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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    Bioflocculants from wastewater : Insights into adsorption affinity, flocculation mechanisms and mixed particle flocculation based on biopolymer size-fractionation
    Ajao, Victor ; Fokkink, Remco ; Leermakers, Frans ; Bruning, Harry ; Rijnaarts, Huub ; Temmink, Hardy - \ 2020
    Journal of Colloid and Interface Science 581 (2020). - ISSN 0021-9797 - p. 533 - 544.
    Co-adsorption - Dual clay system - Extracellular polymeric substances - Kaolinite - Montmorillonite - Natural flocculants - Optical reflectometry - Polymer adsorption - Polymer mixture - Site blocking

    Hypothesis: Microbial extracellular polymeric substances (EPS) produced from wastewater are generally heterodispersed, which is expected to influence their flocculation performances and mechanism, particularly in mixed particle systems. The different molecular weight (MW) fractions should contribute to the overall adsorption affinity and flocculation mechanism of EPS in single and dual clay systems. Experiments: EPS harvested from bioreactors were size-fractionated into high, medium and low MW fractions (HMW, MMW, LMW, respectively). The harvested mixed EPS and its fractions were characterised by diverse analytical techniques coupled with optical reflectometry to investigate the role of each EPS fraction in the overall flocculation mechanism of EPS in kaolinite and montmorillonite clay systems. Findings: In single clay systems, both the harvested mixed EPS and the HMW-EPS fraction showed comparable flocculation performances. However, mixed EPS proved to be more efficient than the HMW-EPS fraction for dual clay flocculation. Site blocking effects were observed in mixed EPS: the LMW and MMW EPS first adsorbed to the surface due to higher diffusivities and faster mass transfer to the interface, while the HMW-EPS were slowly transported but were attached to the surface irreversibly and stronger than the LMW/MMW-EPS. We propose from this, a mixed EPS adsorption mechanism: extended anionic polymer tails in solution, thereby enhancing particle flocculation.

    Plastome phylogeography in two African rain forest legume trees reveals that Dahomey Gap populations originate from the Cameroon volcanic line
    Demenou, Boris B. ; Migliore, Jérémy ; Heuertz, Myriam ; Monthe, Franck K. ; Ojeda, Dario I. ; Wieringa, Jan J. ; Dauby, Gilles ; Albreht, Laura ; Boom, Arthur ; Hardy, Olivier J. - \ 2020
    Molecular Phylogenetics and Evolution 150 (2020). - ISSN 1055-7903
    African rain forest - Cameroon volcanic line - Colonization origin - Dahomey gap - Phylogeography - Plastid genome sequencing

    Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) – a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments – was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.

    Granule-based immobilization and activity enhancement of anammox biomass via PVA/CS and PVA/CS/Fe gel beads
    Wang, Jinxing ; Liang, Jidong ; Sun, Li ; Li, Gaigai ; Temmink, Hardy ; Rijnaarts, Huub H.M. - \ 2020
    Bioresource Technology 309 (2020). - ISSN 0960-8524
    Aggregation - Anammox - Gel beads - Immobilization

    Granule-based immobilization of anammox biomass assisted by polyvinyl alcohol/chitosan (PVA/CS) and PVA/CS/Fe gel beads was studied, via the operation of three identical up-flow reactors (R1 without gel beads, R2 with PVA/CS, R3 with PVA/CS/Fe) for 203 days. In the end, the nitrogen removal rates (NRR) were 5.3 ± 0.4, 10.0 ± 0.3 and 13.9 ± 0.5 kg-N m−3 d−1 for R1, R2 and R3, respectively. The porous PVA/CS and PVA/CS/Fe created a suitable eco-niche for anammox bacteria to grow and attach, thus being retained in the reactor. The EPS entangles newly grown cells within the gel beads, resulting in compact aggregation. The interaction between Fe ions added to PVA/CS/Fe gel beads and negatively charged EPS groups strongly promoted granule strength and compactness. The immobilization method proposed by this study was found to effectively improve biomass retention in the reactors, which is promising for advanced anammox process applications.

