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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Evolutionary diversity is associated with wood productivity in Amazonian forests
Coelho de Souza, Fernanda ; Dexter, Kyle G. ; Phillips, Oliver L. ; Pennington, Toby R. ; Neves, Danilo ; Sullivan, Martin J.P. ; Alvarez-Davila, Esteban ; Alves, Átila ; Amaral, Ieda ; Andrade, Ana ; Aragao, Luis E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmilla ; Aymard C, Gerardo A. ; Bánki, Olaf ; Baraloto, Christopher ; Barroso, Jorcely G. ; Boot, Rene G.A. ; Brienen, Roel J.W. ; Brown, Foster ; Camargo, José Luís C. ; Castro, Wendeson ; Chave, Jerome ; Cogollo, Alvaro ; Comiskey, James A. ; Cornejo-Valverde, Fernando ; Costa, Antonio Lola da; Camargo, Plínio B. de; Fiore, Anthony Di; Feldpausch, Ted R. ; Galbraith, David R. ; Gloor, Emanuel ; Goodman, Rosa C. ; Gilpin, Martin ; Herrera, Rafael ; Higuchi, Niro ; Honorio Coronado, Eurídice N. ; Jimenez-Rojas, Eliana ; Killeen, Timothy J. ; Laurance, Susan ; Laurance, William F. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Thomas E. ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Mendoza, Casimiro ; Monteagudo-Mendoza, Abel ; Neill, David A. ; Vargas, Percy Núñez ; Peñuela Mora, Maria C. ; Pickavance, Georgia C. ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poorter, Lourens ; Prieto, Adriana ; Ramirez, Freddy ; Roopsind, Anand ; Rudas, Agustin ; Salomão, Rafael P. ; Silva, Natalino ; Silveira, Marcos ; Singh, James ; Stropp, Juliana ; Steege, Hans ter; Terborgh, John ; Thomas-Caesar, Raquel ; Umetsu, Ricardo K. ; Vasquez, Rodolfo V. ; Célia-Vieira, Ima ; Vieira, Simone A. ; Vos, Vincent A. ; Zagt, Roderick J. ; Baker, Timothy R. - \ 2019
Nature Ecology & Evolution (2019). - ISSN 2397-334X - p. 1754 - 1761.

Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera, we investigated the association between taxonomic and evolutionary metrics of diversity and two key measures of ecosystem function: aboveground wood productivity and biomass storage. While taxonomic and phylogenetic diversity were not important predictors of variation in biomass, both emerged as independent predictors of wood productivity. Amazon forests that contain greater evolutionary diversity and a higher proportion of rare species have higher productivity. While climatic and edaphic variables are together the strongest predictors of productivity, our results show that the evolutionary diversity of tree species in diverse forest stands also influences productivity. As our models accounted for wood density and tree size, they also suggest that additional, unstudied, evolutionarily correlated traits have significant effects on ecosystem function in tropical forests. Overall, our pan-Amazonian analysis shows that greater phylogenetic diversity translates into higher levels of ecosystem function: tropical forest communities with more distantly related taxa have greater wood productivity.

Author Correction: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G.J. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Abegg, Meinrad ; Adou Yao, C.Y. ; Alberti, Giorgio ; Almeyda Zambrano, Angelica ; Alvarez-Davila, Esteban ; Alvarez-Loayza, Patricia ; Alves, Luciana F. ; Ammer, Christian ; Antón-Fernández, Clara ; Araujo-Murakami, Alejandro ; Arroyo, Luzmila ; Avitabile, Valerio ; Aymard, Gerardo ; Baker, Timothy ; Bałazy, Radomir ; Banki, Olaf ; Barroso, Jorcely ; Bastian, Meredith ; Bastin, Jean Francois ; Birigazzi, Luca ; Birnbaum, Philippe ; Bitariho, Robert ; Boeckx, Pascal ; Bongers, Frans ; Bouriaud, Olivier ; Brancalion, Pedro H.H.S. ; Decuyper, Mathieu ; Hengeveld, Geerten ; Herold, Martin ; Lu, Huicui ; Parren, Marc ; Poorter, Lourens ; Schelhaas, Mart Jan ; Sheil, Douglas ; Zagt, Roderick - \ 2019
Nature 571 (2019)7765. - ISSN 0028-0836

