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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Irrigation reduces the negative effect of global warming on winter wheat yield and greenhouse gas intensity
Li, Jiazhen ; Dong, Wenxu ; Oenema, Oene ; Chen, Tuo ; Hu, Chunsheng ; Yuan, Haijing ; Zhao, Liying - \ 2019
Science of the Total Environment 646 (2019). - ISSN 0048-9697 - p. 290 - 299.
Global warming potential - Greenhouse gas intensity - Greenhouse gases - Irrigation - Warming - Wheat yield

Global warming may exacerbate drought, decrease crop yield and affect greenhouse gas (GHG) emissions in semi-arid regions. However, the interactive effects of increases in temperature and water availability on winter wheat yield and GHG emissions in semi-arid climates are not well-understood. Here, we report on a two-year field experiment that examined the effects of a mean soil temperature increase of ~2 °C (at 5 cm depth) with and without additional irrigation on wheat yield and GHG emissions. Infrared heaters were placed above the crop canopy at a height of 1.8 m to simulate warming. Fluxes of CH4, CO2 and N2O were measured using closed static chamber technique once per week during the wheat growing seasons. Warming decreased wheat yield by 28% in the relatively dry year of 2015, while supplemental irrigation nullified the warming effect completely. Warming did not alter the wheat yield significantly in the relatively wet year of 2016, but supplemental irrigation with no warming decreased the wheat yield by 25%. Warming increased CO2 emissions by 28% and CH4 uptake by 24% and tended to decrease N2O emissions. Supplemental irrigation increased N2O emissions but had little effect on CO2 emissions and CH4 uptake. Evidently, warming and supplemental irrigation had interactive effects on wheat yield, GHG emissions and GHG emissions intensity. Precision irrigation appears to be a means of simultaneously increasing wheat yield and reducing GHG emissions under warming conditions in semi-arid areas.

Hutten catering : How to organize innovation for vital consumers in a sustainable food system?
Ingenbleek, Paul T.M. ; Zhao, Yuan - \ 2018
International Food and Agribusiness Management Review 21 (2018)5. - ISSN 1096-7508 - p. 583 - 593.
Corporate social responsibility - Food service - Food system - Innovation - Responsible consumption - Sustainability

Hutten Catering is the only family-owned company listed among the top 10 catering companies in the Netherlands, yet it also has been the fastest growing company in this market for more than a decade. Catering companies face small margins and tight R & D budgets, yet their strategic position in the food system offers them unique opportunities to contribute to people's health and improve sustainability. Hutten Catering is located in a region with many potential innovation partners, supporting its integration of multiple suppliers, customers, and third parties in its innovation center, Food Squad. This center focuses on building sustainable supply chains that can reduce food waste; innovating specialist foods, such as for health care patients; and enabling vital lifestyles. With its many opportunities but limited budget, can Food Squad engage in more and larger projects, and thus further its impact on society, if it were to operate as an independent organization?

Influence of stocking density on growth, digestive enzyme activities, immune responses, antioxidant of Oreochromis niloticus fingerlings in biofloc systems
Liu, Gang ; Ye, Zhangying ; Liu, Dezhao ; Zhao, Jian ; Sivaramasamy, Elayaraja ; Deng, Yale ; Zhu, Songming - \ 2018
Fish and Shellfish Immunology 81 (2018). - ISSN 1050-4648 - p. 416 - 422.
Antioxidant - Biofloc - Digestive enzyme activities - Immune responses - Stocking density - Tilapia

A 120-day feeding trial was conducted to evaluate the effect of different stocking densities on growth, the non-specific immunities, antioxidant status and digestive enzyme activities of Oreochromis niloticus fingerlings under a zero-water exchange biofloc system. Tilapias (0.51 ± 0.05 g) were randomly distributed in twelve tanks, each with 300 L water. The experimental design was completely randomized using three replications with four treatments 166 orgs m−3 (LD, low density), 333 orgs m−3 (MD, middle density) and 600 orgs m−3 (HD, high density) with glucose added as biofloc groups, and a clear water group without glucose added as a control 333 orgs m−3. The fish cultured in LD and MD group showed higher final body weight. For the digestive enzymes, the lipase, trypsin, and amylase activities were all depressed in HD group and control group. Regarding the immune and antioxidant abilities, significantly lower values (P < 0.05) of the lysozyme, complement 3, and glutathione were observed for the fish that reared in the control group and HD group. The stress indicator, the cortisol, 5-hydroxytryptamine, and glucose concentrations were also depressed in HD group and control group, meanwhile the alanine aminotransferase, aspartate transaminase and alkaline phosphatase were all higher in HD group and control group. The significant higher survival was observed in the LD and MD group after Vibrio harveyi challenge test. The results of the experiment indicated that the biofloc in situ had the effects of anti-crowding stress.

