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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    The Genetic Architecture of Post-Zygotic Reproductive Isolation Between Anopheles coluzzii and An. quadriannulatus
    Deitz, Kevin C. ; Takken, Willem ; Slotman, Michel A. - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    Anopheles gambiae complex - Dobzhansky–Muller incompatibilities - hybrid - inviability - post-zygotic reproductive isolation - speciation - sterility

    The Anopheles gambiae complex is comprised of eight morphologically indistinguishable species and has emerged as a model system for the study of speciation genetics due to the rapid radiation of its member species over the past two million years. Male hybrids between most An. gambiae complex species pairs are sterile, and some genotype combinations in hybrid males cause inviability. We investigated the genetic basis of hybrid male inviability and sterility between An. coluzzii and An. quadriannulatus by measuring segregation distortion and performing a QTL analysis of sterility in a backcross population. Hybrid males were inviable if they inherited the An. coluzzii X chromosome and were homozygous at one or more loci in 18.9 Mb region of chromosome 3. The An. coluzzii X chromosome has a disproportionately large effect on hybrid sterility when introgressed into an An. quadriannulatus genetic background. Additionally, an epistatic interaction between the An. coluzzii X and a 1.12 Mb, pericentric region of the An. quadriannulatus 3L chromosome arm has a statistically significant contribution to the hybrid sterility phenotype. This same epistatic interaction occurs when the An. coluzzii X is introgressed into the genetic background of An. arabiensis, the sister species of An. quadriannulatus, suggesting that this may represent one of the first Dobzhansky–Muller incompatibilities to evolve early in the radiation of the Anopheles gambiae species complex. We describe the additive effects of each sterility QTL, epistatic interactions between them, and genes within QTL with protein functions related to mating behavior, reproduction, spermatogenesis, and microtubule morphogenesis, whose divergence may contribute to post-zygotic reproductive isolation between An. coluzzii and An. quadriannulatus.

    Ghost Introgression: Spooky Gene Flow in the Distant Past
    Ottenburghs, Jente - \ 2020
    Bioessays 42 (2020)6. - ISSN 0265-9247
    adaptation - demographic modelling - hybridization - macroevolution - phylogenetic networks - reproductive isolation - speciation

    Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. The increasing availability of high-quality genome assemblies for non-model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed.

    The Role of Transcriptional Regulation in Hybrid Vigor
    Botet, Ramon ; Keurentjes, Joost J.B. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    Arabidopsis thaliana - breeding - gene expression - genetic regulation - heterosis - hybrid vigor - natural variation - speciation

    The genetic basis of hybrid vigor in plants remains largely unsolved but strong evidence suggests that variation in transcriptional regulation can explain many aspects of this phenomenon. Natural variation in transcriptional regulation is highly abundant in virtually all species and thus a potential source of heterotic variability. Allele Specific Expression (ASE), which is tightly linked to parent of origin effects and modulated by complex interactions in cis and in trans, is generally considered to play a key role in explaining the differences between hybrids and parental lines. Here we discuss the recent developments in elucidating the role of transcriptional variation in a number of aspects of hybrid vigor, thereby bridging old paradigms and hypotheses with contemporary research in various species.

    Data underlying the research of Geochemical multi-surface modeling of reactive zinc speciation in compost as influenced by extraction conditions
    Klinkert, Susan ; Comans, Rob ; Groenenberg, Bert Jan - \ 2020
    Wageningen University & Research
    compost - extraction conditions - fractionation - geochemical modelling - organic matter - zinc - speciation
    This dataset includes the data and calculations underlying the modeling work carried out for the scientific manuscript "Geochemical multi-surface modeling of reactive zinc speciation in compost as influenced by extraction conditions".
    Crossing species boundaries : the hybrid histories of the true geese
    Ottenburghs, Jente - \ 2016
    Wageningen University. Promotor(en): Herbert Prins; R.C. Ydenburg, co-promotor(en): Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462579781 - 268
    geese - anser - crossing - species - hybridization - speciation - phylogenomics - ganzen - anser - kruisen - soorten - hybridisatie - soortvorming - phylogenomica

    Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or “True Geese”, which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, advocating a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase.

    Methodological approaches for fractionation and speciation to estimate trace element bioavailability in engineered anaerobic digestion ecosystems : An overview
    Hullebusch, Eric D. van; Guibaud, Gilles ; Simon, Stéphane ; Lenz, Markus ; Yekta, Sepehr Shakeri ; Fermoso, Fernando G. ; Jain, Rohan ; Duester, Lars ; Roussel, Jimmy ; Guillon, Emmanuel ; Skyllberg, Ulf ; Almeida, C.M.R. ; Pechaud, Yoan ; Garuti, Mirco ; Frunzo, Luigi ; Esposito, Giovanni ; Carliell-Marquet, Cynthia ; Ortner, Markus ; Collins, Gavin - \ 2016
    Critical Reviews in Environmental Science and Technology 46 (2016)16. - ISSN 1064-3389 - p. 1324 - 1366.
    Anaerobic digestion - analytical methods - bioavailability - fractionation - speciation - trace elements

    Optimal supply of trace elements (TE) is a prerequisite for microbial growth and activity in anaerobic digestion (AD) bioprocesses. However, the required concentrations and ratios of essential TE for AD biotechnologies strongly depend on prevailing operating conditions as well as feedstock composition. Furthermore, TE in AD bioreactors undergo complex physicochemical reactions and may be present as free ions, complex bound or as precipitates depending on pH, or on the presence of sulfur compounds or organic macromolecules. To overcome TE deficiency, various commercial mineral products are typically applied to AD processes. The addition of heavy metals poses the risk of overdosing operating systems, which may be toxic to microbial consortia and ultimately the environment. Adequate supplementation, therefore, requires appropriate knowledge not only about the composition, but also on the speciation and bioavailability of TE. However, very little is yet fully understood on this specific issue. Evaluations of TE typically only include the measurement of total TE concentrations but do not consider the chemical forms in which TE exist. Thus detailed information on bioavailability and potential toxicity cannot be provided. This review provides an overview of the state of the art in approaches to determine bioavailable TE in anaerobic bioprocesses, including sequential fractionation and speciation techniques. Critical aspects and considerations, including with respect to sampling and analytical procedures, as well as mathematical modeling, are examined. The approaches discussed in this review are based on our experiences and on previously published studies in the context of the “COST Action 1302: European Network on Ecological Roles of Trace Metals in Anaerobic Biotechnologies.”

    Asymmetric flow field-flow fractionation of manufactured silver nanoparticles spiked into soil solution
    Koopmans, G.F. ; Hiemstra, T. ; Regelink, I.C. ; Molleman, B. ; Comans, R.N.J. - \ 2015
    Journal of Chromatography. A, Including electrophoresis and other separation methods 1392 (2015). - ISSN 0021-9673 - p. 100 - 109.
    natural organic-matter - engineered nanoparticles - calcium-chloride - ionic-strength - humic acids - molar-mass - aggregation - retention - ph - speciation
    Manufactured metallic silver nanoparticles (AgNP) are intensively utilized in consumer products and this will inevitably lead to their release to soils. To assess the environmental risks of AgNP in soils, quantification of both their concentration and size in soil solution is essential. We developed a methodology consisting of asymmetric flow field-flow fractionation (AF4) in combination with on-line detection by UV–vis spectroscopy and off-line HR-ICP-MS measurements to quantify the concentration and size of AgNP, coated with either citrate or polyvinylpyrrolidone (PVP), in water extracts of three different soils. The type of mobile phase was a critical factor in the fractionation of AgNP by AF4. In synthetic systems, fractionation of a series of virgin citrate- and PVP-coated AgNP (10–90 nm) with reasonably high recoveries could only be achieved with ultrahigh purity water as a mobile phase. For the soil water extracts, 0.01% (w:v) sodium dodecyl sulfate (SDS) at pH 8 was the key to a successful fractionation of the AgNP. With SDS, the primary size of AgNP in all soil water extracts could be determined by AF4, except for PVP-coated AgNP when clay colloids were present. The PVP-coated AgNP interacted with colloidal clay minerals, leading to an overestimation of their primary size. Similar interactions between PVP-coated AgNP and clay colloids can take place in the environment and facilitate their transport in soils, aquifers, and surface waters. In conclusion, AF4 in combination with UV–vis spectroscopy and HR-ICP-MS measurements is a powerful tool to characterize AgNP in soil solution if the appropriate mobile phase is used.
    The butterfly plant arms-race escalated by gene and genome duplications
    Edger, P.P. ; Heidel-Fischer, H.M. ; Bekaert, K.M. ; Rota, J. ; Glockner, G. ; Platts, A.E. ; Heckel, D.G. ; Der, J.P. ; Wafula, E.K. ; Tang, M. ; Hofberger, J.A. ; Smithson, A. ; Hall, J.C. ; Blanchette, M. ; Bureau, T.E. ; Wright, S.I. ; dePamphilis, C.W. ; Schranz, M.E. ; Conant, G.C. ; Barker, M.S. ; Wahlberg, N. ; Vogel, H. ; Pires, J.C. ; Wheat, C.W. - \ 2015
    Proceedings of the National Academy of Sciences of the United States of America 112 (2015)27. - ISSN 0027-8424 - p. 8362 - 8366.
    evolutionaire genetica - co-evolutie - diversificatie - brassica - pieridae - papilionidae - glucosinolaten - fylogenie - evolutionary genetics - coevolution - diversification - brassica - pieridae - papilionidae - glucosinolates - phylogeny - diversity - defense - cytochrome-p450 - polymorphism - arabidopsis - metabolism - expression - speciation
    Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.
    Mesocosm validation of the marine No Effect Concentration of dissolved copper derived from a species sensivity distribution
    Foekema, E.M. ; Kaag, N.H.B.M. ; Kramer, K.J.M. ; Long, K. - \ 2015
    Science of the Total Environment 521-522 (2015). - ISSN 0048-9697 - p. 173 - 182.
    principal response curves - organic-matter - toxicity - water - carbon - speciation - exposure - ph
    The Predicted No Effect Concentration (PNEC) for dissolved copper based on the species sensitivity distribution (SSD) of 24 marine single species tests was validated in marine mesocosms. To achieve this, the impact of actively maintained concentrations of dissolved copper on a marine benthic and planktonic community was studied in 18 outdoor 4.6 m3 mesocosms. Five treatment levels, ranging from 2.9 to 31 µg dissolved Cu/L, were created in triplicate and maintained for 82 days. Clear effects were observed on gastropod and bivalve molluscs, phytoplankton, zooplankton, sponges and sessile algae. The most sensitive biological endpoints; reproduction success of the bivalve Cerastoderma edule, copepod population development and periphyton growth were significantly affected at concentrations of 9.9 µg Cu/L and higher. The No Observed Effect Concentration (NOEC) derived from this study was 5.7 µg dissolved Cu/L. Taking into account the DOC concentration of the mesocosm water this NOEC is comparable to the PNEC derived from the SSD.
    Genomics and the challenging translation into conservation practice
    Shafer, A.B.A. ; Wolf, J.B.W. ; Alves, P.C. ; Bergstrom, L. ; Bruford, M.W. ; Brannstrom, I. ; Colling, G. ; Dalen, L. van; Meester, L. de; Ekblom, R. ; Vergeer, P. - \ 2015
    Trends in Ecology and Evolution 30 (2015)2. - ISSN 0169-5347 - p. 78 - 87.
    genetic diversity - background selection - population genomics - insular population - dna - divergence - speciation - evolution - sequence - markers
    The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
    Structural variations in pig genomes
    Paudel, Y. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572171 - 204
    varkens - dierveredeling - genomen - genomica - single nucleotide polymorphism - dna-sequencing - fenotypische variatie - chromosoomafwijkingen - evolutie - soortvorming - pigs - animal breeding - genomes - genomics - single nucleotide polymorphism - dna sequencing - phenotypic variation - chromosome aberrations - evolution - speciation

    Abstract

    Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands

    Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.

    Speciation and domestication in Suiformes: a genomic perspective
    Frantz, L.A.F. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572546 - 227
    domesticatie - suiformes - soortvorming - dierveredeling - genomica - evolutie - genenstroom - dna-sequencing - moleculaire fylogenetica - domestication - suiformes - speciation - animal breeding - genomics - evolution - gene flow - dna sequencing - molecular phylogenetics

    Abstract

    Frantz, L.A.F. (2015). Speciation and Domestication in Suiformes: a genomic perspective. PhD thesis, Wageningen University, the Netherlands

    The diversity of life on earth owes its existence to the process of speciation. The concept of speciation is primordial for evolutionary biologists because it provides a framework to understand how contemporary biodiversity came to be. Moreover, not only natural phenomena can result in the differentiation of life forms. Indeed, biodiversity can also be the result of direct and indirect human influence such as domestication. In this thesis, I investigate these evolutionary processes (speciation and domestication) in the Suiformes superfamily (pigs and related species). I use complete genome sequences to illuminate many specific aspects of the speciation and domestication in Suiformes as well as to draw general conclusions on these crucial processes. In chapter 2 I show how genomes provide an essential source of information to retrieve deep taxonomic relationships among Suiformes. This allows me to describe multiple novel aspects of their early evolutionary history such as the fact that Suiformes colonised North America at least twice. In this chapter, I further highlight and discuss novel methodological limitations that are inherent to phylogenomics. In chapters 3, 4 and 5 I use genome sequences to resolve the evolutionary history of the genus Sus (domestic pigs and wild boars species). More precisely, I show that, contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. In addition, these chapters also provide novel insights into the process of speciation by demonstrating that genetic differentiation between species can be achieved, even when gene-flow is strong. Lastly, in chapter 6 I tested multiple models of domestication for S. scrofa. In this chapter I show that models involving reproductive isolation between wild and domestic forms are incompatible with genomic data. Moreover, this chapter demonstrates that, while domestic pigs are morphologically homogenous, they are not genetically homogenous. Together, these findings have important implications for our understanding of the process of domestication because it shows that this process was not solely the result of captivity. Together, the results of this work not only provide a comprehensive evolutionary history for the Suiformes, but also novel insights into the complex processes (speciation and domestication) that are responsible for the diversity of life on earth.

    Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
    Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Groenen, M. ; Lohse, H. - \ 2014
    Wageningen UR
    speciation - hybridization - population genetics - empirical - phylogeography - genomics / proteomics - conservation genetics
    In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed signatures of inter-specific admixture between these Sus species (Frantz et al. (2013) Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome biology, 14, R107). However, the timing, directionality and extent of this admixture remain unknown. Here we use a likelihood based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that inter-specific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
    Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
    Lohse, K. ; Frantz, L.A.F. - \ 2014
    Genetics 196 (2014)4. - ISSN 0016-6731 - p. 1241 - 1251.
    ancestral population sizes - dna-sequences - divergence - speciation - history - number - recombination - coalescent - migration - inference
    Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.
    Adsorption of levofloxacin onto goethite: Effects of pH, calcium and phosphate
    Qin, X.P. ; Liu, F. ; Wang, G.C. ; Weng, L. ; Li, L. - \ 2014
    Colloids and Surfaces. B: Biointerfaces 116 (2014). - ISSN 0927-7765 - p. 591 - 596.
    fluoroquinolone antibacterial agents - water interface - ciprofloxacin removal - antibiotic ofloxacin - humic substances - iron-oxides - sorption - complexation - tetracycline - speciation
    Adsorption of levofloxacin (LEV), one of the extensively used antibiotics, onto goethite was investigated using batch experiments. The adsorption of LEV on goethite was pH-dependent. A maximum adsorption was reached at pH 6. Above or below pH 6, the adsorption decreased. In the presence of calcium (Ca2+), a decrease in adsorption was observed, due to probably formation of Ca2+-LEV complexes in solutions. Phosphate also showed a significant inhibition on LEV adsorption over a pH range of 3-10. Phosphate competed with LEV for binding sites on the surface of goethite, and the electrostatic competition between LEV and phosphate on goethite surface might be another reason for the decrease in adsorption. These results indicated that Ca2+ and phosphate have a great influence on the distribution of LEV in soils and waters, which will eventually affect its antibacterial activity in the environment. (C) 2013 Elsevier B.V. All rights reserved.
    A decade of uncertainty: Resolving the phyologenetic position of Diclinanona (Annonaceae), inlcuding taxonomic notes and a key to the species
    Erkens, R.H.J. ; Chatrou, L.W. ; Chaowasku, T. ; Westra, L.I.T. ; Maas, J.W. ; Maas, P.J.M. - \ 2014
    Taxon 63 (2014)6. - ISSN 0040-0262 - p. 1244 - 1252.
    palms sheds light - historical biogeography - global biogeography - evolution - diversification - speciation - genus - taxa - biodiversity - convergence
    The molecular phylogenetic placement of Diclinanona (Annonaceae) has been debated in the literature for a decade. On the basis of morphological studies the genus was thought to be related to genera now all placed in subfam. Annonoideae. This early hypothesis was supported by the first phylogenetic analyses of Annonaceae. However, more recently a placement in subfam. Malmeoideae was hypothesised based on an analysis of more plastid data, thus contradicting older but also new morphological findings and previous phylogenetic work. The current study uses newly sequenced plastid data for two species of Diclinanona to show that the earlier hypothesised placement was correct and discusses the (little) anatomical and morphological data on Diclinanona that is available in a phylogenetic framework. Furthermore, an online revision of the three species of Diclinanona is presented in order to update the taxonomic knowledge of this genus.
    Genetic divergence and evidence for sympatric host-races in the highly polyphagous brown tail moth, Euproctis chrysorrhoea (Lepidoptera: Erebidae)
    Marques, J.F. ; Wang, H.L. ; Svensson, G.P. ; Frago Clols, E. ; Anderbrant, O. - \ 2014
    Evolutionary Ecology 28 (2014)5. - ISSN 0269-7653 - p. 829 - 848.
    plant-feeding insects - tree arbutus-unedo - evolutionary history - mitochondrial - populations - speciation - refugia - time - diversification - differentiation
    The brown tail moth (BTM) Euproctis chrysorrhoea (Linnaeus 1758) (Lepidoptera: Erebidae) is a forest and ornamental pest in Europe and the United States. Its extreme polyphagy, and documented phenological shift associated with host use suggest the presence of distinct host-races. To test this hypothesis, we sampled BTM infesting different host species in several locations along its distribution, and used DNA sequence data (a total of 1,672 bp from cytochrome c oxidase subunit I, elongation factor 1-alpha, and wingless) to produce haplotype networks and reconstruct the phylogenetic relationships between individuals. Population genetic diversity indices pointed out a higher genetic diversity in Europe, particularly in the samples from southern Spain and southern England. Lower F ST values were found between geographically closer populations when compared to more distant ones, but analyses of molecular variance and Mantel tests failed to reveal geographically associated genetic differentiation. However, haplotype networks and phylogenetic reconstructions revealed a previously unknown genetic differentiation within the BTM, with one lineage circumscribed to southern Europe. Although BTM haplotypes did not cluster according to their host plant, host-associated haplotypes were observed within certain geographic regions. Hence, our data support the existence of host-races of BTM within southern Spain and southern England, where populations from different hosts occur in sympatry.
    Characterization of colloidal Fe from soils using field-flow fractionation and Fe K-edge X-ray absorption spectroscopy
    Regelink, I.C. ; Voegelin, A. ; Weng, L. ; Koopmans, G.F. ; Comans, R.N.J. - \ 2014
    Environmental Science and Technology 48 (2014)8. - ISSN 0013-936X - p. 4307 - 4316.
    iron-oxide nanoparticles - natural organic-matter - acid forest soils - exafs spectroscopy - mineral nanoparticles - trace-metals - speciation - surface - ferrihydrite - associations
    Colloids may facilitate the transport of trace elements and nutrients like phosphate in soil. In this study, we characterized soil colloids (
    Differences in olfactory species recognition in the females of two Australian songbird species
    Krause, E.T. ; Brummel, C. ; Kohlwey, S. ; Baier, M.C. ; Müller, C. ; Bonadonna, F. ; Caspers, B.A. - \ 2014
    Behavioral Ecology and Sociobiology 68 (2014)11. - ISSN 0340-5443 - p. 1819 - 1827.
    finches taeniopygia-guttata - zebra finches - odor recognition - kin recognition - wild - birds - nest - cues - discrimination - speciation
    Although birds have recently been shown to possess olfactory abilities and to use chemical cues in communication, limited effort has been made to demonstrate the use of odorants in social contexts. Even less is known regarding the use of odorants in species recognition. The ability to recognize conspecifics should be more pronounced in social species. This study investigated the importance of olfactory cues in species recognition in females of two estrildid finch species with different levels of sociality. Combining odor preference tests with chemical analyses, we surveyed whether female zebra finches and diamond firetails are able to distinguish between the species based on volatile traits and whether individuals exhibit species-specific differences in body odorants. Zebra finches are more social than diamond firetails; nevertheless, both species have an overlapping distribution area. Applying an experimental Y-maze paradigm, we showed that zebra finches can use differences in their species odor fingerprints and displayed a significant preference for the odor of conspecifics over that of heterospecifics, whereas diamond firetails did not reveal a preference. Using gas chromatography and mass spectrometry, we demonstrated that body odorants of the two species were significantly different in relative composition. This finding demonstrates the potential importance of olfactory cues in species recognition, at least in social bird species. Even these two closely related species displayed remarkable differences in their responsiveness to similar chemical cues, which might be caused by species-specific differences in ecology, physiology, or evolution. Keywords Songbird . Zebra finch . Taeniopygia guttata . Diamond firetail . Stagonopleura guttata . Sociality . Olfaction . Smell . Scent . Olfactory fingerprint
    Oral bioaccessibility and human exposure to anthropogenic and geogenic mercury in urban, industrial and mining areas
    Rodrigues, S.M. ; Coelho, C. ; Cruz, N. ; Monteiro, R.J.R. ; Henriques, B. ; Duarte, A.C. ; Romkens, P.F.A.M. ; Pereira, E. - \ 2014
    Science of the Total Environment 496 (2014). - ISSN 0048-9697 - p. 649 - 661.
    atomic-absorption-spectrometry - potentially toxic elements - chloralkali plant - inorganic mercury - part i - contaminated soils - asturias spain - speciation - sediments - portugal
    The objective of this study was to characterize the link between bioaccessibility and fractionation of mercury (Hg) in soils and to provide insight into human exposure to Hg due to inhalation of airborne soil particles and hand-to-mouth ingestion of Hg-bearing soil. Mercury in soils from mining, urban and industrial areas was fractionated in organometallic forms; mobile; semi-mobile; and non-mobile forms as well as HCl-extractable Hg. The in vitro bioaccessibility of Hg was obtained by extracting soils with (1) a simulated human gastric fluid (pH 1.5), and (2) a simulated human lung fluid (pH 7.4). Total soil Hg concentrations ranged from 0.72 to 1.8 mg kg- 1 (urban areas), 0.28 to 94 mg kg- 1 (industrial area) and 0.92 to 37 mg kg- 1 (mining areas). Both organometallic Hg as well as 0.1 M HCl extractable Hg were lower (<0.5% of total Hg) than Hg extracted by gastric fluid (up to 1.8% of total Hg) and lung fluid (up to 12% of total Hg). In addition, Hg extracted by lung fluid was significantly higher in urban and industrial soils (average 5.0–6.6% of total Hg) compared to mining soils. Such differences were related to levels of mobile Hg species in urban and industrial soils compared to mining soils. These results strengthen the need to measure site-specific Hg fractionation when determining Hg bioaccessibility. Results also show that ingestion and/or inhalation of Hg from soil particles can contribute up to 8% of adult total Hg intake when compared to total Hg intake via consumption of contaminated fish and animal products from contaminated areas.
    Chemical communication in tilapia: A comparison of Oreochromis mossambicus with O. niloticus
    Hubbard, P.C. ; Mota, V.C. ; Keller-Costa, T. ; Paulo da Silva, J. ; Canário, A.V.M. - \ 2014
    General and Comparative Endocrinology 207 (2014). - ISSN 0016-6480 - p. 13 - 20.
    maturation-inducing hormone - african cichlid fish - mozambique tilapia - olfactory sensitivity - speciation - pheromone - signals - urine - radiations - evolution
    In allopatric speciation species differentiation generally results from different selective pressures in different environments, and identifying the traits responsible helps to understand the isolation mechanism(s) involved. Male Mozambique tilapia (Oreochromis mossambicus) use urine to signal dominance; furthermore, 5b-pregnane-3a,17,20b-triol-3a-glucuronide (and its a-epimer, 5b-pregnane-3a,17,20atriol-3a-glucuronide), in their urine is a potent pheromone, the concentration of which is correlated with social status. The Nile tilapia (Oreochromis niloticus) is a close relative; species divergence probably resulted from geographical separation around 6 million years ago. This raises the question of whether the two species use similar urinary chemical cues during reproduction. The olfactory potency of urine, and crude extracts, from either species was assessed by the electro-olfactogram and the presence of the steroid glucuronides in urine from the Nile tilapia by liquid-chromatography/mass-spectrometry. Both species showed similar olfactory sensitivity to urine and respective extracts from either species, and similar sensitivity to the steroid glucuronides. 5b-Pregnan-3a,17a,20b-triol-3a-glucuronide was present at high concentrations (approaching 0.5 mM) in urine from Nile tilapia, with 5b-pregnan-3a,17a,20a-triol-3a-glucuronide present at lower concentrations, similar to the Mozambique tilapia. Both species also had similar olfactory sensitivity to estradiol-3-glucuronide, a putative urinary cue from females. Together, these results support the idea that reproductive chemical cues have not been subjected to differing selective pressure. Whether these chemical cues have the same physiological and behavioural roles in O. niloticus as O. mossambicus remains to be investigated.
    Terrestrial selenium distribution in China is potentially linked to monsoonal climate
    Blazina, T. ; Sun, Y. ; Voegelin, A. ; Lenz, M. ; Berg, M. ; Winkel, L.H.E. - \ 2014
    Nature Communications 5 (2014). - ISSN 2041-1723
    red clay formation - loess plateau - atmospheric selenium - trace-metals - adsorption - speciation - pliocene - records - water - soil
    The prevalence of terrestrial environments low in the essential trace element selenium (Se) results in large-scale Se deficiency worldwide. However, the underlying processes leading to Se-depleted environments have remained elusive. Here we show that over the last 6.8 million years (Ma) climatic factors have played a key role in the Se distribution in loess–paleosol sequences in the Chinese Loess Plateau (CLP), which lies in a severely Se-depleted region with a history of Se deficiency-related diseases. We use a combination of geochemical and paleoclimate data to demonstrate that during interglacial periods between 2.30 and 0.16¿Ma, variations in the Se concentration in the CLP are potentially related to variability in Se input via East Asian monsoon-derived precipitation. Our results identify precipitation as an important controlling factor of Se distribution in monsoonal China. We suggest that atmospheric Se inputs via precipitation could also play an important role in other regions worldwide.
    Influence of pH on the redox chemistry of metal (hydr)oxides and organic matter in paddy soils
    Pan, Y. ; Koopmans, G.F. ; Bonten, L.T.C. ; Song, J. ; Luo, Y. ; Temminghoff, E.J.M. ; Comans, R.N.J. - \ 2014
    Journal of Soils and Sediments 14 (2014)10. - ISSN 1439-0108 - p. 1713 - 1726.
    flooded soil - ion-binding - cadmium - iron - speciation - manganese - reduction - sorption - dynamics - mobilization
    The primary purpose of this study was to determine how flooding and draining cycles affect the redox chemistry of metal (hydr)oxides and organic matter in paddy soils and how the pH influences these processes. Our secondary purpose was to determine to what extent a geochemical thermodynamic equilibrium model can be used to predict the solubility of Mn and Fe during flooding and draining cycles in paddy soils. We performed a carefully designed column experiment with two paddy soils with similar soil properties but contrasting pH.We monitored the redox potential (Eh) continuously and took soil solution samples regularly at four depths along the soil profile during two successive flooding and drainage cycles. To determine dominant mineral phases of Mn and Fe under equilibrium conditions, stability diagrams of Mn and Fe were constructed as a function of Eh and pH. Geochemical equilibrium model calculations were performed to identify Mn and Fe solubility-controlling minerals and to compare predicted total dissolved concentrations with their measured values. Flooding led to strong Eh gradients in the columns of both soils. In the acidic soil, pH increased with decreasing Eh and vice versa, whereas pH in the alkaline soil was buffered by CaCO3. In the acidic soil, Mn and Fe solubility increased during flooding due to reductive dissolution of their (hydr)oxides and decreased during drainage because of re-oxidation. In the alkaline soil, Mn and Fe solubility did not increase during flooding due to Mn(II) and Fe(II) precipitation as MnCO3, FeCO3, and FeS. The predicted levels of soluble Mn and Fe in the acidic soil were much higher than their measured values, but predictions and measurements were rather similar in the alkaline soil. This difference is likely due to kinetically limited reductive dissolution of Mn and Fe (hydr)oxides in the acidic soil. During flooding, the solubility of dissolved organic matter increased in both soils, probably because of reductive dissolution of Fe (hydr)oxides and the observed increase in pH. Conclusions Under alternating flooding and draining conditions, the pH greatly affected Mn and Fe solubility via influencing either reductive dissolution or carbonate formation. Comparison between measurements and geochemical equilibrium model predictions revealed that reductive dissolution of Mn and Fe (hydr)oxides was kinetically limited in the acidic soil. Therefore, when applying such models to systems with changing redox conditions, such rate-limiting reactions should be parameterized and implemented to enable more accurate predictions of Mn and Fe solubility.
    Characterization of Phosphorus in Animal Manures Collected from Three (Dairy, Swine, and Broiler) Farms in China
    Li, G. ; Li, H. ; Leffelaar, P.A. ; Shen, J. ; Zhang, F. - \ 2014
    PLoS ONE 9 (2014)7. - ISSN 1932-6203
    magnetic-resonance-spectroscopy - enzymatic-hydrolysis - organic phosphorus - northwest germany - poultry litter - forms - soil - diets - speciation - fractions
    In order to identify the phosphorus species and concentration in animal manure, we comparatively characterized phosphorus in dairy manure, swine manure, and broiler litter, using a sequential procedure, a simplified two-step procedure (NaHCO3/NaOH+EDTA), and a solution Phosphorus-31 Nuclear Magnetic Resonance (31P-NMR) spectroscopy procedure. In the sequential procedure, deionized water extracted 39, 22, and 32%; NaHCO3 extracted 48, 26, and 37%; NaOH extracted 8, 9, and 13.8%; and HCl extracted 3, 42.8, and 17% of the total phosphorus in dairy manure, swine manure and broiler litter, respectively. Total phosphorus extracted by the NaHCO3/NaOH+EDTA procedure was 7.5, 32.4, and 15.8 g P kg-1 for dairy manure, swine manure, and broiler litter, respectively. The solution 31P-NMR procedure detected that 9, 34, and 29% of total phosphorus was phytic acid in dairy manure, swine manure, and broiler litter, respectively. These results show that phosphorus forms, availability, and quantities differ between animal manures, which provides valuable information for P characterization of animal manures in China.
    Multi-face modeling to predict free zinc ion concentrations in low-zinc soils
    Duffner, A. ; Weng, L. ; Hoffland, E. ; Zee, S.E.A.T.M. van der - \ 2014
    Environmental Science and Technology 48 (2014)10. - ISSN 0013-936X - p. 5700 - 5708.
    donnan membrane technique - organic-matter - heavy-metals - contaminated soils - isotopic exchange - humic substances - trace-metals - sandy soil - adsorption - speciation
    Multi-surface models are widely used to assess the potential ecotoxicological risk in metal-contaminated soils. Their accuracy in predicting metal speciation in soils with low metal levels was not yet tested. Now highly sensitive analytical techniques are available to experimentally validate such models at low concentration levels. The objective of this study was to test the accuracy of a multi-surface model to predict the Zn2+ concentration and to improve our understanding of Zn bioavailability in low-Zn soils. High-Zn soils were included as controls. Model parameters were determined independently on the basis of earlier peer-reviewed publications. Model output was validated against free Zn2+ concentrations determined with the soil column Donnan membrane technique in a range of soils varying in potentially available Zn, organic matter, clay silicate, and iron (hydr)oxide contents and pH. Deviations between predicted Zn2+ concentrations and experimentally determined values over the whole Zn concentration range were less or equal to the experimental standard error, except for one low-Zn soil. The Zn2+ concentration was mainly controlled by adsorption, where organic matter was predicted to be the dominant soil sorbent. The predicted Zn2+ concentration depends more sensitively upon changes of the reactive Zn pool (application of 0.6, 1.2, 2.4, and 3.6 mg of Zn kg–1 of soil) and organic matter content (±0.2 and 0.4%) than pH changes (±0.5 and 1 pH unit).