In this Letter, the middle initial of author G. J. Nabuurs was omitted, and he should have been associated with an additional affiliation: ‘Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands’ (now added as affiliation 182). In addition, the following two statements have been added to the Supplementary Acknowledgements. (1): ‘We would particularly like to thank The French NFI for the work of the many field teams and engineers, who have made extraordinary efforts to make forest inventory data publicly available.’ (1): ‘Sergio de Miguel benefited from a Serra- Húnter Fellowship provided by the Generalitat of Catalonia.’ Finally, the second sentence of the Methods section should have cited the French NFI, which provided a national forestry database used in our analysis, to read as follows: ‘The GFBi database consists of individual-based data that we compiled from all the regional and national GFBi forest-inventory datasets, including the French NFI (IGN—French National Forest Inventory, raw data, annual campaigns 2005 and following, https://inventaire-forestier.ign.fr/spip.php?rubrique159, site accessed on 01 January 2015)’. All of these errors have been corrected online.

Intraspecific variability in response to phosphorus depleted conditions in the cyanobacteria Microcystis aeruginosa and Raphidiopsis raciborskii
Guedes, Iame Alves ; Pacheco, Ana Beatriz F. ; Vilar, Mauro C.P. ; Mello, Mariana M. ; Marinho, Marcelo Manzi ; Lurling, Miquel ; Azevedo, Sandra M.F.O. - \ 2019
Harmful Algae 86 (2019). - ISSN 1568-9883 - p. 96 - 105.
Cylindrospermopsis - Ecotypes - Phosphorus uptake - Strain variability

Phosphorus loading plays an important role in the occurrence of cyanobacterial blooms and understanding how this nutrient affects the physiology of cyanobacteria is imperative to manage these phenomena. Microcystis aeruginosa and Raphidiopsis raciborskii are cyanobacterial species that form potentially toxic blooms in freshwater ecosystems worldwide. Blooms comprise numerous strains with high trait variability, which can contribute to the widespread distribution of these species. Here, we explored the intraspecific variability in response to phosphorus depleted conditions (P-)testing five strains of each species. Strains could be differentiated by cell volume or genetic profiles except for those of the same species, sampling location and date, though these presented differences in their response to (P-). Although differently affected by (P-)over 10 days, all strains were able to grow and maintain photosynthetic activity. For most M. aeruginosa and R. raciborskii strains growth rates were not significantly different comparing (P+)and (P-)conditions. After ten days in (P-), only one M. aeruginosa strain and two R. raciborskii strains showed reduction in biovolume yield as compared to (P+)but in most strains chlorophyll-a concentrations were lower in (P-)than in (P+). Reduced photosystem II efficiency was found for only one R. raciborskii strain while all M. aeruginosa strains were affected. Only two M. aeruginosa and one R. raciborskii strain increased alkaline phosphatase activity under (P-)as compared to (P+). Variation in P-uptake was also observed but comparison among strains yielded homogeneous groups comprised of representatives of both species. Comparing the response of each species as a whole, the (P-)condition affected growth rate, biovolume yield and chlorophyll yield. However, these parameters revealed variation among strains of the same species to the extent that differences between M. aeruginosa and R. raciborskii were not significant. Taken together, these results do not support the idea that R. raciborskii, as a species, can withstand phosphorus limitation better than M. aeruginosa and also point that the level of intraspecific variation may preclude generalizations based on studies that use only one or few strains.

Prospects for upgrading european seaweeds; a value chain perspective
Burg, S.W.K. van den; Selnes, T. ; Dias, Ana ; Alves, Liliana ; Nuhoff-Isakhanyan, Gohar ; Helmes, Roel ; Daniel, Ana - \ 2019
In: Seaweeds: from tradition to innovation! 23rd international seaweed symposium. - - p. 137 - 138.
Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour
Alves, Mara Lisa ; Carbas, Bruna ; Gaspar, Daniel ; Paulo, Manuel ; Brites, Cláudia ; Mendes-Moreira, Pedro ; Brites, Carla Moita ; Malosetti, Marcos ; Eeuwijk, Fred Van; Vaz Patto, Maria Carlota - \ 2019
BMC Plant Biology 19 (2019)1. - ISSN 1471-2229
Bread - Candidate genes - Nutritional quality - Pasting behavior - Plant breeding - Portuguese maize germplasm - Zea mays L.