The intelligent delivery systems for bioactive compounds in foods : Physicochemical and physiological conditions, absorption mechanisms, obstacles and responsive strategies
Chai, Jingjing ; Jiang, Ping ; Wang, Pengjie ; Jiang, Yumeng ; Li, Dan ; Bao, Weier ; Liu, Bingxue ; Liu, Bin ; Zhao, Liyun ; Norde, Willem ; Yuan, Qipeng ; Ren, Fazheng ; Li, Yuan - \ 2018
Trends in Food Science and Technology 78 (2018). - ISSN 0924-2244 - p. 144 - 154.
Bioaccessibility - Bioactive compounds - Bioavailability - Delivery barriers - Encapsulation - Intelligent delivery systems

Background: Bioactive natural compounds have received considerable attention due to their health benefits, including anti-oxidant, anti-cancer, anti-diabetes and cardiovascular disease-preventing functions. However, the stability of these sensitive compounds can be influenced by unfavourable environmental conditions during processing and storage. In addition, delivery of bioactive compounds via the oral route is restricted by various physiological barriers, including a harsh pH, gastrointestinal enzymes, the mucus layer, and the epithelium. Intelligent delivery systems are a promising method to protect bioactive molecules from degradation and improve their bioavailability. Scope and approach: We have demonstrated the physicochemical and physiological GI conditions. The structural composition of the epithelium and transport mechanisms of bioactives and nanoparticles across the intestinal epithelium were discussed. The effects of enhanced aqueous solubility, stability, bioaccessibility and bioavailability after encapsulation were illustrated. Furthermore, novel intelligent carriers that are responsive to the oral route, pH, enzymes and cell receptors were also discussed. Key findings and conclusions: This comprehensive multidisciplinary review provides useful guidelines for the application of bioactive compounds in the food industry. Intelligent carrier systems are designed to improve the low solubility, poor stability and low permeability of the gastrointestinal tract, and they have the potential to improve oral bioavailability.

Regulation of myostatin expression is associated with growth and muscle development in commercial broiler and DMC muscle
Dou, Tengfei ; Li, Zhengtian ; Wang, Kun ; Liu, Lixian ; Rong, Hua ; Xu, Zhiqiang ; Huang, Ying ; Gu, Dahai ; Chen, Xiaobo ; Hu, Wenyuan ; Zhang, Jiarong ; Zhao, Sumei ; Jois, Markandeya ; Li, Qihua ; Ge, Changrong ; Pas, Marinus F.W. te; Jia, Junjing - \ 2018
Molecular Biology Reports 45 (2018)4. - ISSN 0301-4851 - p. 511 - 522.
Commercial broiler chicken - Daweishan mini chicken - Growth rate - mRNA expression - Muscle weight - Myostatin
Myostatin is a negative regulator of skeletal muscle growth. Muscle tissue is the largest tissue in the body and influences body growth. Commercial Avian broiler chickens are selected for high growth rate and muscularity. Daweishan mini chickens are a slow growing small-sized chicken breed. We investigated the relations between muscle (breast and leg) myostatin mRNA expression and body and muscle growth. Twenty chickens per breed were slaughtered at 0, 30, 60, 90, 120, and 150 days of age. Body and muscle weights were higher at all times in Avian chickens. Breast muscle myostatin expression was higher in Avian chickens than in Daweishan mini chickens at day 30. Myostatin expression peaked at day 60 in Daweishan mini chickens and expression remained higher in breast muscle. Daweishan mini chickens myostatin expression correlated positively with carcass weight, breast and leg muscle weight from day 0 to 60, and correlated negatively with body weight from day 90 to 150, while myostatin expression in Avian chickens was negatively correlated with carcass and muscle weight from day 90 to 150. The results suggest that myostatin expression is related to regulation of body growth and muscle development, with two different regulatory mechanisms that switch between days 30 and 60.
Use of the beta growth function to quantitatively characterize the effects of plant density and a growth regulator on growth and biomass partitioning in cotton
Mao, Lili ; Zhang, Lizhen ; Sun, Xuezhen ; Werf, Wopke van der; Evers, Jochem B. ; Zhao, Xinhua ; Zhang, Siping ; Song, Xianliang ; Li, Zhaohu - \ 2018
Field Crops Research 224 (2018). - ISSN 0378-4290 - p. 28 - 36.
Beta growth function - Biomass partitioning - Growth rate - Mepiquat chloride - Plant population density
Allocation of newly formed biomass towards plant organs is a key determinant of plant performance that is affected by agronomic practices such as plant population density and use of growth regulators. Here we quantified biomass allocation of intercropped cotton (Gossypium hirsutum) growing at two population densities (3.0 and 7.5 plants m−2) and with or without application of the growth regulator mepiquat chloride (MC) in three consecutive years. The beta growth function was used to quantitatively characterize the dynamics of biomass partitioning. Compared to low density, high density increased daily growth rate and final above-ground dry matter, but decreased allocation to fruits. Application of MC did not affect dry matter accumulation but increased allocation to fruits by 22%. The parameters of the beta growth function have a clear biological interpretation, providing a useful quantitative characterization of the effect of management on dry matter allocation in cotton. The function may also be used to model organ-specific daily assimilate partitioning as a component in models of plant growth and crop production with the consideration of discussed caveats.
