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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The red bayberry genome and genetic basis of sex determination
Jia, Hui Min ; Jia, Hui Juan ; Cai, Qing Le ; Wang, Yan ; Zhao, Hai Bo ; Yang, Wei Fei ; Wang, Guo Yun ; Li, Ying Hui ; Zhan, Dong Liang ; Shen, Yu Tong ; Niu, Qing Feng ; Chang, Le ; Qiu, Jie ; Zhao, Lan ; Xie, Han Bing ; Fu, Wan Yi ; Jin, Jing ; Li, Xiong Wei ; Jiao, Yun ; Zhou, Chao Chao ; Tu, Ting ; Chai, Chun Yan ; Gao, Jin Long ; Fan, Long Jiang ; Weg, Eric van de; Wang, Jun Yi ; Gao, Zhong Shan - \ 2018
Plant Biotechnology Journal (2018). - ISSN 1467-7644
genome - Morella rubra - sex-determining region - sex-linked marker

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

Apparent ileal digestibility of Maillard reaction products in growing pigs
Salazar-Villanea, Sergio ; Butré, Claire I. ; Wierenga, Peter A. ; Bruininx, Erik M.A.M. ; Gruppen, Harry ; Hendriks, Wouter H. ; Poel, Antonius F.B. van der - \ 2018
PLoS One 13 (2018)7. - ISSN 1932-6203

The absorption of Maillard reaction products (MRP) from dietary origin has been linked to the occurrence of chronic diseases. The aim of the present study was to determine the effects of toasting time of rapeseed meal (RSM) and the processing method of the diets (pelleting and extrusion) that included RSM on the apparent ileal digestibility (AID) of total lysine, fructosyl-lysine (FL), carboxymethyl-lysine (CML), carboxyethyl-lysine (CEL), lanthionine (LAN) and lysinoalanine (LAL) in growing pigs. The study consisted of a 2×3 factorial design with toasting time of RSM (60, 120 min) and diet processing method (mash, pelleted, extruded) as factors. Fifty growing pigs were individually fed one of the experimental diets for 4.5 consecutive days. Following euthanasia, samples of digesta were collected from the terminal 1.5 m of the small intestine. Increasing the toasting time of RSM increased the contents of FL, CML and CEL, whereas the additional effects of the diet processing methods were relatively small. Lysinoalanine and lanthionine were not detected in the diets; therefore, digestibility of these compounds could not be determined. The contents of FL, CML and CEL in the ileal chyme were positively correlated to their contents in the diets. The AID of the MRP from thermally-treated RSM were overall low and were not related to their contents in the diets. The AID of FL ranged between -8.5 and 19.1%, whilst AID of CML and CEL ranged from -0.2 to 18.3 and 3.6 to 30%, respectively. In conclusion, thermal treatments have clear effects on the contents of MRP in the diets. These compounds have relatively low digestibility in growing pigs.

Effects of different solid carbon sources on water quality, biofloc quality and gut microbiota of Nile tilapia (Oreochromis niloticus) larvae
Li, Jiawei ; Liu, Gang ; Li, Changwei ; Deng, Yale ; Tadda, Musa Abubakar ; Lan, Lihua ; Zhu, Songming ; Liu, Dezhao - \ 2018
Aquaculture 495 (2018). - ISSN 0044-8486 - p. 919 - 931.
Biofloc technology - Gut microbiota - Solid carbon source - Water quality

