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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    Transfer of pyrrolizidine alkaloids from ragwort, common groundsel and viper’s bugloss to milk from dairy cows
    Mulder, Patrick P.J. ; Klijnstra, Mirjam D. ; Goselink, Roselinde M.A. ; Vuuren, Ad M. van; Cone, John W. ; Stoopen, Geert ; Hoogenboom, Ron L.A.P. - \ 2020
    Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment (2020). - ISSN 1944-0049
    dairy cows - feed - Pyrrolizidine alkaloids - rumen - transfer

    To investigate the transfer of pyrrolizidine alkaloids (PAs) from feed to milk, rumen-cannulated dairy cows were intra-ruminally fed with 200 g/day of dried plant material of either ragwort (mixture of Jacobaea vulgaris and Senecio inaequidens), common groundsel (Senecio vulgaris) or viper’s bugloss (Echium vulgare) for a period of 4 days. PA levels in the plant materials were 3767, 2792 and 1674 µg g−1 respectively. Feed intake, milk yield and several blood parameters indicative for liver function were not influenced by the treatment. When fed ragwort, increased levels of PAs were detected in the milk, in particular jacoline and an unidentified cyclic diester, possibly a hydroxylated metabolite from retrorsine. The latter was the most important PA in milk from cows fed common groundsel. For viper’s bugloss, echimidine was the most abundant identified PA but in addition several hydroxylated PA metabolites were detected. For ragwort, the overall PA transfer was estimated at 0.05% and 1.4% for jacoline (N-oxide). Transfer rates were similar for viper’s bugloss (0.05%) but lower for common groundsel (0.01%). Only a small portion of the administered PAs was quantified in milk, urine and faeces, with an overall balance of 4.5%, 2.9% and 5.8%, for ragwort, common groundsel and viper’s bugloss, respectively. Samples taken from the rumen indicated that the N-oxides were converted into the free bases, which was confirmed by in vitro studies with the same plant species incubated with ruminal fluid. These results confirm that the transfer of PAs to milk is relatively low but may be of concern for human health regarding the genotoxic and carcinogenic properties of these compounds. The transfer rate depends on the type of PAs present in the weeds. The incomplete balance of input vs output stresses the need to further investigate the metabolism and the potential transfer of metabolites into edible products.

    Detection of QTL for apple fruit acidity and sweetness using sensorial evaluation in multiple pedigreed full-sib families
    Rymenants, Marijn ; Weg, Eric van de; Auwerkerken, Annemarie ; Wit, Inge De; Czech, Andrzej ; Nijland, Bart ; Heuven, Henri ; Storme, Nico De; Keulemans, Wannes - \ 2020
    Tree Genetics and Genomes 16 (2020)5. - ISSN 1614-2942
    Acidity - Ma and Ma3 - QTL - Sweetness

    Acidity and sweetness are important qualities for apple breeders and understanding their genetic regulation can improve the breeding process. In previous QTL studies, fruit quality assessments were performed using instrumental measurements, leading to the identification of two major QTL Ma and Ma3. Here, we use sensorial data to investigate the role of known and unknown genetic factors in the perception of acidity and sweetness in three pedigreed full-sib families. For 2 years, these families were phenotyped by a trained panel, at harvest and after 2 months of cold storage, and genotyped with a new 50 K SNP array. FlexQTLTM analyses using both an additive and an additive + dominance model resulted in the identification of Ma and Ma3 for acidity as well as sweetness, whereas the use of the additive model yielded decisive evidence for the discovery of two additional QTL on LG1 and LG6 for acidity. QTL genotypes were qualified as the inverse of each other, which indicates that individuals with the less-acidity alleles of Ma and Ma3 are perceived sweeter. Due to the genetic configuration in the families studied, resulting from a link with the Pale Green Disorder locus, no incomplete dominance effect could be detected for the Ma locus, although previously reported in the literature. For the Ma3 locus, however, an incomplete dominance effect (58%) is reported here for the first time. The Ma3 locus was also further confined to a 2–4-cM region and a predictive marker for this locus was identified.

