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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Land-Management Options for Greenhouse Gas Removal and Their Impacts on Ecosystem Services and the Sustainable Development Goals
Smith, Pete ; Adams, Justin ; Beerling, David J. ; Beringer, Tim ; Calvin, Katherine V. ; Fuss, Sabine ; Griscom, Bronson ; Hagemann, Nikolas ; Kammann, Claudia ; Kraxner, Florian ; Minx, Jan C. ; Popp, Alexander ; Renforth, Phil ; Vicente Vicente, Jose Luis ; Keesstra, Saskia - \ 2019
Annual Review of Environment and Resources 44 (2019). - ISSN 1543-5938 - p. 255 - 286.
afforestation/reforestation - BECCS - biochar - bioenergy with carbon capture and storage - carbon dioxide removal - CDR - ecosystem services - greenhouse gas removal - Nature's Contributions to People - NCPs - negative emission technology - NET - SDG - soil carbon sequestration - terrestrial enhanced weathering - UN Sustainable Development Goals - wetland restoration

Land-management options for greenhouse gas removal (GGR) include afforestation or reforestation (AR), wetland restoration, soil carbon sequestration (SCS), biochar, terrestrial enhanced weathering (TEW), and bioenergy with carbon capture and storage (BECCS). We assess the opportunities and risks associated with these options through the lens of their potential impacts on ecosystem services (Nature's Contributions to People; NCPs) and the United Nations Sustainable Development Goals (SDGs). We find that all land-based GGR options contribute positively to at least some NCPs and SDGs. Wetland restoration and SCS almost exclusively deliver positive impacts. A few GGR options, such as afforestation, BECCS, and biochar potentially impact negatively some NCPs and SDGs, particularly when implemented at scale, largely through competition for land. For those that present risks or are least understood, more research is required, and demonstration projects need to proceed with caution. For options that present low risks and provide cobenefits, implementation can proceed more rapidly following no-regrets principles.

8th International Symposium on "Delivery of Functionality in Complex Food Systems"
Linden, E. van der; Marangoni, Alejandro ; Vicente, António ; Singh, Harjinder ; Ubbink, Job ; Mezzenga, Raffaele ; Livney, Yoav ; Axelos, Monique A.V. ; Boland, Mike ; Relkin, Perla - \ 2019
Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Bioturbation and erosion rates along the soil-hillslope conveyor belt, part 2: Quantification using an analytical solution of the diffusion–advection equation
Román-Sánchez, Andrea ; Laguna, Ana ; Reimann, Tony ; Giráldez, Juan Vicente ; Peña, Adolfo ; Vanwalleghem, Tom - \ 2019
Earth Surface Processes and Landforms 44 (2019)10. - ISSN 0197-9337 - p. 2066 - 2080.
bioturbation - critical zone - deposition - diffusivity - erosion - feldspar luminescence dating - sensitivity and uncertainty - soil formation

Particles on soil-mantled hillslopes are subject to downslope transport by erosion processes and vertical mixing by bioturbation. Both are key processes for understanding landscape evolution and soil formation, and affect the functioning of the critical zone. We show here how the depth–age information, derived from feldspar-based single grain post-infrared infrared stimulated luminescence (pIRIR), can be used to simultaneously quantify erosion and bioturbation processes along a hillslope. In this study, we propose, for the first time, an analytical solution for the diffusion–advection equation to calculate the diffusivity constant and erosion–deposition rates. We have fitted this model to age–depth data derived from 15 soil samples from four soil profiles along a catena located under natural grassland in the Santa Clotilde Critical Zone Observatory, in the south of Spain. A global sensitivity analysis was used to assess the relative importance of each model parameter in the output. Finally, the posterior probability density functions were calculated to evaluate the uncertainty in the model parameter estimates. The results show that the diffusivity constant at the surface varies from 11.4 to 81.9 mm2 a-1 for the hilltop and hill-base profile, respectively, and between 7.4 and 64.8 mm2 a-1 at 50 cm depth. The uncertainty in the estimation of the erosion–deposition rates was found to be too high to make a reliable estimate, probably because erosion–deposition processes are much slower than bioturbation processes in this environment. This is confirmed by a global sensitivity analysis that shows how the most important parameters controlling the age–depth structure in this environment are the diffusivity constant and regolith depth. Finally, we have found a good agreement between the soil reworking rates proposed by earlier studies, considering only particle age and depth, and the estimated diffusivity constants. The soil reworking rates are effective rates, corrected for the proportion of particles actually participating in the process.

