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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Effect of nickel and cobalt on methanogenic enrichment cultures and role of biogenic sulphide in metal toxicity attenuation
Luz Ferreira Martins Paulo, Lara da; Ramiro Garcia, Javier ; Mourik, Simon van; Stams, Fons ; Machado de Sousa, Diana - \ 2019
Wageningen University
PRJEB20620 - ERP022789
Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. The amount of methane produced from H2/CO2 was reduced in 50% in the presence of 8 mM of Ni or 30 mM of Co (after 6 days of incubation), compared to controls without metal supplementation. When acetate was used as substrate, methane production was also reduced: in 18% with 8 mM of Ni and in 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulphide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8mM) in the presence of sulphate or sulphide. The addition of sulphide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulphate, possibly due to strong competition of hydrogenotrophic methanogens by sulphate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenic sulphide had a positive effect and higher amounts of methane were produced in these incubations than in similar assays without sulphate addition. The degree of competition between methanogens and sulphate-reducing bacteria is a determinant factor for the success of using biogenic sulphide as detoxification method.
Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Adaptation and application of a two-plasmid inducible CRISPR-Cas9 system in Clostridium beijerinckii
Diallo, M. ; Hocq, Rémi ; Collas, Florent ; Chartier, Gwladys ; Wasels, François ; Wijaya, Hani Surya ; Werten, Marc W.T. ; Wolbert, Emil J.H. ; Kengen, Servé W.M. ; Oost, John van der; Ferreira, Nicolas Lopes ; López-Contreras, A.M. - \ 2019
Methods : a companion to Methods in enzymology (2019). - ISSN 1046-2023 - 10 p.
Clostridium beijerinckii - CRISPR-Cas9 - Genome editing - Nuclease

Recent developments in CRISPR technologies have opened new possibilities for improving genome editing tools dedicated to the Clostridium genus. In this study we adapted a two-plasmid tool based on this technology to enable scarless modification of the genome of two reference strains of Clostridium beijerinckii producing an Acetone/Butanol/Ethanol (ABE) or an Isopropanol/Butanol/Ethanol (IBE) mix of solvents. In the NCIMB 8052 ABE-producing strain, inactivation of the SpoIIE sporulation factor encoding gene resulted in sporulation-deficient mutants, and this phenotype was reverted by complementing the mutant strain with a functional spoIIE gene. Furthermore, the fungal cellulase-encoding celA gene was inserted into the C. beijerinckii NCIMB 8052 chromosome, resulting in mutants with endoglucanase activity. A similar two-plasmid approach was next used to edit the genome of the natural IBE-producing strain C. beijerinckii DSM 6423, which has never been genetically engineered before. Firstly, the catB gene conferring thiamphenicol resistance was deleted to make this strain compatible with our dual-plasmid editing system. As a proof of concept, our dual-plasmid system was then used in C. beijerinckii DSM 6423 ΔcatB to remove the endogenous pNF2 plasmid, which led to a sharp increase of transformation efficiencies.

Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.
Merot-L'anthoene, Virginie ; Tournebize, Rémi ; Darracq, Olivier ; Rattina, Vimel ; Lepelley, Maud ; Bellanger, Laurence ; Tranchant-Dubreuil, Christine ; Coulée, Manon ; Pégard, Marie ; Metairon, Sylviane ; Fournier, Coralie ; Stoffelen, Piet ; Janssens, Steven B. ; Kiwuka, Catherine ; Musoli, Pascal ; Sumirat, Ucu ; Legnaté, Hyacinthe ; Kambale, Jean Léon ; Ferreira da Costa Neto, João ; Revel, Clara ; Kochko, Alexandre de; Descombes, Patrick ; Crouzillat, Dominique ; Poncet, Valérie - \ 2019
Plant Biotechnology Journal 17 (2019)7. - ISSN 1467-7644 - p. 1418 - 1430.
C. canephora - C. eugenioides - Coffea arabica origin - genetic map - single-nucleotide polymorphism - SNP array

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.

