotes. Although HAT genes have been studied in many fungi, few of them have been functionally characterized. In this study, we identified and characterized four putative HATs (FgGCN5, FgRTT109, FgSAS2, FgSAS3) in the plant pathogenic ascomycete Fusarium graminearum, the causal agent of Fusarium head blight of wheat and barley. We replaced the genes and all mutant strains showed reduced growth of F. graminearum. The ΔFgSAS3 and ΔFgGCN5 mutant increased sensitivity to oxidative and osmotic stresses. Additionally, ΔFgSAS3 showed reduced conidia sporulation and perithecium formation. Mutant ΔFgGCN5 was unable to generate any conidia and lost its ability to form perithecia. Our data showed also that FgSAS3 and FgGCN5 are pathogenicity factors required for infecting wheat heads as well as tomato fruits. Importantly, almost no Deoxynivalenol (DON) was produced either in ΔFgSAS3 or ΔFgGCN5 mutants, which was consistent with a significant downregulation of TRI genes expression. Furthermore, we discovered for the first time that FgSAS3 is indispensable for the acetylation of histone site H3K4, while FgGCN5 is essential for the acetylation of H3K9, H3K18, and H3K27. H3K14 can be completely acetylated when FgSAS3 and FgGCN5 were both present. The RNA-seq analyses of the two mutant strains provide insight into their functions in development and metabolism. Results from this study clarify the functional divergence of HATs in F. graminearum, and may provide novel targeted strategies to control secondary metabolite expression and infections of F. graminearum.
Host and Cropping System Shape the Fusarium Population: 3ADON-Producers Are Ubiquitous in Wheat Whereas NIV-Producers Are More Prevalent in Rice
Yang, Meixin ; Zhang, Hao ; Kong, Xiangjiu ; Lee, T.A.J. van der; Waalwijk, C. ; Diepeningen, A.D. van; Xu, Jin ; Xu, Jingsheng ; Chen, Wanquan ; Feng, Jie - \ 2018
Toxins 10 (2018)3. - ISSN 2072-6651
In recent years, Fusarium head blight (FHB) outbreaks have occurred much more frequently in China. The reduction of burning of the preceding crop residues is suggested to contribute to more severe epidemics as it may increase the initial inoculum. In this study, a large number of Fusarium isolates was collected from blighted wheat spikes as well as from rice stubble with perithecia originating from nine sampling sites in five provinces in Southern China. Fusarium asiaticum dominated both wheat and rice populations, although rice populations showed a higher species diversity. Chemotype analysis showed that rice is the preferred niche for NIV mycotoxin producers that were shown to be less virulent on wheat. In contrast, 3ADON producers are more prevalent on wheat and in wheat producing areas. The 3ADON producers were shown to be more virulent on wheat, revealing the selection pressure of wheat on 3ADON producers. For the first time, members of the Incarnatum-clade of Fusarium Incarnatum-Equiseti Species Complex (FIESC) were found to reproduce sexually on rice stubble. The pathogenicity of FIESC isolates on wheat proved very low and this may cause the apparent absence of this species in the main wheat producing provinces. This is the first report of the Fusarium population structure including rice stubble as well as a direct comparison with the population on wheat heads in the same fields. Our results confirm that the perithecia on rice stubble are the primary inoculum of FHB on wheat and that cropping systems affect the local Fusarium population.
A global climate niche for giant trees
Scheffer, Marten ; Xu, Chi ; Hantson, Stijn ; Holmgren, Milena ; Los, Sietse O. ; Nes, Egbert H. van - \ 2018
Global Change Biology 24 (2018)7. - ISSN 1354-1013 - p. 2875 - 2883.
alternative ecosystem state - canopy height - LiDAR - precipitation temperate rainforest - remote sensing - resilience - threshold - tropical rainforest

Rainforests are among the most charismatic as well as the most endangered ecosystems of the world. However, although the effects of climate change on tropical forests resilience is a focus of intense research, the conditions for their equally impressive temperate counterparts remain poorly understood, and it remains unclear whether tropical and temperate rainforests have fundamental similarities or not. Here we use new global data from high precision laser altimetry equipment on satellites to reveal for the first time that across climate zones ‘giant forests’ are a distinct and universal phenomenon, reflected in a separate mode of canopy height (~40 m) worldwide. Occurrence of these giant forests (cutoff height > 25 m) is negatively correlated with variability in rainfall and temperature. We also demonstrate that their distribution is sharply limited to situations with a mean annual precipitation above a threshold of 1,500 mm that is surprisingly universal across tropical and temperate climates. The total area with such precipitation levels is projected to increase by ~4 million km2 globally. Our results thus imply that strategic management could in principle facilitate the expansion of giant forests, securing critically endangered biodiversity as well as carbon storage in selected regions.