Background: Maize is a crop in high demand for food purposes and consumers worldwide are increasingly concerned with food quality. However, breeding for improved quality is a complex task and therefore developing tools to select for better quality products is of great importance. Kernel composition, flour pasting behavior, and flour particle size have been previously identified as crucial for maize-based food quality. In this work we carried out a genome-wide association study to identify genomic regions controlling compositional and pasting properties of maize wholemeal flour. Results: A collection of 132 diverse inbred lines, with a considerable representation of the food used Portuguese unique germplasm, was trialed during two seasons, and harvested samples characterized for main compositional traits, flour pasting parameters and mean particle size. The collection was genotyped with the MaizeSNP50 array. SNP-trait associations were tested using a mixed linear model accounting for genetic relatedness. Fifty-seven genomic regions were identified, associated with the 11 different quality-related traits evaluated. Regions controlling multiple traits were detected and potential candidate genes identified. As an example, for two viscosity parameters that reflect the capacity of the starch to absorb water and swell, the strongest common associated region was located near the dull endosperm 1 gene that encodes a starch synthase and is determinant on the starch endosperm structure in maize. Conclusions: This study allowed for identifying relevant regions on the maize genome affecting maize kernel composition and flour pasting behavior, candidate genes for the majority of the quality-associated genomic regions, or the most promising target regions to develop molecular tools to increase efficacy and efficiency of quality traits selection (such as "breadability") within maize breeding programs.