Dynamics of archaeal community in soil with application of composted tannery sludge
Miranda, Ana Roberta Lima ; Mendes, Lucas William ; Lemos, Leandro Nascimento ; Antunes, Jadson Emanuel Lopes ; Amorim, Marineide Rodrigues ; Melo, Vania Maria Maciel ; Melo, Wanderley Jose de; Brink, Paul J. van den; Araujo, Ademir Sergio Ferreira - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Application of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7 th year by using different rates (0, 2.5, 5, 10 and 20 ton ha −1 ). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.

Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
Importance of details in food descriptions in estimating population nutrient intake distributions
Zhang, Liangzi ; Geelen, Anouk ; Boshuizen, Hendriek C. ; Ferreira, José ; Ocké, Marga C. - \ 2019
Nutrition Journal 18 (2019)1. - ISSN 1475-2891
24-h recall - Dietary assessment - Food consumption survey - Food descriptions - Population nutrient intake distributions - Variable importance measure

Background: National food consumption surveys are important policy instruments that could monitor food consumption of a certain population. To be used for multiple purposes, this type of survey usually collects comprehensive food information using dietary assessment methods like 24-h dietary recalls (24HRs). However, the collection and handling of such detailed information require tremendous efforts. We aimed to improve the efficiency of data collection and handling in 24HRs, by identifying less important characteristics of food descriptions (facets) and assessing the impact of disregarding them on energy and nutrient intake distributions. Methods: In the Dutch National Food Consumption Survey 2007-2010, food consumption data were collected through interviewer-administered 24HRs using GloboDiet software in 3819 persons. Interviewers asked participants about the characteristics of each food item according to applicable facets. Food consumption data were subsequently linked to the food composition database. The importance of facets for predicting energy and each of the 33 nutrients was estimated using the random forest algorithm. Then a simulation study was performed to determine the influence of deleting less important facets on population nutrient intake distributions. Results: We identified 35% facets as unimportant and deleted them from the total food consumption database. The majority (79.4%) of the percent difference between percentile estimates of the population nutrient intake distributions before and after facet deletion ranged from 0 to 1%, while 20% cases ranged from 1 to 5% and 0.6% cases more than 10%. Conclusion: We concluded that our procedure was successful in identifying less important food descriptions in estimating population nutrient intake distributions. The reduction in food descriptions has the potential to reduce the time needed for conducting interviews and data handling while maintaining the data quality of the survey.

iSQAPER task WP 3.3 soil quality indicators : Influence of soil type and land management on chemical, physical and biological soil parameters assessed visually and analytically
Hoek, J. ; Berg, W. van den; Wesselink, M. ; Sukkel, W. ; Mäder, P. ; Bünemann, E. ; Bongiorno, G. ; Goede, R. de; Brussaard, L. ; Bai, Z. ; Haagsma, W. ; Verstegen, H. ; Glavan, M. ; Ferreira, C.S. ; Garcia Orenes, F. ; Toth, Z. ; Zhang, W. ; Fan, H. ; Fu, H. ; Gao, H. ; Xu, M. - \ 2019
Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Wageningen Plant Research Report 783) - 114
Feedbacks from Filter Feeders: Review on the Role of Mussels in Cycling and Storage of Nutrients in Oligo- Meso- and Eutrophic Cultivation Areas
Jansen, Henrice Maria ; Strand, Øivind ; Broekhoven, Wouter Van; Strohmeier, Tore ; Verdegem, Marc C. ; Smaal, Aad C. - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 143 - 177.
Cultured and wild bivalve stocks provide ecosystem services through regulation of nutrient dynamics; both by regeneration of nutrients that become available again for phytoplankton production (positive feedback), and by extraction
of nutrients through filtration and storage in tissue (negative feedback). Consequently, bivalves may fulfil a role in water quality management. The magnitude of regulating services by filter feeding bivalves varies between coastal ecosystems. This review uses the blue mussel as a model species and evaluates how cultured mussel stocks regulate nutrient dynamics in oligo- meso- and eutrophic ecosystems. We thereby examine (i) the eco-physiological response of mussels, and (ii) the positive and negative feedback mechanisms between mussel stocks and the surrounding ecosystem. Mussel culture in nutrient-poor areas (deep Norwegian fjords) are compared with cultures in other coastal systems with medium- to rich nutrient conditions. It was found that despite differences in eco-physiological rates under nutrient-poor conditions (higher clearance, lower egestion, similar excretion and tissue storage rates), the proportion of nutrients regenerated was similar between (deep) nutrient-poor
and (shallow) nutrient-rich areas. Of the filtered nutrients, 40–50% is regenerated
and thus made available again for phytoplankton growth, and 10–50% of the
filtered nutrients is stored in tissue and could be removed from the system by harvest. A priori, we inferred that as a consequence of low background nutrient levels, mussels would potentially have a larger effect on ecosystem functioning in nutrient-poor systems and/or seasons. However, this review showed that due to the physical characteristics (volume, water residence time) and low mussel densities in nutrient-poor Norwegian fjord systems, the effects were lower for these sites, while estimates were more profound in shallow nutrient-rich areas with more intensive aquaculture activities, especially in terms of the negative feedback mechanisms (filtration intensity).
An insight into antidiabetic properties of six medicinal and edible mushrooms : Inhibition of α-amylase and α-glucosidase linked to type-2 diabetes
Stojkovic, D. ; Smiljkovic, M. ; Ciric, A. ; Glamoclija, J. ; Griensven, L. van; Ferreira, I.C.F.R. ; Sokovic, M. - \ 2019
South African Journal of Botany 120 (2019). - ISSN 0254-6299 - p. 100 - 103.
Diabetes mellitus - Edible and medicinal - Mushroom - α-Amylase - α-Glucosidase