External carbon source is needed for biofloc system to maintain an optimal C/N ratio for the growth of bacteria biomass. In this study, three solid-phase biodegradable compounds, including Longan powder (LP), polyhydroxybutyrate-hydroxyvalerate/LP (PHBVL) and Poly(butylene succinate)/LP (PBSL), were utilized to feed biofloc-based aquaculture systems in triplicates for nine Nile tilapia (Oreochromis niloticus) larvae culture tanks. LP was applied in the in-situ biofloc system as a “control group” (3 tanks), while PHBVL and PBSL were used in the ex-situ biofloc systems (6 tanks). During the 120-days experiment, the C/N ratio was maintained at 24.87 ± 5.66, 22.93 ± 3.20 and 23.12 ± 3.54 for the LP, PHBVL and PBSL groups, respectively. There were no significant differences (P >.05) of the averaged total ammonia nitrogen (TAN) concentration among the LP, PHBVL and PBSL groups (1.10 ± 1.18, 0.67 ± 0.38 and 1.18 ± 1.40 mg L−1). Significant differences of the averaged NO2 -N concentrations (0.26 ± 0.38, 0.01 ± 0.01 and 0.08 ± 0.12 mg L−1) were detected among the LP, PHBVL and PBSL groups (P <.05). The accumulation of NO3 -N in LP group (>40 mg L−1 on day 120) was significantly higher than that of PHBVL and PBSL groups (about 2–3 mg L−1 on day 120) (P <.05). To characterize the quality of biofloc, the median diameters (D50) and essential amino acids index (EAAI) were measured for three treatments. The D50 (124.7 ± 4.24, 131.6 ± 2.83 and 175.5 ± 9.19 μm) and EAAI (0.969 ± 0.011, 1.007 ± 0.014 and 0.995 ± 0.012) showed that the high quality bioflocs in the LP, PHBVL and PBSL groups could meet the requirement for feeding the aquatic animals. In addition, high throughput sequencing test showed that solid carbon source not only had a significant effect on the microbial community in bioflocs, but also on the composition of fish gut microbiota. Bacillus was the dominating genus discovered in all treatments (48.34% in LP, 49.24% in PHBVL and 50.47% in PBSL) by 16S rRNA sequencing. Overall, blending LP with biodegradable polymers as carbon source showed significantly higher removal efficiency of nitrate and nitrite nitrogen, and higher biofloc quality than using LP as the only carbon source. How exactly various solid carbon sources influence fish growth performance and health need further study.