    Prioritization of adaptation measures for improved agricultural water management in Northwest Bangladesh
    Acharjee, T.K. ; Hellegers, P.J.G.J. ; Ludwig, F. ; Halsema, G.E. van; Mojid, M.A. ; Terwisscha van Scheltinga, C.T.H.M. - \ 2020
    Climatic Change (2020). - ISSN 0165-0009
    Adaptation strategies are essential to manage water demand and ensure optimal use of available water resources under climate change. Identification and prioritization of adaptation options would greatly support decision-making in drought-prone Northwest Bangladesh. This study identified climate adaptation options by literature review and stakeholder consultation, then used multi-criteria analysis to evaluate and prioritize the options. The complexity of the options was also evaluated, specifically social, institutional, and technical obstacles to their local uptake. Seventy-two adaptation options were identified, spanning six sector categories. The options were further classified as in-system dependent, i.e., options that could be implemented by local actors, or as out-system dependent, i.e., options reliant on actions by external actors. Finally, they were defined as on-farm or off-farm strategies. Transboundary cooperation to increase surface water flows was ranked as the overall top-priority option, though this option is very complex and out-system dependent. Integrated water resources management and integrated crop management were the top-ranked options in the water management and crop production management sectors, respectively. Clustering scattered households and offering training programs in on-farm water management were the most and least complex measures, respectively. Stakeholders exhibited a clear preference for higher scale out-system dependent strategies, rather than in-system dependent options focused on changing the agricultural system itself to cope with climate change. Nonetheless, it is recommended that short-term and medium-term planning focus on opportunities to implement achievable adaptation measures within the local agricultural system. Investment in complex, externally dependent strategies is important for long-term planning.
    Watering techniques and zero-valent iron biochar pH effects on As and Cd concentrations in rice rhizosphere soils, tissues and yield
    Islam, Md Shafiqul ; Chen, Yali ; Weng, Liping ; Ma, Jie ; Khan, Zulqarnain Haider ; Liao, Zhongbin ; Magid, Abdoul Salam Issiaka Abdoul ; Li, Yongtao - \ 2020
    Journal of Environmental Sciences 100 (2020). - ISSN 1001-0742 - p. 144 - 157.
    Brown rice As - Brown rice Cd - Grain yield - Paddy soils - Water management - Zero-valent iron biochar

    Zero-valent iron amended biochar (ZVIB) has been proposed as a promising material in immobilizing heavy metals in paddy fields. In this study, the impacts of pH of ZVIB (pH 6.3 and pH 9.7) and watering management techniques (watering amount in the order of CON (control, 5/72)>3/72>1–3/72>3/100>1/72, with 5/72, for example, representing irrigation given to 5 cm above soil surface in 72 hr regular interval) on As and Cd bioavailability for rice and its grain yield (YieldBR) were investigated in a pot experiment. Brown rice As (AsBR) content was irrelative to the watering treatments, while significantly decreased (>50%) with the addition of both ZVIB materials. The diminutions of brown rice Cd (CdBR) content as well as the YieldBR were highly dependent on both the soil amendment materials’ pH and watering amount. Among all the watering treatments, 3/72 treatment (15% less irrigation water than the CON) with ZVIB 6.3 amendment was the optimum fit for simultaneous reduction of AsBR (50%) and CdBR contents (19%) as well as for significant increment (12%) of the YieldBR. Although high pH (9.7) ZVIB application could also efficiently decrease As and Cd contents in brown rice, it might risk grain yield lost if appropriate (e.g. 3/72 in our study) watering management technique was not chosen. Therefore, ZVIB would be an environmentally friendly option as an amendment material with proper selection of watering management technique to utilize As and Cd co-contaminated arable soils safely for paddy cultivation.