Science-based wildlife disease response
Vicente, Joaquín ; Apollonio, Marco ; Blanco-Aguiar, Jose A. ; Borowik, Tomasz ; Brivio, Francesca ; Casaer, Jim ; Croft, Simon ; Ericsson, Göran ; Ferroglio, Ezio ; Gavier-Widen, Dolores ; Gortázar, Christian ; Jansen, Patrick A. ; Keuling, Oliver ; Kowalczyk, Rafał ; Petrovic, Karolina ; Plhal, Radim ; Podgórski, Tomasz ; Sange, Marie ; Scandura, Massimo ; Schmidt, Krzysztof ; Smith, Graham C. ; Soriguer, Ramon ; Thulke, Hans Hermann ; Zanet, Stefania ; Acevedo, Pelayo - \ 2019
Science 364 (2019)6444. - ISSN 0036-8075 - p. 943 - 944.
Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium
Orsi, Enrico ; Folch, Pauline L. ; Monje-López, Vicente T. ; Fernhout, Bas M. ; Turcato, Alessandro ; Kengen, Servé W.M. ; Eggink, Gerrit ; Weusthuis, Ruud A. - \ 2019
Journal of Industrial Microbiology and Biotechnology 46 (2019)8. - ISSN 1367-5435 - p. 1179 - 1190.
Amorphadiene - MEP - Mevalonate - PHB - Rhodobacter sphaeroides

Rhodobacter sphaeroides is a metabolically versatile bacterium capable of producing terpenes natively. Surprisingly, terpene biosynthesis in this species has always been investigated in complex media, with unknown compounds possibly acting as carbon and nitrogen sources. Here, a defined medium was adapted for R. sphaeroides dark heterotrophic growth, and was used to investigate the conversion of different organic substrates into the reporter terpene amorphadiene. The amorphadiene synthase was cloned in R. sphaeroides, allowing its biosynthesis via the native 2-methyl-d-erythritol-4-phosphate (MEP) pathway and, additionally, via a heterologous mevalonate one. The latter condition increased titers up to eightfold. Consequently, better yields and productivities to previously reported complex media cultivations were achieved. Productivity was further investigated under different cultivation conditions, including nitrogen and oxygen availability. This novel cultivation setup provided useful insight into the understanding of terpene biosynthesis in R. sphaeroides, allowing to better comprehend its dynamics and regulation during chemoheterotrophic cultivation.

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)4. - ISSN 0340-6717 - p. 307 - 326.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
Erratum to: The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
GigaScience 7 (2018)12. - ISSN 2047-217X
Improvement of clay and sand quantification based on a novel approach with a focus on multispectral satellite images
Fongaro, Caio T. ; Demattê, José A.M. ; Rizzo, Rodnei ; Safanelli, José Lucas ; Sousa Mendes, Wanderson de; Dotto, André Carnieletto ; Vicente, Luiz Eduardo ; Franceschini, Marston H.D. ; Ustin, Susan L. - \ 2018
Remote Sensing 10 (2018)10. - ISSN 2072-4292
Bare soil - Digital soil mapping - Precision agriculture - Reflectance spectroscopy - Satellite imagery - Soil degradation