A Migratory Divide Among Red-Necked Phalaropes in the Western Palearctic Reveals Contrasting Migration and Wintering Movement Strategies
Bemmelen, Rob S.A. van; Kolbeinsson, Yann ; Ramos, Raül ; Gilg, Olivier ; Alves, José A. ; Smith, Malcolm ; Schekkerman, Hans ; Lehikoinen, Aleksi ; Petersen, Ib Krag ; Þórisson, Böðvar ; Sokolov, Aleksandr A. ; Välimäki, Kaisa ; Meer, Tim Van Der; Okill, J.D. ; Bolton, Mark ; Moe, Børge ; Hanssen, Sveinn Are ; Bollache, Loïc ; Petersen, Aevar ; Thorstensen, Sverrir ; González-Solís, Jacob ; Klaassen, Raymond H.G. ; Tulp, Ingrid - \ 2019
Frontiers in Ecology and Evolution 7 (2019). - ISSN 2296-701X - 17 p.
flexibility - itinerancy - migration strategy - Phalaropus lobatus - red-necked phalarope
Non-breeding movement strategies of migratory birds may be expected to be flexibly adjusted to the distribution and quality of habitat, but few studies compare movement strategies among populations using distinct migration routes and wintering areas. In our study, individual movement strategies of red-necked phalaropes (Phalaropus lobatus), a long-distance migratory wader which uses saline waters in the non-breeding period, were studied using light-level geolocators. Results revealed a migratory divide between two populations with distinct migration routes and wintering areas: one breeding in the north-eastern North Atlantic and migrating ca. 10,000 km oversea to the tropical eastern Pacific Ocean, and the other breeding in Fennoscandia and Russia migrating
ca. 6,000 km—largely over land—to the Arabian Sea (Indian Ocean). In line with our expectations, the transoceanic migration between the North Atlantic and the Pacific was associated with proportionately longer wings, a more even spread of stopovers in autumn and a higher migration speed in spring compared to the migration between Fennoscandian-Russian breeding grounds and the Arabian Sea. In the wintering period, van Bemmelen et al. Contrasting Movement Strategies in Phalaropes birds wintering in the Pacific were stationary in roughly a single area, whereas individuals wintering in the Arabian Sea moved extensively between different areas, reflecting differences in spatio-temporal variation in primary productivity between the two wintering areas. Our study is unique in showing how habitat distribution shapes movement strategies over the entire non-breeding period within a species.
Anaerobic biological fermentation of urine as a strategy to enhance the performance of a microbial electrolysis cell (MEC)
Barbosa, Sónia G. ; Rodrigues, Telma ; Peixoto, Luciana ; Kuntke, Philipp ; Alves, Maria Madalena ; Pereira, Maria Alcina ; Heijne, Annemiek Ter - \ 2019
Renewable Energy 139 (2019). - ISSN 0960-1481 - p. 936 - 943.
H NMR - Anaerobic digestion - Fermented human urine - Microbial electrolysis cell - Raw human urine - Two-stage bioconversion process
This study investigated the effect of pre-fermented urine on anode performance of a two-chambered microbial electrolysis cells (MECs) compared to raw urine. Pre-fermentation of urine was performed by anaerobic digestion. The effect of this pre-fermentation on anode performance of a MEC was assessed by measuring the removal of chemical oxygen demand (COD), current density and Coulombic efficiency (CE). The MEC using fermented urine achieved a higher average current density (218 ± 6 mA m−2) and a higher CE (17%). Although no significant differences were observed in the COD removal efficiency between both urines, the MEC using fermented urine displayed the highest COD removal rate (0.14 ± 0.02 g L−1 d −1). The organic compounds initially found in both urines, as well as the metabolic products associated to the biodegradation of the organic matter were analyzed by proton nuclear magnetic resonance (H NMR). The main compounds initially identified in the raw urine were urea, creatinine and acetate. In the fermented urine, the main compounds identified were methylamine, acetate and propionic acid demonstrating the effectiveness of the anaerobic fermentation step.
Antibiotics-induced monodominance of a novel gut bacterial order
Hildebrand, Falk ; Moitinho-Silva, Lucas ; Blasche, Sonja ; Jahn, Martin Thomas Thomas ; Gossmann, Toni Ingolf ; Heuerta Cepas, Jaime ; Hercog, Rajna ; Luetge, Mechthild ; Bahram, Mohammad ; Pryszlak, Anna ; Alves, Renato J. ; Waszak, Sebastian M. ; Zhu, Ana ; Ye, Lumeng ; Costea, Paul Igor ; Aalvink, Steven ; Belzer, Clara ; Forslund, Sofia K. ; Sunagawa, Shinichi ; Hentschel, Ute ; Merten, Christoph ; Patil, Kiran Raosaheb ; Benes, Vladimir ; Bork, Peer - \ 2019
Gut 68 (2019)10. - ISSN 0017-5749
antibiotics - bacterial overgrowth - intestinal microbiology - molecular genetics

Objective: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species. Design: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria. Results: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals. Conclusion: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.

Inhibition Studies with 2-Bromoethanesulfonate Reveal a Novel Syntrophic Relationship in Anaerobic Oleate Degradation
Salvador, A.F. ; Cavaleiro, A.J. ; Paulo, A.M.S. ; Silva, S.A. ; Guedes, A.P. ; Pereira, M.A. ; Stams, A.J.M. ; Sousa, D.Z. ; Alves, M.M. - \ 2019
Applied and Environmental Microbiology 85 (2019)2. - ISSN 0099-2240
2-bromoethanesulfonate (BrES) - desulfonation - Desulfovibrio - isethionate - oleate - Syntrophomonas - syntrophy

Degradation of long-chain fatty acids (LCFAs) in methanogenic environments is a syntrophic process involving the activity of LCFA-degrading bacteria and hydrogen-utilizing methanogens. If methanogens are inhibited, other hydrogen scavengers are needed to achieve complete LCFA degradation. In this work, we developed two different oleate (C18:1 LCFA)-degrading anaerobic enrichment cultures, one methanogenic (ME) and another in which methanogenesis was inhibited (IE). Inhibition of methanogens was attained by adding a solution of 2-bromoethanesulfonate (BrES), which turned out to consist of a mixture of BrES and isethionate. Approximately 5 times faster oleate degradation was accomplished by the IE culture compared with the ME culture. A bacterium closely related to Syntrophomonas zehnderi (99% 16S rRNA gene identity) was the main oleate degrader in both enrichments, in syntrophic relationship with hydrogenotrophic methanogens from the genera Methanobacterium and Methanoculleus (in ME culture) or with a bacterium closely related to Desulfovibrio aminophilus (in IE culture). A Desulfovibrio species was isolated, and its ability to utilize hydrogen was confirmed. This bacterium converted isethionate to acetate and sulfide, with or without hydrogen as electron donor. This bacterium also utilized BrES but only after 3 months of incubation. Our study shows that syntrophic oleate degradation can be coupled to desulfonation.IMPORTANCE In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria.