    Microbial Community Drivers in Anaerobic Granulation at High Salinity
    Gagliano, Maria Cristina ; Sudmalis, Dainis ; Pei, Ruizhe ; Temmink, Hardy ; Plugge, Caroline M. - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    16S rRNA gene sequencing - Defluviitaleaceae - EPS - filamentous microorganisms - fluorescence in situ hybridization - granular sludge - Methanosaeta - UASB

    In the recent years anaerobic sludge granulation at elevated salinities in upflow anaerobic sludge blanket (UASB) reactors has been investigated in few engineering based studies, never addressing the microbial community structural role in driving aggregation and keeping granules stability. In this study, the combination of different techniques was applied in order to follow the microbial community members and their structural dynamics in granules formed at low (5 g/L Na+) and high (20 g/L Na+) salinity conditions. Experiments were carried out in four UASB reactors fed with synthetic wastewater, using two experimental set-ups. By applying 16S rRNA gene analysis, the comparison of granules grown at low and high salinity showed that acetotrophic Methanosaeta harundinacea was the dominant methanogen at both salinities, while the dominant bacteria changed. At 5 g/L Na+, cocci chains of Streptoccoccus were developing, while at 20 g/L Na+ members of the family Defluviitaleaceae formed long filaments. By means of Fluorescence in Situ Hybridization (FISH) and Scanning Electron Microscopy (SEM), it was shown that aggregation of Methanosaeta in compact clusters and the formation of filaments of Streptoccoccus and Defluviitaleaceae during the digestion time were the main drivers for the granulation at low and high salinity. Interestingly, when the complex protein substrate (tryptone) in the synthetic wastewater was substituted with single amino acids (proline, leucine and glutamic acid), granules at high salinity (20 g/L Na+) were not formed. This corresponded to a decrease of Methanosaeta relative abundance and a lack of compact clustering, together with disappearance of Defluviitaleaceae and consequent absence of bacterial filaments within the dispersed biomass. In these conditions, a biofilm was growing on the glass wall of the reactor instead, highlighting that a complex protein substrate such as tryptone can contribute to granules formation at elevated salinity.

    Adaptive decision-making under conditions of uncertainty: the case of farming in the Volta delta, Ghana
    Sarku, Rebecca ; Dewulf, Art ; Slobbe, Erik van; Termeer, Katrien ; Kranjac-Berisavljevic, Gordana - \ 2020
    Journal of integrative Environmental Sciences 17 (2020)1. - ISSN 1943-815X - p. 1 - 33.
    Ada East District - Adaptive decision-making - deltas - farming - uncertainty - weather conditions

    Farming in Ghana’s Volta delta is increasingly affected by variability in rainfall conditions and changes in land-use patterns. Under such socio-ecological conditions, little is known about farmers’ decision-making in response to uncertainties in uncertain rainfall conditions. To fill this gap and add to the literature on adaptive decision-making, we addressed the central question: what are the existing patterns of farming decision-making under uncertain rainfall conditions, and which decision-making strategies are adaptive? We developed an adaptive decision-making framework to investigate the behavior of farmers under variable rainfall conditions in Ghana’s Volta delta in the Ada East District. We conducted 5 interviews with agricultural extension agents, 44 in-depth interviews and 4 focus group discussion with farmers. Subsequently, we interviewed a sub-selection of 32 farmers. Findings of the study shows that farmers carry out different decision-making patterns in response to the variable rainfall conditions. We distinguished six strategies: three based on flexibility and three based on robustness. Flexible adaptive decision-making strategies are switching dates for sowing seeds through wait-and-see or delay strategy, muddling through the farming season with the application of various options and alternative irrigation strategies. Robust adaptive decision-making strategies are portfolio strategy of transplanting seedlings in batches, selection of robust (hardy) crops, and intercropping or diversification. Based on how farmers select strategies in response to uncertainty in rainfall conditions, we argue that some decision-making strategies are more adaptive than others. Findings of this study are relevant for the design and implementation of climate related agricultural projects.

