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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    Seed Sector Review in Nigeria : End of project report
    Thijssen, M.H. ; Boef, Walter de - \ 2020
    Wageningen Centre for Development Innovation, Wageningen University & Research (WCDI-20-109 ) - 28 p.
    The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
    Pastorello, Gilberto ; Trotta, Carlo ; Canfora, Eleonora ; Chu, Housen ; Christianson, Danielle ; Cheah, You Wei ; Poindexter, Cristina ; Chen, Jiquan ; Elbashandy, Abdelrahman ; Humphrey, Marty ; Isaac, Peter ; Polidori, Diego ; Ribeca, Alessio ; Ingen, Catharine van; Zhang, Leiming ; Amiro, Brian ; Ammann, Christof ; Arain, M.A. ; Ardö, Jonas ; Arkebauer, Timothy ; Arndt, Stefan K. ; Arriga, Nicola ; Aubinet, Marc ; Aurela, Mika ; Baldocchi, Dennis ; Barr, Alan ; Beamesderfer, Eric ; Marchesini, Luca Belelli ; Bergeron, Onil ; Beringer, Jason ; Bernhofer, Christian ; Berveiller, Daniel ; Billesbach, Dave ; Black, Thomas Andrew ; Blanken, Peter D. ; Bohrer, Gil ; Boike, Julia ; Bolstad, Paul V. ; Bonal, Damien ; Bonnefond, Jean Marc ; Bowling, David R. ; Bracho, Rosvel ; Brodeur, Jason ; Brümmer, Christian ; Buchmann, Nina ; Burban, Benoit ; Burns, Sean P. ; Buysse, Pauline ; Cale, Peter ; Cavagna, Mauro ; Cellier, Pierre ; Chen, Shiping ; Chini, Isaac ; Christensen, Torben R. ; Cleverly, James ; Collalti, Alessio ; Consalvo, Claudia ; Cook, Bruce D. ; Cook, David ; Coursolle, Carole ; Cremonese, Edoardo ; Curtis, Peter S. ; Andrea, Ettore D'; Rocha, Humberto da; Dai, Xiaoqin ; Davis, Kenneth J. ; Cinti, Bruno De; Grandcourt, Agnes de; Ligne, Anne De; Oliveira, Raimundo C. De; Delpierre, Nicolas ; Desai, Ankur R. ; Bella, Carlos Marcelo Di; Tommasi, Paul di; Dolman, Han ; Domingo, Francisco ; Dong, Gang ; Dore, Sabina ; Duce, Pierpaolo ; Dufrêne, Eric ; Dunn, Allison ; Dušek, Jiří ; Eamus, Derek ; Eichelmann, Uwe ; ElKhidir, Hatim Abdalla M. ; Eugster, Werner ; Ewenz, Cacilia M. ; Ewers, Brent ; Famulari, Daniela ; Fares, Silvano ; Feigenwinter, Iris ; Feitz, Andrew ; Fensholt, Rasmus ; Filippa, Gianluca ; Fischer, Marc ; Frank, John ; Galvagno, Marta ; Gharun, Mana ; Gianelle, Damiano ; Gielen, Bert ; Gioli, Beniamino ; Gitelson, Anatoly ; Goded, Ignacio ; Goeckede, Mathias ; Goldstein, Allen H. ; Gough, Christopher M. ; Goulden, Michael L. ; Graf, Alexander ; Griebel, Anne ; Gruening, Carsten ; Grünwald, Thomas ; Hammerle, Albin ; Han, Shijie ; Han, Xingguo ; Hansen, Birger Ulf ; Hanson, Chad ; Hatakka, Juha ; He, Yongtao ; Hehn, Markus ; Heinesch, Bernard ; Hinko-Najera, Nina ; Hörtnagl, Lukas ; Hutley, Lindsay ; Ibrom, Andreas ; Ikawa, Hiroki ; Jackowicz-Korczynski, Marcin ; Janouš, Dalibor ; Jans, Wilma ; Jassal, Rachhpal ; Jiang, Shicheng ; Kato, Tomomichi ; Khomik, Myroslava ; Klatt, Janina ; Knohl, Alexander ; Knox, Sara ; Kobayashi, Hideki ; Koerber, Georgia ; Kolle, Olaf ; Kosugi, Yoshiko ; Kotani, Ayumi ; Kowalski, Andrew ; Kruijt, Bart ; Kurbatova, Julia ; Kutsch, Werner L. ; Kwon, Hyojung ; Launiainen, Samuli ; Laurila, Tuomas ; Law, Bev ; Leuning, Ray ; Li, Yingnian ; Liddell, Michael ; Limousin, Jean Marc ; Lion, Marryanna ; Liska, Adam J. ; Lohila, Annalea ; López-Ballesteros, Ana ; López-Blanco, Efrén ; Loubet, Benjamin ; Loustau, Denis ; Lucas-Moffat, Antje ; Lüers, Johannes ; Ma, Siyan ; Macfarlane, Craig ; Magliulo, Vincenzo ; Maier, Regine ; Mammarella, Ivan ; Manca, Giovanni ; Marcolla, Barbara ; Margolis, Hank A. ; Marras, Serena ; Massman, William ; Mastepanov, Mikhail ; Matamala, Roser ; Matthes, Jaclyn Hatala ; Mazzenga, Francesco ; McCaughey, Harry ; McHugh, Ian ; McMillan, Andrew M.S. ; Merbold, Lutz ; Meyer, Wayne ; Meyers, Tilden ; Miller, Scott D. ; Minerbi, Stefano ; Moderow, Uta ; Monson, Russell K. ; Montagnani, Leonardo ; Moore, Caitlin E. ; Moors, Eddy ; Moreaux, Virginie ; Moureaux, Christine ; Munger, J.W. ; Nakai, Taro ; Neirynck, Johan ; Nesic, Zoran ; Nicolini, Giacomo ; Noormets, Asko ; Northwood, Matthew ; Nosetto, Marcelo ; Nouvellon, Yann ; Novick, Kimberly ; Oechel, Walter ; Olesen, Jørgen Eivind ; Ourcival, Jean Marc ; Papuga, Shirley A. ; Parmentier, Frans Jan ; Paul-Limoges, Eugenie ; Pavelka, Marian ; Peichl, Matthias ; Pendall, Elise ; Phillips, Richard P. ; Pilegaard, Kim ; Pirk, Norbert ; Posse, Gabriela ; Powell, Thomas ; Prasse, Heiko ; Prober, Suzanne M. ; Rambal, Serge ; Rannik, Üllar ; Raz-Yaseef, Naama ; Reed, David ; Dios, Victor Resco de; Restrepo-Coupe, Natalia ; Reverter, Borja R. ; Roland, Marilyn ; Sabbatini, Simone ; Sachs, Torsten ; Saleska, Scott R. ; Sánchez-Cañete, Enrique P. ; Sanchez-Mejia, Zulia M. ; Schmid, Hans Peter ; Schmidt, Marius ; Schneider, Karl ; Schrader, Frederik ; Schroder, Ivan ; Scott, Russell L. ; Sedlák, Pavel ; Serrano-Ortíz, Penélope ; Shao, Changliang ; Shi, Peili ; Shironya, Ivan ; Siebicke, Lukas ; Šigut, Ladislav ; Silberstein, Richard ; Sirca, Costantino ; Spano, Donatella ; Steinbrecher, Rainer ; Stevens, Robert M. ; Sturtevant, Cove ; Suyker, Andy ; Tagesson, Torbern ; Takanashi, Satoru ; Tang, Yanhong ; Tapper, Nigel ; Thom, Jonathan ; Tiedemann, Frank ; Tomassucci, Michele ; Tuovinen, Juha Pekka ; Urbanski, Shawn ; Valentini, Riccardo ; Molen, Michiel van der; Gorsel, Eva van; Huissteden, Ko van; Varlagin, Andrej ; Verfaillie, Joseph ; Vesala, Timo ; Vincke, Caroline ; Vitale, Domenico ; Vygodskaya, Natalia ; Walker, Jeffrey P. ; Walter-Shea, Elizabeth ; Wang, Huimin ; Weber, Robin ; Westermann, Sebastian ; Wille, Christian ; Wofsy, Steven ; Wohlfahrt, Georg ; Wolf, Sebastian ; Woodgate, William ; Li, Yuelin ; Zampedri, Roberto ; Zhang, Junhui ; Zhou, Guoyi ; Zona, Donatella ; Agarwal, Deb ; Biraud, Sebastien ; Torn, Margaret ; Papale, Dario - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463 - 1 p.