Aspergillus species from Brazilian dry beans and their toxigenic potential
Santos-Ciscon, Bárbara Alves dos; Diepeningen, Anne van; Cruz Machado, José da; Dias, Iara Eleutéria ; Waalwijk, Cees - \ 2019
International Journal of Food Microbiology 292 (2019). - ISSN 0168-1605 - p. 91 - 100.
A. flavus - A. luchuensis - A. niger - Aflatoxin - Fumonisin - Ochratoxin A

Aspergilli are common contaminants of food and feed and a major source of mycotoxins. In this study, 87 Aspergillus strains were isolated from beans from 14 different cities in Brazil and identified to the species level based on partial calmodulin and β-tubulin sequence data. All green spored isolates belonged to section Flavi and were identified as A. flavus (n = 39) or A. pseudocaelatus (n = 1). All black spored isolates belonged to section Nigri and were identified as A. niger (n = 24) or A. luchuensis (n = 10), while the yellow spored strains were identified as A. westerdijkiae (n = 7), A. ostianus (n = 3), A. ochraceus (n = 1) or A. wentii (n = 2). The toxigenic potential of these Aspergillus strains from beans was studied by the prospection of genes in three of the major mycotoxin clusters: aflatoxin (seven genes checked), ochratoxin A (four genes) and fumonisin (ten genes and two intergenic regions). Genes involved in the biosynthesis of aflatoxin were only detected in A. flavus isolates: 17/39 A. flavus isolates proved to contain all the aflatoxin genes tested, the others missed one or more genes. The full complement of fumonisin biosynthesis genes was identified in all A. niger isolates. Finally, no genes for ochratoxin A were detected in any of the isolates. Our work suggests that aflatoxin production by some A. flavus strains and fumonisin production by A. niger isolates form the largest mycotoxin risks in Brazilian beans.

A matric flux potential approach to assess plant water availability in two climate zones in Brazil
Pinheiro, Everton Alves Rodrigues ; Jong van Lier, Quirijn de; Metselaar, Klaas - \ 2018
Vadose Zone Journal 17 (2018)1. - ISSN 1539-1663

Predicting soil water availability to plants is important for agricultural and ecological models. Models that explicitly take into account root water uptake and transpiration reduction describe the ability of soil to supply water to plants based on soil hydraulic properties that depend on soil water content. The objective of this study was to further develop an existing single-layer root water uptake model based on matric flux potential to allow for multi-layer scenarios; and to illustrate its functionality using soil hydraulic properties from layered soils from two climate zones in Brazil: a semiarid zone and a humid zone. For each soil layer, the hydraulic properties were determined by inverse modeling of laboratory evaporation experiment data available for pressure heads between −165 and −1.5 m. The water supplying capacities of soils were evaluated using the newly developed multi-layer root water uptake model. Soils from the semiarid zone were able to supply water to plants over a wider range of pressure heads. Soils from the humid zone showed slightly stronger hydraulic restrictions for supplying transpirable water. For the analyzed soils, only a negligible increase in available water results from decreasing the root water potential below −150 m. Therefore, based on this analysis, it is reasonable to expect plant adaptation to move toward an increase of root length density rather than to a decrease of minimum root water potential.