Soil mapping demands large-scale surveys that are costly and time consuming. It is necessary to identify strategies with reduced costs to obtain detailed information for soil mapping. We aimed to compare multispectral satellite image and relief parameters for the quantification and mapping of clay and sand contents. The Temporal Synthetic Spectral (TESS) reflectance and Synthetic Soil Image (SYSI) approaches were used to identify and characterize texture spectral signatures at the image level. Soil samples were collected (0-20 cm depth, 919 points) from an area of 14,614 km2 in Brazil for reference and model calibration. We compared different prediction approaches: (a) TESS and SYSI; (b) Relief-Derived Covariates (RDC); and (c) SYSI plus RDC. The TESS method produced highly similar behavior to the laboratory convolved data. The sandy textural class showed a greater increase in average spectral reflectance from Band 1 to 7 compared with the clayey class. The prediction using SYSI produced a better result for clay (R2 = 0.83; RMSE = 65.0 g kg-1) and sand (R2 = 0.86; RMSE = 79.9 g kg-1). Multispectral satellite images were more stable for the identification of soil properties than relief parameters.

Comparative proteome analysis of propionate degradation by Syntrophobacter fumaroxidans in pure culture and in coculture with methanogens
Sedano-Núñez, Vicente T. ; Boeren, Sjef ; Stams, Alfons J.M. ; Plugge, Caroline M. - \ 2018
Environmental Microbiology 20 (2018)5. - ISSN 1462-2912 - p. 1842 - 1856.
Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate axenically or in syntrophic interaction with methanogens or other sulfate-reducing bacteria. We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio desulfuricans. Special attention was put on the role of hydrogen and formate in interspecies electron transfer (IET) and energy conservation. Formate dehydrogenase Fdh1 and hydrogenase Hox were the main confurcating enzymes used for energy conservation. In the periplasm, Fdh2 and hydrogenase Hyn play an important role in reverse electron transport associated with succinate oxidation. Periplasmic Fdh3 and Fdh5 were involved in IET. The sulfate reduction pathway was poorly regulated and many enzymes associated with sulfate reduction (Sat, HppA, AprAB, DsrAB and DsrC) were abundant even at conditions where sulfate was not present. Proteins similar to heterodisulfide reductases (Hdr) were abundant. Hdr/Flox was detected in all conditions while HdrABC/HdrL was exclusively detected when sulfate was available; these complexes most likely confurcate electrons. Our results suggest that S. fumaroxidans mainly used formate for electron release and that different confurcating mechanisms were used in its sulfidogenic metabolism.
Energy conservation mechanisms and electron transfer in syntrophic propionate-oxidizing microbial consortia
Sedano Núñez, Vicente Tonamellotl - \ 2018
Wageningen University. Promotor(en): A.J.M. Stams, co-promotor(en): Caroline M. Plugge. - Wageningen : Wageningen University - ISBN 9789463432634 - 206
Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway
Balanzà, Vicente ; Martínez-Fernández, Irene ; Sato, Shusei ; Yanofsky, Martin F. ; Kaufmann, Kerstin ; Angenent, Gerco C. ; Bemer, Marian ; Ferrándiz, Cristina - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Monocarpic plants have a single reproductive cycle in their lives, where life span is determined by the coordinated arrest of all meristems, or global proliferative arrest (GPA). The molecular bases for GPA and the signaling mechanisms involved are poorly understood, other than systemic cues from developing seeds of unknown nature. Here we uncover a genetic pathway regulating GPA in Arabidopsis that responds to age-dependent factors and acts in parallel to seed-derived signals. We show that FRUITFULL (FUL), a MADS-box gene involved in flowering and fruit development, has a key role in promoting meristem arrest, as GPA is delayed and fruit production is increased in ful mutants. FUL directly and negatively regulates APETALA2 expression in the shoot apical meristem and maintains the temporal expression of WUSCHEL which is an essential factor for meristem maintenance.