    Natural wetland emissions of methylated trace elements
    Vriens, B. ; Lenz, M. ; Charlet, L. ; Berg, M. ; Winkel, L.H.E. - \ 2014
    Nature Communications 5 (2014). - ISSN 2041-1723
    yellowstone-national-park - selenium volatilization - atmospheric selenium - biomethylation - soil - speciation - bacterium - products - sulfide - sulfur
    Natural wetlands are well known for their significant methane emissions. However, trace element emissions via biomethylation and subsequent volatilization from pristine wetlands are virtually unstudied, even though wetlands constitute large reservoirs for trace elements. Here we show that the average volatile fluxes of selenium (
    Data from: Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis
    Jonker, R.M. ; Kraus, Robert ; Zhang, Q. ; Hooft, Pim van; Larsson, K. ; Jeugd, H.P. van der; Kurvers, Ralf ; Wieren, Sip van; Loonen, M.J.J.E. ; Crooijmans, Richard ; Ydenberg, Ron ; Groenen, Martien ; Prins, Herbert - \ 2013
    Wageningen University & Research
    population genetics - SNP - admixture - Branta leucopsis - migration modelling - speciation - cultural evolution
    Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions, new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 single nucleotide polymorphism (SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used discriminant analysis of principal components, FST, linkage disequilibrium and a comparison of geneflow models using migrate-n to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations, we also show that genetic exchange occurs between all populations. The newly established nonmigratory population in the Netherlands is characterized by high emigration into other populations, which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of nonmigration probably resulted from developmental plasticity.
    Mechanisms contributing to the thermal analysis of waste incineration bottom ash and quantification of idfferent carbon species
    Rocca, S. ; Zomeren, A. van; Costa, G. ; Dijkstra, J.J. ; Comans, R.N.J. ; Lombardi, F. - \ 2013
    Waste Management 33 (2013)2. - ISSN 0956-053X - p. 373 - 381.
    loss-on-ignition - fly-ash - unburned carbon - behavior - speciation - residues - coal
    The focus of this study was to identify the main compounds affecting the weight changes of bottom ash (BA) in conventional loss on ignition (LOI) tests and to obtain a better understanding of the individual processes in heterogeneous (waste) materials such as BA. Evaluations were performed on BA samples from a refuse derived fuel incineration (RDF-I) plant and a hospital waste incineration (HW-I) plant using thermogravimetric analysis and subsequent mass spectrometry (TG–MS) analysis of the gaseous thermal decomposition products. Results of TG–MS analysis on RDF-I BA indicated that the LOI measured at 550 °C was due to moisture evaporation and dehydration of Ca(OH)2 and hydrocalumite. Results for the HW-I BA showed that LOI at 550 °C was predominantly related to the elemental carbon (EC) content of the sample. Decomposition of CaCO3 around 700 °C was identified in both materials. In addition, we have identified reaction mechanisms that underestimate the EC and overestimate the CaCO3 contents of the HW-I BA during TG–MS analyses. These types of artefacts are expected to occur also when conventional LOI methods are adopted, in particular for materials that contain CaO/Ca(OH)2 in combination with EC and/or organic carbon, such as e.g. municipal solid waste incineration (MSWI) bottom and fly ashes. We suggest that the same mechanisms that we have found (i.e. in situ carbonation) can also occur during combustion of the waste in the incinerator (between 450 and 650 °C) demonstrating that the presence of carbonate in bottom ash is not necessarily indicative for weathering. These results may also give direction to further optimization of waste incineration technologies with regard to stimulating in situ carbonation during incineration and subsequent potential improvement of the leaching behavior of bottom ash.
    Arsenate and phosphate adsorption in relation to oxides composition in soils: LCD modelling
    Cui, Y. ; Weng, L. - \ 2013
    Environmental Science and Technology 47 (2013)13. - ISSN 0013-936X - p. 7269 - 7276.
    charge-distribution - humic substances - competitive adsorption - ion adsorption - heavy-metals - speciation - parameters - minerals - sorption - binding
    The pH dependent solid-solution distribution of arsenate and phosphate in five Dutch agricultural soil samples was measured in the pH range 4–8, and the results were interpreted using the LCD (ligand and charge distribution) adsorption modeling. The pH dependency is similar for both oxyanions, with a minimum soluble concentration observed around pH 6–8. This pH dependency can be successfully described with the LCD model and it is attributed mainly to the synergistic effects from Ca adsorption. The solubility of phosphate is much lower than that of arsenate. This big difference cannot be sufficiently explained by the reduction of small amount of As(V) into As(III), neither by slow desorption/adsorption. The difference between phosphate and arsenate in their solid-solution distribution becomes larger with the increase of aluminum (hydr)oxides (Al-oxides) contribution to the total amount of metal (Al and Fe) (hydr)oxides. The influence of Al-oxides is much larger than its relative amount extracted from the soils. When Al-oxides account for >40% of the soil oxides, the whole adsorbents behave apparently similarly to that of pure Al-oxides. These results indicated that surface coating and substitution may have modified significantly oxyanion adsorption to Fe-oxides in soils, and how to account for this complexity is a challenge for geochemical modeling.
    The effect of phosphorus binding clay (Phoslock) in mitigating cyanobacterial nuisance: A laboratory study on the effects on water quality variables and plankton
    Oosterhout, J.F.X. ; Lurling, M. - \ 2013
    Hydrobiologia 710 (2013)1. - ISSN 0018-8158 - p. 265 - 277.
    rare-earth-elements - organic-matter - lake restoration - eutrophication - microcystis - netherlands - sediments - blooms - complexation - speciation
    This laboratory study examined the lanthanum modified clay Phoslock® for its effectiveness to bind soluble reactive phosphorus (SRP), release of nutrients from this modified clay, its influence on water quality variables (pH, oxygen saturation %, conductivity and turbidity), effects on phytoplankton growth (green alga Scenedesmus obliquus, cyanobacteria Microcystis aeruginosa and Anabaena sp.), and, lastly, its effect on the population growth of the rotifer Brachionus calyciflorus. A clear dose–response for SRP binding by the modified clay was observed. A small amount of ammonium is released from Phoslock®. We found no effect of Phoslock® on pH or oxygen saturation. Conductivity increased with the increasing concentration of Phoslock®. An application of Phoslock® caused a transient increase of turbidity up to 211 NTU. However, due to rapid settlement, turbidity fell below 13 NTU (~1 m Secchi depth), after 6 h. Phoslock® addition caused a reduction in growth of all phytoplankton species tested that we attribute to the combined effects of light limitation, flocculation with the bentonite and binding of SRP to Phoslock®. We estimated the EC50 of Phoslock® on the population growth of rotifer B. calyciflorus to be 0.15 g Phoslock® l-1. Overall, the results of our study indicate Phoslock® seems to be suitable for field applications.
    Biovailability of copper and zinc in pig and cattle slurries
    Jakubus, M. ; Dach, J. ; Starmans, D.A.J. - \ 2013
    Fressenius Environmental Bulletin 22 (2013)4. - ISSN 1018-4619 - p. 995 - 1002.
    sequential extraction procedures - heavy-metals - soils - fractionation - speciation - sediments - manganese - sludge - nickel - lead
    Slurry is an important source of macronutrients, micro-nutrients and organic matter. Despite the considerable fertilizer value of slurry, it may be abundant in amounts of copper and zinc originating from dietary. The study presents quantitative changes in copper and zinc in individual slurries (pig and cattle slurries). The bioavailability of copper and zinc was estimated on the basis of amounts of the metals in isolated fractions using the sequential extraction method. Sequential techniques identify fractions which describe different connections of metals with the compost solid phase beginning with those that are easiest soluble up to those that dissolve with the greatest difficulties.Pig slurry was characterized by 2-fold higher amounts of copper and zinc in comparison to the levels detected in cattle slurries. Quantitative changes of the elements in the sequentially isolated fractions of analyzed slurries differed. First of all, this was dependent on the chemical character of a given metal, followed by the animal species, or the type of management. Irrespective of the type of slurry, 40-56% of the total amounts of copper were found in hardly available combinations, while available copper forms accounted for only 6.6–10.9%. Zinc was found predominantly in com-binations with iron and manganese oxides which, irrespective of the tested slurry, ranged from 130.64 mg·kg-1 to 293.60 mg·kg-1. Bioavailable metal contents, potentially introduced to soil with slurry doses, calculated as 170 kg total N/ha/year, ranged from 63.6 to 124.5 g for copper, and from 349.5 to 696.4 g for zinc. The estimated amounts of metal inputs to agricultural land demonstrate that soils are potentially at risk of heavy metal accumulation from the application of pig and cattle slurries.
    Crossability patterns in Asia Pacific Oryza series Sativae
    Banaticla-Hilario, M.C.N. ; Sackville Hamilton, R. ; Berg, R.G. van den; McNally, K.L. - \ 2013
    Genetic Resources and Crop Evolution 60 (2013)6. - ISSN 0925-9864 - p. 1899 - 1914.
    reproductive isolation - rice oryza - wild-rice - genome - hybridization - evolution - speciation - diversity - rufipogon - differentiation
    Reproductive barriers are thought to intensify with increasing genetic distance between species. To assess the extent of post-pollination reproductive isolation within and among the Asia Pacific species of Oryza series Sativae, crossing experiments using 15 accessions of O. meridionalis Ng, O. nivara Sharma et Shastry, and O. rufipogon Griff. were conducted. Intra- and interspecific crosses of the selfing species O. meridionalis and O. nivara had very low seed set and produced inviable F1 seeds indicative of strong pre- and post-zygotic barriers. Contrastingly, the outcrossing O. rufipogon exhibited high intraspecific crossability and modest compatibility with O. nivara and O. meridionalis in terms of seed set suggesting substantial pre-zygotic reproductive isolation of the species. O. rufipogon was asymmetrically compatible with O. meridionalis and symmetrically with O. nivara. The two inbreeding species manifested comparable degrees of isolation from O. rufipogon despite differences in strength of several post-zygotic barriers. Mating compatibility within and between the Asia Pacific species of Oryza series Sativae is not strongly spatially influenced, but some resistance to gene flow under sympatric conditions was observed. Intraspecific O. rufipogon F1s were more vegetatively robust and more late-flowering than their parents. Intra- and interspecific hybrids of Australasian O. rufipogon differed phenotypically from crosses with non-Australasian populations. Interspecific hybrids displayed both intermediate and parental character traits. O. nivara and O. rufipogon generated early-flowering F1s that are more similar to the former. O. meridionalis and O. rufipogon produced F1s that varied in phenology and morphology depending on the maternal and paternal species.
    Corresponding Mitochondrial DNA and Niche Divergence for Crested Newt Candidate Species
    Wielstra, B.M. ; Beukema, W. ; Arntzen, J.W. ; Skidmore, A.K. ; Toxopeus, A.G. ; Raes, N. - \ 2012
    PLoS ONE 7 (2012)9. - ISSN 1932-6203
    absence data - models - phylogeography - delimitation - speciation - ecology - areas
    Genetic divergence of mitochondrial DNA does not necessarily correspond to reproductive isolation. However, if mitochondrial DNA lineages occupy separate segments of environmental space, this supports the notion of their evolutionary independence. We explore niche differentiation among three candidate species of crested newt (characterized by distinct mitochondrial DNA lineages) and interpret the results in the light of differences observed for recognized crested newt species. We quantify niche differences among all crested newt (candidate) species and test hypotheses regarding niche evolution, employing two ordination techniques (PCA-env and ENFA). Niche equivalency is rejected: all (candidate) species are found to occupy significantly different segments of environmental space. Furthermore, niche overlap values for the three candidate species are not significantly higher than those for the recognized species. As the three candidate crested newt species are, not only in terms of mitochondrial DNA genetic divergence, but also ecologically speaking, as diverged as the recognized crested newt species, our findings are in line with the hypothesis that they represent cryptic species. We address potential pitfalls of our methodology.
    Determination of free Zn2+ concentration in synthetic and natural samples with AGNES (Absence of Gradients and Nernstian Equilibrium Stripping) and DMT (Donnan Membrane Techniques)
    Chito, D. ; Weng, L.P. ; Galceran, J. ; Companys, E. ; Puy, J. ; Riemsdijk, W.H. van; Leeuwen, H.P. van - \ 2012
    Science of the Total Environment 421-422 (2012). - ISSN 0048-9697 - p. 238 - 244.
    dissolved organic-matter - metal-ion concentrations - humic-acid - electroanalytical technique - lolium-perenne - soil solution - trace-metals - speciation - binding - waters
    The determination of free Zn2+ ion concentration is a key in the study of environmental systems like river water and soils, due to its impact on bioavailability and toxicity. AGNES (Absence of Gradients and Nernstian Equilibrium Stripping) and DMT (Donnan Membrane Technique) are emerging techniques suited for the determination of free heavy metal concentrations, especially in the case of Zn2+, given that there is no commercial Ion Selective Electrode. In this work, both techniques have been applied to synthetic samples (containing Zn and NTA) and natural samples (Rhine river water and soils), showing good agreement. pH fluctuations in DMT and N2/CO2 purging system used in AGNES did not affect considerably the measurements done in Rhine river water and soil samples. Results of DMT in situ of Rhine river water are comparable to those of AGNES in the lab. The comparison of this work provides a cross-validation for both techniques.
    Olivine Weathering in Soil, and Its Effects on Growth and Nutrient Uptake in Ryegrass (lolium perenne L.): A Pot Experiment
    Berge, H.F.M. ten; Meer, H.G. van der; Steenhuizen, J.W. ; Goedhart, P.W. ; Knops, P. ; Verhagen, J. - \ 2012
    PLoS ONE 7 (2012)8. - ISSN 1932-6203
    carbon-dioxide - plant - bioavailability - sequestration - phytotoxicity - serpentine - nickel - co2 - speciation - models
    Mineral carbonation of basic silicate minerals regulates atmospheric CO2 on geological time scales by locking up carbon. Mining and spreading onto the earth's surface of fast-weathering silicates, such as olivine, has been proposed to speed up this natura
    Age structure in neutral theory resolves inconsistencies related to reproductive size threshold
    Rosindell, J. ; Jansen, P.A. ; Etienne, R.S. - \ 2012
    Journal of Plant Ecology 5 (2012)1. - ISSN 1752-9921 - p. 64 - 71.
    species-area relationships - biodiversity - speciation - model - biogeography - limitation - dispersal - diversity - abundance - forests
    Neutral theory consists of a suite of models that assume ecological equivalence among individual organisms. They have been most commonly applied to tropical forest tree communities either as null models or as approximations. Neutral models typically only include reproductive adults; therefore, fitting to empirical tree community data requires defining a reproductive-size threshold, which for trees is usually set arbitrarily to a diameter at breast height (DBH) of 100 mm. The inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model fits. Here, we investigate this problem and resolve it by introducing simple age structure into a neutral model.
    Environmental Selenium Research: From Microscopic Processes to Global Understanding
    Winkel, L.H.E. ; Johnson, C.A. ; Lenz, M. ; Grundl, T. ; Leupin, O.X. ; Amini, M. ; Charlet, L. - \ 2012
    Environmental Science and Technology 46 (2012)2. - ISSN 0013-936X - p. 571 - 579.
    plasma-mass spectrometry - icp-ms - arsenic contamination - agricultural soils - sewage-sludge - speciation - se - chromatography - groundwater - metabolism
    Selenium is a natural trace element that is of fundamental importance to human health. The extreme geographical variation in selenium concentrations in soils and food crops has resulted in significant health problems related to deficient or excess levels of selenium in the environment. To deal with these kinds of problems in the future it is essential to get a better understanding of the processes that control the global distribution of selenium. The recent development of analytical techniques and methods enables accurate selenium measurements of environmental concentrations, which will lead to a better understanding of biogeochemical processes. This improved understanding may enable us to predict the distribution of selenium in areas where this is currently unknown. These predictions are essential to prevent future Se health hazards in a world that is increasingly affected by human activities.
    Hg transfer from contaminated soils to plants and animals
    Rodrigues, S.M. ; Henriques, B. ; Reis, A.T. ; Duarte, A.C. ; Pereira, E. ; Romkens, P.F.A.M. - \ 2012
    Environmental Chemistry Letters 10 (2012)1. - ISSN 1610-3653 - p. 61 - 67.
    potentially toxic elements - chloralkali plant - available pools - total mercury - part ii - speciation - transport - portugal - slovenia - samples
    Understanding the transfer of mercury (Hg) from soil to crops is crucial due to Hg toxicity and Hg occurrence in terrestrial systems. Previous research has shown that available Hg in soils contributes to plant Hg levels. Plant Hg concentrations are related to soil conditions and plant characteristics. Mechanistic models describing such soil–plant interactions are however difficult to quantify. Here we performed a field study in agricultural, mining and industrial areas in Portugal to evaluate potential food chain risks. The uptake of Hg by Italian ryegrass, ryegrass, orchard grass, collard greens and rye was measured to calculate daily intakes (DI) of Hg for cows and sheep grazing. A total of 136 soil samples and 129 plant samples were analysed. Results show that total Hg concentrations ranged from 0.01 to 98 mg kg-1 in soils; 0.01–5.4 mg kg-1 in shoots and 0.01–42 mg kg-1 in roots. Calculated DI ranged from 0.18 to 132 mg d-1 for cows, and from 0.028 to 23 mg d-1 for sheep. In 27 grassland sites, daily intakes exceeded the acceptable daily intake of both cows and sheep in view of food safety considering Hg in animal kidneys evidencing potential risks to human health. The transfer of Hg from soil to crops was described using empirical Freundlich-type functions. For ryegrass, orchard grass and collard greens, the soil-to-root or soil-to-shoot transfer of Hg appeared to be controlled by the total soil Hg concentration and levels of Alox and Feox. Empirical functions allowed us to obtain realistic estimates of Hg levels in crops and can be used as an alternative to mechanistic models when evaluating food chain risks of Hg contamination in agricultural soils.
    Pyrrolizidine alkaloid variation in shoots and roots of segregating hybrids between Jacobaea vulgaris and Jacobaea aquatica
    Cheng, D. ; Kirk, H. ; Mulder, P.P.J. ; Vrieling, K. ; Klinkhamer, P.G.L. - \ 2011
    New Phytologist 192 (2011)4. - ISSN 0028-646X - p. 1010 - 1023.
    senecionine n-oxide - british-isles - natural hybridization - plant hybridization - chemical diversity - tyria-jacobaeae - asteraceae - speciation - evolution - translocation