New insights into the phylogeny of the TMBIM superfamily across the three of life : Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants
Gamboa-Tuz, Samuel D. ; Pereira-Santana, Alejandro ; Zhao, Tao ; Schranz, M.E. ; Castano, Enrique ; Rodriguez-Zapata, Luis C. - \ 2018
Molecular Phylogenetics and Evolution 126 (2018). - ISSN 1055-7903 - p. 266 - 278.
Bax inhibitor 1 - Gene family evolution - Lifeguard - Programmed cell death - Synteny network - TMBIM
The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. However, no research has focused on the evolution of this superfamily in plants. We identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. Then, we used orthology and synteny network analyses to further investigate the evolution and expansion of the BI and LFG families in 48 plants from diverse taxa. Plant BI family forms a single monophyletic group; however, monocot BI sequences transposed to another genomic context during evolution. Plant LFG family, which expanded trough whole genome and tandem duplications, is subdivided in LFG I, LFG IIA, and LFG IIB major phylogenetic groups, and retains synteny in angiosperms. Moreover, two orthologous groups (OGs) are shared between bryophytes and seed plants. Other several lineage-specific OGs are present in plants. This work clarifies the phylogenetic classification of the TMBIM superfamily across the three domains of life. Furthermore, it sheds new light on the evolution of the BI and LFG families in plants providing a benchmark for future research.
The Hot Serial Cereal Experiment for modeling wheat response to temperature: field experiments and AgMIP-Wheat multi-model simulations
Martre, Pierre ; Kimball, Bruce A. ; Ottman, Michael J. ; Wall, Gerard W. ; White, Jeffrey W. ; Asseng, Senthold ; Ewert, Frank ; Cammarano, Davide ; Maiorano, Andrea ; Aggarwal, Pramod K. ; Anothai, Jakarat ; Basso, Bruno ; Biernath, Christian ; Challinor, Andrew J. ; Sanctis, Giacomo De; Doltra, Jordi ; Dumont, Benjamin ; Fereres, Elias ; Garcia-Vila, Margarita ; Gayler, Sebastian ; Hoogenboom, Gerrit ; Hunt, Leslie A. ; Izaurralde, Roberto C. ; Jabloun, Mohamed ; Jones, Curtis D. ; Kassie, Belay T. ; Kersebaum, Kurt C. ; Koehler, Ann-Kristin ; Müller, Christoph ; Kumar, Soora Naresh ; Liu, Bing ; Lobell, David B. ; Nendel, Claas ; O'Leary, Garry ; Olesen, Jørgen E. ; Palosuo, Taru ; Priesack, Eckart ; Rezaei, Ehsan Eyshi ; Ripoche, Dominique ; Rötter, Reimund P. ; Semenov, Mikhail A. ; Stöckle, Claudio ; Stratonovitch, Pierre ; Streck, Thilo ; Supit, Iwan ; Tao, Fulu ; Thorburn, Peter ; Waha, Katharina ; Wang, Enli ; Wolf, Joost ; Zhao, Zhigan ; Zhu, Yan - \ 2018
ODjAR : open data journal for agricultural research 4 (2018). - ISSN 2352-6378 - p. 28 - 34.
The data set reported here includes the part of a Hot Serial Cereal Experiment (HSC) experiment recently used in the AgMIP-Wheat project to analyze the uncertainty of 30 wheat models and quantify their response to temperature. The HSC experiment was conducted in an open-field in a semiarid environment in the southwest USA. The data reported herewith include one hard red spring wheat cultivar (Yecora Rojo) sown approximately every six weeks from December to August for a two-year period for a total of 11 planting dates out of the 15 of the entire HSC experiment. The treatments were chosen to avoid any effect of frost on grain yields. On late fall, winter and early spring plantings temperature free-air controlled enhancement (T-FACE) apparatus utilizing infrared heaters with supplemental irrigation were used to increase air temperature by 1.3°C/2.7°C (day/night) with conditions equivalent to raising air temperature at constant relative humidity (i.e. as expected with global warming) during the whole crop growth cycle. Experimental data include local daily weather data, soil characteristics and initial conditions, detailed crop measurements taken at three growth stages during the growth cycle, and cultivar information. Simulations include both daily in-season and end-of-season results from 30 wheat models.
Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens
Jia, Junjing ; Ahmed, Irfan ; Liu, Lixian ; Liu, Yong ; Xu, Zhiqiang ; Duan, Xiaohua ; Li, Qihua ; Dou, Tengfei ; Gu, Dahai ; Rong, Hua ; Wang, Kun ; Li, Zhengtian ; Talpur, Mir Zulqarnain ; Huang, Ying ; Wang, Shanrong ; Yan, Shixiong ; Tong, Huiquan ; Zhao, Sumei ; Zhao, Guiping ; Pas, Marinus F.W. te; Su, Zhengchang ; Ge, Changrong - \ 2018
PLoS One 13 (2018)4. - ISSN 1932-6203
The growth hormone / insulin-like growth factor-1 (GH/IGF-1) pathway of the somatotropic axis is the major controller for growth rate and body size in vertebrates, but the effect of selection on the expression of GH/IGF-1 somatotropic axis genes and their association with body size and growth performance in farm animals is not fully understood. We analyzed a time series of expression profiles of GH/IGF-1 somatotropic axis genes in two chicken breeds, the Daweishan mini chickens and Wuding chickens, and the commercial Avian broilers hybrid exhibiting markedly different body sizes and growth rates. We found that growth rate and feed conversion efficiency in Daweishan mini chickens were significantly lower than those in Wuding chickens and Avian broilers. The Wuding and Daweishan mini chickens showed higher levels of plasma GH, pituitary GH mRNA but lower levels of hepatic growth hormone receptor (GHR) mRNA than in Avian broilers. Daweishan mini chickens showed significantly lower levels of plasma IGF-1, thigh muscle and hepatic IGF-1 mRNA than did Avian broilers and Wuding chickens. These results suggest that the GH part of the somatotropic axis is the main regulator of growth rate, while IGF-1 may regulate both growth rate and body weight. Selection for growth performance and body size have altered the expression profiles of somatotropic axis genes in a breed-, age-, and tissue-specific manner, and manner, and alteration of regulatory mechanisms of these genes might play an important role in the developmental characteristics of chickens.
Ecological succession drives the structural change of seed-rodent interaction networks in fragmented forests
Yang, Xifu ; Yan, Chuan ; Zhao, Qingjian ; Holyoak, Marcel ; Fortuna, Miguel A. ; Bascompte, Jordi ; Jansen, Patrick A. ; Zhang, Zhibin - \ 2018
Forest Ecology and Management 419-420 (2018). - ISSN 0378-1127 - p. 42 - 50.
Ecological networks - Forest succession - Habitat fragmentation - Habitat loss - Interaction strength - Nestedness - Network complexity - Seed-dispersal
While deforestation and fragmentation can cause massive species loss in forest ecosystems, forest regeneration can also drive successional changes in species composition. Although studies have sometimes documented the effects of these compositional changes on interspecific interactions, few studies have investigated changes in the structure of plant-animal networks. We investigated how interaction networks of assemblages of rodents and tree seeds changed with forest fragmentation and succession in a subtropical region. We compared seed-rodent interactions between 14 secondary forest patches that ranged in area from 2 to 58 ha, and from 10 to at least 100 years old, representing a successional gradient. We expected that deforestation and fragmentation would reduce seed production and diversify rodent communities, resulting in higher interaction strengths and connectivity, but weak nestedness (i.e., specialists interact with subsets of the species interaction of generalists). We measured the frequency of rodents eating and removing seeds (interaction strength) in each patch during 3 successive years, using seed tagging and infrared camera trapping, and calculated the properties of the seed-rodent networks. We found that the relative abundances of seeds and rodents changed with stand age not patch size, as did seed-rodent interactions: older patches produced more seeds, contained fewer individuals and species of rodents, and had seed-rodent networks with lower connectance and interaction strength, but higher nestedness. Connectance and interaction strength decreased with metabolic per capita seed availability (as measured by seed energy value); nestedness increased with seed richness, but decreased with rodent abundance. At species level, we found stand age and patch size showed significant effects on seed or rodent abundance of a few species. We also found seed coat thickness and starch contents had significant effects on network metrics. Our results suggest that during succession after deforestation, seed-rodent interactions in these sub-tropical forests change from a state dominated by high seed removal and highly connected seed-rodent networks to a state with more seeds and highly nested networks. From a management perspective of our study region, succession age, not fragment size, and network structure should be paid more attention so as to facilitate the restoration processes of degraded forests. Rodent management should be applied to protect native forest species and exclude incursive ones from farmlands and human residences at early succession stage.
RXLR effector diversity in Phytophthora infestans isolates determines recognition by potato resistance proteins; the case study AVR1 and R1
Du, Y. ; Weide, R. ; Zhao, Z. ; Msimuko, P. ; Govers, F. ; Bouwmeester, K. - \ 2018
Studies in Mycology 89 (2018). - ISSN 0166-0616 - p. 85 - 93.