    The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

    The global abundance of tree palms
    Muscarella, Robert ; Emilio, Thaise ; Phillips, Oliver L. ; Lewis, Simon L. ; Slik, Ferry ; Baker, William J. ; Couvreur, Thomas L.P. ; Eiserhardt, Wolf L. ; Svenning, Jens Christian ; Affum-Baffoe, Kofi ; Aiba, Shin Ichiro ; Almeida, Everton C. de; Almeida, Samuel S. de; Oliveira, Edmar Almeida de; Álvarez-Dávila, Esteban ; Alves, Luciana F. ; Alvez-Valles, Carlos Mariano ; Carvalho, Fabrício Alvim ; Guarin, Fernando Alzate ; Andrade, Ana ; Aragão, Luis E.O.C. ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Ashton, Peter S. ; Corredor, Gerardo A.A. ; Baker, Timothy R. ; Camargo, Plinio Barbosa de; Barlow, Jos ; Bastin, Jean François ; Bengone, Natacha Nssi ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Böhning-Gaese, Katrin ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brambach, Fabian ; Brearley, Francis Q. ; Brewer, Steven W. ; Camargo, Jose L.C. ; Campbell, David G. ; Castilho, Carolina V. ; Castro, Wendeson ; Catchpole, Damien ; Cerón Martínez, Carlos E. ; Chen, Shengbin ; Chhang, Phourin ; Cho, Percival ; Chutipong, Wanlop ; Clark, Connie ; Collins, Murray ; Comiskey, James A. ; Medina, Massiel Nataly Corrales ; Costa, Flávia R.C. ; Culmsee, Heike ; David-Higuita, Heriberto ; Davidar, Priya ; Aguila-Pasquel, Jhon del; Derroire, Géraldine ; Fiore, Anthony Di; Do, Tran Van; Doucet, Jean Louis ; Dourdain, Aurélie ; Drake, Donald R. ; Ensslin, Andreas ; Erwin, Terry ; Ewango, Corneille E.N. ; Ewers, Robert M. ; Fauset, Sophie ; Feldpausch, Ted R. ; Ferreira, Joice ; Ferreira, Leandro Valle ; Fischer, Markus ; Franklin, Janet ; Fredriksson, Gabriella M. ; Gillespie, Thomas W. ; Gilpin, Martin ; Gonmadje, Christelle ; Gunatilleke, Arachchige Upali Nimal ; Hakeem, Khalid Rehman ; Hall, Jefferson S. ; Hamer, Keith C. ; Harris, David J. ; Harrison, Rhett D. ; Hector, Andrew ; Hemp, Andreas ; Herault, Bruno ; Pizango, Carlos Gabriel Hidalgo ; Honorio Coronado, Eurídice N. ; Hubau, Wannes ; Hussain, Mohammad Shah ; Ibrahim, Faridah Hanum ; Imai, Nobuo ; Joly, Carlos A. ; Joseph, Shijo ; Anitha, K. ; Kartawinata, Kuswata ; Kassi, Justin ; Killeen, Timothy J. ; Kitayama, Kanehiro ; Klitgård, Bente Bang ; Kooyman, Robert ; Labrière, Nicolas ; Larney, Eileen ; Laumonier, Yves ; Laurance, Susan G. ; Laurance, William F. ; Lawes, Michael J. ; Levesley, Aurora ; Lisingo, Janvier ; Lovejoy, Thomas ; Lovett, Jon C. ; Lu, Xinghui ; Lykke, Anne Mette ; Magnusson, William E. ; Mahayani, Ni Putu Diana ; Malhi, Yadvinder ; Mansor, Asyraf ; Peña, Jose Luis Marcelo ; Marimon-Junior, Ben H. ; Marshall, Andrew R. ; Melgaco, Karina ; Bautista, Casimiro Mendoza ; Mihindou, Vianet ; Millet, Jérôme ; Milliken, William ; Mohandass, D. ; Mendoza, Abel Lorenzo Monteagudo ; Mugerwa, Badru ; Nagamasu, Hidetoshi ; Nagy, Laszlo ; Seuaturien, Naret ; Nascimento, Marcelo T. ; Neill, David A. ; Neto, Luiz Menini ; Nilus, Rueben ; Vargas, Mario Percy Núñez ; Nurtjahya, Eddy ; Araújo, R.N.O. de; Onrizal, Onrizal ; Palacios, Walter A. ; Palacios-Ramos, Sonia ; Parren, Marc ; Paudel, Ekananda ; Morandi, Paulo S. ; Pennington, R.T. ; Pickavance, Georgia ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poedjirahajoe, Erny ; Poorter, Lourens ; Poulsen, John R. ; Prasad, P.R.C. ; Prieto, Adriana ; Puyravaud, Jean Philippe ; Qie, Lan ; Quesada, Carlos A. ; Ramírez-Angulo, Hirma ; Razafimahaimodison, Jean Claude ; Reitsma, Jan Meindert ; Requena-Rojas, Edilson J. ; Correa, Zorayda Restrepo ; Rodriguez, Carlos Reynel ; Roopsind, Anand ; Rovero, Francesco ; Rozak, Andes ; Lleras, Agustín Rudas ; Rutishauser, Ervan ; Rutten, Gemma ; Punchi-Manage, Ruwan ; Salomão, Rafael P. ; Sam, Hoang Van; Sarker, Swapan Kumar ; Satdichanh, Manichanh ; Schietti, Juliana ; Schmitt, Christine B. ; Marimon, Beatriz Schwantes ; Senbeta, Feyera ; Nath Sharma, Lila ; Sheil, Douglas ; Sierra, Rodrigo ; Silva-Espejo, Javier E. ; Silveira, Marcos ; Sonké, Bonaventure ; Steininger, Marc K. ; Steinmetz, Robert ; Stévart, Tariq ; Sukumar, Raman ; Sultana, Aisha ; Sunderland, Terry C.H. ; Suresh, Hebbalalu Satyanarayana ; Tang, Jianwei ; Tanner, Edmund ; Steege, Hans ter; Terborgh, John W. ; Theilade, Ida ; Timberlake, Jonathan ; Torres-Lezama, Armando ; Umunay, Peter ; Uriarte, María ; Gamarra, Luis Valenzuela ; Bult, Martin van de; Hout, Peter van der; Martinez, Rodolfo Vasquez ; Vieira, Ima Célia Guimarães ; Vieira, Simone A. ; Vilanova, Emilio ; Cayo, Jeanneth Villalobos ; Wang, Ophelia ; Webb, Campbell O. ; Webb, Edward L. ; White, Lee ; Whitfeld, Timothy J.S. ; Wich, Serge ; Willcock, Simon ; Wiser, Susan K. ; Young, Kenneth R. ; Zakaria, Rahmad ; Zang, Runguo ; Zartman, Charles E. ; Zo-Bi, Irié Casimir ; Balslev, Henrik - \ 2020
    Global Ecology and Biogeography (2020). - ISSN 1466-822X
    above-ground biomass - abundance patterns - Arecaceae - local abiotic conditions - Neotropics - pantropical biogeography - tropical rainforest - wood density