    Automated Processing of Sentinel-2 Products for Time-Series Analysis in Grassland Monitoring
    Hardy, Tom ; Franceschini, Marston Domingues ; Kooistra, Lammert ; Novani, Marcello ; Richter, Sebastiaan - \ 2020
    In: International Symposium on Environmental Software Systems (ISESS 2020) Wageningen : Springer (IFIP Advances in Information and Communication Technology ) - ISBN 9783030398149 - p. 48 - 56.
    Effective grassland management practices require a good understanding of soil and vegetation properties, that can be quantified by farmers’ knowledge and remote sensing techniques. Many systems have been proposed in the past for grassland monitoring, but open-source alternatives are increasingly being preferred. In this paper, a system is proposed to process data in an open-source and automated way. This system made use of Sentinel-2 data to support grassland management at Haus Riswick in the region around Kleve, Germany, retrieved with help of a platform called Sentinelsat that was developed by ESA. Consecutive processing steps consisted of atmospheric correction, cloud masking, clipping the raster data, and calculation of vegetation indices. First results from 2018 resembled the mowing regime of the area with four growing cycles, although outliers were detected due to a lack of data caused by cloud cover. Moreover, that year’s extremely dry summer was visible in the time-series pattern as well. The proposed script is a primary version of a processing chain, which is suitable to be further expanded for more advanced data pre-processing and data analysis in the future.
    Regeneration and reuse of microbial extracellular polymers immobilised on a bed column for heavy metal recovery
    Ajao, Victor ; Nam, Kang ; Chatzopoulos, Paraschos ; Spruijt, Evan ; Bruning, Harry ; Rijnaarts, Huub ; Temmink, Hardy - \ 2020
    Water Research 171 (2020). - ISSN 0043-1354
    Biosorption - Column - Extracellular polymeric substances - Ion exchange mechanism - Metal adsorption

    Microbial extracellular polymeric substances (EPS) have gained increasing attention for various water treatment applications. In this study, EPS produced from nitrogen-limited glycerol/ethanol-rich wastewater were used to recover Cu2+ and Pb2+ from aqueous solutions. Continuous flow-through tests were conducted on a column packed with silica gel coated with polyethyleneimine, to which EPS were irreversibly attached as shown by optical reflectometry. These immobilised EPS excellently adsorbed Cu2+ and Pb2+, with 99.9% of influent metal adsorbed before the breakthrough points. Metal desorption was achieved with 0.1M HCl, with an average recovery of 86% for Cu2+ and 90% recovery for Pb2+. For the first time, we successfully showed the possibility to regenerate and reuse the immobilised EPS for five adsorption-desorption cycles (using Cu2+ as an example) with no reduction in the adsorbed amount at the breakthrough point (qbp). Based on the mass balance of the associated metal ions participating in the adsorption process, ion exchange was identified as the major mechanism responsible for Cu2+ and Pb2+ adsorption by EPS. The results demonstrate the potential of wastewater-produced EPS as an attractive and perhaps, cost-effective biosorbent for heavy metal removal (to trace effluent concentrations) and recovery (86–99%).

    Calcium effect on microbial activity and biomass aggregation during anaerobic digestion at high salinity
    Gagliano, Maria Cristina ; Sudmalis, Dainis ; Temmink, Hardy ; Plugge, Caroline M. - \ 2020
    New Biotechnology 56 (2020). - ISSN 1871-6784 - p. 114 - 122.
    Anaerobic digestion - Anaerobic granules - Ca - High salinity - Methanosaeta - Microbial aggregation

    The potential effect of different Ca2+ additions (150, 300, 450, 600 and 1000 mg/L) on microbial activity and aggregation, during anaerobic digestion at moderate (8 g/L Na+) and high salinity (20 g/L Na+) has been investigated. Batch tests were carried out in duplicate serum bottles and operated for 30 days at 37 °C. At 8 g/L Na+, methanogenic activity and protein degradation were comparable from 150 to 450 mg/L Ca2+, and a significant inhibition was only observed at a Ca2+concentration of 1000 mg/L. In contrast, at 20 g/L Na+, 150 to 300 mg/L were the only Ca2+ concentrations to maintain chemical oxygen demand (COD) removal, protein hydrolysis and methane production. Overall, increasing Ca2+ concentrations had a larger impact on acetotrophic methanogenesis at 20 g/L than at 8 g/L Na+. Increasing Ca2+ had a negative effect on the aggregation behaviour of the dominant methanogen Methanosaeta when working at 8 g/L Na+. At 20 g/L Na+ the aggregation of Methanosaeta was less affected by addition of Ca2+ than at 8 g/L Na+. The negative effect appeared to be connected with Ca2+ precipitation and its impact on cell-to cell communication. The results highlight the importance of ionic balance for microbial aggregation at high salinity, bringing to the forefront the effect on Methanosaeta cells, known to be important to obtain anaerobic granules.

    Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies
    Koenen, Erik J.M. ; Ojeda, Dario I. ; Steeves, Royce ; Migliore, Jérémy ; Bakker, Freek T. ; Wieringa, Jan J. ; Kidner, Catherine ; Hardy, Olivier J. ; Pennington, R.T. ; Bruneau, Anne ; Hughes, Colin E. - \ 2020
    New Phytologist 225 (2020)3. - ISSN 0028-646X - p. 1355 - 1369.
    Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data is lacking.We generated alignments of 72 chloroplast genes and 7621 homologous nuclear‐encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees.
    We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting.
    All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as ‘basal’ or ‘early‐diverging’ with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.
    Protein hydrolysis and fermentation under methanogenic and acidifying conditions
    Duong, Thu Hang ; Grolle, Katja ; Nga, Tran Thi Viet ; Zeeman, Grietje ; Temmink, Hardy ; Eekert, Miriam Van - \ 2019
    Biotechnology for Biofuels 12 (2019)1. - ISSN 1754-6834
    Amino acid fermentation - Hydrolysis - Methanogenic conditions - Non-methanogenic conditions - Proteins

    Background: Many kinds of wastewaters contain appreciable quantities of protein. Anaerobic processes are suitable for the treatment of wastewater high in organics to achieve pollution control and recovery of energy as methane and hydrogen, or intermediates for production of biofuels and valuable biochemicals. A distinction between protein hydrolysis and amino acid fermentation, especially for dissolved proteins, is needed to target which one is truly rate-limiting and to effectively harvest bioproducts during anaerobic conversion of these wastewaters. This study explored mesophilic anaerobic hydrolysis and amino acid fermentation of gelatine, as a model for dissolved proteins, at pH 7 and at pH 5. Results: The results showed that at pH 7, protein hydrolysis (first-order rate of 0.15 h-1) was approximately 5 times faster than acidification of the hydrolysis products (first-order rate of 0.03 h-1), implying that not hydrolysis but acidification was the rate-limiting step in anaerobic dissolved protein degradation. This was confirmed by (temporary) accumulation of amino acids. Nineteen different amino acids were detected during the first 8 incubation hours of gelatine at neutral pH and the total chemical oxygen demand (COD) of these 19 amino acids was up to approximately 40% of the COD of the gelatine that was added. Protein hydrolysis at pH 5 was 2-25 times slower than at pH 7. Shifting the initial pH from neutral to acidic conditions (pH 5) inhibited protein degradation and changed the volatile fatty acids (VFA) product profile. Furthermore, the presence or absence of methanogenic activity did not affect the rates of protein hydrolysis and acidification. Conclusions: The findings in this study can help to set a suitable solid retention time to accomplish anaerobic degradation of protein-rich wastewaters in continuous reactor systems. For example, if the target is harvesting VFAs, methanogens can be washed-out for a shorter retention time while amino acid fermentation, instead of hydrolysis as assumed previously, will govern the design and solutions to improve the system dealing with dissolved proteins.[Figure not available: see fulltext].

    Optimization of algae production on urine
    Tuantet, Kanjana ; Temmink, Hardy ; Zeeman, Grietje ; Wijffels, René H. ; Buisman, Cees J.N. ; Janssen, Marcel - \ 2019
    Algal Research 44 (2019). - ISSN 2211-9264
    Microalgae production - Nutrient removal - Photobioreactor control - Urine treatment

    Urine is a potential source of nutrients to grow microalgal biomass to be re-used as fertilizer and soil conditioner. In this study the impact of photobioreactor dilution rate on microalgae productivity and photosynthetic efficiency was assessed and used to determine operating conditions to reach both full nitrogen removal from urine and high biomass productivity. In addition, the possibility to work under day/night cycling was tested. To this end, the microalga Chlorella sorokiniana was grown on artificial urine and real human urine in bench-scale panel photobioreactors with short optical paths. At a light intensity of 1530 μmol⋅ m−2⋅s-1 photobioreactor productivity and photosynthetic efficiency was demonstrated to be maximal at reactor dilution rates between 0.10 and 0.15 h-1. A biomass yield of 1 g dry matter per mol of PAR photons was achieved. Biomass concentration, and accordingly nutrient removal efficiency, decreased at increasing reactor dilution rate. The experimental results could be reproduced by model simulations. These simulations allowed to demonstrate that the system must be operated at a dilution rate of less than 0.01 h-1 in order to reach complete nitrogen removal. In that scenario more than half of the potential biomass productivity is lost due to severe self-shading within the algal culture. Experiments with real human urine illustrated the problem of incomplete nitrogen removal and ammonium inhibition of growth at too high dilution rates. It is therefore suggested to apply an optimized pre-dilution of pure urine prior to treatment in a photobioreactor. Experiments under day-night cycles demonstrated that microalgal cultures quickly acclimate to such variable light conditions. Additional model simulations illustrated that a phototrophic system is most effective when diluted urine is fed to the photobioreactor during day time only. In that situation the lowest nitrogen concentration in the effluent can be reached at a maximal areal removal rate and photosynthetic efficiency.