The preferential retention of VIZn over IVZn on birnessite during dissolution/desorption
Qin, Zhangjie ; Yin, Hui ; Wang, Xiaoming ; Zhang, Qin ; Lan, Shuai ; Koopal, Luuk K. ; Zheng, Lirong ; Feng, Xionghan ; Liu, Fan - \ 2018
Applied Clay Science 161 (2018). - ISSN 0169-1317 - p. 169 - 175.
Birnessite - Desorption - Dissolution - Extended X-ray absorption fine structure spectroscopy - Zinc coordination
Zn is a common heavy metal in soils and sediments. In this study, the release behaviors of octahedral (VIZn) and tetrahedral (IVZn) Zn complexes on synthesized hexagonal birnessite were explored by solution chemistry method in combination with spectroscopic analysis. In acidic dissolution processes, the release of adsorbed Zn2+ from birnessite occurred into two stages: in the first stage, ~60% of Zn2+ was desorbed rapidly, with only 8% of Mn being released, and the ratio of VIZn/IVZn increased with time; in the second stage, the residual Zn2+ was mostly VIZn and released slowly at a nearly constant rate until complete dissolution of the matrix mineral was observed. During desorption of Zn2+ by Pb2+, the ratio of VIZn/IVZn on birnessite also increased, while the residual percentage of VIZn remained nearly constant. However, it is known that IVZn-triple corner-sharing (TCS) is more stable than VIZn-TCS, suggesting that part of the remaining IVZn-TCS on birnessite might transform to VIZn-TCS immediately when VIZn-TCS is replaced by H+ or Pb2+. Additionally, the possible distribution of Mn3+ and IVZn or the partial charge compensation by protons can lead to the preferential retention of VIZn on birnessite or the preferential re-adsorption of VIZn at the new edge sites. These results can provide new insights into the geochemical behavior of Zn2+ contaminant in soil and aquatic environments.
How do land rental markets affect household income? Evidence from rural Jiangsu, P.R. China
Zhang, Lan ; Feng, Shuyi ; Heerink, Nico ; Qu, Futian ; Kuyvenhoven, Arie - \ 2018
Land Use Policy 74 (2018). - ISSN 0264-8377 - p. 151 - 165.
China - Household income - Income components - Income distribution - Land rental market - Quantile regression
The development of land rental markets in developing countries attracts much attention, but little is known about its impact on household income. This study empirically examines the effects of land rental decisions of farm households on their income and income components, i.e. farm, off-farm and transfer income, taking into account potential endogeneity of land rental decisions. Rural household survey data for 1080 households in 128 villages in Jiangsu Province, China are used to estimate these effects. Quantile regressions are used to examine to what extent effects differ between income groups. Results indicate that lessor households surprisingly obtain lower total income as compared to autarkic households. Among the lessee households, who gain on average from land rentals, the lower income groups obtain the largest total income gains. As to the sources of income, no significant differences in off-farm income between transacting households (i.e. lessee or lessor households) and autarkic households are found while differences in farm income between transacting households are as expected. Transfer income of lessor households is significantly lower than that of autarkic households. We explain these findings from some typical features of the rural land rental market in China and discuss the policy implications.
Phylogenetic classification of the world's tropical forests
Slik, J.W.F. ; Franklin, Janet ; Arroyo-Rodríguez, Víctor ; Field, Richard ; Aguilar, Salomon ; Aguirre, Nikolay ; Ahumada, Jorge ; Aiba, Shin Ichiro ; Alves, Luciana F. ; Anitha, K. ; Avella, Andres ; Mora, Francisco ; Aymard, Gerardo A.C. ; Báez, Selene ; Balvanera, Patricia ; Bastian, Meredith L. ; Bastin, Jean François ; Bellingham, Peter J. ; Berg, Eduardo Van Den; Conceição Bispo, Polyanna Da; Boeckx, Pascal ; Boehning-Gaese, Katrin ; Bongers, Frans ; Boyle, Brad ; Brambach, Fabian ; Brearley, Francis Q. ; Brown, Sandra ; Chai, Shauna Lee ; Chazdon, Robin L. ; Chen, Shengbin ; Chhang, Phourin ; Chuyong, George ; Ewango, Corneille ; Coronado, Indiana M. ; Cristóbal-Azkarate, Jurgi ; Culmsee, Heike ; Damas, Kipiro ; Dattaraja, H.S. ; Davidar, Priya ; DeWalt, Saara J. ; Din, Hazimah ; Drake, Donald R. ; Duque, Alvaro ; Durigan, Giselda ; Eichhorn, Karl ; Eler, Eduardo Schmidt ; Enoki, Tsutomu ; Ensslin, Andreas ; Fandohan, Adandé Belarmain ; Farwig, Nina ; Feeley, Kenneth J. ; Fischer, Markus ; Forshed, Olle ; Garcia, Queila Souza ; Garkoti, Satish Chandra ; Gillespie, Thomas W. ; Gillet, Jean Francois ; Gonmadje, Christelle ; Granzow-De La Cerda, Iñigo ; Griffith, Daniel M. ; Grogan, James ; Hakeem, Khalid Rehman ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andy ; Hemp, Andreas ; Homeier, Jürgen ; Hussain, M.S. ; Ibarra-Manríquez, Guillermo ; Hanum, I.F. ; Imai, Nobuo ; Jansen, Patrick A. ; Joly, Carlos Alfredo ; Joseph, Shijo ; Kartawinata, Kuswata ; Kearsley, Elizabeth ; Kelly, Daniel L. ; Kessler, Michael ; Killeen, Timothy J. ; Kooyman, Robert M. ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Letcher, Susan G. ; Lindsell, Jeremy ; Lovett, Jon ; Lozada, Jose ; Lu, Xinghui ; Lykke, Anne Mette ; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana ; Mansor, Asyraf ; Marshall, Andrew R. ; Martin, Emanuel H. ; Matos, Darley Calderado Leal ; Meave, Jorge A. ; Melo, Felipe P.L. ; Mendoza, Zhofre Huberto Aguirre ; Metali, Faizah ; Medjibe, Vincent P. ; Metzger, Jean Paul ; Metzker, Thiago ; Mohandass, D. ; Munguía-Rosas, Miguel A. ; Muñoz, Rodrigo ; Nurtjahy, Eddy ; Oliveira, Eddie Lenza De; Onrizal, ; Parolin, Pia ; Parren, Marc ; Parthasarathy, N. ; Paudel, Ekananda ; Perez, Rolando ; Pérez-García, Eduardo A. ; Pommer, Ulf ; Poorter, Lourens ; Qi, Lan ; Piedade, Maria Teresa F. ; Pinto, José Roberto Rodrigues ; Poulsen, Axel Dalberg ; Poulsen, John R. ; Powers, Jennifer S. ; Prasad, Rama Chandra ; Puyravaud, Jean Philippe ; Rangel, Orlando ; Reitsma, Jan ; Rocha, Diogo S.B. ; Rolim, Samir ; Rovero, Francesco ; Rozak, Andes ; Ruokolainen, Kalle ; Rutishauser, Ervan ; Rutten, Gemma ; Mohd Said, Mohd Nizam ; Saiter, Felipe Z. ; Saner, Philippe ; Santos, Braulio ; Santos, João Roberto Dos; Sarker, Swapan Kumar ; Schmitt, Christine B. ; Schoengart, Jochen ; Schulze, Mark ; Sheil, Douglas ; Sist, Plinio ; Souza, Alexandre F. ; Spironello, Wilson Roberto ; Sposito, Tereza ; Steinmetz, Robert ; Stevart, Tariq ; Suganuma, Marcio Seiji ; Sukri, Rahayu ; Sultana, Aisha ; Sukumar, Raman ; Sunderland, Terry ; Supriyadi, S. ; Suresh, H.S. ; Suzuki, Eizi ; Tabarelli, Marcelo ; Tang, Jianwei ; Tanner, Ed V.J. ; Targhetta, Natalia ; Theilade, Ida ; Thomas, Duncan ; Timberlake, Jonathan ; Morisson Valeriano, Márcio De; Valkenburg, Johan Van; Do, Tran Van; Sam, Hoang Van; Vandermeer, John H. ; Verbeeck, Hans ; Vetaas, Ole Reidar ; Adekunle, Victor ; Vieira, Simone A. ; Webb, Campbell O. ; Webb, Edward L. ; Whitfeld, Timothy ; Wich, Serge ; Williams, John ; Wiser, Susan ; Wittmann, Florian ; Yang, Xiaobo ; Yao, C.Y.A. ; Yap, Sandra L. ; Zahawi, Rakan A. ; Zakaria, Rahmad ; Zang, Runguo - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)8. - ISSN 0027-8424 - p. 1837 - 1842.
Biogeographic legacies - Forest classification - Forest functional similarity - Phylogenetic community distance - Tropical forests

Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northernhemisphere forests.

Field methods for sampling tree height for tropical forest biomass estimation
Sullivan, Martin J.P. ; Lewis, Simon L. ; Hubau, Wannes ; Qie, Lan ; Baker, Timothy R. ; Banin, Lindsay F. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Feldpausch, Ted R. ; Lopez-Gonzalez, Gabriela ; Arets, Eric ; Ashton, Peter ; Bastin, Jean François ; Berry, Nicholas J. ; Bogaert, Jan ; Boot, Rene ; Brearley, Francis Q. ; Brienen, Roel ; Burslem, David F.R.P. ; Canniere, Charles de; Chudomelová, Markéta ; Dančák, Martin ; Ewango, Corneille ; Hédl, Radim ; Lloyd, Jon ; Makana, Jean Remy ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Junior, Ben Hur Marimon ; Metali, Faizah ; Moore, Sam ; Nagy, Laszlo ; Vargas, Percy Nuñez ; Pendry, Colin A. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Rutishauser, Ervan ; Salim, Kamariah Abu ; Sonké, Bonaventure ; Sukri, Rahayu S. ; Sunderland, Terry ; Svátek, Martin ; Umunay, Peter M. ; Martinez, Rodolfo Vasquez ; Vernimmen, Ronald R.E. ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Phillips, Oliver L. - \ 2018
Methods in Ecology and Evolution 9 (2018)5. - ISSN 2041-210X - p. 1179 - 1189.
Above-ground biomass estimation - Allometry - Carbon stocks - Forest inventory - Forest structure - Sample size
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.
Additive effects of the herbicide glyphosate and elevated temperature on the branched coral Acropora formosa in Nha Trang, Vietnam
Amid, C. ; Olstedt, M. ; Gunnarsson, J.S. ; Lan, H. Le; Tran Thi Minh, H. ; Brink, P.J. van den; Hellström, M. ; Tedengren, M. - \ 2018
Environmental Science and Pollution Research 25 (2018)14. - ISSN 0944-1344 - p. 13360 - 13372.
Adaptation - Chlorophyll - Climate change - Coral bleaching - Digital image analysis - Genotype - Global warming - Pesticides - Tolerance - Zooxanthellae