As a continuation of our search for biologically active mushroom species the present study investigates in vitro antidiabetic properties of six edible and medicinal mushroom species: Agaricus blazei Murrill, Coprinus comatus (O.F. Müll.) Pers., Cordyceps militaris (L.) Fr., Inonotus obliquus (Ach. ex Pers.) Pilát, Morchella conica Pers. and Phellinus linteus Berk. & M.A. Curtis. In vitro assays on α-amylase and α-glucosidase enzymes inhibition were performed with methanolic extracts of the selected mushrooms. Furthermore, we calculated the necessary daily intake of mushroom extracts and dry mushroom powders based on the equivalent doses of therapeutic drug acarbose given to diabetic patients per day. Our comparative study on enzymes inhibition showed that the most promising potential is ascribed to Inonotus obliquus extract, while no inhibition of α-amylase was recorded with Morchella conica and Cordyceps militaris methanolic extract at the tested concentration. This comparative study is the first highlighting in vitro antidiabetic potential by inhibition of α-amylase and α-glucosidase with methanolic extracts; which makes the investigated species more promising for the diabetes type-2 treatment by an additional and different mechanism of action.

Perceptions of integrated crop-livestock systems for sustainable intensification in the Brazilian Amazon
Cortner, O. ; Garrett, R.D. ; Valentim, J.F. ; Ferreira, J. ; Niles, M.T. ; Reis, J. ; Gil, J. - \ 2019
Land Use Policy 82 (2019). - ISSN 0264-8377 - p. 841 - 853.
Farmer decision-making - Innovation - Integrated systems - Pasture intensification - Supply chains - Sustainable agriculture - Technology diffusion