    Applying ecosystem services for pre-market environmental risk assessments of regulated stressors
    Devos, Y. ; Munns Jr., W.R. ; Forbes, V.E. ; Maltby, Lorraine ; Stenseke, Marie ; Brussaard, L. ; Streissl, F. ; Hardy, A. - \ 2019
    In: Proceedings of the Third EFSA Scientific Conference: Science, Food and Society Guest / Devos, Y., Elliott, K.C., Hardy, A., John Wiley and Sons (EFSA Journal S1)
    Ecosystem services (ES) are the benefits that people obtain from ecosystems. Investigating the environment through an ES framework has gained wide acceptance in the international scientific community and is applied by policymakers to protect biodiversity and safeguard the sustainability of ecosystems. This approach can enhance the ecological and societal relevance of pre‐market/prospective environmental risk assessments (ERAs) of regulated stressors by: (1) informing the derivation of operational protection goals; (2) enabling the integration of environmental and human health risk assessments; (3) facilitating horizontal integration of policies and regulations; (4) leading to more comprehensive and consistent environmental protection; (5) articulating the utility of, and trade‐offs involved in, environmental decisions; and (6) enhancing the transparency of risk assessment results and the decisions based upon them. Realisation of these advantages will require challenges that impede acceptance of an ES approach to be overcome. Particularly, there is concern that, if biodiversity only matters to the extent that it benefits humans, the intrinsic value of nature is ignored. Moreover, our understanding of linkages among ecological components and the processes that ultimately deliver ES is incomplete, valuing ES is complex, and there is no standard ES lexicon and limited familiarity with the approach. To help overcome these challenges, we encourage: (1) further research to establish biodiversity–ES relationships; (2) the development of approaches that (i) quantitatively translate responses to chemical stressors by organisms and groups of organisms to ES delivery across different spatial and temporal scales, (ii) measure cultural ES and ease their integration into ES valuations, and (iii) appropriately value changes in ES delivery so that trade‐offs among different management options can be assessed; (3) the establishment of a standard ES lexicon; and (4) building capacity in ES science and how to apply ES to ERAs. These development needs should not prevent movement towards implementation of an ES approach in ERAs, as the advantages we perceive of using this approach render it more than worthwhile to tackle those challenges. Society and the environment stand to benefit from this shift in how we conduct the ERA of regulated stressors.
    Valorization of glycerol/ethanol-rich wastewater to bioflocculants: recovery, properties, and performance
    Ajao, Victor ; Millah, Siti ; Gagliano, Maria Cristina ; Bruning, Harry ; Rijnaarts, Huub ; Temmink, Hardy - \ 2019
    Journal of Hazardous Materials 375 (2019). - ISSN 0304-3894 - p. 273 - 280.
    Biodegradable flocculants - Extracellular polymeric substance - Nitrogen limitation - Resource recovery

    Microbial extracellular polymeric substances (EPS)were produced in two membrane bioreactors, each separately treating fresh and saline synthetic wastewater (consisting of glycerol and ethanol), with the purpose of applying them as sustainable bioflocculants. The reactors were operated under nitrogen-rich (COD/N ratios of 5 and 20)and limited (COD/N ratios of 60 and 100)conditions. Under both conditions, high COD removal efficiencies of 87–96% were achieved. However, nitrogen limitation enhanced EPS production, particularly the polysaccharide fraction. The maximum EPS recovery (g EPS−COD/g COD influent )from the fresh wastewater was 54% and 36% recovery was obtained from the saline (30 g NaCl/L)wastewater. The biopolymers had molecular weights up to 2.1 MDa and anionic charge densities of 2.3–4.7 meq/g at pH 7. Using kaolin clay suspensions, high flocculation efficiencies of 85–92% turbidity removal were achieved at EPS dosages below 0.5 mg/g clay. Interestingly, EPS produced under saline conditions proved to be better flocculants in a saline environment than the corresponding freshwater EPS in the same environment. The results demonstrate the potential of glycerol/ethanol-rich wastewater, namely biodiesel/ethanol industrial wastewater, as suitable substrates to produce EPS as effective bioflocculants.