The combined effects of the herbicide glyphosate and elevated temperature were studied on the tropical staghorn coral Acropora formosa, in Nha Trang bay, Vietnam. The corals were collected from two different reefs, one close to a polluted fish farm and one in a marine-protected area (MPA). In the laboratory, branches of the corals were exposed to the herbicide glyphosate at ambient (28 °C) and at 3 °C elevated water temperatures (31 °C). Effects of herbicide and elevated temperature were studied on coral bleaching using photography and digital image analysis (new colorimetric method developed here based on grayscale), chlorophyll a analysis, and symbiotic dinoflagellate (Symbiodinium, referred to as zooxanthellae) counts. All corals from the MPA started to bleach in the laboratory before they were exposed to the treatments, indicating that they were very sensitive, as opposed to the corals collected from the more polluted site, which were more tolerant and showed no bleaching response to temperature increase or herbicide alone. However, the combined exposure to the stressors resulted in significant loss of color, proportional to loss in chlorophyll a and zooxanthellae. The difference in sensitivity of the corals collected from the polluted site versus the MPA site could be explained by different symbiont types: the resilient type C3u and the stress-sensitive types C21 and C23, respectively. The additive effect of elevated temperatures and herbicides adds further weight to the notion that the bleaching of coral reefs is accelerated in the presence of multiple stressors. These results suggest that the corals in Nha Trang bay have adapted to the ongoing pollution to become more tolerant to anthropogenic stressors, and that multiple stressors hamper this resilience. The loss of color and decrease of chlorophyll a suggest that bleaching is related to concentration of chloro-pigments. The colorimetric method could be further fine-tuned and used as a precise, non-intrusive tool for monitoring coral bleaching in situ.