Volatile organic molecules from Fusarium oxysporum strain 21 with nematicidal activity against Meloidogyne incognita
Terra, Willian César ; Campos, Vicente Paulo ; Martins, Samuel Julio ; Costa, Lilian Simara Abreu S. ; Silva, Júlio Carlos Pereira da; Barros, Aline Ferreira ; Lopez, Liliana Estupiñan ; Santos, Thaisa Conrado Nunes ; Smant, Geert ; Oliveira, Denilson Ferreira - \ 2018
Crop Protection 106 (2018). - ISSN 0261-2194 - p. 125 - 131.
Bioprospecting - Fusarium oxysporum - Plant-parasitic nematodes - Volatiles
Volatile organic compounds (VOCs) produced by microorganisms are potential alternatives for the development of new nematicides. In a previous study, we identified VOCs produced by Fusarium oxysporum strain 21 (F.o–21). In this study, we tested the eight most abundant VOCs produced by F.o-21 against Meloidogyne incognita. Compounds 2-methylbutyl acetate (1), 3-methylbutyl acetate (2), ethyl acetate (7), and 2-methylpropyl acetate (8) led to in vitro mortality of 100%, 91%, 100%, and 82%, respectively, in second-stage juveniles (J2) of M. incognita at a concentration of 500 μg/mL. The lethal concentration (LC50) for compounds 1, 2, 7, and 8 in M. incognita J2, was 236, 198, 213, and 218 μg/mL, respectively. Under the same conditions, the commercial nematicide called carbofuran (2,3-dihydro-2,2-dimethyl-1-benzofuran-7-yl N-methyl carbamate) showed an LC50 of 191 μg/mL. Eggs exposed to compounds 2 and 7, for 72 h showed up to a 90% reduction in hatching, and the compounds 1, 2, 7, and 8 reduced M. incognita infectivity by 52%, 52%, 36% and 41%, respectively. When the compounds were applied in tomato seedlings infested by M. incognita, compound 1 reduced the number of galls per root gram by 22% when compared to the negative control (without the application of nematicide). The compound 2-methylbutyl acetate (1) showed potential to be used in the field after improvements in the application technology.
An assessment of policies affecting Sustainable Soil Management in Europe and selected member states
Turpin, Nadine ; Berge, Hein ten; Grignani, Carlo ; Guzmán, Gema ; Vanderlinden, Karl ; Steinmann, Horst-Henning ; Siebielec, Grzegorz ; Spiegel, Adelheid ; Perret, Eric ; Ruysschaert, Greet ; Laguna, Ana ; Giráldez, Juan Vicente ; Werner, Magdalena ; Raschke, Isabell ; Zavattaro, Laura ; Costamagna, Chiara ; Schlatter, Norman ; Berthold, Helen ; Sandén, Taru ; Baumgarten, Andreas - \ 2017
Land Use Policy 66 (2017). - ISSN 0264-8377 - p. 241 - 249.
This paper analyses soils-related policies in Europe and in selected member states and regions. Our approach breaks down policy packages at European, national and regional levels into strategic objectives, operational objectives, policy measures and expected impacts, and assesses the relationships between these elements and soil stakes. Four major policy packages, both at EU and national level (CAP-I, RDP, Environment, national initiatives) were analysed. A numerical scale was developed to quantify the level of “embeddedness” of soil stakes in these policy packages. We found that countries better embed soil stakes into their policies when they also put more efforts on environmental innovation. In turn, countries with a high embeddedness level, with high trust in European institutions and that make more efforts towards renewable energy, tend to propose a wider variety of management practices to farmers for dealing with soil stakes.
The sponge microbiome project
Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
GigaScience 6 (2017)10. - ISSN 2047-217X
16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
Agronomic effects of bovine manure : A review of long-term European field experiments
Zavattaro, Laura ; Bechini, Luca ; Grignani, Carlo ; Evert, Frits K. van; Mallast, Janine ; Spiegel, Heide ; Sandén, Taru ; Pecio, Alicja ; Giráldez Cervera, Juan Vicente ; Guzmán, Gema ; Vanderlinden, Karl ; Hose, Tommy D'; Ruysschaert, Greet ; Berge, Hein F.M. ten - \ 2017
European Journal of Agronomy 90 (2017). - ISSN 1161-0301 - p. 127 - 138.
Efficiency - Farmyard manure - Nitrogen - Response ratio - Slurry - Soil organic carbon