Identification of the Bisabolol Synthase in the Endangered Candeia Tree (Eremanthus erythropappus (DC) McLeisch)
Alves Gomes Albertti, Leticia ; Delatte, T.L. ; Souza Farias, Katyuce de; Boaretto, A.G. ; Verstappen, F.W.A. ; Houwelingen, A.M.M.L. van; Cankar, K. ; Bouwmeester, H.J. ; Beekwilder, M.J. - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
Candeia (Eremanthus erythropappus (DC) McLeisch, Asteraceae) is a Brazilian tree, mainly occurring in the cerrado areas. From ethnobotanical information its essential oil is known to have wound healing and nociceptive properties. These properties are ascribed to result from a sesquiterpene alcohol, (–)-α-bisabolol, which is present at high concentrations in this oil. Bisabolol is highly valued by the cosmetic industry because of its antibacterial, anti-inflammatory, skin-smoothing and wound healing properties. Over the past decades, Candeia timber has been collected at large scale for bisabolol extraction from wild reserves and the species is thereby at risk of extinction. To support the development of breeding and nursing practices that would facilitate sustainable cultivation of Candeia, we identified a terpene synthase gene, EeBOS1, that appears to control biosynthesis (–)-α-bisabolol in the plant. Expression of this gene in E. coli showed that EeBOS1 protein is capable of producing (–)-α-bisabolol from farnesyl pyrophosphate in vitro. Analysis of gene expression in different tissues from Candeia plants in different life stages showed a high correlation of EeBOS1 expression and accumulation of (–)-α-bisabolol. This work is the first step to unravel the pathway toward (–)-α-bisabolol in Candeia, and in the further study of the control of (–)-α-bisabolol production
Considerations and consequences of allowing DNA sequence data as types of fungal taxa
Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
In depth investigation of the metabolism of Nectandra megapotamica chemotypes
S. Farias, Katyuce de; Delatte, Thierry ; C. de O. Arruda, Rosani do; Alves, Flavio M. ; Silva, Denise B. ; Beekwilder, Jules ; Carollo, Carlos A. - \ 2018
PLoS ONE 13 (2018)8. - ISSN 1932-6203

Plants produce a wide range of secondary metabolites. Within a single species, chemotypes can be distinguished by the differences in the composition of the secondary metabolites. Herein, we evaluated Nectandra megapotamica (Spreng.) chemotypes and the balance of different classes of metabolites to verify how significant differences in plant metabolism are regarding chemotypes. We collected N. megapotamica leaves from eight adult plants in two Brazilian states. The essential oils and ethanol/water extracts were analyzed by GC-MS and LC-DAD-MS, respectively. Histochemical tests were performed, as well as chemical analyses of leaves from adaxial and abaxial foliar surfaces of N. megapotamica, and the stereochemistry of α-bisabolol was determined. Two different chemotypes, based on volatile compounds, were identified, distinguished by the presence of isospathulenol, α-bisabolol, β-bisabolene, and (E)-nerolidol for chemotype A, and bicyclogermacrene and elemicin for chemotype B. A stereochemical analysis of chemotype A extract revealed (+)-α-bisabolol enantiomer. Histochemical tests of chemotypes showed similar results and suggested the presence of essential oil in idioblasts stained with the dye NADI. The analyses of chemotype A leaves by GC-MS revealed similar compositions for abaxial and adaxial surfaces, such pattern was also observed for chemotype B. Medium and high polarity metabolites showed high chemical similarities between the chemotypes, highlighting the presence of proanthocyanidins and glycosylated flavonoids (O- and C-glycosides). Thus, N. megapotamica produced distinct volatile chemotypes with highly conserved medium to high polarity compounds. Such results suggest that phenolic derivatives have a basal physiological function, while genetic or environmental differences lead to differentiation in volatile profiles of N. megapotamica.

The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon
Maezumi, S.Y. ; Alves, Daiana ; Robinson, Mark ; Souza, Jonas Gregorio de; Levis, Carolina ; Barnett, Robert L. ; Almeida de Oliveira, Edemar ; Urrego, Dunia ; Schaan, Denise ; Iriarte, José - \ 2018
Nature Plants 4 (2018)8. - ISSN 2055-026X - p. 540 - 547.

The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social1–10 and natural sciences11,12. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data8, modern vegetation13, modern ethnographic data3 or a limited integration of archaeological and palaeoecological data12. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered11. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

Insight into the Role of Facultative Bacteria Stimulated by Microaeration in Continuous Bioreactors Converting LCFA to Methane
Duarte, M.S. ; Silva, Sérgio A. ; Salvador, Andreia F. ; Cavaleiro, Ana J. ; Stams, Alfons J.M. ; Alves, M.M. ; Pereira, M.A. - \ 2018
Environmental Science and Technology 52 (2018)11. - ISSN 0013-936X - p. 6497 - 6507.