    Aim: Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location: Tropical and subtropical moist forests. Time period: Current. Major taxa studied: Palms (Arecaceae). Methods: We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co-occurring non-palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results: On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long-term climate stability. Life-form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non-tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above-ground biomass, but the magnitude and direction of the effect require additional work. Conclusions: Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

    Impact and Opportunities of Agroecological Intensification Strategies on Farm Performance : A Case Study of Banana-Based Systems in Central and South-Western Uganda
    Gambart, Clara ; Swennen, Rony ; Blomme, Guy ; Groot, Jeroen C.J. ; Remans, Roseline ; Ocimati, Walter - \ 2020
    Frontiers in Sustainable Food Systems 4 (2020). - ISSN 2571-581X
    agroecology - farm optimization - farm performance - farm typology - FarmDESIGN - nutritional yield - profitability - sustainability

    Agroecological intensification (AEI) practices relying on on-farm diversity tend to close nutrient cycles and reduce dependency on external inputs in agricultural systems. These practices improve the productivity of banana-based systems in Uganda, but their extent of implementation differs between and within regions. However, the impact of AEI practices on a broader range of objectives including environmental and nutritional objectives, is hardly quantified. Additionally, recommendations to improve the farm performance, given these options, are lacking. We, therefore, analyzed the current farm performance for these broad range of objectives and explored optimal farm reconfigurations in two Ugandan districts, one in Central Uganda and one in Southwestern (SW) Uganda. Given the heterogeneity of smallholder farms, a farm typology based on the applied AEI practices was developed. It classified the subsistence farms in Central Uganda into two extreme groups with an average of 11.0 and 16.4 AEI practices applied per farm. Farms in SW Uganda were moderately intensified (i.e., 13.0 practices). The FarmDESIGN model revealed a higher species diversity, relatively higher profitability (2,039 – 3,270 $/ha/year) and nutritional yield on farms in Central Uganda. However, relatively high soil erosion levels (0.243 – 0.240) and negative nitrogen (N) balances (−72 to −50 kg N/ha/year) were indicative of unsustainable practices. In contrast, farms in SW Uganda were less diverse and more market oriented. Their commercial orientation allowed investments in soil fertility management, resulting in more sustainable [low soil erosion level (0.172) and positive N balance (5 kg/ha/year)], but less profitable (506 $/ha/year) systems. To improve farm performance, bananas and other perennials played a key role. Explorations with Calliandra calothyrsus (Calliandra) hedgerow or Mucuna pruriens (Mucuna) cover crop increased on-farm mulch production, improved sustainability indicators and profitability. We conclude that AEI practices can improve farm performance, and a more intensive use would be beneficial. In addition, the FarmDESIGN model provides a useful tool for redesigning these farms, proposing different redesigns depending on farmers' objectives (profitability, productivity or sustainability), and for evaluating ex ante the impact of new agricultural measures on farm performance.