    Hybridization can lead to novel qualitative or quantitative variation of secondary metabolite (SM) expression that can have ecological and evolutionary consequences.•We measured pyrrolizidine alkaloid (PA) expression in the shoots and roots of a family including one Jacobaea vulgaris genotype and one Jacobaea aquatica genotype (parental genotypes), two F1 hybrid genotypes, and 102 F2 hybrid genotypes using liquid chromatography–tandem mass spectrometry (LC-MS/MS).•We detected 37 PAs in the roots and shoots of J. vulgaris, J. aquatica and the hybrids. PA concentrations and compositions differed between genotypes, and between roots and shoots. Three otosenine-like PAs that only occurred in the shoots of parental genotypes were present in the roots of F2 hybrids; PA compositions were sometimes novel in F2 hybrids compared with parental genotypes, and in some cases transgressive PA expression occurred. We also found that PAs from within structural groups covaried both in the roots and in the shoots, and that PA expression was correlated between shoots and roots.•Considerable and novel variation present among F2 hybrids indicates that hybridization has a potential role in the evolution of PA diversity in the genus Jacobaea, and this hybrid system is useful for studying the genetic control of PA expression
    Unraveling the rapid radiation of crested newts, Triturus cristatus superspecies, using complete mitogenomic sequences
    Wielstra, B.M. ; Arntzen, J.W. - \ 2011
    BMC Evolutionary Biology 11 (2011). - ISSN 1471-2148 - 8 p.
    complete mitochondrial genomes - historical biogeography - phylogenetic analysis - mixed models - dna - salamandridae - phylogeography - nuclear - mtdna - speciation
    Background - The rapid radiation of crested newts (Triturus cristatus superspecies) comprises four morphotypes: 1) the T. karelinii group, 2) T. carnifex - T. macedonicus, 3) T. cristatus and 4) T. dobrogicus. These vary in body build and the number of rib-bearing pre-sacral vertebrae (NRBV). The phylogenetic relationships of the morphotypes have not yet been settled, despite several previous attempts, employing a variety of molecular markers. We here resolve the crested newt phylogeny by using complete mitochondrial genome sequences. Results - Bayesian inference based on the mitogenomic data yields a fully bifurcating, significantly supported tree, though Maximum Likelihood inference yields low support values. The internal branches connecting the morphotypes are short relative to the terminal branches. Seen from the root of Triturus (NRBV = 13), a basal dichotomy separates the T. karelinii group (NRBV = 13) from the remaining crested newts. The next split divides the latter assortment into T. carnifex - T. macedonicus (NRBV = 14) versus T. cristatus (NRBV = 15) and T. dobrogicus (NRBV = 16 or 17). Conclusions - We argue that the Bayesian full mitochondrial DNA phylogeny is superior to previous attempts aiming to recover the crested newt species tree. Furthermore, our new phylogeny involves a maximally parsimonious interpretation of NRBV evolution. Calibrating the phylogeny allows us to evaluate potential drivers for crested newt cladogenesis. The split between the T. karelinii group and the three other morphotypes, at ca. 10.4 Ma, is associated with the separation of the Balkan and Anatolian landmasses (12-9 Ma). No currently known vicariant events can be ascribed to the other two splits, first at ca. 9.3 Ma, separating T. carnifex - T. macedonicus, and second at ca. 8.8 Ma, splitting T. cristatus and T. dobrogicus. The crested newt morphotypes differ in the duration of their annual aquatic period. We speculate on the role that this ecological differentiation could have played during speciation
    The contribution of organic and mineral colloidal nanoparticles to element transport in a podzol soil.
    Regelink, I.C. ; Weng, L.P. ; Riemsdijk, W.H. van - \ 2011
    Applied Geochemistry 26 (2011)Suppl.. - ISSN 0883-2927 - p. S241 - S244.
    field-flow fractionation - montmorillonite - competition - separation - adsorption - speciation - water - fe
    The aim of this work is to analyze the size-distribution and composition of nanoparticles in a water-extract of a podzol B horizon. AsFlowFFF coupled to ICP–MS and a UV/VIS detector was used for particle fractionation and simultaneous measurement of the composition of the nanoparticles. Detected nanoparticles were organic and mineral particles; the mineral particles were dominated by clay and Fe-(hydr)oxides. Both organic- and inorganic particles contributed to the mobility of Fe, Al, trace metals and P. For Zn, Pb and P respectively 73%, 92% and 72% of the colloidal concentrations were associated with clay minerals. The large contribution of clay particles to the mobility of trace metals and P can be partly explained by the high amount of dispersed clay due to drying, sieving and rewetting of the soil. Inorganic nanoparticles can contribute significantly to the mobility of metals and P in soils.
    Transfer functions for solid solution partitioning of cadmium for Australian soils
    Vries, W. de; Mc Laughlin, M.J. ; Groenenberg, J.E. - \ 2011
    Environmental Pollution 159 (2011)12. - ISSN 0269-7491 - p. 3583 - 3594.
    metal-ion activities - contaminated soils - humic substances - organic-matter - heavy-metals - surface waters - fresh-waters - pore-water - copper - speciation
    To assess transport and ecotoxicological risks of metals, such as cadmium (Cd) in soils, models are needed for partitioning and speciation. We derived regression-based “partition-relations” based on adsorption and desorption experiments for main Australian soil types. First, batch adsorption experiments were carried out over a realistic range of dissolved Cd concentrations in agricultural soils in Australia. Results showed linear sorption relationships, implying the adequacy of using Kd values to describe partitioning. Desorption measurements were then carried out to assess in-situ Kd values and relate these to soil properties The best transfer functions for solid–solution partitioning were found for Kd values relating total dissolved Cd concentration to total soil Cd concentrations, accounting for the variation in pH, SOM contents and DOC concentrations. Model predictions compared well with measurements of an independent data set, but there was a tendency to underestimate dissolved Cd concentrations of highly polluted soils.
    Using advanced surface complexation models for modelling soil chemistry under forests: Solling forest, Germany
    Bonten, L.T.C. ; Groenenberg, J.E. ; Vries, W. de - \ 2011
    Environmental Pollution 159 (2011)10. - ISSN 0269-7491 - p. 2831 - 2839.
    acid deposition - heavy-metals - hydraulic conductivity - contaminated soils - atmosphere models - ion-binding - speciation - ecosystems - water - acidification
    Various dynamic soil chemistry models have been developed to gain insight into impacts of atmospheric deposition of sulphur, nitrogen and other elements on soil and soil solution chemistry. Sorption parameters for anions and cations are generally calibrated for each site, which hampers extrapolation in space and time. On the other hand, recently developed surface complexation models (SCMs) have been successful in predicting ion sorption for static systems using generic parameter sets. This study reports the inclusion of an assemblage of these SCMs in the dynamic soil chemistry model SMARTml and applies this model to a spruce forest site in Solling Germany. Parameters for SCMs were taken from generic datasets and not calibrated. Nevertheless, modelling results for major elements matched observations well. Further, trace metals were included in the model, also using the existing framework of SCMs. The model predicted sorption for most trace elements well.
    Bioavailability pathways underlying zinc-induced avoidance behavior and reproduction toxicity in Lumbricus rubellus earthworms.
    Ma, W.C. ; Bonten, L.T.C. - \ 2011
    Ecotoxicology and Environmental Safety 74 (2011)6. - ISSN 0147-6513 - p. 1721 - 1726.
    metal accumulation - organic-matter - eisenia-andrei - contaminated field - heavy-metals - soils - copper - ph - speciation - calcium
    We investigated possible bioavailability pathways underlying zinc-induced avoidance behavior and sublethal reproduction impairment in Lumbricus rubellus. Clay-loam (pH 7.3) and sandy soil (three pH values of 4.3–6.0) were amended with zinc sulfate at six soil concentrations of total Zn ranging from 0.1 to 36 mmol/kg dw. Estimated and measured concentrations of free and exchangeable Zn ranged 10-4 to 7.1 mmol/l. Avoidance behavior responses were fast and could be directly predicted from the activity of free zinc ions without a modifying pH effect. The repellent effect is thus likely mediated by a direct action of Zn2+ ions on epidermal chemosensitive receptors. Body zinc uptake, however, was determined by proton competition with free Zn2+ sorption. Excess accumulation of body Zn was a good predictor of reproduction decline, which is indicative of internal zinc poisoning. The results indicated that zinc affects earthworms via both direct and indirect mechanisms of external and internal exposure.
    Sulfate reduction during the acidification of sucrose at pH 5 under thermophilic (55 degrees C) conditions. I: Effect of trace metals
    Lopes, S.I.C. ; Capela, M.I. ; Lens, P.N.L. - \ 2010
    Bioresource Technology 101 (2010)12. - ISSN 0960-8524 - p. 4269 - 4277.
    anaerobic granular sludge - desulfovibrio-desulfuricans - waste-water - inhibition - speciation - toxicity - degradation - 8-degrees-c - reactors - methanol
    This work studied the effect of supplying trace metals (7.5 mu M Fe and 0.5 mu M Co, Ni, Mn, Zn, Cu, B, Se, Mo and W) on sulfate reduction and acidification in thermophilic (55 degrees C) UASB reactors fed with sucrose (4 gCOD (I-reactor d)(-1)) operated at a reactor mixed liquor pH controlled at 5. Trace metals were supplied to one UASB reactor and were omitted from the influent of a second UASB reactor. The influence of different trace metal concentrations was further assessed in batch tests performed with the sludge from the UASB reactor receiving no trace metals. The absence of trace metals in the influent did not affect the performance of the acidifying UASB reactor throughout the 305 day long reactor run, but supplying low concentrations of trace metals inhibited sulfate reduction.
    Evaluation of an approach for the characterization of reactive and available pools of 20 potentially toxic elements in soils: Part II – Solid-solution partition relationships and ion activity in soil solutions
    Rodrigues, S.M. ; Henriques, B. ; Ferreira da Silva, E. ; Pereira, M.E. ; Duarte, A.C. ; Groenenberg, J.E. ; Romkens, P.F.A.M. - \ 2010
    Chemosphere 81 (2010)11. - ISSN 0045-6535 - p. 1560 - 1570.
    organic-matter - contaminated soils - heavy-metals - trace-elements - speciation - extraction - copper - adsorption - mercury - field
    To assess environmental risks related to contaminants in soil it is essential to predict the available pool of inorganic contaminants at regional scales, accounting for differences between soils from variable geologic and climatic origins. An approach composed of a well-accepted soil extraction procedure (0.01 M CaCl2) and empirical Freundlich-type models in combination with mechanistically based models which to date have been used only in temperate regions was applied to 136 soils from a South European area and evaluated for its possible general use in risk assessment. Empirical models based on reactive element pools and soil properties (pH, organic carbon, clay, total Al, Fe and Mn) provided good estimations of available concentrations for a broad range of contaminants including As, Ba, Cd, Co, Cu, Hg, Mo, Ni, Pb, Sb, Se and Zn (r2: 0.46–0.89). The variation of the pools of total Al in soils expressed the sorptive capacity of aluminosilicates and Al oxides at the surfaces and edges of clay minerals better than the actual variability of clay contents. The approach has led to recommendations for further research with particular emphasis on the impact of clay on the solubility of As and Sb, on the mechanisms controlling Cr and U availability and on differences in binding properties of soil organic matter from different climatic regions. This study showed that such approach may be included with a good degree of certainty for first step risk assessment procedures to identify potential risk areas for leaching and uptake of inorganic contaminants in different environmental settings.
    Evaluation of an approach for the characterization of reactive and available pools of twenty potentially toxic elements in soils: Part I – The role of key soil properties in the variation of contaminants’ reactivity
    Rodrigues, S.M. ; Henriques, B. ; Ferreira da Silva, E. ; Pereira, M.E. ; Duarte, A.C. ; Romkens, P.F.A.M. - \ 2010
    Chemosphere 81 (2010)11. - ISSN 0045-6535 - p. 1549 - 1559.
    iberian pyrite belt - heavy-metals - acid soils - organic-matter - trace-elements - mercury - extraction - sediments - desorption - speciation
    Harmful effects of potentially toxic elements (PTE’s) in soils relate to their geochemically reactive fraction. To assess the degree of the reactivity, specific extractions or models are needed. Here we applied a 0.43 M HNO3 chemical extraction to assess reactive pools of a broad range of PTE’s in 136 contaminated and non-contaminated soils. Furthermore we derived Freundlich-type models based on commonly available soil properties (pH, organic carbon and clay) as well as extended models that used other properties such as amorphous Al and Fe oxides and evaluated their possible use in risk assessment. The approach allowed to predict the reactivity of As, Hg, Co, U, Ba, Se, Sb, Mo, Li, Be (r2: 0.55–0.90) elements not previously included in such studies, as well as that of Cd, Zn, Cu, Pb, Ni and Cr (r2: 0.73–0.90). The inclusion of pH, organic carbon and clay improved the performance of all models except for Be and Mo, although the role of clay is not completely clear and requires further investigation. The ability of amorphous metal oxides to affect the reactivity of As, Hg, Cu, Ni, Cr, Sb, Mo and Li was expressed by the models in agreement with known geochemical processes leading to the retention of PTE’s by the solid matrix. Hence, such approach can be a useful tool to account for regional differences in soil properties during the identification of risk areas and constitute a significantly more powerful tool than the analysis of total pools of PTE’s in soils.
    Assessment of in situ immobilization of Lead (Pb) and Arsenic (As) in contaminated soils with phosphate and iron: solubility and bioaccessibility
    Cui, Y.S. ; Du, X. ; Weng, L.P. ; Riemsdijk, W.H. van - \ 2010
    Water Air and Soil Pollution 213 (2010)1-4. - ISSN 0049-6979 - p. 95 - 104.
    competitive interaction - amendments - bioavailability - phosphorus - stabilization - speciation - cement - china - adsorption - extraction
    The effect of in situ immobilization of lead (Pb) and arsenic (As) in soil with respectively phosphate and iron is well recognized. However, studies on combined Pb and As-contaminated soil are fewer, and assessment of the effectiveness of the immobilization on mobility and bioaccessibility is also necessary. In this study, a Pb and As-contaminated soil was collected from an abandoned lead/zinc mine in Shaoxing, Zhejiang province of China, which has been treated with three phosphates, i.e., calcium magnesium phosphate (CMP), phosphate rock, and single super-phosphate (SSP) for 6 months in a field study. The ferrous sulfate (FeSO4) at 20 g kg-1 was then amended to the soil samples and incubated for 8 weeks in a greenhouse. The solubility and bioaccessibility tests were used to assess the effectiveness of the in situ immobilization. The result showed that phosphates addition decreased the concentrations of CaCl2-extractable Pb; however, the concentrations of water-soluble As increased upon CMP and SSP addition. With the iron addition, the water-soluble As concentrations decreased significantly, but CaCl2-extractable Pb concentrations increased. The bioaccessibility of As and Pb measured in artificial gastric and small intestinal solutions decreased with phosphate and iron application except for the bioaccessibility of As in the gastric phase with SSP addition. Combined application of phosphates and iron can be an effective approach to lower bioaccessibility of As and Pb, but has opposing effects on mobility of As and Pb in contaminated soils
    Enrichment of the African catfish Clarias gariepinus (Burchell) with functional selenium originating from garlic: effect of enrichment period and depuration on total selenium level and sensory properties
    Schram, E. ; Schelvis-Smit, A.A.M. ; Heul, J.W. van der; Luten, J.B. - \ 2010
    Aquaculture Research 41 (2010)6. - ISSN 1355-557X - p. 793 - 803.
    fatty-acid-composition - oil finishing diet - cancer prevention - fish-oil - speciation
    We wanted to optimize the procedure for the selenium enrichment of farmed African catfish, using garlic as dietary selenium source. In the first experiment we established the relation between the length of the selenium enrichment period and the resulting total selenium level in the fillet of the fish. It was found that at a dietary level of 11.7 mg kg-1 Se, a total selenium level in the fillet of 0.7 mg kg-1 was reached in a relatively short enrichment period of 10 days before harvest. In the second experiment we studied the effect of depuration on the selenium level in the fillet and the sensory properties of selenium-enriched African catfish. It was found that total selenium levels in the fillet were not affected during a 7-day depuration period, while garlic odours and flavours in the raw and cooked fillets were significantly reduced after 2 days of depuration. We concluded that selenium enrichment of farmed African catfish can be obtained by selenium-enriched finishing diets, while garlic odours and flavours resulting from dietary garlic can be effectively reduced in the fillet during a short depuration period without negatively affecting fillet levels of total selenium.
    Modelling ion composition in simulated milk ultrafiltrate (SMUF). I: Influence of calcium phosphate precipitation.
    Gao, R. ; Halsema, F.E.D. van; Temminghoff, E.J.M. ; Leeuwen, H.P. van; Valenberg, H.J.F. van; Eisner, M.D. ; Giesbers, M. ; Boekel, M.A.J.S. van - \ 2010
    Food Chemistry 122 (2010)3. - ISSN 0308-8146 - p. 700 - 709.
    donnan membrane technique - salt solution - ph - 50-degrees-c - equilibria - speciation - additives
    Freshly prepared simulated milk ultrafiltrate (SMUF) is a solution that is supersaturated with respect to various calcium phosphate phases that precipitate in time. As a consequence, the ion composition of equilibrated SMUF was found to be significantly different from that of freshly prepared SMUF. This study proposes a thermodynamic ion-speciation model that is able to describe ion equilibria in SMUF. Moreover, it is also able to describe calcium phosphate precipitation in fresh SMUF on its way to equilibrium by using an apparent solubility product for CaHPO4·2H2O as a function of time. The model was validated by experiments in which CaCl2 and Na2HPO4 were added to freshly prepared SMUF. The changes in calcium activity and pH were followed and the precipitates were characterised by X-ray diffraction. The model was able to predict the observed changes
    The genus Phytophthora; phylogeny, speciation and host specificity
    Kroon, L.P.N.M. - \ 2010
    Wageningen University. Promotor(en): Francine Govers; Pierre de Wit, co-promotor(en): W.G. Flier. - [S.l. : S.n. - ISBN 9789085856689 - 184
    phytophthora - plantenziekteverwekkers - fylogenie - soortvorming - gastheerspecificiteit - plantenziekten - plantenziekteverwekkende schimmels - phytophthora infestans - phytophthora - plant pathogens - phylogeny - speciation - host specificity - plant diseases - plant pathogenic fungi - phytophthora infestans
    Pormotie-onderzoek naar de fylogenie, soortsvorming en waardplantspecificiteit in het geslacht Phytophthora.
    Genomic support for speciation and specificity of baculoviruses
    Jakubowska, A.K. - \ 2010
    Wageningen University. Promotor(en): Just Vlak, co-promotor(en): Monique van Oers. - [S.l. : S.n. - ISBN 9789085856207 - 136
    baculovirus - baculoviridae - insecten - soortvorming - fylogenie - gastheerspecificiteit - genexpressieanalyse - baculovirus - baculoviridae - insects - speciation - phylogeny - host specificity - genomics
    Keywords: baculovirus, insects, speciation, genomics, phylogeny, host specificity