    FitTetra 2.0 - Improved genotype calling for tetraploids with multiple population and parental data support
    Zych, Konrad ; Gort, Gerrit ; Maliepaard, Chris A. ; Jansen, Ritsert C. ; Voorrips, Roeland E. - \ 2019
    BMC Bioinformatics 20 (2019)1. - ISSN 1471-2105
    Autotetraploids - fitPoly - Genomics - Genotype calling - Genotyping - Polyploids

    Background: Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data. Results: Our upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60 k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated. Conclusion: Our updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.

    Increased virulence of Globodera pallida during repeated rearing on different resistant potato cultivars explained by a simple model
    Beniers, J.E. ; Nöllen, Y. ; Eck, H.J. van; Schouten, H.J. - \ 2019
    Plant Pathology 68 (2019)3. - ISSN 0032-0862 - p. 445 - 453.
    Globodera pallida - model - potato cyst nematodes - resistance - selection - virulence

    Selection for virulence of Globodera pallida on potato cultivars was studied for four generations under controlled conditions. The reproduction rate (Pf/Pi) of a mixed Pa2/3 population increased by a factor of 61 during rearing on the partially resistant potato cv. Darwina compared to rearing on the susceptible cv. Irene. This was a result of selection for virulence on cv. Darwina, and achieving the Hardy–Weinberg equilibrium on cv. Irene. Increased virulence also significantly raised the reproduction rate on several other Solanum genotypes. These changes could be explained reasonably well by the monogenic inheritance of a virulence factor breaking the Grp1 locus. The virulence changes were probably mainly evoked by this gene only, inherited from S. vernei 1-3 or S. vernei 24/20. The Grp1 locus has probably provided the differential S. vernei hybrid (VTn)2 62-33-3 with its resistance to the Pa2 group and not to the Pa3 group. Alternation of cultivars did not halt selection if the cultivars highly differentiated between the Pa2 and Pa3 populations. Only when alternation was with cultivars that harboured a different resistance gene against Pa3 was selection for virulence delayed. Differences in virulence levels (i.e. reproduction rates) within the nematode population determined the rate of selection, not the resistance level itself. Selection of a Pa3 population for three generations on cv. Karakter not only increased the reproduction rate on cv. Karakter itself by a factor 4.2, but also raised the reproduction on other potato genotypes. A simple monogenic model could explain these changes in virulence.

    Sensor-based management of container nursery crops irrigated with fresh or saline water
    Incrocci, Luca ; Marzialetti, Paolo ; Incrocci, Giorgio ; Vita, Andrea Di; Balendonck, Jos ; Bibbiani, Carlo ; Spagnol, Serafino ; Pardossi, Alberto - \ 2019
    Agricultural Water Management 213 (2019). - ISSN 0378-3774 - p. 49 - 61.
    The objective of this study was to design and test a prototype fertigation controller for the management of container ornamental nursery stocks irrigated with different water sources, including saline water or reclaimed municipal/industrial wastewater. The prototype could schedule irrigation in various ways, i.e. as a time clock, or by means of a soil moisture dielectric sensor, or using a crop evapotranspiration (ET) model. The prototype also monitored the salinity in the root zone using a dielectric sensor that measured both substrate moisture and electrical conductivity (EC), or a probe measuring the EC of the water draining out of the containers. Excessive substrate salinization of the containers irrigated with saline water (containing 10 mM of sodium chloride) was prevented by the automated adoption of a series of measures: irrigation with fresh water or a mixture of fresh water and saline water; progressive increase of irrigation dose for each event, and progressive reduction of fertilizer concentration in the nutrient solution delivered to the crop. The system was tested in three experiments conducted in Pistoia (Italy) between 2008 and 2010 with two ornamental species: Photinia × fraseri Dress (a salt-medium tolerant species) and Prunus laurocerasus L. (a salt-sensitive species). When irrigation with fresh water was controlled with a dielectric sensor or an ET model, total irrigation water use and the loss of both N and P were reduced by 17% to 84% compared with the time-controlled irrigation. The sensor-based control of saline water irrigation reduced the salinity effects on dry matter accumulation in both species; however, it did not prevent the occurrence of leaf damages (leaf scorch) on Prunus plants, which were unmarketable by the end of growing season. On the contrary, no leaf damages were visible on Photinia plants irrigated with saline and/or fresh water, such that all were classified in the top quality market category. The controller developed in this work could be used in commercial nurseries to improve profitability and sustainability of container hardy ornamental nursery stock production.
    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    The Effect of Bioinduced Increased pH on the Enrichment of Calcium Phosphate in Granules during Anaerobic Treatment of Black Water
    Cunha, Jorge Ricardo ; Tervahauta, Taina ; Weijden, Renata D. van der; Temmink, Hardy ; Hernández Leal, Lucía ; Zeeman, Grietje ; Buisman, Cees J.N. - \ 2018
    Environmental Science and Technology 52 (2018)22. - ISSN 0013-936X - p. 13144 - 13154.