To evaluate the agronomic value of animal manure, we quantified the effects of pedo-climatic, crop and management factors on crop productivity, N use efficiency, and soil organic matter, described with simple indicators that compare manures with mineral fertilizers. We selected 80 European long-term field experiments that used bovine farmyard manure or bovine liquid slurry, alone (FYM and SLU) or combined with mineral fertilizers (FYMm and SLUm), and compared them to mineral fertilizer only reference treatments. We collected 5570 measurements from 107 papers. FYM produced slightly lower crop yields (−9.5%) when used alone and higher (+11.3%) yields when used in combination with N fertilizer (FYMm), compared to those obtained using mineral fertilizers only. Conditions promoting manure-N mineralization (lighter soil texture, warmer temperature, longer growing season, and shallower incorporation depth) significantly increased the effect of FYM/FYMm on crop yield and yield N. The production efficiency of FYM (yield:N applied ratio) was slightly lower than that of mineral fertilizers (-1.6%). The apparent N recoveries of FYM and FYMm were 59.3% and 78.7%, respectively, of mineral fertilizers. Manured soils had significantly higher C (+32.9% on average for FYM and FYMm) and N (+21.5%) concentrations. Compared to mineral fertilizers, yield was reduced by 9.1% with SLU, but not with SLUm. Influencing factors were similar to those of FYM/FYMm. Efficiency indicators indicated SLU (but not SLUm) was less effective than mineral fertilizers. Slurry significantly increased SOC (on average for SLU and SLUm by +17.4%) and soil N (+15.7%) concentrations. In conclusion, compared to mineral N fertilizers, bovine farmyard manure and slurry were slightly less effective on the crop, but determined marked increases to SOC and soil N, and thus, to long-term soil fertility maintenance.

The NSm proteins of phylogenetically related tospoviruses trigger Sw-5b–mediated resistance dissociated of their cell-to-cell movement function
Leastro, Mikhail Oliveira ; Oliveira, Athos Silva De; Pallás, Vicente ; Sánchez-Navarro, Jesús A. ; Kormelink, Richard ; Resende, Renato Oliveira - \ 2017
Virus Research 240 (2017). - ISSN 0168-1702 - p. 25 - 34.
Avr - Hypersensitive response - NS protein - Resistance - Sw-5b gene - Tospovirus

The cell-to-cell movement protein (NSM) in members of the tospovirus species Tomato spotted wilt virus (TSWV) has been recently identified as the effector of the single dominant Sw-5b resistance gene from tomato (Solanum lycopersicum L.). Although most TSWV isolates shows a resistance-inducing (RI) phenotype, regular reports have appeared on the emergence of resistance-breaking (RB) isolates in tomato fields, and suggested a strong association with two point mutations (C118Y and T120N) in the NSM protein. In this study the Sw-5b gene has been demonstrated to confer not only resistance against TSWV but to members of five additional, phylogenetically-related tospovirus species classified within the so-called “American” evolutionary clade, i.e. Alstroemeria necrotic streak virus (ANSV), Chrysanthemum stem necrosis virus (CSNV), Groundnut ringspot virus (GRSV), Impatiens necrotic spot virus (INSV) and Tomato chlorotic spot virus (TCSV). Remarkably, a member of the species Bean necrotic mosaic virus (BeNMV), a recently discovered tospovirus classified in a distinct American subclade and circulating on the American continent, did not trigger a Sw-5b-mediated hypersensitive (HR) response. Introduction of point mutations C118Y and T120N into the NSM protein of TSWV, TCSV and CSNV abrogated the ability to trigger Sw-5b-mediated HR in both transgenic-N. benthamiana and tomato isolines harboring the Sw-5b gene whereas it had no effect on BeNMV NSM. Truncated versions of TSWV NSM lacking motifs associated with tubule formation, cell-to-cell or systemic viral movement were made and tested for triggering of resistance. HR was still observed with truncated NSM proteins lacking 50 amino acids (out of 301) from either the amino- or carboxy-terminal end. These data altogether indicate the importance of amino acid residues C118 and T120 in Sw-5b-mediated HR only for the NSM proteins from one cluster of tospoviruses within the American clade, and that the ability to support viral cell-to-cell movement is not required for effector functionality.