Sustainable intensification of existing global croplands and rangelands is a pressing challenge to reconcile competing demands on land systems for food production and conservation of natural ecosystems. In Brazil, the world's second-largest beef-producing country, intensification of pasture-based production systems is central to both improving livelihoods and reducing deforestation, since low-productivity, low-income cattle ranches occupy a majority of the agricultural land area. Integrated crop-livestock systems (ICLS) present a promising opportunity in the array of possible agricultural intensification strategies for Brazil because they have the potential to reclaim vast areas of degraded pastures while mitigating greenhouse gas emissions. Much of the previous research on ICLS, particularly in Brazil, has focused on agronomic and economic aspects. Here we examine local perspectives of ICLS to better illuminate what other concerns, besides agronomic and economic outcomes, might guide farmers’ decisions to adopt this (and other) agricultural intensification strategies. We are particularly interested in the degree to which structural factors interact with personal experiences to shape information and values and farmers’ understanding of the costs and benefits of adopting a new technology. Using semi-structured interviews with a diverse sample of producers in four states in the Brazilian Amazon, we find that existing adopters perceived ICLS as a beneficial strategy for increasing the economic value and competitiveness of their farm, while most non-adopters did not. Ranchers in particular perceived intensification as a necessity to maintain their livelihood amidst declining profits and increased environmental oversight. However, both adopters and non-adopters described numerous structural barriers that impeded greater adoption of ICLS in the region, including problems obtaining qualified labor, a lack of marketing options, poor infrastructure, an unsupportive regulatory environment, and in some regions, poorly drained soils. Furthermore, non-monetary motives, such as maintaining one's existing quality of life and traditions, often drove decisions regardless of expected profit-maximization pathways. This work underscores the need to employ a more diverse set of policy tools beyond credit subsidies to encourage adoption of sustainable intensification strategies, including education programs, payments for the ecosystem services, and improved transportation and supply chain infrastructure that can support intensification and help create a climate of innovation.