Effector variation - Effector-triggered immunity (ETI) - Host defence - Late blight disease - Nucleotide-binding and leucine-rich repeat (NLR) protein - Potato resistance
Late blight disease caused by the plant pathogenic oomycete pathogen Phytophthora infestans is one of the most limiting factors in potato production. P. infestans is able to overcome introgressed late blight resistance by adaptation of effector genes. AVR1 is an RXLR effector that triggers immune responses when recognized by the potato resistance protein R1. P. infestans isolates avirulent on R1 plants were found to have AVR1 variants that are recognized by R1. Virulent isolates though, lack AVR1 but do contain a close homologue of AVR1, named A-L, of which all variants escape recognition by R1. Co-expression of AVR1 and R1 in Nicotiana benthamiana results in a hypersensitive response (HR). In contrast, HR is not activated when A-L is co-expressed with R1. AVR1 and A-L are highly similar in structure. They share two W motifs and one Y motif in the C-terminal part but differ in the T-region, a 38 amino acid extension at the carboxyl-terminal tail of AVR1 lacking in A-L. To pinpoint what determines R1-mediated recognition of AVR1 we tested elicitor activity of AVR1 and A-L chimeric and deletion constructs by co-expression with R1. The T-region is important as it enables R1-mediated recognition of A-L, not only when fused to A-L but also via trans-complementation. Yet, AVR1 lacking the T-region is still active as an elicitor of HR, but this activity is lost when certain motifs are swapped with A-L. These data show that A-L circumvents R1 recognition not only because it lacks the T-region, but also because of differences in the conserved C-terminal effector motifs.
Genetically engineering Crambe abyssinica- A potentially high-value oil crop for salt land improvement
Qi, W. ; Tinnenbroek-Capel, I.E.M. ; Salentijn, E.M.J. ; Zhang, Zhao ; Huang, Bangquan ; Cheng, Jihua ; Shao, Hongbo ; Visser, R.G.F. ; Krens, F.A. ; Loo, E.N. van - \ 2018
Land Degradation and Development 29 (2018)4. - ISSN 1085-3278 - p. 1096 - 1106.
Crambe abyssinica (crambe) is a new industrial oil crop that can grow on saline soil and tolerates salty water irrigation. Genetically engineered crambe in which the seed‐oil composition is manipulated for more erucic acid and less polyunsaturated fatty acid (PUFA) would be highly beneficial to industry. In this research, lysophosphatidic acid acyltransferase 2 RNA interference (CaLPAT2‐RNAi) was introduced into the crambe genome to manipulate its oil composition. The result showed in comparison with wild type, CaLPAT2‐RNAi could significantly reduce linoleic and linolenic acid content, simultaneously increasing erucic acid content. Systematic metabolism engineering was then carried out to further study CaLPAT2‐RNAi, combined with the overexpression of Brassica napus fatty acid elongase (BnFAE), Limnanthes douglasii LPAT (LdLPAT), and RNAi of endogenous fatty acid desaturase 2 (CaFAD2‐RNAi). Oil composition analysis on the tranformants' seeds showed that (a) with CaFAD2‐RNAi, PUFA content could be dramatically decreased, in comparison with BnFAE + LdLPAT + CaFAD2‐RNAi, and BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi seeds showed lower linolenic acid content; (b) BnFAE + LdLPAT + CaFAD2‐RNAi + CaLPAT2‐RNAi could increase the erucic acid content in crambe seed oil from less than 66.6% to 71.6%, whereas the highest erucic acid content of BnFAE + LdLPAT + CaFAD2‐RNAi was 79.2%; (c) although the four‐gene combination could not increase the erucic acid content of seed oil to a higher level than the others, it led to increased carbon resource deposited into C22:1 and C18:1 moieties and lower PUFA. Summarily, the present research indicates that suppression of LPAT2 is a new, promising strategy for seed‐oil biosynthesis pathway engineering, which would increase the value of crambe oil.
Publisher Correction : Enterotypes in the landscape of gut microbial community composition
Costea, Paul I. ; Hildebrand, Falk ; Arumugam, Manimozhiyan ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O’Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276
In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
Greenhouse gas and ammonia emissions and mitigation options from livestock production in peri-urban agriculture : Beijing – A case study
Wei, S. ; Bai, Z.H. ; Chadwick, D. ; Hou, Y. ; Qin, W. ; Zhao, Z.Q. ; Jiang, R.F. ; Ma, L. - \ 2018
Journal of Cleaner Production 178 (2018). - ISSN 0959-6526 - p. 515 - 525.