    Natuurinclusief bouwen: wat beweegt de Nederlandse vastgoedsector? : Onderzoek naar motieven, barrières en gedrag in de transitie naar meer groen
    Haaster-de Winter, M.A. van; Dijkshoorn-Dekker, M.W.C. ; Polman, N.B.P. ; Mattijssen, T.J.M. ; Kortstee, H. - \ 2020
    Wageningen : Wageningen Economic Research (Rapport / Wageningen Economic Research 2020-047) - ISBN 9789463954167 - 21
    To find out what the current role of nature-inclusive building is in the real estate sector and how the sector can be supported to build more nature-inclusive, a survey is conducted among companies in the Dutch real estate sector in 2019. Based on the results, we conclude that there is a positiveattitude towards nature-inclusive construction; its appeal lies in both social and business interests andthere are leverage points for behavioural change towards nature-inclusive construction in the following pack.
    Structural basis for diamide modulation of ryanodine receptor
    Ma, Ruifang ; Haji-Ghassemi, Omid ; Ma, Dan ; Jiang, Heng ; Lin, Lianyun ; Yao, Li ; Samurkas, Arthur ; Li, Yuxin ; Wang, Yiwen ; Cao, Peng ; Wu, Shian ; Zhang, Yan ; Murayama, Takashi ; Moussian, Bernard ; Petegem, Filip Van; Yuchi, Zhiguang - \ 2020
    Nature Chemical Biology (2020). - ISSN 1552-4450

    The diamide insecticide class is one of the top-selling insecticides globally. They are used to control a wide range of pests by targeting their ryanodine receptors (RyRs). Here, we report the highest-resolution cryo-electron microscopy (cryo-EM) structure of RyR1 in the open state, in complex with the anthranilic diamide chlorantraniliprole (CHL). The 3.2-Å local resolution map facilitates unambiguous assignment of the CHL binding site. The molecule induces a conformational change by affecting the S4–S5 linker, triggering channel opening. The binding site is further corroborated by mutagenesis data, which reveal how diamide insecticides are selective to the Lepidoptera group of insects over honeybee or mammalian RyRs. Our data reveal that several pests have developed resistance via two mechanisms, steric hindrance and loss of contact. Our results provide a foundation for the development of highly selective pesticides aimed at overcoming resistance and therapeutic molecules to treat human myopathies. [Figure not available: see fulltext.].

    Author Correction: Global status and conservation potential of reef sharks
    MacNeil, M.A. ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, C.S. ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, M.S. ; Ali, Khadeeja ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; Barcia, Laura García ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcy ; Brooks, Edd ; Brown, J.J. ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabaugh, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, B.M. ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Sjamsul Quamar, L.M. ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature (2020). - ISSN 0028-0836

    An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Understanding the psychological and social environmental determinants driving infant and young child feeding practices among Rwandan households: a salutogenic approach
    Ahishakiye, Jeanine - \ 2020
    Wageningen University. Promotor(en): M.A. Koelen; H.W. Vaandrager, co-promotor(en): I.D. Brouwer. - Wageningen : Wageningen University - ISBN 9789463954563 - 166
    Long-term effects of folic acid and vitamin-B12 supplementation on fracture risk and cardiovascular disease : Extended follow-up of the B-PROOF trial
    Oliai Araghi, Sadaf ; Kiefte-de Jong, Jessica C. ; Dijk, Suzanne C. van; Swart, Karin M.A. ; Ploegmakers, Kim J. ; Zillikens, M.C. ; Schoor, Natasja M. van; Groot, Lisette C.P.G.M. de; Lips, Paul ; Stricker, Bruno H. ; Uitterlinden, André G. ; Velde, Nathalie van der - \ 2020
    Clinical Nutrition (2020). - ISSN 0261-5614
    B-vitamins - Cardiovascular disease - Fracture - Long-term follow-up