    The Baculoviridae comprise a large family of double-stranded DNA viruses infecting
    arthropods. In this thesis two baculoviruses, Leucoma salicis nucleopolyhedrovirus
    (LesaNPV) and Agrotis segetum (Agse) NPV, were characterized in detail. Both viruses are
    potential biocontrol agents of the insects from which they were isolated. A close genetic
    relationship between LesaNPV and Orgyia pseudotsugata multiple NPV (OpMNPV) was
    found. O. pseudotsugata is known from North America and contains two baculoviruses,
    OpSNPV and OpMNPV. L. salicis is a European insect species that was accidentally
    introduced in the beginning of the 20th century into North America. Results from the current
    study suggest that LesaNPV was imported along with L. salicis into North America, where it
    infected O. pseudotsugata and adapted to this new host in coexistence with OpSNPV. As
    such, this case provides a snapshot of baculovirus evolution through speciation. The genome
    sequence of AgseNPV showed a striking co-linearity with Spodoptera exigua (Se) MNPV,
    although these viruses vary in biological properties such as host specificity. AgseNPV can
    infect S. exigua orally, but SeMNPV is not infectious for A. segetum larvae. SeMNPV causes
    a systemic infection in A.segetum only when the midgut barrier is bypassed through injection
    of the virus into the hemocoel. SeMNPV was able to enter A. segetum midgut epithelial cells
    and to transcribe its early genes, but was unable to replicate and produce progeny virus in
    these cells. The AgseNPV / SeMNPV case provides an excellent model to study baculovirus
    specificity by analyzing the changes in the genome sequence that lead to the differences in
    host range. The collected data support the view that molecular characterization is essential for
    proper virus classification and for assessing the phylogenetic relationships with other viruses.
    Preliminary insight into the age and origin of the Labeobarbus fish species flock from Lake Tana (Ethiopia) using the mtDNA cytochrome b gene
    Graaf, M. de; Megens, H.J.W.C. ; Samallo, J. ; Sibbing, F.A. - \ 2010
    Molecular Phylogenetics and Evolution 54 (2010)2. - ISSN 1055-7903 - p. 336 - 343.
    late pleistocene desiccation - barbus-intermedius complex - cichlid fishes - molecular phylogeny - reproductive segregation - ecological divergence - dna-sequences - east-africa - cyprinidae - speciation
    The high diversity of Cyprinid fish in Ethiopia’s Lake Tana appears to be an example of ecological differentiation and assortative mating leading to rapid sympatric speciation. Lake Tana’s Labeobarbus species flock consists of 15 morphological and ecological distinct species. This is the first attempt to determine the age and origin and inter-species relationships of Lake Tana’s Labeobarbus species using the mtDNA cytochrome b gene. Analysis of cytchrome b sequences shows that Lake Tana’s species flock appears to be young but the present dataset did not unequivocally support monophyly of Lake Tana’s species. Additional markers are needed to determine whether Lake Tana’s labeobarbs originated from a single or multiple incursion(s) of ancestral L. intermedius in the Lake Tana drainage basin, or the disruption of an ancient continuous riverine population by the emergence of the Tissisat waterfalls. Adaptive radiation and speciation within Lake Tana’s Labeobarbus species flock may have occurred in the last 10,000–25,000 years, following the desiccation of Lake Tana around 17,000 years ago, at the same time as Lake Victoria, however, obtaining more data using other (nuclear) markers is urgently required
    Evaluation of a Generic Multisurface Sorption Model for Inorganic Soil Contaminants
    Dijkstra, J.J. ; Meeussen, J.C.L. ; Comans, R.N.J. - \ 2009
    Environmental Science and Technology 43 (2009)16. - ISSN 0013-936X - p. 6196 - 6201.
    incinerator bottom ash - surface complexation - heavy-metals - organic-matter - ion-binding - sandy soil - speciation - ferrihydrite - iron
    The performance of a multisurface sorption model approach, composed of well-accepted surface complexation models in combination with published “generic” parameter sets, is evaluated for its possible use in risk assessment. For that purpose, the leaching of a broad range of potential soil contaminants (Ni, Cu, Zn, Cd, Pb, Ba, Cr, Co, Mo, V, Sn, Sb, S, As, Se) from eight diffusely and industrially contaminated soils is predicted simultaneously without any parameter optimization. The model approach includes aqueous speciation in combination with sorption to organic matter (NICA-Donnan model), Fe/Al-(hydr)oxides (Generalized Two-Layer Model), and clay (Donnan model). Independent data generated by pH-static leaching experiments, performed with individual subsamples over a wide pH range (pH 0.4-12), provide a sensitive evaluation of the model performance. Root-mean-squared error values between predicted and measured log concentrations over the entire pH range, RMSElog, are
    Effects of Fulvic and Humic Acids on Arsenate Adsorption of Goethite: Experiments and Modeling
    Weng, L.P. ; Riemsdijk, W.H. van; Hiemstra, T. - \ 2009
    Environmental Science and Technology 43 (2009)19. - ISSN 0013-936X - p. 7198 - 7204.
    natural organic-matter - surface structural approach - charge-distribution - ion adsorption - water interface - iron-oxides - binding - speciation - ph - competition
    Data for interactions between arsenate (AsO43-) and fulvic acids (FA) or humic acids (HA) at the surface of goethite are presented (pH 3-7, ionic strength 2 mM and 10 mM). Adsorption of FA and HA leads to desorption of arsenate and a correspondingly strong increase of arsenic concentration in solution. Adsorption of both FA and HA is mutually decreased by the competition with arsenate. The competition between FA and arsenate is much stronger than that between HA and arsenate. Using an advanced model, the LCD model (Ligand and Charge Distribution), arsenate adsorption to goethite in the presence of both adsorbed FA and HA can be predicted reasonably well. The stronger effects of FA on arsenate adsorption are caused, according to the model, by its spatial location which is closer to the oxide surface, and as a consequence, the electrostatic interactions between adsorbed FA particles and arsenate ions are much stronger than those for HA particles. The results show that site and electrostatic competition are the major mechanisms explaining the effects of natural organic matter on the arsenic speciation, whereas other possible mechanisms, such as a chemical reduction of arsenate to arsenite and formation of ternary organic arsenic complexes, are of minor significance.
    Allopatric origin of cryptic butterfly species that were discovered feeding on distinct host plants in sympatry.
    McBride, L.C. ; Velzen, R. van; Larsen, T.B. - \ 2009
    Molecular Ecology 18 (2009)17. - ISSN 0962-1083 - p. 3639 - 3651.
    parasitoid flies diptera - dna barcodes - mitochondrial-dna - reproductive isolation - astraptes-fulgerator - phytophagous insects - speciation - evolution - lepidoptera - divergence
    Surveys of tropical insects are increasingly uncovering cryptic species ¿ morphologically similar yet reproductively isolated taxa once thought to comprise a single interbreeding entity. The vast majority of such species are described from a single location. This leaves us with little information on geographic range and intraspecific variation and limits our ability to infer the forces responsible for generating such diversity. For example, in herbivorous and parasitic insects, multiple specialists are often discovered within what were thought to be single more generalized species. Host shifts are likely to have contributed to speciation in these cases. But when and where did those shifts occur, and were they facilitated by geographic isolation? We attempted to answer these questions for two cryptic species within the butterfly Cymothoe egesta that were recently discovered on different host plants in central Cameroon. We first used mtDNA markers to separate individuals collected on the two hosts within Cameroon and then extended our analysis to incorporate individuals collected across the entire pan-Afrotropical range of the original taxon. To our surprise, we found that the species are almost entirely allopatric, dividing the original range and overlapping only in the narrow zone of West-Central Africa where they were first discovered in sympatry. This finding, combined with analyses of genetic variation within each butterfly species, strongly suggests that speciation occurred in allopatry, probably during the Pleistocene. We discuss the implications of our results for understanding speciation among other cryptic species recently discovered in the tropics and argue that more work is needed on geographic patterns and host usage in such taxa
    Screening of selenium containing proteins in the Tris-buffer soluble fraction of African catfish (Clarias gariepinus) fillets by laser ablation-ICP-MS after SDS-PAGE and electroblotting onto membranes
    Pedrero, Z. ; Madrid, Y. ; Camara, C. ; Schram, E. ; Luten, J.B. ; Feldmann, I. ; Waentig, L. ; Hayen, H. ; Jakubowski, N. - \ 2009
    Journal of Analytical Atomic Spectrometry 24 (2009)6. - ISSN 0267-9477 - p. 775 - 784.
    plasma-mass spectrometry - 2-dimensional gel-electrophoresis - liquid-chromatography - isotope-dilution - cell disruption - size-exclusion - rich yeast - speciation - identification - tissues
    The anti-carcinogenic properties of selenium against certain types of cancer when present in organic forms justify the increasing interest in development of selenium fortified food. In this particular study, African catfish (Clarias gariepinus) were fed with a Se-enriched diet in order to enhance the selenium concentration in the fish fillet up to 0.85 ± 0.06 mg Se kg-1 (0.26 ± 0.02 mg Se kg-1 in control). Selenium distribution in proteins separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was studied for better understanding of the metabolism of this element in the organism. Soluble proteins (Tris buffer) were investigated by conventional application of a glass homogenizer in comparison to application of ultrasound probe sonication, and the latter was convincing due to higher protein extraction efficiency and the ease and speed of application. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was successfully applied for screening of selenium in proteins in fillets of African catfish separated by one-dimensional SDS-PAGE and after electroblotting onto nitrocellulose membranes, with a total Se amount below 0.4 ng loaded into a well. Selenium was detected in more than 11 protein spots. In order to improve the protein separation of one-dimensional SDS-PAGE, pre-fractionation of the Tris buffer soluble protein extract by size exclusion was carried out. Tryptic digestion of the Se-containing bands was performed for protein identification by nano-HPLC coupled to electrospray-MS/MS. A database search revealed several proteins which are located in muscle tissue. However, the very low Se concentration circumvents the detection of selenium containing amino acids in the tryptic peptides by electrospray-MS/MS
    Simultaneous determination of free calcium, magnesium, sodium and potassium ion concentrations in simulated milk ultrafiltrate and reconstituted skim milk using the Donnan Membrane Technique
    Gao, R. ; Temminghoff, E.J.M. ; Leeuwen, H.P. van; Valenberg, H.J.F. van; Eisner, M.D. ; Boekel, M.A.J.S. van - \ 2009
    International Dairy Journal 19 (2009)8. - ISSN 0958-6946 - p. 431 - 436.
    selective electrode - salt solution - speciation - stability - minerals
    This study focused on determination of free Ca2+, Mg2+, Na+ and K+ concentrations in a series of CaCl2 solutions, simulated milk ultrafiltrate and reconstituted skim milk using a recently developed Donnan Membrane Technique (DMT). A calcium ion selective electrode was used to compare the DMT results. The study showed that the free Ca2+ concentrations measured by the DMT agreed well with calcium electrode data. Concentrations of free Ca2+, Mg2+, Na+ and K+ measured by the DMT agreed with concentrations predicted by existing ion speciation models. It is concluded that the DMT is suitable to measure various free metal ion concentrations simultaneously in complex milk-type systems
    De evolutionaire dimensie van duurzaam visserijbeheer
    Rijnsdorp, A.D. - \ 2008
    IJmuiden : IMARES (Rapport / Wageningen IMARES C105/08) - 19
    visserij - visserijbeheer - evolutionaire genetica - adaptatiefysiologie - soortvorming - duurzaamheid (sustainability) - fisheries - fishery management - evolutionary genetics - adaptation physiology - speciation - sustainability
    Dit rapport behandelt de evolutionaire consequenties van visserij en de implicaties hiervan voor het duurzaam beheer. Visserij verhoogt de kans dat vissen worden weggevangen voordat ze volwassen worden en zich kunnen voortplanten. Dit betekent dat de dieren die genetisch geprogrammeerd zijn om op jongere leeftijd volwassen te meer nakomelingen zullen produceren dan dieren die pas op latere leeftijd volwassen worden. Een andere eigenschap die beïnvloed kan worden is de voortplantingsinspanning (aantal eieren) en de groeisnelheid. Dieren die meer eieren produceren zijn in het voordeel. Een verlaging van de geslachtsrijpe leeftijd en een verhoging van de voortplantingsinspanning resulteert in een afname van de groeisnelheid. Visserij leidt dus tot verschuivingen in de genetische eigenschappen (evolutionaire veranderingen) van de geëxploiteerde bestanden. In dit rapport wordt een overzicht gegevens van de huidige wetenschappelijk inzichten in de door de visserijgeïnduceerde evolutie en de implicaties die dit heeft voor het visserijbeheer. Speciale aandacht wordt gegeven aan de beschikbare kennis over Noordzee platvis en de mogelijkheden die er zijn om op basis van deze kennis tot een Evolutionair Impact Assessment voor deze bestanden te komen.
    Species of Botryosphaeriaceae occurring on Proteaceae
    Marincowitz, S. ; Groenewald, J.Z. ; Wingfield, M.J. ; Crous, P.W. - \ 2008
    Persoonia 21 (2008). - ISSN 0031-5850 - p. 111 - 118.
    south-africa - western-cape - sp-nov - pathogens - fungi - endophytes - morphology - speciation - australia - canker
    The Botryosphaeriaceae includes several species that are serious canker and leaf pathogens of Proteaceae. In the present study, sequence data for the ITS nrDNA region were used in conjunction with morphological observations to resolve the taxonomy of species of Botryosphaeriaceae associated with Proteaceae. Neofusicoccum luteum was confirmed from Buckinghamia and Banksia in Australia, and on Protea cynaroides in South Africa. A major pathogen of Banksia coccinea in Australia was shown to be N. australe and not N. luteum as previously reported. Neofusicoccum protearum was previously reported on Proteaceae from Australia, Madeira, Portugal and South Africa, and is shown here to also occur in Hawaii and Tenerife (Canary Islands). Furthermore, several previous records of N. ribis on Proteaceae were shown to be N. parvum. Saccharata capensis is described as a new species that is morphologically similar to S. proteae. There is no information currently available regarding its potential importance as plant pathogen and pathogenicity tests should be conducted with it in the future.
    Chalcone Synthase Gene Lineage Diversification confirms allopolyploid evolutionary relationships of European Rostrate Violets
    Hof, K. van den; Berg, R.G. van den; Gravendeel, B. - \ 2008