Climate change - Manure management - Mitigation option - Temporal and spatial variation - Urban livestock production
Livestock production in peri-urban areas constitutes an important sub-sector of the agricultural production system in China, and contributes to environmental degradation and local air borne pollution contributing to smog. As a result, local policies are being implemented to safeguard the environment. However, there has been little attempt to quantify the impact of environmental policies on livestock production structure, spatial distribution and their related greenhouse gases (GHGs) and ammonia (NH3) emissions. Here, we calculated the inventories of GHGs and NH3 emissions for 2010 and 2014 for peri-urban livestock production in Beijing, using reliable spatially explicit data, which was collected from 1748 industrial farms in 2010 and 2351 industrial farms in 2014, including pig, dairy, beef cattle, poultry and sheep farms. Our estimates indicated that total industrial livestock production increased by 17% between 2010 and 2014, even under the more strict environmental protection polices, with farm size decreasing by between 7% and 47%. Up to 50% of the industrial livestock farms have remained in operation, with the rest closing down or being moved to other regions. Following this trend, total GHGs emission decreased from 5.0 to 4.5 Tg CO2-eq between 2010 and 2014. Most of the GHGs emission reduction was due to the lowering of energy related carbon dioxide (CO2) emission in 2014. Total NH3 emission decreased from 102 to 96 Gg between 2010 and 2014, mainly due to more stringent environmental regulations for new and extended farms (increased in farm size), e.g. Discharge standard for pollutants for livestock and poultry breeding. Our study identified that GHGs and NH3 emission hotspots were concentrated in suburban areas (around the city centre and with less agricultural resource and population density) in 2010. However, between 2010 and 2014 these hotspots moved to the exurban plain and mountain area following the closure or sub-division of intensive farms in suburban regions and construction of new and small farms in exurban areas (around the suburban and with more agricultural resource and lower population density). Scenario analysis suggests that total GHGs emission can be reduced by up to 1.0 Tg CO2-eq (23% of total livestock sector emissions) in Beijing, using a combination of modifications of farm type, livestock diet and manure management. The integrated scenario can reduce CH4, N2O and NH3 emissions by 27%, 9% and 35%, compared to the reference scenario. Within this short period of time (5 years), policies have had direct impacts on peri-urban livestock production in Beijing, resulting in marked changes in the structure of different livestock sectors, as well as the GHGs and NH3 emission inventories and their spatial distribution. Our analysis clearly shows that the success of these (and future) polices relies on optimizing spatial management of new livestock production systems. Policy and farmer guidance should focus on optimizing livestock diet and on-farm manure management, industrial production systems and the pig and poultry sectors in peri-urban regions.
Global environmental costs of China's thirst for milk
Bai, Zhaohai ; Lee, Michael R.F. ; Ma, Lin ; Ledgard, Stewart ; Velthof, Gerard L. ; Ma, Wenqi ; Guo, Mengchu ; Zhao, Zhanqing ; Wei, Sha ; Li, Shengli ; Liu, Xia ; Havlík, Petr ; Luo, Jiafa ; Hu, Chunsheng ; Zhang, Fusuo - \ 2018
Global Change Biology 24 (2018)5. - ISSN 1354-1013 - p. 2198 - 2211.
Cattle feed - Greenhouse gas - Land use, nitrogen losses - Milk trade - Shared socio-economic pathways scenarios
China has an ever-increasing thirst for milk, with a predicted 3.2-fold increase in demand by 2050 compared to the production level in 2010. What are the environmental implications of meeting this demand, and what is the preferred pathway? We addressed these questions by using a nexus approach, to examine the interdependencies of increasing milk consumption in China by 2050 and its global impacts, under different scenarios of domestic milk production and importation. Meeting China's milk demand in a business as usual scenario will increase global dairy-related (China and the leading milk exporting regions) greenhouse gas (GHG) emissions by 35% (from 565 to 764 Tg CO 2eq ) and land use for dairy feed production by 32% (from 84 to 111 million ha) compared to 2010, while reactive nitrogen losses from the dairy sector will increase by 48% (from 3.6 to 5.4 Tg nitrogen). Producing all additional milk in China with current technology will greatly increase animal feed import; from 1.9 to 8.5 Tg for concentrates and from 1.0 to 6.2 Tg for forage (alfalfa). In addition, it will increase domestic dairy related GHG emissions by 2.2 times compared to 2010 levels. Importing the extra milk will transfer the environmental burden from China to milk exporting countries; current dairy exporting countries may be unable to produce all additional milk due to physical limitations or environmental preferences/legislation. For example, the farmland area for cattle-feed production in New Zealand would have to increase by more than 57% (1.3 million ha) and that in Europe by more than 39% (15 million ha), while GHG emissions and nitrogen losses would increase roughly proportionally with the increase of farmland in both regions. We propose that a more sustainable dairy future will rely on high milk demanding regions (such as China) improving their domestic milk and feed production efficiencies up to the level of leading milk producing countries. This will decrease the global dairy related GHG emissions and land use by 12% (90 Tg CO 2eq reduction) and 30% (34 million ha land reduction) compared to the business as usual scenario, respectively. However, this still represents an increase in total GHG emissions of 19% whereas land use will decrease by 8% when compared with 2010 levels, respectively.