    Bioconversion efficiencies, greenhouse gas and ammonia emissions during black soldier fly rearing – A mass balance approach
    Parodi, Alejandro ; Boer, Imke J.M. de; Gerrits, Walter J.J. ; Loon, Joop J.A. van; Heetkamp, Marcel J.W. ; Schelt, Jeroen van; Bolhuis, J.E. ; Zanten, Hannah H.E. van - \ 2020
    Journal of Cleaner Production 271 (2020). - ISSN 0959-6526
    Ammonia - Bioconversion - Emissions - GHG - Hermetia illucens - Nitrogen

    Black soldier fly larvae (BSFL) are acknowledged for their potential to upcycle waste biomass into animal feed, human food or biofuels. To ensure sustainable BSFL rearing, insight into nutrient bioconversion efficiencies and nutrient losses via gaseous emissions is key. This study used a mass balance approach to quantify nutrient bioconversion efficiencies (i.e., carbon, energy, nitrogen, phosphorus and potassium) and gaseous emissions (i.e., greenhouse gasses and ammonia) of BSFL reared on a substrate used in industrial production. On this substrate, bioconversion efficiencies ranged from 14% (potassium) to 38% (nitrogen). The proportion of dietary inputs found in the residues ranged from 55% (energy) to 86% (potassium), while the proportion of dietary inputs lost via gaseous emissions ranged from 1% (nitrogen) to 24% (carbon). Direct emissions of methane and nitrous oxide during rearing were 16.8 ± 8.6 g CO2-equivalents per kg of dry BSFL biomass. Even though ammonia emissions were minimal, these could have been avoided if larvae would have been harvested before the CO2 peak was reached. Our results provide the first complete mass balance and comprehensive quantification of BSF larval metabolism and GHG emissions, required to assess and improve the environmental sustainability of BSFL production systems.

    Corporate Social Respondibly Manager: Job Roles, challenges and individual compentencies
    Osagie, E.R. ; Wesselink, R. - \ 2020
    In: Decent Work and Economic Growth / Filho, Walter Leal, Azul, Anabela Marisa, Brandli, Luciana, Lange Salvia, Amanda, Wall, Tony, Springer
    Effect of dietary fiber fermentation on short-chain fatty acid production and microbial composition in vitro
    Bai, Yu ; Zhao, Jin Biao ; Tao, Shi Yu ; Zhou, Xing Jian ; Pi, Yu ; Gerrits, Walter J.J. ; Johnston, Lee J. ; Zhang, Shi Yi ; Yang, Hong Jian ; Liu, Ling ; Zhang, Shuai ; Wang, Jun Jun - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)11. - ISSN 0022-5142 - p. 4282 - 4291.
    fiber-rich co-products - gas production - in vitro fermentation - microbial community - short chain fatty acid

    BACKGROUND: The efficient utilization of fiber-rich co-products is important for optimizing feed resource utilization and animal health. This study was conducted to evaluate the fermentation characteristics of fiber-rich co-products, which had equal quantities of total dietary fiber (TDF), at different time points using batch in vitro methods. It considered their gas production, short-chain fatty acid (SCFA) production, and microbial composition. RESULTS: The fermentation of wheat bran (WB) and oat bran (OB) showed higher and faster (P < 0.05) gas and SCFA production than corn bran (CB), sugar beet pulp (SBP), and soybean hulls (SH). The α-diversity was higher in the CB, SBP, and SH groups than in the WB and OB groups (P < 0.05). At the phylum level, OB and WB fermentation showed lower (P < 0.05) relative abundance of Actinobacteria than the CB, SBP, and SH groups. At the genus level, OB and WB fermentation increased the Enterococcus population in comparison with the CB, SBP, and SH groups, whereas CB and SBP fermentation improved the relative abundance of the Christensenellaceae R-7 group more than the WB, OB, and SH groups (P < 0.05). CONCLUSION: Overall, WB and OB were rapidly fermented by fecal microbiota, in contrast with SBP, SH, and CB. Fermentation of different fiber-rich co-products with an equal TDF content gives different responses in terms of microbial composition and SCFA production due to variations in their physicochemical properties and molecular structure.

    Caracterización de unidades de producción familiar agropecuarias mesoamericanas
    Reyna-Ramírez, Cristian A. ; Fuentes-Ponce, Mariela H. ; Rossing, Walter A.H. ; López-Ridaura, Santiago - \ 2020
    Agrociencia / Colegio de Postgraduados * Programa de Genetica I R E G E P 54 (2020)2. - ISSN 1405-3195 - p. 259 - 277.
    Dependence - Economic poly-activity - Family system - Multivariate analysis

    Farming policies tend to be homogeneous for an entire sector and encourage the implementation of technological innovations without considering the particular characteristics of smallholder farm systems (SFS). The objective of this study was to characterize the SFSs in the Oaxacan Mixteca, Mexico, and the highlands of Guatemala based on typologies, to know their diversity and to have elements to provide guidelines to generate development alternatives. The typology was constructed with information obtained from workshops, surveys and multivariate methods (PCA, cluster analysis and K-means). The variables that determined the diversity of the SFSs were investment capacity, remittances, type of work and livestock activities. The types of SFS identified in the Oaxacan Mixteca were: 1) farming, 2) dependent on external agricultural labours and low monetary income, 3) dependent on government programs, 4) with high non-agricultural income, and 5) medium external income. In the highlands of Guatemala: 1) semi-commercial farming, 2) commercial agriculture, 3) small subsistence, 4) small diversified income, and 5) semi-commercial agriculture. In the Oaxacan Mixteca region, the SFSs are self-consumption systems, dependent on external income (remittances and government programs), in which the potential for development lies in policies, according to the diversity of types and more efficient production systems. In Guatemala, the characteristics of the SFSs comply with global market chains, which regulate production and commercialization conditions, in which the potential for change lies in generating fairer market conditions and more efficient production systems linked to local non-governmental organizations (NGOs). The information obtained based on the typologies is useful for generating specific policies and programs of differentiated support, according to the types of systems and their context.