    Molecular Biology and Evolution 25 (2008)10. - ISSN 0737-4038 - p. 2099 - 2108.
    chs gene - family - dna - plant - genome - trees - hybridization - superfamily - duplication - speciation
    Phylogenetic relationships among and within the subsections of the genus Viola are still far from resolved. We present the first organismal phylogeny of predominantly western European species of subsection Rostratae based on the plastid trnS¿trnG intron and intergenic spacer and the nuclear low-copy gene chalcone synthase (CHS) sequences. CHS is a key enzyme in the synthesis of flavonoids, which are important for flower pigmentation. Genes encoding for CHS are members of a multigene family. In Viola, 3 different CHS copies are present. CHS gene lineages obtained confirmed earlier hypotheses about reticulate relationships between species of Viola subsection Rostratae based on karyotype data. Comparison of the CHS gene lineage tree and the plastid species phylogeny of Viola reconstructed in this study indicates that the different CHS copies present in Viola are the products of both recent and more ancient duplications
    A consistent geochemical modelling approach for the leaching and reactive transport of major and trace elements in MSWI bottom ash
    Dijkstra, J.J. ; Meeussen, J.C.L. ; Sloot, H.A. van der; Comans, R.N.J. - \ 2008
    Applied Geochemistry 23 (2008)6. - ISSN 0883-2927 - p. 1544 - 1562.
    affecting leachate composition - natural organic-matter - humic substances - heavy-metals - fulvic-acid - surface complexation - landfill lostorf - ion-binding - adsorption - speciation
    To improve the long-term environmental risk assessment of waste applications, a predictive "multi-surface" modelling approach has been developed to simultaneously predict the leaching and reactive transport of a broad range of major and trace elements (i.e., pH, Na, Al, Fe, Ca, SO4, Mg, Si, PO4, CO3, Cl, Ni, Cu, Zn, Cd, Pb, Mo) and fulvic acids from MSWI bottom ash. The geochemical part of the model approach incorporates surface complexation/precipitation on Fe/Al (hydr)oxides, complexation with humic and fulvic acids (HA and FA, respectively) and mineral dissolution/precipitation. In addition, a novel approach is used to describe the dynamic leaching of FA, based on the surface complexation of FA on Fe/Al (hydr)oxides. To enable reactive transport calculations, the geochemical part of the model is combined with advective/dispersive transport of water and first-order mass transfer between mobile and stagnant zones. Using a single, independently determined set of input parameters, adequate model predictions are obtained for the leaching of a broad range of elements under widely different conditions, as verified with data from the European standardised pH-static and percolation leaching tests (TS 14997 and TS 14405, respectively). The percolation tests were operated at different flow velocities and with flow interruptions to enable verification of the local equilibrium assumption. Although the combination of experimental and modelling results indicates that the leaching of major solubility-controlled elements occurs largely under local equilibrium conditions, this study has led to the identification of physical non-equilibrium processes for non-reactive soluble salts, as well as possible sorption-related non-equilibrium processes for the leaching of Mo, FA and associated trace metals. Further improvement of the reactive transport model can be achieved by a more mechanistic description of the (dynamic) leaching behaviour of humic substances. As the modelling approach outlined in this study is based on the fundamental processes that underlie leaching, the approach is expected to be also applicable to other granular contaminated materials application scenarios and conditions. Therefore, the combination of standardized leaching test methods, selective chemical extractions and mechanistic modelling, constitutes a promising generic approach to assess the long-term environmental impact of the application of granular contaminated materials in the environment.
    Eigen kinetics in surface complexation of aqueous metal ions
    Leeuwen, H.P. van - \ 2008
    Langmuir 24 (2008)20. - ISSN 0743-7463 - p. 11718 - 11721.
    solution/gamma-alumina interface - debye-huckel theory - adsorption-desorption - gamma-al2o3 surface - cobalt ions - goethite - equilibrium - reactivity - speciation - geometries
    The mechanism of chemisorption of aqueous metal ions at surfaces has long been a topical issue in such fields as soil chemistry and bioenvironmental science. Here it is quantitatively demonstrated for the first time that release of water from the inner hydration shell is the rate-limiting step in inner-sphere surface complexation. The reactive intermediate is an outer-sphere complex between metal ion and surface site, with an electrostatically controlled stability defined by Boltzmann statistics. Using tabulated dehydration rate constants for metal ions, the resulting scheme allows for prediction of rates of sorption of aqueous metal ions at any type of complexing surface
    Resolving the phylogenetic and taxonomic status of dark-spored teleomorph genera in the Botryosphaeriaceae
    Phillips, A.J.L. ; Alves, A. ; Pennycook, S.R. ; Johnston, P.R. ; Ramaley, A. ; Akulov, A. ; Crous, P.W. - \ 2008
    Persoonia 21 (2008). - ISSN 0031-5850 - p. 29 - 55.
    sp-nov - primer sets - anamorph - characters - confidence - speciation - inference - prunus - trees - spp.
    Species in the Botryosphaeriaceae are common plant pathogens and saprobes found on a variety of mainly woody hosts. Teleomorphs typically have hyaline, aseptate ascospores. However, some have been reported with brown ascospores and their taxonomic status is uncertain. A multi-gene approach (SSU, ITS, LSU, EF1-a and ß-tubulin) was used to resolve the correct phylogenetic position of the dark-spored 'Botryosphaeria' teleomorphs and related asexual species. Neodeightonia and Phaeobotryon are reinstated for species with brown ascospores that are either 1-septate (Neodeightonia) or 2-septate (Phaeobotryon). Phaeobotryosphaeria is reinstated for species with brown, aseptate ascospores that bear an apiculus at either end. The status of Sphaeropsis is clarified and shown to be the anamorph of Phaeobotryosphaeria. Two new genera, namely Barriopsis for species having brown, aseptate ascospores without apiculi and Spencermartinsia for species having brown, 1-septate ascospores with an apiculus at either end are introduced. Species of Dothiorella have brown, 1-septate ascospores and differ from Spencermartinsia in the absence of apiculi. These six genera can also be distinguished from one another based on morphological characters of their anamorphs. Although previously placed in the Botryosphaeriaceae, Dothidotthia, was shown to belong in the Pleosporales, and the new family Dothidotthiaceae is introduced to accommodate it
    Partitioning of organic matter and heavy metals in a sandy soil: Effects of extracting solution, solid to liquid ratio and pH
    Fest, P.M.J. ; Temminghoff, E.J.M. ; Comans, R.N.J. ; Riemsdijk, W.H. van - \ 2008
    Geoderma 146 (2008)1-2. - ISSN 0016-7061 - p. 66 - 74.
    donnan membrane technique - low-molecular-weight - humic substances - contaminated soils - model parameters - fulvic-acids - trace-metals - bottom ash - copper - speciation
    In sandy soils the behavior of heavy metals is largely controlled by soil organic matter (solid and dissolved organic matter; SOC and DOC). Therefore, knowledge of the partitioning of organic matter between the solid phase and soil solution is essential for adequate predictions of the total dissolved metal concentration in the soil solution. At present, only a few studies have incorporated solid/liquid partitioning of organic matter in metal mobility predictions. In order to gain more insight in the behavior of DOC, we have studied the effect of the extraction solution, solid to liquid ratio (SLR), pH and storage time on the extractability of DOC and related metal concentration in the soil solution of a sandy soil. Furthermore, the composition of the DOC was measured and free metal concentrations were analyzed in the soil solution with the Donnan Membrane Technique. Extraction solution, SLR and pH affected the extracted amount of both DOC and metals. The DOC concentrations were highest in pore water and decreased further from water extracts to CaCl2 extracts. In general, with increasing SLR the metal/DOC ratio decreased, which indicated that the increased DOC at higher SLR had a lower average metal binding capacity than DOC released at the lowest SLR. Storage time of the samples and changes in the field greatly affected the extracted amount of DOC; the DOC concentration of samples taken 20 years ago and stored for a long period of time are 10 times higher than for samples from the same area and stored for less than one year. The extracted DOC is comprised mainly of fulvic acids (FA) and hydrophilic acids. Humic acids (HA) played a minor role in the DOC, which is in contrast to the often used assumptions on the DOC compositions in modeling studies. The composition of DOC is also affected by the soil pH; at low pH the contribution of FA to the total DOC concentration is lower because more FA is adsorbed to Fe-oxides in the soil. Speciation calculations assuming that DOC comprised of HA, FA and citric acid (as a model substance for hydrophilic acids) showed that for Cu the citrate-bound Cu could be up to 20% of the total Cu in solution. This study shows that more research is needed to gain more insight in the composition, concentration and behavior of DOC under field conditions in order to improve the prediction of metal leaching in the field.
    Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana
    Arzanlou, M. ; Groenewald, J.Z. ; Fullerton, R.A. ; Abeln, E.C.A. ; Carlier, J. ; Zapater, M.F. ; Buddenhagen, I.W. ; Viljoen, A. ; Crous, P.W. - \ 2008
    Persoonia 20 (2008). - ISSN 0031-5850 - p. 19 - 37.
    leaf-spot - var-difformis - eucalyptus - spp. - cercospora - fijiensis - disease - colletogloeopsis - population - speciation
    Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.
    Adaptive radiation of Lake Tana's (Ethiopia) Labeobarbus species flock (Pisces, Cyprinidae)
    Graaf, M. de; Dejen, E. ; Osse, J.W.M. ; Sibbing, F.A. - \ 2008
    Marine and Freshwater Research 59 (2008)5. - ISSN 1323-1650 - p. 391 - 407.
    late pleistocene desiccation - tropical fish assemblage - cichlid fishes - barbs barbus - east-africa - reproductive segregation - ecological divergence - victoria - speciation - origin
    Studying species flocks (e.g. Darwin¿s finches, Caribbean anoline lizards, East African cichlid fishes) has proven to be highly successful in understanding the forces driving speciation. The only known, intact species flock of cyprinid fishes, the 15 Labeobarbus species in Lake Tana (Ethiopia), includes eight piscivorous species. Piscivory is a rare specialisation among the highly successful (>2000 species) but mostly benthivorous Cyprinidae. The extent and mechanisms of diversification of this remarkable Labeobarbus species flock, particularly among the unexpected piscivorous species, are still largely unknown. In the present study we demonstrate that all 15 Labeobarbus species are segregated to a great extent along spatial, trophic and/or temporal dimensions. The spatial distribution, diet (prey species but not prey size), time of active feeding and predation techniques differed significantly among the eight piscivores. Lake Tana¿s cyprinids displayed their retained potential for ecological diversification and speciation, including the uncommon specialisation of piscivory. The latter is probably a result of the absence of common African specialist piscivores in Lake Tana. We suggest that the evolution of Lake Tana¿s Labeobarbus species flock at this stage is predominantly structured by ecological selection models. The labeobarbs most likely underwent sequential stages of radiation and speciation: habitat divergence followed by trophic divergence.
    Enrichment of African catfish with functional selenium originating from garlic
    Schram, E. ; Pedrero, Z. ; Camara, C. ; Heul, J.W. van der; Luten, J.B. - \ 2008
    Aquaculture Research 39 (2008)8. - ISSN 1355-557X - p. 850 - 860.
    rainbow-trout salmo - enzymatic probe sonication - cancer prevention - dietary selenium - tissue selenium - channel catfish - selenomethionine - speciation - gairdneri - requirement
    We wanted to create functional seafood with high concentrations of organic selenium (seleno-methyl-selenocysteine and ¿-glutamyl-seleno-methyl-selenocysteine) with anti-carcinogenic properties for human consumers. Garlic containing high concentrations of these organic selenium compounds was used as a selenium source in five experimental feeds for African catfish (1.9, 2.8, 3.9, 5.1 and 8.5 mg kg¿1 Se); a sixth experimental feed was formulated without garlic (1.9 mg kg¿1 Se). The experimental feeds were fed to African catfish [initial mean (SD) weight 100.7 (2.7) g] for 43 days with three replicates per treatment. Whole fish fillets were sampled for total selenium analysis (start and end) and selenium speciation (end). We found a positive linear relationship between dietary and fillet concentrations for total selenium and selenomethionine. The dietary total selenium concentration of 8.5 mg kg¿1 resulted in a total selenium concentration of 0.9 mg kg¿1 in the fillet (wet tissue). The majority of the selenium compounds recovered in an extract made from the fillet consisted of selenomethionine, considered to be important from a nutritional point of view. Seleno-methyl-selenocysteine, one of the organic selenium species to which superior anti-carcinogenic properties are attributed, was detected in the fillet but could not be quantified.
    Groundwater chemistry of Al under Dutch acid sandy soils: effects of land use and depth.
    Fest, E. ; Temminghoff, E.J.M. ; Griffioen, J. ; Grift, B. ; Riemsdijk, W.H. van - \ 2007
    Applied Geochemistry 22 (2007)7. - ISSN 0883-2927 - p. 1427 - 1438.
    dissolved organic-matter - acid forest soils - aluminum solubility - bs horizons - unsaturated zone - natural-waters - surface waters - heavy-metals - nica-donnan - speciation
    Aluminium has received great attention in the second half of the 20th century, mainly in the context of the acid rain problem mostly in forest soils. In this research the effect of land use and depth of the groundwater on Al, pH and DOC concentration in groundwater under Dutch sandy soils has been studied. Both pH and DOC concentration play a major role in the speciation of Al in solution. Furthermore, the equilibrium with mineral phases like gibbsite, amorphous Al(OH)3 and imogolite, has been considered. Agricultural and natural land use were expected to have different effects on the pH and DOC concentration, which in turn could influence the total Al concentration and the speciation of Al in groundwater at different depths (phreatic, shallow and deep). An extensive dataset (n = 2181) from the national and some provincial monitoring networks on soil and groundwater quality was used. Land use type and groundwater depth did influence the pH, and Al and DOC concentrations in groundwater samples. The Al concentration ranged from 7 to 1941 ¿mol L¿1 at pH <4; highest Al concentrations were found for natural-phreatic groundwater. The DOC concentration decreased and the median pH increased with depth of the groundwater. Natural-phreatic groundwater showed lower pH than the agricultural-phreatic groundwater. Highest DOC concentrations were found for the agricultural-phreatic groundwater, induced by the application of organic fertilizers. Besides inorganic complexation, the NICA-Donnan model was used to calculate Al3+ concentrations for complexation with DOC. Below pH 4.5 groundwater samples were mainly in disequilibrium with a mineral phase. This disequilibrium is considered to be the result of kinetic constraints or equilibrium with organic matter. Log K values were derived by linear regression and were close to theoretical values for Al(OH)3 minerals (e.g. gibbsite or amorphous Al(OH)3), except for natural-phreatic groundwater for which lower log K values were found. Complexation of Al with DOC is shown to be an important factor for the Al concentrations, especially at high DOC concentrations as was found for agricultural-phreatic groundwater.