Blockchain for agriculture and food : Findings from the pilot study
Ge, Lan ; Brewster, Christopher ; Spek, Jacco ; Smeenk, Anton ; Top, Jan ; Diepen, Frans van; Klaase, Bob ; Graumans, Conny ; Ruyter de Wildt, Marieke de - \ 2017
Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2017-112) - ISBN 9789463438179 - 33
This report documents experiences and findings from the public private partnership (PPP) project ‘Blockchain for Agrifood’ that was started in March 2017. The project aims to contribute to a better understanding of the blockchain technology (BCT) and its implications for agrifood, especially how it can impact specific aspects of supply chains and what is needed to apply BCT in agrifood chains. A second aim of this project is to conceptualise and develop a proof of concept in an application based on a use case concerning table grapes from South Africa where BCT could be applied. This has been done by building a demonstrator that keeps track of different certificates involved in the table grapes supply chain. The code of this demonstrator is published at Github. Furthermore, the project explored issues regarding the relevance, applicability and implications of BCT for the agrifood sector through literature study and stakeholder consultation.
Nitrogen Fertilizer Replacement Value of Concentrated Liquid Fraction of Separated Pig Slurry Applied to Grassland
Middelkoop, J.C. Van; Holshof, G. - \ 2017
Communications in Soil Science and Plant Analysis 48 (2017)10. - ISSN 0010-3624 - p. 1132 - 1144.
Fertilizer replacement value - grassland - mineral concentrate - nitrogen
Seven grassland experiments on sandy and clay soils were performed during a period of 4 years to estimate the nitrogen (N) fertilizer replacement value (NFRV) of concentrated liquid fractions of separated pig slurry (mineral concentrate: MC). The risk of nitrate leaching when applying MC was compared to when applying mineral fertilizers. Grassland yields in 2009–2012 fertilized with MC were compared with grassland fertilized with two mineral fertilizers: granulated calcium ammonium nitrate and liquid ammonium nitrate (LAN). The mineral fertilizers comprised 50% nitrate-N and 50% ammonium-N, and MC comprised 95–100% ammonium-N. Treatment application rates included zero N and three incremental rates of N fertilization. The liquid fertilizers were shallow injected (0–5 cm). The NFRV of MCs was 75% on sandy and 58% on clay soil with granulated ammonium nitrate as reference, and 89% on sandy and 92% on clay soil with LAN as reference. Risk of nitrate leaching after application of MC, measured in residual soil mineral N post-growing season and N in the upper groundwater in the following spring, was equal to that for mineral fertilizers.
Self-amplified Amazon forest loss due to vegetation-atmosphere feedbacks
Zemp, Delphine Clara ; Schleussner, Carl Friedrich ; Barbosa, Henrique M.J. ; Hirota, Marina ; Montade, Vincent ; Sampaio, Gilvan ; Staal, Arie ; Wang-Erlandsson, Lan ; Rammig, Anja - \ 2017
Nature Communications 8 (2017). - ISSN 2041-1723
Big Data in Smart Farming – A review
Wolfert, Jacques ; Ge, Lan ; Verdouw, Cor ; Bogaardt, Marc Jeroen - \ 2017
Agricultural Systems 153 (2017). - ISSN 0308-521X - p. 69 - 80.
Agriculture - Business modelling - Data - Data infrastructure - Governance - Information and communication technology
Smart Farming is a development that emphasizes the use of information and communication technology in the cyber-physical farm management cycle. New technologies such as the Internet of Things and Cloud Computing are expected to leverage this development and introduce more robots and artificial intelligence in farming. This is encompassed by the phenomenon of Big Data, massive volumes of data with a wide variety that can be captured, analysed and used for decision-making. This review aims to gain insight into the state-of-the-art of Big Data applications in Smart Farming and identify the related socio-economic challenges to be addressed. Following a structured approach, a conceptual framework for analysis was developed that can also be used for future studies on this topic. The review shows that the scope of Big Data applications in Smart Farming goes beyond primary production; it is influencing the entire food supply chain. Big data are being used to provide predictive insights in farming operations, drive real-time operational decisions, and redesign business processes for game-changing business models. Several authors therefore suggest that Big Data will cause major shifts in roles and power relations among different players in current food supply chain networks. The landscape of stakeholders exhibits an interesting game between powerful tech companies, venture capitalists and often small start-ups and new entrants. At the same time there are several public institutions that publish open data, under the condition that the privacy of persons must be guaranteed. The future of Smart Farming may unravel in a continuum of two extreme scenarios: 1) closed, proprietary systems in which the farmer is part of a highly integrated food supply chain or 2) open, collaborative systems in which the farmer and every other stakeholder in the chain network is flexible in choosing business partners as well for the technology as for the food production side. The further development of data and application infrastructures (platforms and standards) and their institutional embedment will play a crucial role in the battle between these scenarios. From a socio-economic perspective, the authors propose to give research priority to organizational issues concerning governance issues and suitable business models for data sharing in different supply chain scenarios.
Digital compliance: perspectives of key stakeholders : (D3.2.2 & D3.2.3 Analysis of workshops and interviews)
Hoes, Anne-Charlotte ; Lan, Ge - \ 2017
Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2017-015) - ISBN 9789463430999 - 27
Different actors involved in organising agrifood chain transparency hold different views and expectations of farm data sharing and digital compliance in general and AgriPlace in particular. The findings are summarised into Strength, Weakness, Opportunity, and Threat (SWOT) matrices that enable the analysis of agreements and differences among different stakeholders. Reducing administrative burden alone provides limited value for farmers as the key users of the compliance platform. More value creation mechanisms should be explored, for example, by developing tools and methods for analysing compliance data and providing benchmarking information for improving farm performance. At the same time, concerns of privacy and data security should be adequately addressed. As a prototype compliance platform, the business case of Agriplace faces some uncertainties in the current phase of development. Proactive actions are recommended to establish alliance and align with key stakeholders in the value network in seeking collaborative value propositions. In particular, alignments with cooperatives, trade, retail and standards organisations (including compliance scheme owners) on data requirements and with other solution providers on data registration and re-use deserve top priority.
Business modelling for a digital compliance platform: taking stock and looking forward : (D3.2.1 Desk study and interviews)
Ge, Lan ; Doorneweert, Bart ; Bogaardt, Marc-Jeroen - \ 2017
Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2017-014) - ISBN 9789463430982 - 37
This study consists of a desk study on business models related to Ag data platforms and stakeholder consultation through interviews and stakeholder workshops (information on the interviews can be found in the Section References). An Ag data platform is interpreted as an IT-based interorganisational arrangement dealing with the collection, storage, exchange and use of Ag data. The scope of the desk study is limited to Ag data platforms with publicly available information on their key features. 8 | Wageningen Economic Research Report 2017-014 The objective of this study is to examine main types of business models that are used for developing Ag data platforms in agrifood chains and identify viable options that can be used for future development of the compliance platform envisaged by FarmDigital. More specifically, the research intends to provide answers to the following questions: What types of business models are being used for Ag data platforms? What features characterise the current landscape of Ag data platforms? What are the analogs and antilogs of the compliance platform envisaged by FarmDigital? What are the challenges and enabling options for future development of a compliance platform?
Diversity and carbon storage across the tropical forest biome
Sullivan, Martin J.P. ; Talbot, Joey ; Lewis, Simon L. ; Phillips, Oliver L. ; Qie, Lan ; Begne, Serge K. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Hubau, Wannes ; Lopez-Gonzalez, Gabriela ; Bongers, Frans ; Peña-Claros, Marielos ; Sheil, Douglas - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322

Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-Tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity.

Climate Change Adaptation Strategies for Freshwater Agriculture in the Coastal Mekong Delta : Farm-scale Opportunities and Water Management Challenges
Nhan, D.K. ; Phuong, To Lan ; Son, Nguyen Ngoc ; Ha, Vo Van ; Tin, Nguyen Hong ; Pham Dang Tri, V. ; Trung, Nguyen Hieu ; Bosma, R.H. ; Halsema, G.E. van - \ 2016
Tropicultura 34 (2016)special. - ISSN 0771-3312 - p. 120 - 120.
Climate Change - Water productivity - Rice - Aquaculture - southern vietnam
Impact assessment for digital compliance platform: a conceptual model (D3.1.1 Conceptual model for impact assessment)
Ge, Lan ; Hennen, Wil ; Doorneweert, Bart ; Bogaardt, Marc-Jeroen - \ 2016
Den Haag : Wageningen Economic Research (Report / Wageningen Economic Research 2016-063) - ISBN 9789462579545 - 21 p.
Nut van ICT-gebruik voor tuinbouwondernemers
Robbemond, Robbert ; Ge, Lan ; Puister, Linda ; Verdouw, Cor - \ 2016
Wageningen : Wageningen Economic Research (Rapport / Wageningen Economic Research 2016-051) - 98 p.
Functional ratios among leaf, xylem and phloem areas in branches change with shade tolerance, but not with local light conditions, across temperate tree species
Zhang, Lan ; Copini, Paul ; Weemstra, Monique ; Sterck, Frank - \ 2016
New Phytologist 209 (2016)4. - ISSN 0028-646X - p. 1566 - 1575.
Biomass allocation - Functional ratios - Leaf area - Phloem area - Ray parenchyma - Shade tolerance - Tree - Xylem area

Leaf, xylem and phloem areas drive the water and carbon fluxes within branches and trees, but their mutual coordination is poorly understood. We test the hypothesis that xylem and phloem areas increase relative to leaf area when species are selected for, or branches are exposed to, higher levels of light intensity. Trees of 10 temperate, broadleaved and deciduous, tree species were selected. Fifty-centimetre-long branches were collected from shaded and exposed conditions at a height of 3-4 m. We measured the total leaf area, xylem area, phloem area and leaf traits, as well as the area of the constituent cell types, for a stem section at the branch base. Xylem area : leaf area and phloem area : leaf area ratios did not differ consistently between sun and shade branches, but, as expected, they decreased with species' shade tolerance. Similar trends were observed for conductive cell areas in xylem and phloem. Trees of light-demanding species maintain higher water loss and carbon gain rates per leaf area by producing more xylem area and phloem area than shade-tolerant species. We call for more comparative branch studies as they provide an integrated biological perspective on functional traits and their role in the ecology of tree species.

Climate change: A virtual special issue with commentary for COP21 : Current Opinion in Environmental Sustainability provides free access to 29 articles on climate change
Brondizio, Eduardo S. ; Solecki, William ; Leemans, R. ; Song, Lan - \ 2015
Amsterdam : Elsevier
To support the efforts of the UN Conference on Climate Change 2015 (COP-21) in Paris, the Editors-in-Chief of Current Opinion in Environmental Sustainability (COSUST) have organized a Virtual Special Issue focusing on climate change.
Under the headings below, you will find their editorial, presenting the purpose of this special issue and current thinking about climate change and the challenges and opportunities for societal response.
The editors have selected a series of 29 articles that represent relevant themes in climate change research and policy. For each article, authors comment on recent developments related to their topic. All selected articles are freely available for six months until the middle of June 2016.
Check title to add to marked list
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