    The importance of amylase action in the porcine stomach to starch digestion kinetics
    Martens, Bianca M.J. ; Bruininx, Erik M.A.M. ; Gerrits, Walter J.J. ; Schols, Henk A. - \ 2020
    Animal Feed Science and Technology 267 (2020). - ISSN 0377-8401
    Bacteria - Dynamic stomach model - Extrusion - In vitro - pH dependency - Saliva

    Starch digestion in the proximal small intestine of pigs exceeds in vitro predictions, suggesting a currently underestimated role for the stomach in starch digestion kinetics. This study aimed to investigate the role of amylase action in the porcine stomach on starch digestion kinetics, including hydrolysis by porcine saliva and degradation by bacterial enzymes present in the stomach. We studied the hydrolysis of starch in pigs fed barley based diets, in which starch was included as isolated powder, ground barley, or extruded barley. We identified soluble maltodextrins originating from starch breakdown in stomach digesta, especially in pigs fed extruded barley. Furthermore, we observed bacterial cells embedded in granular starch with electron microscopy, for pigs fed diets containing isolated barley starch. These observations lead us to measure starch hydrolysis in a dynamic stomach model over the course of a 225 min incubation, in which the pH was step-wise decreased from 6.5 to 2.0. Using this method, feed was either exposed to an enzyme extract obtained from stomach digesta or to porcine saliva. Up to 30 % of starch was hydrolysed into maltodextrins with a degree of polymerisation (DP) <6 when starch was incubated with the enzyme extract obtained from the stomach. Under the same conditions, saliva amylase, with an optimum pH around 7.8, hydrolysed up to 10 % of processed starch into maltodextrins with DP < 6. We conclude that a substantial part of starch may be degraded into oligomers in the porcine stomach by both salivary and bacterial amylases. This implies a considerable role for the stomach on starch digestion kinetics, which is overlooked in current feed evaluation systems.

    Using 3D turbulence-resolving simulations to understand the impact of surface properties on the energy balance of a debris-covered glacier
    Bonekamp, Pleun N.J. ; Heerwaarden, Chiel C. Van; Steiner, Jakob F. ; Immerzeel, Walter W. - \ 2020
    Cryosphere 14 (2020)5. - ISSN 1994-0416 - p. 1611 - 1632.

    Debris-covered glaciers account for almost onefifth of the total glacier ice volume in High Mountain Asia; however, their contribution to the total glacier melt remains uncertain, and the drivers controlling this melt are still largely unknown. Debris influences the properties (e.g. albedo, thermal conductivity, roughness) of the glacier surface and thus the surface energy balance and glacier melt. In this study we have used sensitivity tests to assess the effect of surface properties of debris on the spatial distribution of micrometeorological variables such as wind fields, moisture and temperature. Subsequently we investigated how those surface properties drive the turbulent fluxes and eventually the conductive heat flux of a debris-covered glacier. We simulated a debris-covered glacier (Lirung Glacier, Nepal) at a 1m resolution with the MicroHH model, with boundary conditions retrieved from an automatic weather station (temperature, wind and specific humidity) and unmanned aerial vehicle flights (digital elevation map and surface temperature). The model was validated using eddy covariance data. A sensitivity analysis was then performed to provide insight into how heterogeneous surface variables control the glacier microclimate. Additionally, we show that ice cliffs are local melt hot spots and that turbulent fluxes and local heat advection amplify spatial heterogeneity on the surface. The high spatial variability of small-scale meteorological variables suggests that point-based station observations cannot be simply extrapolated to an entire glacier. These outcomes should be considered in future studies for a better estimation of glacier melt in High Mountain Asia.