    Soil texture effects on the transport of phosphorus from agricultural land in river deltas of Northern Belgium, The Netherlands and North-West Germany
    Chardon, W.J. ; Schoumans, O.F. - \ 2007
    Soil Use and Management 23 (2007)suppl.1. - ISSN 0266-0032 - p. 16 - 24.
    animal manure applications - sorption capacity - amended soils - phosphate - water - losses - saturation - speciation - release - peat
    The loss of phosphorus (P) from agricultural soils can lead to serious eutrophication of surface water. Within the large river delta areas in Northern Belgium, The Netherlands and North-West Germany, a number of representative soil textures are found (sandy, peaty and clayey soils), each with its own specific combination of pathways for P loss. Based on a literature review, this paper describes for these areas the main eutrophication issues and the factors affecting P loss from these agricultural soils. Aspects of P input, legislation and water quality are discussed. On sandy soils, intensive animal production systems have led to the localized build-up of P in the soil profile with subsequent leaching to shallow groundwaters, and seepage into surface waters. Regulations for production and application of manure on these soils have led to improvements in surface water quality in the last decade, but P concentrations are still too high to maintain satisfactory ecological standards in water. On peat soils, the mineralization of organic matter in the topsoil or in the subsoil can release large amounts of P, leading to high concentrations of P in surface water. However, large P losses can also occur in seepage water from peat deposits in marine sediments containing easily-soluble calcareous P minerals. On clays, incidental losses of P are dominant: surface runoff or preferential flow can lead to loss of freshly applied P, even from soils that are known to have a large retention capacity for P.
    Bonding Form Analysis of Metals and Sulfur Fractionation in Methanol-Grown Anaerobic Granular Sludge
    Veen, A. van der; Gonzalez Fermoso, F. ; Lens, P.N.L. - \ 2007
    Engineering in Life Sciences 7 (2007)5. - ISSN 1618-0240 - p. 480 - 489.
    acid volatile sulfide - sequential extraction - anoxic sediments - dissolved-oxygen - uasb reactors - heavy-metals - cobalt - nickel - degradation - speciation
    This study investigates the metal and sulfur bonding form distribution in mesophilic (30 °C, pH 7) methanol-grown anaerobic granular sludge from upflow anaerobic sludge bed reactors operating at an organic loading rate of 3.8 g CH3OH-COD/L d. This was achieved by applying a modified Tessier sequential extraction scheme to investigate the metal bonding forms and a sequential extraction scheme for sulfur and simultaneously extracted metals to granular sludge samples of the reactors after 0, 22, 35 and 43 days of operation. Metals were also determined in the sulfur extracts. Co and Ni predominated in their oxidizable bonding forms, which increased together with the pseudo-total content during reactor operation. An omission of Co and Ni from the influent led to only a minor decline of the pseudo-total content in the sludge, mainly from the acid-soluble fraction. The ratio of simultaneously extracted metals (Co, Fe, Mn, Ni) to acid-volatile sulfides was lower than 1, indicating that the sludge contained sufficient sulfide to bind the metals as metal monosulfides. The bioavailability of metals in the methanol-grown anaerobic granular sludge investigated is therefore mainly controlled by sulfide formation/dissolution.
    Adsorptive stripping chronopotentiometry (AdSCP). Part 1: Fundamental features
    Leeuwen, H.P. van; Town, R.M. - \ 2007
    Journal of Electroanalytical Chemistry 610 (2007)1. - ISSN 1572-6657 - p. 9 - 16.
    deposition potential sscp - mercury drop electrode - bismuth film electrode - cyclic chronopotentiometry - complex-systems - voltammetry - speciation - accumulation - kinetics - cobalt
    Direct heterogeneous electron transfer reactions and the molecular orientation of d-fructose dehydrogenase (FDH, from Gluconobacter sp.) adsorbed onto electrodes were investigated. Catalytic oxidation currents based on the direct electron transfer reactions of FDH adsorbed onto basal-plane, highly oriented pyrolytic graphite (basal-plane HOPG), plastic formed carbon plate and tin-doped indium oxide electrodes were observed from a potential around ¿0.1 V (vs. Ag/AgCl/saturated KCl) in phosphate solution (pH 5.0) in the presence of fructose as a substrate for FDH. The catalytic current for the FDH adsorbed onto basal-plane HOPG electrodes indicated a pH dependence. The catalytic oxidation currents were only observed in acidic solutions (pH 6), and were not observed in neutral and alkaline solutions. The reason why the catalytic current was not obtained in neutral and alkaline solutions was because the FDH complex decomposed in neutral and alkaline solutions based on the AFM measurements. The differential pulse voltammetric investigations for FDH adsorbed onto basal-plane HOPG electrode together with the AFM and electrophoresis results indicated that the flavin-containing subunit in FDH accepts electrons from d-fructose, and transfers these electrons to the heme c-containing subunit, and then the direct electron transfer reaction of FDH occurred at the heme c site.
    Adsorptive stripping chronopotentiometry (AdSCP). Part 2: Basic experimental features
    Leeuwen, H.P. van; Town, R.M. - \ 2007
    Journal of Electroanalytical Chemistry 610 (2007)1. - ISSN 1572-6657 - p. 17 - 27.
    deposition potential sscp - competitive ligand-exchange - xylenol-orange - cyclic chronopotentiometry - diffusion-coefficients - natural-waters - voltammetry - speciation - complex - trace
    AdSCP determines a metal ion, M, by reaction with added ligand, Lad, to form a surface active MLad which is accumulated on an electrode surface, then quantified by constant current reduction. The chronopotentiometric stripping curves for Pb(II), with xylenol orange (XO) as the added ligand, are scrutinized in the context of a recently developed theoretical framework. The experimental curves are well described by expressions for the general case of an adsorbed reactant and a dissolved product, Pb0, at a conventional mercury drop electrode. The shape of the potential/time transient is substantially influenced by convergency in the diffusion of Pb0 into the electrode volume. The mercury drop electrode lies in between the limits for a macroscale electrode (with planar diffusion) and a microelectrode (where diffusion of product is immaterial). Practical borders to the various experimental conditions are identified, e.g. in the maximum value of the stripping transition time as compared to the accumulation time, and in the strength of adsorption of PbXO to ensure a constant accumulation flux. The measured position of the E/t transient is in good agreement with that predicted on the basis of the extent of convergence together with the adsorption coefficient and the stability constant for PbXO. The suitability of the area under the dt/dE peak for obtaining the magnitude of the stripping transition time and the ensuing amount of PbXO is evaluated in detail.
    Fate of airborne metal pollution in soils as related to agricultural management. 1. Zn and Pb distributions in soil profiles
    Fernandez, C. ; Labanowski, J. ; Cambier, P. ; Jongmans, A.G. ; Oort, F. van - \ 2007
    European Journal of Soil Science 58 (2007)3. - ISSN 1351-0754 - p. 547 - 559.
    contaminated soils - land-use - solubility - mobility - lead - decomposition - speciation - patterns - france - exafs
    The fate of airborne metal pollutants in soils is still relatively unknown. We studied the incorporation of such airborne metal pollution in two soils under long-term permanent pasture (PP) and conventional arable land (CA). Both soils were located at an almost equal distance from a former zinc smelter complex and developed under comparable pedogenetic conditions. Profiles of total concentrations of Zn, chosen as a mobile, and Pb as a little- or non-mobile element, were examined and compared with macro- and micromorphological soil characteristics (soil colour, biological activity). The two soils showed different profiles of total Zn and Pb concentrations, with a marked decrease of concentrations of both elements under the plough layer in CA, whereas the decrease was more progressive in PP. However, the stocks of Zn and Pb for the 1-m soil profiles of CA and PP were comparable. Correlation of Zn and Pb concentration at different depths with total Fe contents and comparison with estimated data for the local geochemical background (LGCB), suggests transport of Zn from the surface to depth in CA and PP, and Pb movement in PP. In CA, 53% of Zn and 92.5% of Pb stocks derived from airborne metal pollution were located at depths <26 cm. In PP, only 40% of Zn and 82% of Pb, derived from airborne pollution, were found in the A11 and A12 horizons (<26 cm), the remaining 18% of the Pb stock being incorporated until 50 cm depth; one-third of total Zn stock ascribed to airborne pollution was found at depths > 50 cm. Studies of the composition of gravitational water collected in soils from the same study area suggest two mechanisms for metal movement. First, mobile metal ions (Zn2+) move in the soil solution and are intercepted by iron-clay complexes in deeper soil horizons. Second, observed only in PP, simultaneous movement of Zn and Pb is ascribed to bioturbation by earthworms.
    Microgeographic evolution of snail shell shape and predator behavior
    Schilthuizen, M. ; Til, A. Van; Salverda, M. ; Liew, T.S. ; James, S. ; Elahan, B. Bin; Vermeulen, J.J. - \ 2006
    Evolution 60 (2006)9. - ISSN 0014-3820 - p. 1851 - 1858.
    land-snails - sexual selection - gene flow - speciation - dna - diversification - biodiversity - population - diversity - sequences
    AbstractGenetic divergence in geographically isolated populations is a prerequisite for allopatric speciation, one of the most common modes of speciation. In ecologically equivalent populations existing within a small, environmentally homogeneous area, an important role for environmentally neutral divergence is often found or inferred. We studied a species complex of conspicuously shaped Opisthostoma land snails on scattered limestone outcrops within a small area of lowland rainforest in Borneo. We used shell morphometrics, mitochondrial and nuclear DNA sequences, and marks of predation to study the factors involved in allopatric divergence. We found that a striking geographic divergence exists in shell morphology, which is partly associated with neutral genetic divergence. We also found geographic differentiation in the behavior of the snails' invertebrate predator and evidence of an evolutionary interaction between aspects of shell shape and predator behavior. Our study shows that adaptation to biotic aspects of the environment may play a more important role in allopatric speciation than previously suspected, even on a geographically very small scale.
    The leaching of major and trace elements from MSWI bottom ash as a function of pH and time
    Dijkstra, J.J. ; Sloot, H.A. van der; Comans, R.N.J. - \ 2006
    Applied Geochemistry 21 (2006)2. - ISSN 0883-2927 - p. 335 - 351.
    nica-donnan model - metal-ion binding - natural organic-matter - humic substances - heavy-metals - aqueous-solutions - fly-ash - waste - speciation - dissolution
    In this paper, the leaching behaviour of major components (Al, Ca, SO4, Mg, Si, Fe, Na and DOC) and trace elements (Ni, Zn, Cd, Cu, Pb, Mo and Sb) from MSWI bottom ash is studied as a function of time over a wide range of pH, under pH-controlled conditions. Equilibrium geochemical modelling using the modelling framework ORCHESTRA is used to enable a process-based interpretation of the results and to investigate whether 'equilibrium' is attained during the time scale of the experiments. Depending on the element and setpoint-pH value, net concentration increases or decreases of up to one order of magnitude were observed. Different concentration-time trends (increase or decrease) are observed in different pH ranges. The direction of the concentration-time trends depends on: (1) the shape of the 'equilibrium' solubility curve, and (2) the position of the setpoint-pH in the leaching test relative to the natural pH of the sample. Although the majority of the elements do not reach steady state, leached concentrations over a wide pH range have been shown to closely approach 'equilibrium' model curves within an equilibration time of 168 h. The different effects that leaching kinetics may have on the pH dependent leaching patterns have been identified for a wide range of elements, and can generally be explained in a mechanistic way. The results are in support of the currently prescribed equilibration time of 48 h in the European standard for the pH-static leaching test (TS14997). Finally, this study demonstrates that pH-static leaching experiments such as described in the European standards (TS14497 and TS14429), in combination with selective chemical extractions and a mechanistically based modelling approach, constitute a powerful set of tools for the characterization of leaching processes in waste materials over a wide range of conditions.
    Effect of accelerated aging of MSWI bottom ash on the leaching mechanisms of copper and molybdenum
    Dijkstra, J.J. ; Zomeren, A. van; Meeussen, J.C.L. ; Comans, R.N.J. - \ 2006
    Environmental Science and Technology 40 (2006)14. - ISSN 0013-936X - p. 4481 - 4487.
    natural organic-matter - humic substances - fulvic-acid - trace-elements - ion-binding - adsorption - surface - complexation - carbonation - speciation
    The effect of accelerated aging of Municipal Solid Waste Incinerator (MSWI) bottom ash on the leaching of Cu and Mo was studied using a "multisurface" modeling approach, based on surface complexation to iron/aluminum (hydr) oxides, mineral dissolution/precipitation, and metal complexation by humic substances. A novel experimental method allowed us to identify that the solid/liquid partitioning of fulvic acids (FA) quantitatively explains the observed beneficial effect of accelerated aging on the leaching of Cu. Our results suggest that iron/aluminum (hydr)oxides are the major reactive surfaces that retain fulvic acid in the bottom ash matrix, of which the aluminum (hydr)oxides were found to increase after aging. A new modeling approach, based on the surface complexation of FA on iron/aluminum (hydr) oxides is developed to describe the pH-dependent leaching of FA from MSWI bottom ash. Accelerated aging results in enhanced adsorption of FA to (neoformed) iron/aluminum (hydr) oxides, leading to a significant decrease in the leaching of FA and associated Cu. Accelerated aging was also found to reduce the leaching of Mo, which is also attributed to enhanced adsorption to (neoformed) iron/aluminum (hydr) oxides. These findings provide important new insights that may help to improve accelerated aging technology.