Conversion of unsaturated long chain fatty acids (LCFA) to methane in continuous bioreactors is not fully understood. Palmitate (C16:0) often accumulates during oleate (C18:1) biodegradation in methanogenic bioreactors, and the reason why this happens and which microorganisms catalyze this reaction remains unknown. Facultative anaerobic bacteria are frequently found in continuous reactors operated at high LCFA loads, but their function is unclear. To get more insight on the role of these bacteria, LCFA conversion was studied under microaerophilic conditions. For that, we compared bioreactors treating oleate-based wastewater (organic loading rates of 1 and 3 kg COD m-3 d-1), operated under different redox conditions (strictly anaerobic-AnR, -350 mV; microaerophilic-MaR, -250 mV). At the higher load, palmitate accumulated 7 times more in the MaR, where facultative anaerobes were more abundant, and only the biomass from this reactor could recover the methanogenic activity after a transient inhibition. In a second experiment, the abundance of facultative anaerobic bacteria, particularly Pseudomonas spp. (from which two strains were isolated), was strongly correlated (p < 0.05) with palmitate-to-total LCFA percentage in the biofilm formed in a continuous plug flow reactor fed with very high loads of oleate. This work strongly suggests that microaeration stimulates the development of facultative bacteria that are critical for achieving LCFA conversion to methane in continuous bioreactors. Microbial networks and interactions of facultative and strict anaerobes in microbial communities should be considered in future studies.

Photographic comparison : a method for qualitative outdoor thermal perception surveys
Cortesão, João ; Brandão Alves, Fernando ; Raaphorst, Kevin - \ 2018
International Journal of Biometeorology (2018). - ISSN 0020-7128 - 13 p.
Field survey - Outdoor - Photographic comparison - Qualitative methods - Thermal perception - Visual semiotics

This article addresses the use of photographic comparison as a complementary visual appraisal method in an outdoor thermal perception survey. This survey was carried out during a Ph.D. research exploring how materials and vegetation influence thermal comfort in outdoor public spaces. Objective and subjective thermal perception parameters were combined and quantitative and qualitative research methods were used. The quantitative methods included microclimatic measurements, whilst the qualitative methods comprised observations and spatially localised interviews based on a questionnaire and the photographic comparison. This article explores how such visual research method allowed triangulating findings of this field survey. Three non-edited photographs of outdoor public spaces, under similar summer meteorological conditions but with contrasting spatial features, were shown to respondents to the questionnaire. The photographs depicted undisclosed locations for preventing biased emotional appreciations. Respondents were asked to select the potentially most comfortable and uncomfortable environments depicted. The choice of photographs matched the previous answers on the thermal sensation and evaluation judgement scales. Hence, we discuss the way the visual interpretations by respondents allowed the triangulation of in situ thermal perception data. The extent to which thermal comfort can be interpreted from thermal environments depicted in photographs containing clear visual signs is further discussed. The article concludes on how such a visual appraisal method can be valuable for enriching future qualitative outdoor thermal perception surveys with subjective interpretation of visual data.

Engineering storage capacity for volatile sesquiterpenes in Nicotiana benthamiana leaves
Delatte, Thierry L. ; Scaiola, Giulia ; Molenaar, Jamil ; Sousa Farias, Katyuce de; Alves Gomes Albertti, Leticia ; Busscher, Jacqueline ; Verstappen, Francel ; Carollo, Carlos ; Bouwmeester, Harro ; Beekwilder, Jules - \ 2018
Plant Biotechnology Journal 16 (2018)12. - ISSN 1467-7644 - p. 1997 - 2006.
Nicotiana benthamiana - Lipid bodies - Secondary metabolites - Sesquiterpene - Storage - Triacylglycerol