    Fermentative N-Methylanthranilate Production by Engineered Corynebacterium glutamicum
    Walter, Tatjana ; Medani, Nour Al; Burgardt, Arthur ; Cankar, K. ; Ferrer, Lenny ; Kerbs, Anastasia ; Lee, Jin-Ho ; Mindt, Melanie ; Risse, Joe Max ; Wendisch, Volker F. - \ 2020
    Microorganisms 8 (2020)6. - ISSN 2076-2607
    N-functionalized amines; N-methylanthranilate; Corynebacterium glutamicum; metabolic engineering; sustainable production of quinoline precursors; acridone; quinazoline alkaloid drugs
    The N-functionalized amino acid N-methylanthranilate is an important precursor for bioactive compounds such as anticancer acridone alkaloids, the antinociceptive alkaloid O-isopropyl N-methylanthranilate, the flavor compound O-methyl-N-methylanthranilate, and as a building block for peptide-based drugs. Current chemical and biocatalytic synthetic routes to N-alkylated amino acids are often unprofitable and restricted to low yields or high costs through cofactor regeneration systems. Amino acid fermentation processes using the Gram-positive bacterium Corynebacterium glutamicum are operated industrially at the million tons per annum scale. Fermentative processes using C. glutamicum for N-alkylated amino acids based on an imine reductase have been developed, while N-alkylation of the aromatic amino acid anthranilate with S-adenosyl methionine as methyl-donor has not been described for this bacterium. After metabolic engineering for enhanced supply of anthranilate by channeling carbon flux into the shikimate pathway, preventing by-product formation and enhancing sugar uptake, heterologous expression of the gene anmt encoding anthranilate N-methyltransferase from Ruta graveolens resulted in production of N-methylanthranilate (NMA), which accumulated in the culture medium. Increased SAM regeneration by coexpression of the homologous adenosylhomocysteinase gene sahH improved N-methylanthranilate production. In a test bioreactor culture, the metabolically engineered C. glutamicum C1* strain produced NMA to a final titer of 0.5 g·L−1 with a volumetric productivity of 0.01 g·L−1·h−1 and a yield of 4.8 mg·g−1 glucose.
    Long-term thermal sensitivity of Earth's tropical forests
    Sullivan, Martin J.P. ; Lewis, Simon L. ; Affum-Baffoe, Kofi ; Castilho, Carolina ; Costa, Flávia ; Sanchez, Aida Cuni ; Ewango, Corneille E.N. ; Hubau, Wannes ; Marimon, Beatriz ; Monteagudo-Mendoza, Abel ; Qie, Lan ; Sonké, Bonaventure ; Martinez, Rodolfo Vasquez ; Baker, Timothy R. ; Brienen, Roel J.W. ; Feldpausch, Ted R. ; Galbraith, David ; Gloor, Manuel ; Malhi, Yadvinder ; Aiba, Shin Ichiro ; Alexiades, Miguel N. ; Almeida, Everton C. ; Oliveira, Edmar Almeida de; Dávila, Esteban Álvarez ; Loayza, Patricia Alvarez ; Andrade, Ana ; Vieira, Simone Aparecida ; Aragão, Luiz E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmila ; Ashton, Peter ; Aymard C, Gerardo ; Baccaro, Fabrício B. ; Banin, Lindsay F. ; Baraloto, Christopher ; Camargo, Plínio Barbosa ; Barlow, Jos ; Barroso, Jorcely ; Bastin, Jean François ; Batterman, Sarah A. ; Beeckman, Hans ; Begne, Serge K. ; Bennett, Amy C. ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Boeckx, Pascal ; Bogaert, Jan ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brearley, Francis Q. ; Brncic, Terry ; Brown, Foster ; Burban, Benoit ; Camargo, José Luís ; Castro, Wendeson ; Céron, Carlos ; Ribeiro, Sabina Cerruto ; Moscoso, Victor Chama ; Chave, Jerôme ; Chezeaux, Eric ; Clark, Connie J. ; Souza, Fernanda Coelho de; Collins, Murray ; Comiskey, James A. ; Valverde, Fernando Cornejo ; Medina, Massiel Corrales ; Costa, Lola da; Dančák, Martin ; Dargie, Greta C. ; Davies, Stuart ; Cardozo, Nallaret Davila ; Haulleville, Thales de; Medeiros, Marcelo Brilhante de; Aguila Pasquel, Jhon Del; Derroire, Géraldine ; Fiore, Anthony Di; Doucet, Jean Louis ; Dourdain, Aurélie ; Droissant, Vincent ; Duque, Luisa Fernanda ; Ekoungoulou, Romeo ; Elias, Fernando ; Erwin, Terry ; Esquivel-Muelbert, Adriane ; Fauset, Sophie ; Ferreira, Joice ; Llampazo, Gerardo Flores ; Foli, Ernest ; Ford, Andrew ; Gilpin, Martin ; Hall, Jefferson S. ; Hamer, Keith C. ; Hamilton, Alan C. ; Harris, David J. ; Hart, Terese B. ; Hédl, Radim ; Herault, Bruno ; Herrera, Rafael ; Higuchi, Niro ; Hladik, Annette ; Coronado, Eurídice Honorio ; Huamantupa-Chuquimaco, Isau ; Huasco, Walter Huaraca ; Jeffery, Kathryn J. ; Jimenez-Rojas, Eliana ; Kalamandeen, Michelle ; Djuikouo, Marie Noël Kamdem ; Kearsley, Elizabeth ; Umetsu, Ricardo Keichi ; Kho, Lip Khoon ; Killeen, Timothy ; Kitayama, Kanehiro ; Klitgaard, Bente ; Koch, Alexander ; Labrière, Nicolas ; Laurance, William ; Laurance, Susan ; Leal, Miguel E. ; Levesley, Aurora ; Lima, Adriano J.N. ; Lisingo, Janvier ; Lopes, Aline P. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Tom ; Lovett, Jon C. ; Lowe, Richard ; Magnusson, William E. ; Malumbres-Olarte, Jagoba ; Manzatto, Ângelo Gilberto ; Marimon, Ben Hur ; Marshall, Andrew R. ; Marthews, Toby ; Almeida Reis, Simone Matias de; Maycock, Colin ; Melgaço, Karina ; Mendoza, Casimiro ; Metali, Faizah ; Mihindou, Vianet ; Milliken, William ; Mitchard, Edward T.A. ; Morandi, Paulo S. ; Mossman, Hannah L. ; Nagy, Laszlo ; Nascimento, Henrique ; Neill, David ; Nilus, Reuben ; Vargas, Percy Núñez ; Palacios, Walter ; Camacho, Nadir Pallqui ; Peacock, Julie ; Pendry, Colin ; Peñuela Mora, Maria Cristina ; Pickavance, Georgia C. ; Pipoly, John ; Pitman, Nigel ; Playfair, Maureen ; Poorter, Lourens ; Poulsen, John R. ; Poulsen, Axel Dalberg ; Preziosi, Richard ; Prieto, Adriana ; Primack, Richard B. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Réjou-Méchain, Maxime ; Correa, Zorayda Restrepo ; Sousa, Thaiane Rodrigues de; Bayona, Lily Rodriguez ; Roopsind, Anand ; Rudas, Agustín ; Rutishauser, Ervan ; Abu Salim, Kamariah ; Salomão, Rafael P. ; Schietti, Juliana ; Sheil, Douglas ; Silva, Richarlly C. ; Espejo, Javier Silva ; Valeria, Camila Silva ; Silveira, Marcos ; Simo-Droissart, Murielle ; Simon, Marcelo Fragomeni ; Singh, James ; Soto Shareva, Yahn Carlos ; Stahl, Clement ; Stropp, Juliana ; Sukri, Rahayu ; Sunderland, Terry ; Svátek, Martin ; Swaine, Michael D. ; Swamy, Varun ; Taedoumg, Hermann ; Talbot, Joey ; Taplin, James ; Taylor, David ; Steege, Hans Ter; Terborgh, John ; Thomas, Raquel ; Thomas, Sean C. ; Torres-Lezama, Armando ; Umunay, Peter ; Gamarra, Luis Valenzuela ; Heijden, Geertje van der; Hout, Peter van der; Meer, Peter van der; Nieuwstadt, Mark van; Verbeeck, Hans ; Vernimmen, Ronald ; Vicentini, Alberto ; Vieira, Ima Célia Guimarães ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Wang, Ophelia ; White, Lee J.T. ; Willcock, Simon ; Woods, John T. ; Wortel, Verginia ; Young, Kenneth ; Zagt, Roderick ; Zemagho, Lise ; Zuidema, Pieter A. ; Zwerts, Joeri A. ; Phillips, Oliver L. - \ 2020
    Science 368 (2020)6493. - ISSN 0036-8075 - p. 869 - 874.