Global Production of Marine Bivalves. Trends and Challenges
Wijsman, J.W.M. ; Troost, K. ; Fang, J. ; Roncarati, A. - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 7 - 26.
The global production of marine bivalves for human consumption is more than 15 million tonnes per year (average period 2010–2015), which is about 14% of the total marine production in the world. Most of the marine bivalve production
(89%) comes from aquaculture and only 11% comes from the wild fishery.
Asia, especially China, is by far the largest producer of marine bivalves, accounting for 85% of the world production and responsible for the production growth. In other continents, the production is stabilizing or decreasing (Europe) the last decades. In order to stimulate growth, sustainability (Planet, Profit, People) of the aquaculture activities is a key issue. Environmental (Planet) aspects for sustainable aquaculture include the fishery on seed resources, carrying capacity, invasive species and organic loading. Food safety issues due to environmental contaminants and biotoxines should be minimized to increase the reliability of marine bivalves as a healthy food source and to stimulate market demands. Properly designed monitoring programs are important tools to accomplish sustainable growth of marine bivalve production.
Perspectives on Bivalves Providing Regulating Services in Integrated Multi-Trophic Aquaculture
Strand, Øivind ; Jansen, Henrice M. ; Jiang, Zengjie ; Robinson, Shawn M.C. - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 209 - 230.
The concept of integrating species into one culture system originates from Asia and the Middle East. Development of integrated aquaculture involving marine bivalves is relatively new, going back to the late 1980s in China and 1990s in the Western world. In this chapter, we present four cases of integrated multi-trophic
aquaculture (IMTA) where bivalves are involved in providing regulating services: i) shrimp culture in ponds, ii) cascading pond systems, iii) open-water caged finfish culture and iv) bay-scale culture systems. The bay-scale integrated
culture system in Sanggou Bay in China represents commercial IMTA where a
range of different regulating services are provided by the bivalves. Bivalves use
degraded fragments derived from cultured kelp and organic waste products from
fish farming, and play an important role in the ecosystem processes of the bay. The provision of regulating services in shrimp and cascading ponds is evident as the system configurations allow for biogeochemical processing of waste to maximize extraction by the bivalves. The current configurations used in open-water finfish cage culture suggest that adaptation of concepts allowing for control of effluent water, producing longer contact times and increased biogeochemical processing of the waste products, will dominate future IMTA development. If global bivalve culture production is sustained, we will likely see more regulating services from bivalves in IMTA systems, as new opportunities may arise for developing novel IMTA configurations and concepts
Habitat Modification and Coastal Protection by Ecosystem-Engineering Reef-Building Bivalves
Ysebaert, Tom ; Walles, Brenda ; Haner, Judy ; Hancock, Boze - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 253 - 273.
Reef-building bivalves like oysters and mussels are conspicuous ecosystem
engineers in intertidal and subtidal coastal environments. By forming complex,
three-dimensional structures on top of the sediment surface, epibenthic bivalve
reefs exert strong bio-physical interactions, thereby influencing local hydro- and morphodynamics as well as surrounding habitats and associated species. The spatial impact of the ecosystem engineering effects of reef-building bivalves is much larger than the size of the reef. By influencing hydrodynamics oysters and mussels modify the sedimentary environment far beyond the boundaries of the reef, affecting morphological and ecological processes up to several hundreds of meters. Being key-stone species in many coastal environments, reef-building bivalves are increasingly recognized for their role in delivering important ecosystem services that serve human wellbeing. Here we focus on two services, namely the regulating service coastal protection (coastal erosion prevention, shoreline stabilization) and the supporting habitat for species service (enhancement of biodiversity and diversification of the landscape). Due to their wave dampening effects, reef-building bivalve reefs are increasingly used for shoreline protection and erosion control along eroding coastlines, as an alternative to artificial shoreline hardening. Thefacilitative interactions at long-distances of bivalve reefs provide biodiversity benefits and more specifically facilitate or protect other valuable habitats such as intertidal flats, sea grasses, saltmarshes and mangroves. Two case studies are used to demonstrate how bivalve reefs can be restored or constructed for shoreline protection and erosion control, thereby focusing on oyster reefs: (1) Oyster reefs for shoreline protection in coastal Alabama, USA, and (2) Oyster reefs as protection against tidal flat erosion, Oosterschelde, The Netherlands. It is argued that bivalve reefs should be promoted as nature-based solutions that provide biodiversity benefits and coastal protection and help in climate change mitigation and adaptation. In order to successfully restore these habitats practitioners should consider a general framework in which habitat requirements, environmental setting and long-distance interdependence between habitats are mutually considered.
Bivalve Assemblages as Hotspots for Biodiversity
Craeymeersch, J.A. ; Jansen, H.M. - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 275 - 294.
Many bivalve species occur in aggregations, and locally cover large parts
of the seafloor. Above a certain density they provide a distinct, three dimensional structure and the aggregations are called bivalve beds or reefs. These persistent aggregations form a biogenic habitat for many other species. Bivalve beds, therefore, often have, in comparison with the surrounding areas, a high biodiversity value and can be seen as hotspots for biodiversity. Bivalve have a wide global distribution, on rocky and sedimentary coasts. Different processes and mechanisms influence the presence of associated benthic fauna. This paper reviewed the main drivers that influence the biodiversity, such as the bivalve species involved, the density, the size and the age of the bed, the depth or height in the tidal zone and the substratum type. Bivalve beds not only occur naturally in many subtidal and intertidal areas around the world, but mussels and oysters are also extensively cultured. Addition of physical cultivation structures in the water column or on the bottom allows for development of substantial and diverse communities that have a structure similar to that of natural beds. Dynamics of culture populations may however differ from natural
bivalve reefs as a result of culture site and/or maintenance and operation like