    Background & aims: In the initial B-proof, we found inconsistent results of B vitamin supplementation. However, the debate regarding the effects of B vitamins on age-related diseases continues. Therefore, our aim was to investigate the long-term effects (5–7 years follow-up) of an intervention with folic acid and vitamin-B12 supplementation on fracture and cardiovascular disease risk. Methods: Extended follow-up of the B-PROOF trial, a multi-center, double-blind randomized placebo-controlled trial designed to assess the effect of 2–3 years daily supplementation with folic acid (400 μg) and vitamin-B12 (500 μg) versus placebo (n = 2,919). Primary outcome was verified self-reported fracture incidence and secondary outcomes were self-reported cardiovascular endpoints, which were collected through a follow-up questionnaires Proportional hazard analyses was used for the effect of the intervention on risk of fracture(s) and logistic regression for the effect of the intervention on risk of cardiovascular disease. Results: A total of 1,298 individuals (44.5%) participated in the second follow-up round with median of 54 months [51–58], (n = 662 and n = 636, treatment versus placebo group). Median age at baseline was 71.0 years [68.0–76.0] for both groups. No effect was observed of the intervention on osteoporotic fracture or any fracture risk after a follow-up (HR: 0.99, 95% CI: 0.62–1.59 and HR: 0.77; 95% CI: 0.50–1.19, respectively), nor on cardiovascular or cerebrovascular disease risk (OR: 1.05; 95%CI: 0.80–1.44 and OR: 0.85; 95%CI: 0.50–1.45, respectively). Potential interaction by baseline homocysteine concentration was observed for osteoporotic- and any fracture (p = 0.10 and 0.06 respectively), which indicated a significantly lower risk of any fracture in the treatment group with higher total homocysteine concentrations (>15.1 μmol/l). No age-dependent effects were present. Conclusions: This study supports and extends previous null-findings of the B-PROOF trial and shows that supplementation of folic acid and vitamin-B12 has no effect on fracture risk, nor on cardiovascular disease in older individuals over a longer follow-up period. However, B-vitamin supplementation may be beneficial in reducing fractures in individuals with high total homocysteine concentrations, a finding which needs to be replicated.

    Onderzoek naar biorationals tegen Fusarium
    Streminska, M.A. - \ 2020
    Onder Glas 2020 / 17 (2020)8. - p. 47 - 47.
    Lignin degradation and modification by laccase/mediator systems : Insights at the molecular level
    Hilgers, Roelant - \ 2020
    Wageningen University. Promotor(en): J.-P. Vincken, co-promotor(en): M.A. Kabel. - Wageningen : Wageningen University - ISBN 9789463953856 - 240

    Lignin degradation and valorization is one of the major challenges in biorefinery. A potential green tool for lignin degradation or modification is the use of laccase/mediator systems (LMS). Treatment of lignin with LMS results in lignin radicals, which may react further via multiple pathways, resulting in lignin degradation, modification or polymerization. The overall outcome of LMS treatments of lignin is, currently, hard to predict, as the reactions of lignin induced by LMS treatments are insufficiently understood. In this thesis, we investigated the reactivity of lignin upon laccase and LMS treatments by using various lignin model compounds as well as lignocellulose and lignin isolates as substrates. We demonstrated that the balance between degradation, Cα-oxidation and polymerization of lignin is dependent on multiple factors, such as the choice of mediator and the initial structure of the lignin substrate. In addition, we revealed that buffer properties play a key role in the balance between Cα-oxidation and degradation of lignin structures by a laccase/hydroxybenzotriazole (HBT) system, and that altering buffer properties allows to enhance bond cleavage of a lignin structure by >1 order of magnitude. Laccase/HBT treatment of wheat straw and corn stover was shown to result in up to 51% delignification of the biomass. Based on the insights obtained from the model compound studies, and by using a combination of HSQC NMR spectroscopy and py-GC-MS, we showed, for the first time, that the laccase/HBT system degrades lignin via cleavage of Cβ-O, O-4’ and Cα-Cβ bonds. Overall, by studying the reactivity of various lignin substructures, this thesis provided in-depth insights into the reactivity of lignin upon laccase and LMS treatments.