Effect of soil surface roughness on infiltration water, ponding and runoff on tilled soils under rainfall simulation experiments
Zhao, Longshan ; Hou, Rui ; Wu, Faqi ; Keesstra, Saskia - \ 2018
Soil & Tillage Research 179 (2018). - ISSN 0167-1987 - p. 47 - 53.
Depression storage - Soil infiltration - Surface runoff - Tillage - Water erosion
Agriculture has a large effect on the properties of the soil and with that on soil hydrology. The partitioning of rainfall into infiltration and runoff is relevant to understand runoff generation, infiltration and soil erosion. Tillage manages soil surface properties and generates soil surface roughness (SSR) that affects the partitioning of the rainfall. The objective of this study was to quantify the amount of rainwater that infiltrates, is temporarily stored in surface depressions and flows out of the surfaces during rainfall events. A set of tillage-induced rough surfaces with slope steepness of 10° and 15° was used under simulated rainfall, and a smooth surface served as a control. Rainfall intensities were 60 and 120 mm h−1, and two soil erosion periods, overland flow erosion period (OFEP) and rill flow erosion period (RFEP), were monitored for each rainfall intensity. The results showed that for OFEP, infiltration water was 58% and 76% of the total rainwater on the rough surfaces and was approximately 1.5 and 2 times greater than that on the smooth surfaces for the different rainfall intensities. The surface runoff was consistently small for the OFEP but significantly increased for the RFEP. For example, for the RFEP, the amount of surface runoff was up to 78.66% of the total rainwater on the rough surfaces under rainfall of 120 mm h−1 in intensity. The amount of rainwater stored in surface depressions was significantly less than infiltration water and surface runoff for all conditions. The mean transformation ratio of rainwater into surface depression storage, infiltration water and surface runoff in the OFEP and RFEP was 0.07:0.49:0.44 for the rough surfaces and 0.01:0.29:0.70 for the smooth surfaces. For the tilled surfaces, more than 50% of rainwater was be harvested through tillage technique during a rainfall event, whereas for the smooth surfaces, only 29% of rainwater. Our result will be useful when evaluating the impact of tillage on soil moisture content and even studying soil erosion in agriculture land.
Soil protist communities form a dynamic hub in the soil microbiome
Xiong, Wu ; Jousset, Alexandre ; Guo, Sai ; Karlsson, Ida ; Zhao, Qingyun ; Wu, Huasong ; Kowalchuk, George A. ; Shen, Qirong ; Li, Rong ; Geisen, Stefan - \ 2018
ISME Journal 12 (2018)2. - ISSN 1751-7362 - p. 634 - 638.
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.
An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple
Xie, Yinpeng ; Chen, Pengxiang ; Yan, Yan ; Bao, Chana ; Li, Xuewei ; Wang, Liping ; Shen, Xiaoxia ; Li, Haiyan ; Liu, Xiaofang ; Niu, Chundong ; Zhu, Chen ; Fang, Nan ; Shao, Yun ; Zhao, Tao ; Yu, Jiantao ; Zhu, Jianhua ; Xu, Lingfei ; Nocker, Steven van; Ma, Fengwang ; Guan, Qingmei - \ 2018
New Phytologist 218 (2018)1. - ISSN 0028-646X - p. 201 - 218.
Apple (Malus × domestica) - C-REPEAT BINDING FACTOR (CBF) - Cold hardiness - MdMYB124 - MdMYB88
Apple (Malus × domestica) trees are vulnerable to freezing temperatures. However, there has been only limited success in developing cold-hardy cultivars. This lack of progress is due at least partly to lack of understanding of the molecular mechanisms of freezing tolerance in apple. In this study, we evaluated the potential roles for two R2R3 MYB transcription factors (TFs), MYB88 and the paralogous FLP (MYB124), in cold stress in apple and Arabidopsis. We found that MYB88 and MYB124 positively regulate freezing tolerance and cold-responsive gene expression in both apple and Arabidopsis. Chromatin-Immunoprecipitation-qPCR and electrophoretic mobility shift assays showed that MdMYB88/MdMYB124 act as direct regulators of the COLD SHOCK DOMAIN PROTEIN 3 (MdCSP3) and CIRCADIAN CLOCK ASSOCIATED 1 (MdCCA1) genes. Dual luciferase reporter assay indicated that MdCCA1 but not MdCSP3 activated the expression of MdCBF3 under cold stress. Moreover, MdMYB88 and MdMYB124 promoted anthocyanin accumulation and H2O2 detoxification in response to cold. Taken together, our results suggest that MdMYB88 and MdMYB124 positively regulate cold hardiness and cold-responsive gene expression under cold stress by C-REPEAT BINDING FACTOR (CBF)-dependent and CBF-independent pathways.