    Simultaneous recovery of calcium phosphate granules (CaP granules) and methane in anaerobic treatment of source separated black water (BW) has been previously demonstrated. The exact mechanism behind the accumulation of calcium phosphate (Cax(PO4)y) in CaP granules during black water treatment was investigated in this study by examination of the interface between the outer anaerobic biofilm and the core of CaP granules. A key factor in this process is the pH profile in CaP granules, which increases from the edge (7.4) to the center (7.9). The pH increase enhances supersaturation for Cax(PO4)y phases, creating internal conditions preferable for Cax(PO4)y precipitation. The pH profile can be explained by measured bioconversion of acetate and H2, HCO3 - and H+ into CH4 in the outer biofilm and eventual stripping of CO2 and CH4 (biogas) from the granule. Phosphorus content and Cax(PO4)y crystal mass quantity in the granules positively correlated with the granule size, in the reactor without Ca2+ addition, indicating that the phosphorus rich core matures with the granule growth. Adding Ca2+ increased the overall phosphorus content in granules >0.4 mm diameter, but not in fine particles (<0.4 mm). Additionally, H+ released from aqueous phosphate species during Cax(PO4)y crystallization were buffered by internal hydrogenotrophic methanogenesis and stripping of biogas from the granule. These insights into the formation and growth of CaP granules are important for process optimization, enabling simultaneous Cax(PO4)y and CH4 recovery in a single reactor. Moreover, the biological induction of Cax(PO4)y crystallization resulting from biological increase of pH is relevant for stimulation and control of (bio)crystallization and (bio)mineralization in real environmental conditions.

    Understanding and improving the reusability of phosphate adsorbents for wastewater effluent polishing
    Suresh Kumar, Prashanth ; Ejerssa, Wondesen Workneh ; Wegener, Carita Clarissa ; Korving, Leon ; Dugulan, Achim Iulian ; Temmink, Hardy ; Loosdrecht, Mark C.M. van; Witkamp, Geert-Jan - \ 2018
    Water Research 145 (2018). - ISSN 0043-1354 - p. 365 - 374.
    Calcium adsorption - Phosphate adsorption - Regeneration - Reusability - Surface precipitation - Wastewater effluent

    Phosphate is a vital nutrient for life but its discharge from wastewater effluents can lead to eutrophication. Adsorption can be used as effluent polishing step to reduce phosphate to very low concentrations. Adsorbent reusability is an important parameter to make the adsorption process economically feasible. This implies that the adsorbent can be regenerated and used over several cycles without appreciable performance decline. In the current study, we have studied the phosphate adsorption and reusability of commercial iron oxide based adsorbents for wastewater effluent. Effects of adsorbent properties like particle size, surface area, type of iron oxide, and effects of some competing ions were determined. Moreover the effects of regeneration methods, which include an alkaline desorption step and an acid wash step, were studied. It was found that reducing the adsorbent particle size increased the phosphate adsorption of porous adsorbents significantly. Amongst all the other parameters, calcium had the greatest influence on phosphate adsorption and adsorbent reusability. Phosphate adsorption was enhanced by co-adsorption of calcium, but calcium formed surface precipitates such as calcium carbonate. These surface precipitates affected the adsorbent reusability and needed to be removed by implementing an acid wash step. The insights from this study are useful in designing optimal regeneration procedures and improving the lifetime of phosphate adsorbents used for wastewater effluent polishing.

    Editorial: Algal technologies for wastewater treatment and resource recovery :
    Muñoz, Raul ; Temmink, Hardy ; Verschoor, Anthony M. ; Steen, Peter Van Der - \ 2018
    Water Science and Technology 78 (2018)1. - ISSN 0273-1223 - 2 p.
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