    The phoma-like dilemma
    Hou, L.W. ; Groenewald, J.Z. ; Pfenning, L.H. ; Yarden, O. ; Crous, P.W. ; Cai, L. - \ 2020
    Studies in Mycology 96 (2020). - ISSN 0166-0616 - p. 309 - 396.
    Al. anatii L.W. Hou & O. Yarden - Allophoma alba L.W. Hou, Pfenning, L. Cai & Crous - Amphisphaeria vincetoxici De Not. - As. koolunga (J.A. Davidson et al.) L.W. Hou, L. Cai & Crous - Ascochyta astragalina (Rehm ex Sacc.) L.W. Hou, L. Cai & Crous - Ascochyta ferulae Pat. - Ascochyta nobilis Kabát & Bubák - Ascochyta pilosella L.W. Hou, L. Cai & Crous - Calophoma parvula L.W. Hou, L. Cai & Crous - Calophoma vincetoxici (De Not.) L.W. Hou, L. Cai & Crous - Chaetasbolisia argentina L.W. Hou, L. Cai & Crous - Chaetasbolisia eupatorii (Died.) L.W. Hou, L. Cai & Crous - Did. guttulata L.W. Hou, L. Cai & Crous - Did. indica L.W. Hou, L. Cai & Crous - Did. mitis L.W. Hou, L. Cai & Crous - Did. prolaticolla L.W. Hou, L. Cai & Crous - Did. prosopidis (Crous & A.R. Wood) L.W. Hou, L. Cai & Crous - Did. subglobispora L.W. Hou, L. Cai & Crous - Did. subrosea L.W. Hou, L. Cai & Crous - Did. variabilis L.W. Hou, L. Cai & Crous - Didymella aloeicola L.W. Hou, L. Cai & Crous - Didymella combreti (Crous) L.W. Hou, L. Cai & Crous - Dimorphoma L.W. Hou, L. Cai & Crous - Dimorphoma saxea (Aveskamp et al.) L.W. Hou, L. Cai & Crous - Ectodidymella L.W. Hou, L. Cai & Crous - Ectodidymella nigrificans (P. Karst.) L.W. Hou, L. Cai & Crous - Ectophoma insulana (Mont.) L.W. Hou, L. Cai & Crous - Ep. dickmanii L.W. Hou & O. Yarden - Ep. longiostiolatum L.W. Hou, L. Cai & Crous - Ep. multiceps L.W. Hou, L. Cai & Crous - Ep. oryzae Ito & Iwadare - Ep. polychromum L.W. Hou, L. Cai & Crous - Ep. purpurascens Ehrenb. - Ep. variabile L.W. Hou, L. Cai & Crous - Epicoccum brahmansense L.W. Hou, L. Cai & Crous - Epicoccum mezzettii Goid. - Epicoccum oryzae S. Ito & Iwadare - Epicoccum tobaicum (Szilv.) L.W. Hou, L. Cai & Crous - Heterophoma verbasci-densiflori L.W. Hou, L. Cai & Crous - Le. sisyrinchiicola L.W. Hou, L. Cai & Crous - Leptosphaerulina obtusispora L.W. Hou, L. Cai & Crous - Lo. vitalbae (Briard & Har.) L.W. Hou, L. Cai & Crous - Longididymella clematidis (Woudenb. et al.) L.W. Hou, L. Cai & Crous - Longididymella L.W. Hou, L. Cai & Crous - Ma. terrestris L.W. Hou, L. Cai & Crous - Macroascochyta grandis L.W. Hou, L. Cai & Crous - Macroascochyta L.W. Hou, L. Cai & Crous - Macroventuria angustispora L.W. Hou, L. Cai & Crous - Mi. taxicola L.W. Hou, L. Cai & Crous - Mi. viridis L.W. Hou, L. Cai & Crous - Microsphaeropsis fusca L.W. Hou, L. Cai & Crous - Multi-locus phylogeny - Neoa. humicola L.W. Hou, L. Cai & Crous - Neoa. longispora L.W. Hou, L. Cai & Crous - Neoa. mortariensis L.W. Hou, L. Cai & Crous - Neoascochyta fusiformis L.W. Hou, L. Cai & Crous - Neodidymelliopsis tiliae L.W. Hou, L. Cai & Crous - New taxa - No. eucalyptigena (Crous) L.W. Hou, L. Cai & Crous - No. prosopidis (Crous & A.R. Wood) L.W. Hou, L. Cai & Crous - Nothophoma acaciae (Crous) L.W. Hou, L. Cai & Crous - Nothophoma infuscata L.W. Hou, L. Cai & Crous - Nothophoma nullicana L.W. Hou, L. Cai & Crous - Paramicrosphaeropsis ellipsoidea L.W. Hou, L. Cai & Crous - Paramicrosphaeropsis L.W. Hou, L. Cai & Crous - Phoma - Phoma eupatorii Died - Phoma eupatorii Died. - Phoma laurina Thüm., Phoma nemophilae Neerg. - Phomatodes pilosa L.W. Hou, L. Cai & Crous - Phyllosticta acetosellae A.L. Sm. & Ramsb. - Phyllosticta arachidis-hypogaeae V.G. Rao - Phyllosticta insulana Mont - Phyllosticta verbascicola Ellis & Kellerm. - Pleosphaerulina briosiana Pollacci - Pseudopeyronellaea eucalypti (Crous & M.J. Wingf.) L.W. Hou, L. Cai & Crous - Pseudopeyronellaea L.W. Hou, L. Cai & Crous - R. humicola L.W. Hou, L. Cai & Crous - Remotididymella brunnea L.W. Hou, L. Cai & Crous - Remotididymella capsici (Bond.-Mont.) L.W. Hou, L. Cai & Crous - rpb2 - Sclerotiophoma L.W. Hou, L. Cai & Crous - Sclerotiophoma versabilis (Boerema et al.) L.W. Hou, L. Cai & Crous - St. sambucella L.W. Hou, L. Cai & Crous - Stagonosporopsis cucumeris L.W. Hou, L. Cai & Crous - Stagonosporopsis nemophilae (Neerg). L.W. Hou, L. Cai & Crous - Taxonomy - Toruloidea tobaica Szilv - Va. laurina (Thüm.) L.W. Hou, L. Cai & Crous - Vacuiphoma ferulae (Pat.) L.W. Hou, L. Cai & Crous - Xenodidymella glycyrrhizicola L.W. Hou, L. Cai & Crous