ICTV virus taxonomy profile : Ophioviridae
García, María Laura ; Bó, Elena Dal; Graça, John V. da; Gago-Zachert, Selma ; Hammond, John ; Moreno, Pedro ; Natsuaki, Tomohide ; Pallás, Vicente ; Navarro, Jose A. ; Reyes, Carina A. ; Luna, Gabriel Robles ; Sasaya, Takahide ; Tzanetakis, Ioannis E. ; Vaira, Anna María ; Verbeek, Martin ; Lefkowitz, Elliot J. ; Davison, Andrew J. ; Siddell, Stuart G. ; Simmonds, Peter ; Adams, Michael J. ; Smith, Donald B. ; Orton, Richard J. ; Sanfaçon, Hélène - \ 2017
Journal of General Virology 98 (2017)6. - ISSN 0022-1317 - p. 1161 - 1162.
Blueberry mosaic associated virus - Citrus psorosis virus - ICTV - Lettuce ring necrosis virus - Mirafiori lettuce big-vein virus - Ophioviridae - Taxonomy
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Ophioviridae, which is available at http://www.ictv.global/report/ophioviridae.
Interfaces of school food procurement and family farming: the social constitution of the “30% Law” 11947/2009
Vicente-Almazan, C. ; Schneider, S. ; Derkzen, P.H.M. ; Sherwood, S.G. - \ 2016
In: ALIMENTAÇÃO ESCOLAR construindo interfaces entre saúde, educação e desenvolvimento, Edition: 1ª, Chapter: 5, Publisher: Argos, Editors: Carla Rosane Paz Arruda Teo, Rozane Marcia Triches / Paz Arruda Teo, Carla Rosane, Triches, Rozane Marcia, Argos - p. 148 - 162.
Prediction of soil properties using imaging spectroscopy: Considering fractional vegetation cover to improve accuracy
Domingues Franceschini, Marston ; Demattê, J.A.M. ; Silva Terra, F. Da; Vicente, L. ; Bartholomeus, H.M. ; Souza Filho, C. De - \ 2015
International Journal of applied Earth Observation and Geoinformation 38 (2015). - ISSN 0303-2434 - p. 358 - 370.
Spectroscopic techniques have become attractive to assess soil properties because they are fast, require little labor and may reduce the amount of laboratory waste produced when compared to conventional methods. Imaging spectroscopy (IS) can have further advantages compared to laboratory or field proximal spectroscopic approaches such as providing spatially continuous information with a high density. However, the accuracy of IS derived predictions decreases when the spectral mixture of soil with other targets occurs. This paper evaluates the use of spectral data obtained by an airborne hyperspectral sensor (ProSpecTIR-VS – Aisa dual sensor) for prediction of physical and chemical properties of Brazilian highly weathered soils (i.e., Oxisols). A methodology to assess the soil spectral mixture is adapted and a progressive spectral dataset selection procedure, based on bare soil fractional cover, is proposed and tested. Satisfactory performances are obtained specially for the quantification of clay, sand and CEC using airborne sensor data (R2 of 0.77, 0.79 and 0.54; RPD of 2.14, 2.22 and 1.50, respectively), after spectral data selection is performed; although results obtained for laboratory data are more accurate (R2 of 0.92, 0.85 and 0.75; RPD of 3.52, 2.62 and 2.04, for clay, sand and CEC, respectively). Most importantly, predictions based on airborne-derived spectra for which the bare soil fractional cover is not taken into account show considerable lower accuracy, for example for clay, sand and CEC (RPD of 1.52, 1.64 and 1.16, respectively). Therefore, hyperspectral remotely sensed data can be used to predict topsoil properties of highly weathered soils, although spectral mixture of bare soil with vegetation must be considered in order to achieve an improved prediction accuracy.
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