    The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate.

    Responding to future regime shifts with agrobiodiversity : A multi-level perspective on small-scale farming in Uganda
    Kozicka, Marta ; Gotor, Elisabetta ; Ocimati, Walter ; Jager, Tamar de; Kikulwe, Enoch ; Groot, Jeroen C.J. - \ 2020
    Agricultural Systems 183 (2020). - ISSN 0308-521X
    Agricultural biodiversity - Banana disease - Climate change - Integrated modelling - Smallholder farmer - Vulnerability and resilience

    We analyse the impact of two large-scale regime shifts caused by disease incidence or climate change, and associated crop productivity and price changes, on banana-based smallholders in Uganda. We evaluate these farmers' vulnerability and assess the potential of using increased crop diversity to improve their resilience. We further explore trade-offs and synergies between environmental, economic and nutritional outcomes faced by the farmers in their decision making when a regime shift occurs. We simulate the large-scale scenarios with the IMPACT model and use the results obtained to assess their effect at the local level using the bio-economic farm-household model, FarmDESIGN. Our results indicate that climate change can lead to a regime shift that expands revenue variance, increases soil erosion and reduces vitamin A yield for farmers. Banana disease can negatively impact income levels and species diversity. We show that under both scenarios farmers have scope to reconfigure their farms and recover farm performance. Specifically, we discuss the benefits of species diversity; increasing agrobiodiversity by adding new crops increases the farm's adaptive capacity and resilience, allowing for much higher revenues, on-farm crop diversity and vitamin A production. The conceptual approach and the method we developed can be applied to assess the local synergies and trade-offs between crop diversity conservation, nutrition, environmental protection and human nutrition that farmers face as a result of global drivers. Our results offer a further understanding of how biodiverse systems respond to regime shifts, which can inform effective policy design. Our method can be also useful to help farmers manage their farms in a way to better meet their complex needs.

    Xanthomonas wilt of banana drives changes in land-use and ecosystem services across infected landscapes
    Ocimati, Walter ; Groot, Jeroen J.C. ; Tittonell, Pablo ; Taulya, Godfrey ; Ntamwira, Jules ; Amato, Serge ; Blomme, Guy - \ 2020
    Sustainability 12 (2020)8. - ISSN 2071-1050 - p. 1 - 20.
    Communities - Disease - Multi-functional - Perceptions - Soil erosion - Uprooting

    Changes in land-use have been observed in banana-based systems in the African Great Lakes region affected by Xanthomonas wilt disease (XW) of banana. Through focus group discussions (FGDs) and the 4-cell method (to map the area under production and the number of households involved), changes in land-use were assessed in 13 XW-affected landscapes/villages along a 230 km transect from Masisi (where XW arrived in 2001) to Bukavu (XW arrived around 2014) in the Eastern Democratic Republic of Congo. Farmers' perceptions on the sustainability of new land uses were also documented. Soil nutrient content and erosion levels were measured for five major land-use options/trajectories on 147 fields across 55 farms in three landscapes along the transect. From banana being ranked the most important crop (92% of landscapes) before XW outbreaks, its importance had declined, with it grown on smaller farms by most households in 36% of the landscapes, while in 64% of cases by few households on smaller plots. Farmers uprooted entire banana mats or fields, expanding land under other crops. Species richness did not change at landscape level, although 21 crops were introduced at farm level. Banana is, however, still perceived as more sustainable due to its multi-functional roles. Soils under banana had better chemical attributes, while high erosion levels (Mg ha-1 year-1) occurred under cassava (1.7-148.9) compared with banana (0.3-10.7) and trees (0.3-5.9). The shifts from banana could thus affect supply of key services and sustainability of the farming systems. This study offers a good basis for interventions in XW-affected landscapes.

    Data and R code: Bioconversion efficiencies, greenhouse gas and ammonia emissions during black soldier fly rearing – a mass balance approach
    Parodi, Alejandro ; Boer, Imke de; Gerrits, Walter ; Loon, Joop van; Heetkamp, Marcel ; Schelt, Jeroen van; Bolhuis, Liesbeth ; Zanten, Hannah van - \ 2020
    Wageningen University & Research
    ammonia - bioconversion - emissions - GHG - Hermetia illucens - nitrogen
    Contains data and R code for analysis and visualizations of the study Bioconversion efficiencies, greenhouse gas and ammonia emissions during black soldier fly rearing.
    A multi-objective optimization model for dairy feeding management
    Notte, Gastón ; Cancela, Héctor ; Pedemonte, Martín ; Chilibroste, Pablo ; Rossing, Walter ; Groot, Jeroen C.J. - \ 2020
    Agricultural Systems 183 (2020). - ISSN 0308-521X
    Dairy production - Evolutionary algorithms - Multi-objective - Pareto front - Resource allocation

    The allocation of feedstuff to intensively managed dairy cows to achieve different objectives is challenging due to the inherent complexity of the system and the combinatorial problem that has to be solved. Pareto-based multi-objective optimization approaches using evolutionary algorithms can help to address these challenges and show the trade-offs and synergies among various objectives. Here we present a framework for multi-objective optimization with the Differential Evolution (DE) algorithm applied to dairy feeding systems with grazing and concentrate supply to generate an approximation of the Pareto front. The available feed resources are located in different feeding areas, and the number of animals and groups of animals with similar feeding requirements are distributed across these areas for feeding purposes. To evaluate the DE algorithm, we performed two in-silico experiments to: (1) compare the solutions quality of single-objective DE with exact Linear Programming (LP) solutions, and (2) assess the influence of different stocking rates (number of cows/ha) on milk production, feed allocation and economic performance indicators. The DE solutions that minimize the feeding costs for different stocking rates (1.1–2.6 cows/ha) closely approached the solutions derived with LP, confirming the quality of the heuristic algorithm. The multi-objective model scenarios demonstrated that increasing stocking density would enhance milk production and gross margin per unit of area at largely unchanged productivity per animal by shifting the feed ration from roughage to a large proportion of supplementary concentrate feed. At low stocking rates solutions with high productivity and gross margin and a large proportion of roughage in the ration and limited supplementary feeding were identified. We conclude that the multi-objective optimization with a Pareto-based DE algorithm is highly effective to explore the interrelations among conflicting objectives and to find suitable solutions.