    Species of Didymellaceae have a cosmopolitan distribution and are geographically widespread, occurring in diverse ecosystems. The family includes several important plant pathogenic fungi associated with fruit, leaf, stem and root diseases on a wide variety of hosts, as well as endophytic, saprobic and clinically relevant species. The Didymellaceae was recently revised based on morphological and phylogenetic analyses of ex-type strains subjected to DNA sequencing of partial gene data of the LSU, ITS, rpb2 and tub2 loci. Several poly- and paraphyletic genera, including Ascochyta, Didymella and Phoma were redefined, along with the introduction of new genera. In the present study, a global collection of 1 124 Didymellaceae strains from 92 countries, 121 plant families and 55 other substrates, including air, coral, human tissues, house dust, fungi, insects, soil, and water were examined via multi-locus phylogenetic analyses and detailed morphological comparisons, representing the broadest sampling of Didymellaceae to date. Among these, 97 isolates representing seven new genera, 40 new species and 21 new combinations were newly introduced in Didymellaceae. In addition, six epitypes and six neotypes were designated to stabilise the taxonomy and use of older names. A robust, multi-locus reference phylogenetic tree of Didymellaceae was generated. In addition, rpb2 was revealed as the most effective locus for the identification of Didymellaceae at species level, and is proposed as a secondary DNA marker for the family.

    5 Factsheet Agroforestry - Agroforestry; wat zijn de mogelijkheden van mechanisatie? : Handreiking voor agrarisch ondernemers die bomen willen planten op hun bedrijf
    Selin Norén, Isabella ; Dawson, A.W. ; Schoutsen, M.A. ; Vijn, M.P. - \ 2020
    Wageningen : Wageningen University & Research - 12 p.
    agroforestry - landscape management - circular agriculture
    Als u als agrarisch ondernemer agroforestry wil toepassen op uw bedrijf en u heeft nog geen ervaring met het telen van houtige gewassen, dan kan het lastig zijn om keuzes te maken voor beheer. Het beheer en de oogst van deze gewassen zal uiteraard heel anders zijn dan u gewend bent en er is veelal andere mechanisatie voor nodig. Vanuit de fruit- en notenteelt zijn er tal van machines beschikbaar om u te helpen. Het is belangrijk om de mogelijkheden voor mechanisering mee te nemen in de ontwerp- en aanlegfase van een agroforestry-systeem. Deze factsheet gaat dieper in op de huidige mogelijkheden om agroforestry-systemen te mechaniseren en op de toekomstige ontwikkelingen. De mogelijkheden voor oogst van noten, hard fruit en zacht fruit, inclusief onkruidbeheersing in de boomstrook, bemesting, snoei en bespuiting worden in deze factsheet toegelicht met een aantal voorbeelden. Per type machine wordt één model en fabrikant getoond. Er zijn echter in de praktijk meer fabrikanten en modellen te vinden met behulp van de aangegeven zoektermen. Bestaande machines voor het aanplanten van bomen en struiken worden in deze factsheet niet behandeld. Ook komen machines voor drogen, schonen, sorteren en andere bewerkingen na de oogst in deze factsheet niet aan bod. Als prijzen genoemd worden zijn deze exclusief BTW.
    Integration of Marine Macroalgae (Chaetomorpha maxima) with a Moving Bed Bioreactor for Nutrient Removal from Maricultural Wastewater
    Li, Xian ; Deng, Yale ; Li, Xueying ; Ma, Xiaona ; Wang, Jinxia ; Li, Jun - \ 2020
    Archaea : an international microbiological journal 2020 (2020). - ISSN 1472-3646