Short communication : Growth of dairy isolates of Geobacillus thermoglucosidans in skim milk depends on lactose degradation products supplied by Anoxybacillus flavithermus as secondary species
Zhao, Y. ; Kumar, M. ; Caspers, M.P.M. ; Nierop Groot, M.N. ; Vossen, J.M.B.M. van der; Abee, T. - \ 2018
Journal of Dairy Science 101 (2018)2. - ISSN 0022-0302 - p. 1013 - 1019.
Symbiosis - Thermophile - Thermoresistant spore
Thermophilic bacilli such as Anoxybacillus and Geobacillus are important contaminants in dairy powder products. Remarkably, one of the common contaminants, Geobacillus thermoglucosidans, showed poor growth in skim milk, whereas significant growth of G. thermoglucosidans was observed in the presence of an Anoxybacillus flavithermus dairy isolate. In the present study, we investigated the underlying reason for this growth dependence of G. thermoglucosidans. Whole-genome sequences of 4 A. flavithermus strains and 4 G. thermoglucosidans strains were acquired, with special attention given to carbohydrate utilization clusters and proteolytic enzymes. Focusing on traits relevant for dairy environments, comparative genomic analysis revealed that all G. thermoglucosidans strains lacked the genes necessary for lactose transport and metabolism, showed poor growth in skim milk, and produced white colonies on X-gal plates, indicating the lack of β-galactosidase activity. The A. flavithermus isolates scored positive in these tests, consistent with the presence of a putative lactose utilization gene cluster. All tested isolates from both species showed proteolytic activity on milk plate count agar plates. Adding glucose or galactose to liquid skim milk supported growth of G. thermoglucosidans isolates, in line with the presence of the respective monosaccharide utilization gene clusters in the genomes. Analysis by HPLC of A. flavithermus TNO-09.006 culture filtrate indicated that the previously described growth dependence of G. thermoglucosidans in skim milk was based on the supply of glucose and galactose by A. flavithermus TNO-09.006.
Effects of temperature, genetic variation and species competition on the sensitivity of algae populations to the antibiotic enrofloxacin
Rico, Andreu ; Zhao, Wenkai ; Gillissen, Frits ; Lürling, Miquel ; Brink, Paul J. van den - \ 2018
Ecotoxicology and Environmental Safety 148 (2018). - ISSN 0147-6513 - p. 228 - 236.
Antibiotics - Cyanobacteria - Green algae - Species competition - Temperature-dependent sensitivity

Primary producers are amongst the most sensitive organisms to antibiotic pollution in aquatic ecosystems. To date, there is little information on how different environmental conditions may affect their sensitivity to antibiotics. In this study we assessed how temperature, genetic variation and species competition may affect the sensitivity of the cyanobacterium Microcystis aeruginosa and the green-algae Scenedesmus obliquus to the antibiotic enrofloxacin. First, we performed single-species tests to assess the toxicity of enrofloxacin under different temperature conditions (20 °C and 30 °C) and to assess the sensitivity of different species strains using a standard temperature (20 °C). Next, we investigated how enrofloxacin contamination may affect the competition between M. aeruginosa and S. obliquus. A competition experiment was performed following a full factorial design with different competition treatments, defined as density ratios (i.e. initial bio-volume of 25/75%, 10/90% and 1/99% of S. obliquus/M. aeruginosa, respectively), one 100% S. obliquus treatment and one 100% M. aeruginosa treatment, and four different enrofloxacin concentrations (i.e. control, 0.01, 0.05 and 0.10 mg/L). Growth inhibition based on cell number, bio-volume, chlorophyll-a concentration as well as photosynthetic activity were used as evaluation endpoints in the single-species tests, while growth inhibition based on measured chlorophyll-a was primarily used in the competition experiment. M. aeruginosa photosynthetic activity was found to be the most sensitive endpoint to enrofloxacin (EC50–72 h =0.02 mg/L), followed by growth inhibition based on cell number. S. obliquus was found to be slightly more sensitive at 20 °C than at 30 °C (EC50–72 h cell number growth inhibition of 38 and 41 mg/L, respectively), whereas an opposite trend was observed for M. aeruginosa (0.047 and 0.037 mg/L, respectively). Differences in EC50–72 h values between algal strains of the same species were within a factor of two. The competition experiment showed that M. aeruginosa growth can be significantly reduced in the presence of S. obliquus at a density ratio of 75/25% M. aeruginosa/S. obliquus, showing a higher susceptibility to enrofloxacin than in the single-species test. The results of this study confirm the high sensitivity of cyanobacteria to antibiotics and show that temperature and inter-strain genetic variation may have a limited influence on their response to them. The results of the competition experiment suggest that the structure of primary producer communities can be affected, at least temporarily, at antibiotic concentrations close to those that have been measured in the environment.

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