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis
Griesmann, Maximilian ; Chang, Yue ; Liu, Xin ; Song, Yue ; Haberer, Georg ; Crook, Matthew B. ; Billault-Penneteau, Benjamin ; Lauressergues, Dominique ; Keller, Jean ; Imanishi, Leandro ; Roswanjaya, Yuda Purwana ; Kohlen, Wouter ; Pujic, Petar ; Battenberg, Kai ; Alloisio, Nicole ; Liang, Yuhu ; Hilhorst, Henk ; Salgado, Marco G. ; Hocher, Valerie ; Gherbi, Hassen ; Svistoonoff, Sergio ; Doyle, Jeff J. ; He, Shixu ; Xu, Yan ; Xu, Shanyun ; Qu, Jing ; Gao, Qiang ; Fang, Xiaodong ; Fu, Yuan ; Normand, Philippe ; Berry, Alison M. ; Wall, Luis G. ; Ané, Jean Michel ; Pawlowski, Katharina ; Xu, Xun ; Yang, Huanming ; Spannagl, Manuel ; Mayer, Klaus F.X. ; Wong, Gane Ka Shu ; Parniske, Martin ; Delaux, Pierre Marc ; Cheng, Shifeng - \ 2018
Science (2018). - ISSN 0036-8075 - 18 p.

The root nodule symbiosis of plants with nitrogen-fixing bacteria impacts global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of ten plant species covering the diversity of nodule morphotypes, bacterial symbionts and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION (NIN) in ten out of 13 genomes of non-nodulating species within this clade. The discovery that multiple independent losses shaped the present day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so far underestimated selection pressure against this symbiosis.

Effects of agricultural management practices on soil quality : A review of long-term experiments for Europe and China
Bai, Zhanguo ; Caspari, Thomas ; Gonzalez, Maria Ruiperez ; Batjes, Niels H. ; Mäder, Paul ; Bünemann, Else K. ; Goede, Ron de; Brussaard, Lijbert ; Xu, Minggang ; Ferreira, Carla Sofia Santos ; Reintam, Endla ; Fan, Hongzhu ; Mihelič, Rok ; Glavan, Matjaž ; Tóth, Zoltán - \ 2018
Agriculture, Ecosystems and Environment 265 (2018). - ISSN 0167-8809 - p. 1 - 7.
Agricultural management practices - Literature review - Long-term field experiments - Response ratio - Soil quality indicators
In this paper we present effects of four paired agricultural management practices (organic matter (OM) addition versus no organic matter input, no-tillage (NT) versus conventional tillage, crop rotation versus monoculture, and organic agriculture versus conventional agriculture) on five key soil quality indicators, i.e., soil organic matter (SOM) content, pH, aggregate stability, earthworms (numbers) and crop yield. We have considered organic matter addition, no-tillage, crop rotation and organic agriculture as “promising practices”; no organic matter input, conventional tillage, monoculture and conventional farming were taken as the respective references or “standard practice” (baseline). Relative effects were analysed through indicator response ratio (RR) under each paired practice. For this we considered data of 30 long-term experiments collected from 13 case study sites in Europe and China as collated in the framework of the EU-China funded iSQAPER project. These were complemented with data from 42 long-term experiments across China and 402 observations of long-term trials published in the literature. Out of these, we only considered experiments covering at least five years. The results show that OM addition favourably affected all the indicators under consideration. The most favourable effect was reported on earthworm numbers, followed by yield, SOM content and soil aggregate stability. For pH, effects depended on soil type; OM input favourably affected the pH of acidic soils, whereas no clear trend was observed under NT. NT generally led to increased aggregate stability and greater SOM content in upper soil horizons. However, the magnitude of the relative effects varied, e.g. with soil texture. No-tillage practices enhanced earthworm populations, but not where herbicides or pesticides were applied to combat weeds and pests. Overall, in this review, yield slightly decreased under NT. Crop rotation had a positive effect on SOM content and yield; rotation with ley very positively influenced earthworms’ numbers. Overall, crop rotation had little impact on soil pH and aggregate stability − depending on the type of intercrop; alternatively, rotation of arable crops only resulted in adverse effects. A clear positive trend was observed for earthworm abundance under organic agriculture. Further, organic agriculture generally resulted in increased aggregate stability and greater SOM content. Overall, no clear trend was found for pH; a decrease in yield was observed under organic agriculture in this review.
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