    Rather than direct nutrient removal from wastewaters, an alternative approach aimed at nutrient recovery from aquacultural wastewaters could enable sustainable management for aquaculture production. This study demonstrated the feasibility of cultivating marine macroalgae (Chaetomorpha maxima) with a moving bed bioreactor (MBBR-MA), to remove nitrogen and phosphorus in aquaculture wastewater as well as to produce macroalgae biomass. MBBR-MA significantly increased the simultaneous removal of nitrate and phosphate in comparison with only MBBR, resulting in an average total nitrogen (TN) and total phosphorus (TP) removal efficiency of 42.8±5.5% and 83.7±7.7%, respectively, in MBBR-MA while MBBR had no capacity for TN and TP removal. No chemical oxygen demand (COD) removal was detected in both reactors. Phosphorus could be a limiting factor for nitrogen uptake when N: P ratio increased. The recovered nitrogen and phosphorus resulted in a specific growth rate of 3.86%-10.35%/day for C. maxima with an uptake N: P ratio of 6. The presence of macroalgae changed the microbial community in both the biofilter and water by decreasing the relative abundance of Proteobacteria and Nitrospirae and increasing the abundance of Bacteroidetes. These findings indicate that the integration of the macroalgae C. maxima with MBBR could represent an effective wastewater treatment option, especially for marine recirculating aquaculture systems.

    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 ICOS Atmosphere use case : From raw data to knowledge of societal relevance
    Hellström, M. ; Karstens, U. ; Pantazatou, K. ; Vermeulen, A. ; Smith, N. - \ 2020
    In: Earth and Environmental Science. - IOP Publishing (IOP Conference Series: Earth and Environmental Science )

    In order to effectively tackle the on-going changes in global climate, stakeholders and policy makers across the globe need timely and accurate information they can trust on a wide range of topics. Here we briefly describe how observational data on greenhouse gas concentrations collected from the ICOS network of measurement stations in Europe is transformed via atmospheric modelling into information on how emission and uptake of greenhouse gases vary over time and space, and interpreted by experts to create knowledge usable by decision makers.

    Multiple and flexible roles of facultative anaerobic bacteria in microaerophilic oleate degradation
    Duarte, M.S. ; Salvador, Andreia F. ; Cavaleiro, Ana J. ; Stams, Alfons J.M. ; Pereira, M.A. ; Alves, M.M. - \ 2020
    Environmental Microbiology (2020). - ISSN 1462-2912