harvesting of the bivalve cultures. We used the outcome of the review on the drivers for wild assemblages to evaluate trade-offs between bivalve aquaculture and biodiversity conservation. Studies comparing natural and cultured assemblages proved to allow for a better understanding of the effect of the culture strategies and, consequently, to forward sustainable bivalve cultures. This is illustrated by a case study in the Dutch Wadden Sea.
Introduction to Cultural Services
Smaal, Aad C. ; Strand, Øivind - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 315 - 316.
Cultural services of marine bivalves are of high value as they provide
well-being in many different ways. These services are more difficult to quantify but
provide a lot of qualities. Shell collectioning, shells as archives, community efforts
for bivalve restoration and gardening are some cases of cultural services. Marine
bivalves have been recognized as a carrier of a variety of cultures since pre-historic
times.
Bivalve Aquaculture Carrying Capacity : Concepts and Assessment Tools
Smaal, Aad C. ; Duren, L.A. Van - \ 2019
In: Goods and Services of Marine Bivalves / Smaal, Aad C., Ferreira, Joao G., Grant, Jon, Petersen, Jens K., Strand, Øivind, Springer International Publishing - ISBN 9783319967752 - p. 451 - 483.
The carrying capacity concept for bivalve aquaculture is used to assess
production potential of culture areas, and to address possible effects of the culture for the environment and for other users. Production potential is depending on physical and production carrying capacity of the ecosystem, while ecological and social carrying capacity determine to what extent the production capacity can be realized. According to current definitions, the ecological carrying capacity is the stocking or farm density of the exploited population above which unacceptable environmental impacts become apparent, and the social capacity is the level of farm development above which unacceptable social impacts are manifested. It can be disputed to what extent social and ecological capacities differ, as unacceptable impacts are social constructs. In the approach of carrying capacity, focus is often on avoiding adverse impacts of bivalve aquaculture. However, bivalve populations also have positive impacts on the ecosystem, such as stimulation of primary production through filtration and nutrient regeneration. These ecosystem services deserve more attention in proper estimation of carrying capacity and therefore we focus on both positive and
negative feedbacks by the bivalves on the ecosystem. We review tools that are available to quantify carrying capacity. This varies from simple indices to complex models. We present case studies of the use of clearance and grazing ratio’s as simple carrying capacity indices. Applications depend on specific management questions in the respective areas, the availability of data and the type of decisions that need to be made. For making decisions on bivalve aquaculture, standards, threshold values or levels of acceptable change (LAC) are used. The FAO framework for aquaculture is formulated as The Ecosystem Approach to Aquaculture. It implies stakeholder involvement, and a carrying capacity management where commercial stocks attribute in a balanced way to production, ecological and social goals. Simulation models are being developed as tools to predict the integrated effect of various levels of bivalve aquaculture for specific management goals, such as improved ecosystem resilience. In practice, bivalve aquaculture management is confronted with different competing stocks of cultured, wild, restoration and invasive origin. Scenario models have been reviewed that are used for finding the balance between maximizing production capacity and optimizing ecological carrying capacity in areas with bivalve aquaculture.
Provisioning of mussel seed and its efficient use in culture
Kamermans, P. ; Capelle, J. - \ 2019
In: Goods and services of marine bivalves / Smaal, A., Ferreira, J.G., Grant, J., Petersen, J.K., Strand, O., Cham : Springer - ISBN 9783319967752 - p. 27 - 49.
Mussel culture largely depends on seed and feed from the natural environment. This paper focusses on seed provisioning and efficient use of these resources in mussel production. Approaches and technologies for seed supply and efficient use of seed in mussel production are described for the different culture techniques. This includes potential interactions and conflicts with the natural environment. Three methods are used to provide seed: wild harvest, use of suspended collectors and hatchery production. Harvest of wild seed from seaweed (in New Zealand) or natural beds is still a major source for culture in some areas, costs are low but provisioning is often unreliable. Most research concerning spat collection deals with comparison of different types of suspended collectors, settlement cues and problems with biofouling. Hatchery seed is more expensive, but hatcheries provide the opportunity for selective breeding and triploid production giving the product an added value. The challenge is to bring hatchery production costs more in line with the actual sale value of mussel seed. Monitoring genetic diversity can give insight in whether collector seed or hatchery seed growth and survival is negatively affected by reduced diversity. Grow-out occurs in bottom culture, bouchot culture and off-bottom longline and raft culture. In bottom-culture, the focus is on developing better seeding techniques, predator control and optimizing culture practices such as timing of relay, substrate use and harvest. For bouchot culture, technical developments are directed to mechanical methods to increase efficiency in size grading, restocking, harvesting and processing. Innovation in growing-out techniques for longline and raft culture are directed towards the investigation of optimal stocking densities, and on material type and configuration of farms. Production efficiency increases from bottom culture to bouchot culture, to rope and raft culture and are related to the sources of mortality and differences in growth rate. Growth rate of mussels is higher in off bottom culture than in on bottom culture and higher when submerged than in intertidal. Mussels from the Perna genus are found to have a higher growth rate but a lower production efficiency than mussels from the Mytilus genus. Efficient use of seed in mussel culture should aim at a reduction of mussel losses and an increase in growth rates. Important tools are adjusting seeding densities in relation to system design, reducing seeding stress, predator control and applying thinning out or relay.
Short communication: detection and molecular characterization of hepatitis E virus in domestic animals of São Tomé and Príncipe
Mesquita, João Rodrigo ; Istrate, Claudia ; Santos-Ferreira, Nânci L. ; Ferreira, Ana S. ; Abreu-Silva, Joana ; Veiga, José ; Poel, Wim H.M. van der; Nascimento, Maria S.J. - \ 2019
Tropical Animal Health and Production 51 (2019). - ISSN 0049-4747 - p. 481 - 485.
Domestic animals - Hepatitis E virus - São Tomé e Príncipe - Zoonoses