Plants store volatile compounds in specialized organs. The properties of these storage organs prevent precarious evaporation and protect neighbouring tissues from cytotoxicity. Metabolic engineering of plants is often carried out in tissues such as leaf mesophyll cells, which are abundant and easily accessible by engineering tools. However, these tissues are not suitable for the storage of volatile and hydrophobic compound such as sesquiterpenes and engineered volatiles are often lost into the headspace. In this study, we show that the seeds of Arabidopsis thaliana, which naturally contain lipid bodies, accumulate sesquiterpenes upon engineered expression. Subsequently, storage of volatile sesquiterpenes was achieved in Nicotiana benthamiana leaf tissue, by introducing oleosin-coated lipid bodies through metabolic engineering. Hereto, different combinations of genes encoding diacylglycerol acyltransferases (DGATs), transcription factors (WRINKL1) and oleosins (OLE1), from the oil seed-producing species castor bean (Ricinus communis) and Arabidopsis, were assessed for their suitability to promote lipid body formation. Co-expression of α-bisabolol synthase with Arabidopsis DGAT1 and WRINKL1 and OLE1 from castor bean promoted storage of α-bisabolol in N. benthamiana mesophyll tissue more than 17-fold. A clear correlation was found between neutral lipids and storage of sesquiterpenes, using synthases for α-bisabolol, (E)-β-caryophyllene and α-barbatene. The co-localization of neutral lipids and α-bisabolol was shown using microscopy. This work demonstrates that lipid bodies can be used as intracellular storage compartment for hydrophobic sesquiterpenes, also in the vegetative parts of plants, creating the possibility to improve yields of metabolic engineering strategies in plants.

Effects of steaming on contaminants of emerging concern levels in seafood
Barbosa, Vera ; Maulvault, Ana Luísa ; Alves, Ricardo N. ; Kwadijk, Christian ; Kotterman, Michiel ; Tediosi, Alice ; Fernández-Tejedor, Margarita ; Sloth, Jens J. ; Granby, Kit ; Rasmussen, Rie R. ; Robbens, Johan ; Witte, Bavo De; Trabalón, Laura ; Fernandes, José O. ; Cunha, Sara C. ; Marques, António - \ 2018
Food and Chemical Toxicology 118 (2018). - ISSN 0278-6915 - p. 490 - 504.
Musk fragrances and UV-Filters - PAHs - PFCs - Seafood - Steaming - Toxic elements
Seafood consumption is a major route for human exposure to environmental contaminants of emerging concern (CeCs). However, toxicological information about the presence of CeCs in seafood is still insufficient, especially considering the effect of cooking procedures on contaminant levels. This study is one among a few who evaluated the effect of steaming on the levels of different CeCs (toxic elements, PFCs, PAHs, musk fragrances and UV-filters) in commercially relevant seafood in Europe, and estimate the potential risks associated with its consumption for consumers. In most cases, an increase in contaminant levels was observed after steaming, though varying according to contaminant and seafood species (e.g. iAs, perfluorobutanoate, dibenzo(ah)anthracene in Mytilus edulis, HHCB-Lactone in Solea sp., 2-Ethylhexyl salicylate in Lophius piscatorius). Furthermore, the increase in some CeCs, like Pb, MeHg, iAs, Cd and carcinogenic PAHs, in seafood after steaming reveals that adverse health effects can never be excluded, regardless contaminants concentration. However, the risk of adverse effects can vary. The drastic changes induced by steaming suggest that the effect of cooking should be integrated in food risk assessment, as well as accounted in CeCs regulations and recommendations issued by food safety authorities, in order to avoid over/underestimation of risks for consumer health.
Insects as Human Food
Huis, Arnold van - \ 2018
In: Ethnozoology Animals in our Lives / Alves, Romulo Romeu Nobrega, Albuquerque, Ulysses Paulino, Elsevier Inc. Academic Press - ISBN 9780128099131 - p. 195 - 213.
Arthropods were an important food source for early hominids. They still are in tropical countries, where about 2000 species are consumed as a sustainable source of food, contributing to food security. Most species are harvested from nature depending on the season, and only some are semidomesticated or farmed. Throughout history local people have developed an intricate knowledge about these species which is reflected by the way how arthropods are harvested and prepared as food. Whether or not some arthropod species are eaten depends not only on taste and nutritional value but also on customs, ethnic preferences, or prohibitions. Its promotion deserves more attention both from national governments and development agencies.
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