    Approaches to identify the value of seminatural habitats for conservation biological control
    Holland, John M. ; Jeanneret, Philippe ; Moonen, Anna Camilla ; Werf, Wopke van der; Rossing, Walter A.H. ; Antichi, Daniele ; Entling, Martin H. ; Giffard, Brice ; Helsen, Herman ; Szalai, Mark ; Rega, Carlo ; Gibert, Caroline ; Veromann, Eve - \ 2020
    Insects 11 (2020)3. - ISSN 2075-4450 - p. 1 - 11.
    Conservation biological control - Crop pests - Field margins - Integrated pest management - Landscape ecology - Natural capital - Natural enemies - Sentinel systems

    Invertebrates perform many vital functions in agricultural production, but many taxa are in decline, including pest natural enemies. Action is needed to increase their abundance if more sustainable agricultural systems are to be achieved. Conservation biological control (CBC) is a key component of integrated pest management yet has failed to be widely adopted in mainstream agriculture. Approaches to improving conservation biological control have been largely ad hoc. Two approaches are described to improve this process, one based upon pest natural enemy ecology and resource provision while the other focusses on the ecosystem service delivery using the QuESSA (Quantification of Ecological Services for Sustainable Agriculture) project as an example. In this project, a predictive scoring system was developed to show the potential of five seminatural habitat categories to provide biological control, from which predictive maps were generated for Europe. Actual biological control was measured in a series of case studies using sentinel systems (insect or seed prey), trade-offs between ecosystem services were explored, and heatmaps of biological control were generated. The overall conclusion from the QuESSA project was that results were context specific, indicating that more targeted approaches to CBC are needed. This may include designing new habitats or modifying existing habitats to support the types of natural enemies required for specific crops or pests.

    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    Microbial Engineering for Production of N-Functionalized Amino Acids and Amines
    Mindt, Melanie ; Walter, Tatjana ; Kugler, Pierre ; Wendisch, Volker F. - \ 2020
    Biotechnology Journal 15 (2020)7. - ISSN 1860-6768
    bioactives - fermentation - metabolic engineering - N-functionalization - natural products

    N-functionalized amines play important roles in nature and occur, for example, in the antibiotic vancomycin, the immunosuppressant cyclosporine, the cytostatic actinomycin, the siderophore aerobactin, the cyanogenic glucoside linamarin, and the polyamine spermidine. In the pharmaceutical and fine-chemical industries N-functionalized amines are used as building blocks for the preparation of bioactive molecules. Processes based on fermentation and on enzyme catalysis have been developed to provide sustainable manufacturing routes to N-alkylated, N-hydroxylated, N-acylated, or other N-functionalized amines including polyamines. Metabolic engineering for provision of precursor metabolites is combined with heterologous N-functionalizing enzymes such as imine or ketimine reductases, opine or amino acid dehydrogenases, N-hydroxylases, N-acyltransferase, or polyamine synthetases. Recent progress and applications of fermentative processes using metabolically engineered bacteria and yeasts along with the employed enzymes are reviewed and the perspectives on developing new fermentative processes based on insight from enzyme catalysis are discussed.

    Assessment of Multi-Image Unmanned Aerial Vehicle Based High-Throughput Field Phenotyping of Canopy Temperature
    Perich, Gregor ; Hund, Andreas ; Anderegg, Jonas ; Roth, Lukas ; Boer, Martin P. ; Walter, Achim ; Liebisch, Frank ; Aasen, Helge - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    anisotropy - low-altitude/high-resolution remote sensing - phenotyping - plant breeding - spatial correction - temperate climate - thermography - unmanned aerial vehicle

    Canopy temperature (CT) has been related to water-use and yield formation in crops. However, constantly (e.g., sun illumination angle, ambient temperature) as well as rapidly (e.g., clouds) changing environmental conditions make it difficult to compare measurements taken even at short time intervals. This poses a great challenge for high-throughput field phenotyping (HTFP). The aim of this study was to i) set up a workflow for unmanned aerial vehicles (UAV) based HTFP of CT, ii) investigate different data processing procedures to combine information from multiple images into orthomosaics, iii) investigate the repeatability of the resulting CT by means of heritability, and iv) investigate the optimal timing for thermography measurements. Additionally, the approach was v) compared with other methods for HTFP of CT. The study was carried out in a winter wheat field trial with 354 genotypes planted in two replications in a temperate climate, where a UAV captured CT in a time series of 24 flights during 6 weeks of the grain-filling phase. Custom-made thermal ground control points enabled accurate georeferencing of the data. The generated thermal orthomosaics had a high spatial accuracy (mean ground sampling distance of 5.03 cm/pixel) and position accuracy [mean root-mean-square deviation (RMSE) = 4.79 cm] over all time points. An analysis on the impact of the measurement geometry revealed a gradient of apparent CT in parallel to the principle plane of the sun and a hotspot around nadir. Averaging information from all available images (and all measurement geometries) for an area of interest provided the best results by means of heritability. Correcting for spatial in-field heterogeneity as well as slight environmental changes during the measurements were performed with the R package SpATS. CT heritability ranged from 0.36 to 0.74. Highest heritability values were found in the early afternoon. Since senescence was found to influence the results, it is recommended to measure CT in wheat after flowering and before the onset of senescence. Overall, low-altitude and high-resolution remote sensing proved suitable to assess the CT of crop genotypes in a large number of small field plots as is required in crop breeding and variety testing experiments.

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