As in most of the African continent, the status of hepatitis E virus (HEV) infection in domestic animals in São Tomé and Príncipe, an archipelago off the western equatorial coast of Central Africa, is also completely unknown. In the present study, we investigated the presence of HEV among domestic animals in São Tomé and Príncipe. A total of 93 stool samples from different animal species (goat, cow, pig, chicken, duck, and monkey) were tested for HEV RNA using two real-time RT-PCR assays, followed by a nested RT-PCR assay for sequencing and phylogenetic analysis. A total of six samples (1 cow stool and 5 pig stools) were found to be positive for HEV RNA of which one pig stool was positive by broad spectrum nested RT-PCR. Phylogenetic analysis showed that the retrieved sequence clustered within HEV subgenotype 3f, similar to zoonotic strains of European countries and posing interesting questions on past introduction of European HEV into São Tomé and Príncipe archipelago. This is the first report describing the presence and molecular characterization of HEV in São Tomé and Príncipe.

Assessment of promising agricultural management practices
Barão, Lúcia ; Alaoui, Abdallah ; Ferreira, Carla ; Basch, Gottlieb ; Schwilch, Gudrun ; Geissen, Violette ; Sukkel, Wijnand ; Lemesle, Julie ; Garcia-Orenes, Fuensanta ; Morugán-Coronado, Alicia ; Mataix-Solera, Jorge ; Kosmas, Costas ; Glavan, Matjaž ; Pintar, Marina ; Tóth, Brigitta ; Hermann, Tamás ; Vizitiu, Olga Petruta ; Lipiec, Jerzy ; Reintam, Endla ; Xu, Minggang ; Di, Jiaying ; Fan, Hongzhu ; Wang, Fei - \ 2019
Science of the Total Environment 649 (2019). - ISSN 0048-9697 - p. 610 - 619.
Environment - Farming systems - Soil threats - Sustainability

iSQAPER project - Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience - aims to develop an app to advise farmers on selecting the best Agriculture Management Practice (AMPs) to improve soil quality. For this purpose, a soil quality index has to be developed to account for the changes in soil quality as impacted by the implementation of the AMPs. Some promising AMPs have been suggested over the time to prevent soil degradation. These practices have been randomly adopted by farmers but which practices are most used by farmers and where they are mostly adopted remains unclear. This study is part of the iSQAPER project with the specific aims: 1) map the current distribution of previously selected 18 promising AMPs in several pedo-climatic regions and farming systems located in ten and four study site areas (SSA) along Europe and China, respectively; and 2) identify the soil threats occurring in those areas. In each SSA, farmers using promising AMP's were identified and questionnaires were used to assess farmer's perception on soil threats significance in the area. 138 plots/farms using 18 promising AMPs, were identified in Europe (112) and China (26).Results show that promising AMPs used in Europe are Crop rotation (15%), Manuring & Composting (15%) and Min-till (14%), whereas in China are Manuring & Composting (18%), Residue maintenance (18%) and Integrated pest and disease management (12%). In Europe, soil erosion is the main threat in agricultural Mediterranean areas while soil-borne pests and diseases is more frequent in the SSAs from France and The Netherlands. In China, soil erosion, SOM decline, compaction and poor soil structure are among the most significant. This work provides important information for policy makers and the development of strategies to support and promote agricultural management practices with benefits for soil quality.

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