    Anaerobic degradation of long-chain fatty acids (LCFA) involves syntrophic bacteria and methanogens, but facultative anaerobic bacteria (FAB) might have a relevant role as well. Here we investigated oleate degradation by a syntrophic synthetic co-culture of Syntrophomonas zehnderi (Sz) and Methanobacterium formicicum (Mf) and FAB (two oleate-degrading Pseudomonas spp. I1 + I2). Sz + Mf were first cultivated in a continuous bioreactor under strict anaerobic conditions. Thereafter, I1 + I2 were inoculated and microaerophilic conditions were provided. Methane and acetate were the main degradation products by Sz + Mf in anaerobiosis and by Sz + Mf + I1 + I2 in microaerophilic conditions. However, acetate production from oleate was higher in microaerophilic conditions (5% O2) with the four microorganisms together (0.41 ± 0.07 mmol day−1) than in anaerobiosis with Sz + Mf (0.23 ± 0.05 mmol day−1). Oleate degradation in batch assays was faster by Sz + Mf + I1 + I2 (under microaerophilic conditions) than by Sz + Mf alone (under strict anaerobic conditions). I1 + I2 were able to grow with oleate and with intermediates of oleate degradation (hydrogen, acetate and formate). This work highlights the importance of FAB, particularly Pseudomonas sp., in anaerobic reactors treating oleate-based wastewater, because they accelerate oleate conversion to methane, by protecting strict anaerobes from oxygen toxicity and also by acting as alternative hydrogen/formate and acetate scavengers for LCFA-degrading anaerobes.

    Electron Storage in Electroactive Biofilms
    Heijne, A. ter; Pereira, M.A. ; Pereira, J. ; Sleutels, T. - \ 2020
    Trends in Biotechnology (2020). - ISSN 0167-7799 - 9 p.
    electroactive biofilms - electron storage - microbial electrochemical technologies - polymers

    Microbial electrochemical technologies (METs) are promising for sustainable applications. Recently, electron storage during intermittent operation of electroactive biofilms (EABs) has been shown to play an important role in power output and electron efficiencies. Insights into electron storage mechanisms, and the conditions under which these occur, are essential to improve microbial electrochemical conversions and to optimize biotechnological processes. Here, we discuss the two main mechanisms for electron storage in EABs: storage in the form of reduced redox active components in the electron transport chain and in the form of polymers. We review electron storage in EABs and in other microorganisms and will discuss how the mechanisms of electron storage can be influenced.

    Review of arrival and lairage management at pig slaughterhouses (version 1.0)
    Holmes, Rebecca ; Gerritzen, M.A. ; Herskin, M.S. ; Schwarzlose, Inga ; Ruis, M.A.W. - \ 2020
    EURCAW-Pigs - 30 p.
    pigs - animal welfare - slaughter - killing of animals - sows - boars - meat animals - finishing - handling - handling - animal nutrition - transport - animal health - animal behaviour - animal production - animal housing
    Plant architectural responses in simultaneous maize/soybean strip intercropping do not lead to a yield advantage
    Li, Shuangwei ; Evers, Jochem B. ; Werf, Wopke van der; Wang, Ruili ; Xu, Zhaoli ; Guo, Yan ; Li, Baoguo ; Ma, Yuntao - \ 2020
    Annals of Applied Biology 177 (2020)2. - ISSN 0003-4746 - p. 195 - 210.
    architectural response - border row effect - growth - intercropping - land equivalent ratio

    Maize/soybean strip intercropping is a commonly used system throughout China with high crop yields at reduced nutrient input compared to sole maize. Maize is the taller crop, and due to its dominance in light capture over soybean in the intercrop, maize is expected to outperform maize in sole cropping. Conversely, soybean is the subordinate crop and intercropped soybean plants are expected to perform worse than sole soybean. Crop plants show plastic responses in plant architecture to their growing conditions to forage for light and avoid shading. There is little knowledge on plant architectural responses to growing conditions in simultaneous (non-relay) intercropping and their relationship to species yields. A two-year field experiment with two simultaneous maize/soybean intercropping systems with narrow and wide strips was conducted to characterise architectural traits of maize and soybean plants grown as intercrop and sole crops. Intercropped maize plants, especially those in border rows, had substantially greater leaf area, biomass and yield than maize plants in sole crops. Intercropped soybean plants, especially those in border rows, had lower leaf area, biomass and yield than sole soybean plants. Overall intercrop performance was similar to that of sole crops, with the land equivalent ratio (LER) being only slightly greater than one (1.03–1.08). Soybean displayed typical shade avoidance responses in the intercrop, such as greater internode elongation and changes in specific leaf area, but these responses could not overcome the consequences of the competition with the taller maize plants. Therefore, in contrast to relay intercrop systems, in the studied simultaneous maize/soybean system, plastic responses did not contribute to practically relevant increases in resource capture and yield at whole system (i.e., intercrop) level.

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