    Macroevolutionary data suggest a role for reinforcement in pollination system shifts
    Niet, T. van der; Johnson, S.D. ; Linder, H.P. - \ 2006
    Evolution 60 (2006)8. - ISSN 0014-3820 - p. 1596 - 1601.
    southern-africa - reproductive isolation - pelargonium geraniaceae - satyrium orchidaceae - cape flora - character displacement - taxonomic revision - fly pollination - speciation - evolution
    Reproductive isolation can evolve either as a by-product of divergent selection or through reinforcement. We used the Cape flora of South Africa, known for its high level of pollination specialization, as a model system to test the potential role of shifts in pollination system in the speciation process. Comparative analysis of 41 sister-species pairs (representing Geraniaceae, Iridaceae, and Orchidaceae) for which complete pollinator, edaphic, and distribution data are available showed that for sister species with overlapping distribution ranges, pollination system shifts are significantly associated with edaphic shifts. In contrast, there is no significant association between pollination system shifts and edaphic shifts for allopatric sister species. These results are interpreted as evidence for reinforcement
    Eucalyptus microfungi known from culture. 2. Alysidiella, Fusculina and Phlogicylindrium genera nova, with notes on some other poorly known taxa
    Summerell, B.A. ; Groenewald, J.Z. ; Carnegie, A.J. ; Summerbell, R.C. ; Crous, P.W. - \ 2006
    Fungal Diversity 23 (2006). - ISSN 1560-2745 - p. 323 - 350.
    south-africa - phylogenetic reassessment - mycosphaerella spp. - cylindrocladium anamorphs - australia - fungi - genus - cryphonectria - speciation - vesicles
    Although numerous microfungi have been described from Eucalyptus in recent years, this plant genus remains a rich substrate colonized by numerous undescribed species. In the present study several species and genera of ascomycetes were collected from symptomatic leaves or from leaf litter of this host in Australia, South Africa and Europe. New genera include those encompassing Alysidiella parasitica and Phlogicylindrium eucalypti genera et spp. nov. (hyphomycetes), and Fusculina eucalypti gen. et sp. nov. (a coelomycete). New species include Colletogloeopsis blakelyi, C. considenianae, C. dimorpha, Elsinoe eucalyptorum, Harknessia rhabdosphaera, Neofusicoccum corticosae and Staninwardia suttonii. A new combination is proposed for Microsphaeropsis eucalypti in Readeriella, while new cultures, hosts and distribution records are reported for Cytospora diatrypelloidea, Mycosphaerella swartii, Plectosphaera eucalypti and Valsa fabianae.
    Bioconversion of Selenate in Methanogenic Anaerobic Granular Sludge
    Astratinei, V. ; Hullebusch, E.D. van; Lens, P.N.L. - \ 2006
    Journal of Environmental Quality 35 (2006). - ISSN 0047-2425 - p. 1873 - 1883.
    soluble selenium removal - bacillus sp sf-1 - elemental selenium - sequential extraction - reducing bacterium - toxic metals - reduction - speciation - oxyanions - reactor
    The capacity of anaerobic granular sludge to remove selenate from contaminated wastewater was investigated. The potential of different types of granular sludge to remove selenate from the liquid phase was compared to that of suspended sludge and contaminated soil and sediment samples. The selenate removal rates ranged from 400 to 1500 µg g VSS¿1 h¿1, depending on the source of biomass, electron donor, and the initial selenate concentration. The granular structure protects the microorganisms when exposed to high selenate concentrations (0.1 to 1 mM). Anaerobic granular sludge "Eerbeek," originating from a UASB reactor treating paper mill wastewater, removed about 90, 50, and 36% of 0.1, 0.5, and 1 mM of Se, respectively, from the liquid phase when incubated with 20 mM lactate at 30°C and pH 7.5. Selenite, elemental Se (Seo), and metal selenide precipitates were the conversion products. Enrichments from the anaerobic granular sludge "Eerbeek" were able to convert 90% of the 10-mM selenate to Seo at a rate of 1505 µg Se(VI) g cells¿1 h¿1, a specific growth rate of 0.0125 g cells h¿1, and a yield of 0.083 g cells mg Se¿1. Both microbial metabolic processes (e.g dissimilatory reduction) as well as microbially mediated physicochemical mechanisms (adsorption and precipitation) contribute to the removal of selenate from the Se-containing medium
    Geochemical modeling of leaching from MSWI air-pollution control residues
    Astrup, T. ; Dijkstra, J.J. ; Comans, R.N.J. ; Sloot, H.A. van der; Christensen, T.H. - \ 2006
    Environmental Science and Technology 40 (2006)11. - ISSN 0013-936X - p. 3551 - 3557.
    incinerator bottom ash - solid-waste combustion - fly-ash - part ii - solubility - speciation - landfill - leachate - field - identification
    This paper provides an improved understanding of the leaching behavior of waste incineration air-pollution-control (APC) residues in a long-term perspective. Leaching was investigated by a series of batch experiments reflecting leaching conditions after initial washout of highly soluble salts from residues. Leaching experiments were performed at a range of pH-values using carbonated and noncarbonated versions of two APC residues. The leaching data were evaluated by geochemical speciation modeling and discussed with respect to possible solubility control. The leaching of major elements as well as trace elements was generally found to be strongly dependent on pH. As leaching characterization was performed in the absence of high salt levels, the presented results represent long-term leaching after initial washout from a disposal site, that is, liquid-to-solid ratios above 1-2 L/kg. The leaching of Al, Ba, Ca, Cr, Pb, S, Si, V, and Zn was found influenced by solubility control from Al2O3, Al(OH)3, Ba(S,Cr)O4 solid solutions, BaSO4, Ca6Al2(SO4)3(OH)12·26H2O, CaAl2Si4O12·2H2O, Ca(OH)2, CaSiO3, CaSO4·2H2O, CaZn2(OH)6·2H2O, KAlSi2O6, PbCO3, PbCrO4, Pb2O3, Pb2V2O7, Pb3(VO4)2, ZnO, Zn2SiO4, and ZnSiO3. The presented dataset and modeling results form a thorough contribution to the assessment of long-term leaching behavior of APC residues under a wide range of conditions.
    Multi-gene phylogenies and phenotypic characters distinguish two species within the Colletogloeopsis zuluensis complex associated with Eucalyptus stem cankers.
    Cortinas, M.N. ; Crous, P.W. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2006
    Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 133 - 146.
    coniothyrium-zuluense - mycosphaerella spp. - dna-sequences - south-africa - primer sets - inference - rates - speciation - mrbayes - models
    Colletogloeopsis zuluensis, previously known as Coniothyrium zuluense, causes a serious stem canker disease on Eucalyptus spp. grown as non-natives in many tropical and sub-tropical countries. This stem canker disease was first reported from South Africa and it has subsequently been found on various species and hybrids of Eucalyptus in other African countries as well as in countries of South America and South-East Asia. In previous studies, phylogenetic analyses based on DNA sequence data of the ITS region suggested that all material of C. zuluensis was monophyletic. However, the occurrence of the fungus in a greater number of countries, and analyses of DNA sequences with additional isolates has challenged the notion that a single species is involved with Coniothyrium canker. The aim of this study was to consider the phylogenetic relationships amongst C. zuluensis isolates from all available locations and to support these analyses with phenotypic and morphological comparisons. Individual and combined phylogenies were constructed using DNA sequences from the ITS region, exons 3 through 6 of the ß-tubulin gene, the intron of the translation elongation factor 1- gene, and a partial sequence of the mitochondrial ATPase 6 gene. Both phylogenetic data and morphological characteristics showed clearly that isolates of C. zuluensis represent at least two taxa. One of these is C. zuluensis as it was originally described from South Africa, and we provide an epitype for it. The second species occurs in Argentina and Uruguay, and is newly described as C. gauchensis. Both fungi are serious pathogens resulting in identical symptoms. Recognising them as different species has important quarantine consequences.
    Microscale and Pb distribution patterns in subsurface soil horizons: an indication for metal transport dynamics
    Oort, F. van; Jongmans, A.G. ; Citeau, L. ; Chevallier, P. - \ 2006
    European Journal of Soil Science 57 (2006)2. - ISSN 1351-0754 - p. 154 - 166.
    smelter-contaminated soils - heavy-metals - exafs spectroscopy - pollution - land - lead - cd - microprobe - solubility - speciation
    In many studies on soil pollution, authors conclude that there is no downward migration of metal elements if no evidence for enrichment can be inferred from profiles of total metal contents. We assessed possible transfer of mobile and less mobile metal pollutants to depth in subsurface horizons of a heavy metal contaminated soil, by a study of specific pedofeatures in thin sections by optical microscopy, and their corresponding Zn and Pb distribution patterns by synchrotron-based X-ray microfluorescence. In the B horizon (70 cm depth), Zn accumulation was predominantly associated with clay-iron coatings. Strong correlation was found between Zn and Fe (r = 0.94), Zn and Mn (r = 0.75), Zn and Ti (r = 0.84), and Zn and K (r = 0.88), but significant correlation was absent between Zn and Pb. In the C horizon (100 cm depth), clear Pb accumulation was observed in distinct iron coatings, with large correlation coefficients found between Pb and Fe (r = 0.94-0.75), whereas correlation between Zn and Fe was absent. Detected Zn concentrations were small and attributed to the local natural geochemical background. These results were then compared with data of the composition of gravitational soil water collected in other soils from the same study area. Thus, Zn accumulation in the B horizon was ascribed to interception of dissolved Zn2+ by negatively charged constituents of clay-iron coatings. In contrast, Pb accumulation in C horizons was related to precipitation of Pb-bearing iron colloids leading to neoformed, optically pure iron oxyhydroxide crystals and coatings. We demonstrate very localized accumulation of almost immobile Pb which occurs at greater depth than the more mobile Zn. The common, but strongly localized, occurrence of Pb-bearing iron coatings in the soil groundmass explained the absence of changes in the total Pb concentrations of the C horizon compared with the concentrations in the B horizon.
    Plant species-level systematics : New perspectives on pattern & process
    Bakker, F.T. ; Chatrou, L.W. ; Gravendeel, B. ; Pelser, P.B. - \ 2005
    Liechtenstein : A.R.G. Gantner Verlag (Regnum vegetabile vol. 143) - ISBN 9783906166391 - 348
    planten - taxonomie - biosystematiek - soorten - evolutie - fylogenetica - soortvorming - genomen - plants - taxonomy - biosystematics - species - evolution - phylogenetics - speciation - genomes
    Measuring marine iron(III) complexes by CLE-AdSV
    Town, R.M. ; Leeuwen, H.P. van - \ 2005
    Environmental Chemistry 2 (2005)2. - ISSN 1448-2517 - p. 80 - 84.
    cathodic stripping voltammetry - natural organic-ligands - iron-limited growth - southern-ocean - north pacific - sea-water - kinetics - seawater - speciation - coordination
    Iron(iii) speciation data, as determined by competitive ligand exchange?adsorptive stripping voltammetry (CLE-AdSV), is reconsidered in the light of the kinetic features of the measurement. The very large stability constants reported for iron(iii) in marine ecosystems are shown to be possibly due to an artefact of the technique, arising from the assumption that equilibrium is achieved between all iron(iii) species of relevance. Particular kinetic properties, related to the special nature of hydroxide as a metal complexant, have the consequence that CLE-AdSV measurements of iron(iii) in seawater generally correspond to the hydroxide complexes only. By the same token, dissolved hydroxide complexes are the key components of the bioavailable iron(iii) pool. The analysis presented herein opens opportunities to exploit CLE-AdSV for more rigorous investigation of the links between the speciation and the bioavailability of iron(iii).
    Distinct species exist within the Cercospora apii morphotype
    Groenewald, M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2005
    Phytopathology 95 (2005)8. - ISSN 0031-949X - p. 951 - 959.
    phylogenetic analysis - beticola resistant - rdna sequence - spot disease - leaf-spot - fungicides - speciation - anamorphs - strains - dna
    The genus Cercospora is one of the largest genera of hyphomycetes. Cercospora apii sensu lato is the oldest name for a large complex of morphologically indistinguishable Cercospora spp. occurring on a wide host range. There are currently 659 recognized Cercospora spp., and names of another 281 morphologically identical species are included in the synonymy of C. apii sensu lato. Two of the species that belong to the C. apii complex, C. apii and C. beticola, cause Cercospora leaf spot on Apium graveolens (celery) and Beta vulgaris (sugar beet), respectively. In the present study, multilocus sequence data, amplified fragment length polymorphism analysis, and cultural characteristics were used as additional features to characterize morphologically similar Cercospora strains occurring on celery and sugar beet. From the data obtained, it is shown that C. apii and C. beticola, although morphologically similar and able to cross-infect each others¿ hosts, are distinct functional species that should be retained as separate entities. Furthermore, a third, as yet undescribed species of Cercospora was detected in celery fields in Korea and Venezuela, suggesting that additional undescribed species also may be found to cause Cercospora leaf spot on celery. A polymerase chain reaction-based diagnostic protocol distinguishes all three Cercospora spp.
    Influence of pH shocks on trace netal dynamics and performance of methanol fed granular sludge bioreactors
    Zandvoort, M.H. ; Hullebusch, E.D. van; Peerbolte, A. ; Golubnic, S. ; Lettinga, G. ; Lens, P.N.L. - \ 2005
    Biodegradation 16 (2005)6. - ISSN 0923-9820 - p. 549 - 567.
    sequential extraction procedure - degradation - reactors - cobalt - methanogenesis - speciation - sediments - acetate - nickel - growth
    The influence of pH shocks on the trace metal dynamics and performance of methanol fed upflow anaerobic granular sludge bed (UASB) reactors was investigated. For this purpose, two UASB reactors were operated with metal pre-loaded granular sludge (1mM Co, Ni and Fe; 30°C; 96h) at an organic loading rate (OLR) of 5gCOD l reactor-1d-1. One UASB reactor (R1) was inoculated with sludge that originated from a full scale reactor treating alcohol distillery wastewater, while the other reactor (R2) was inoculated with sludge from a full scale reactor treating paper mill wastewater. A 30h pH shock (pH 5) strongly affected the metal retention dynamics within the granular sludge bed in both reactors. Iron losses in soluble form with the effluent were considerable: 2.3 and 2.9% for R1 and R2, respectively, based on initial iron content in the reactors, while losses of cobalt and nickel in soluble form were limited. Sequential extraction of the metals from the sludge showed that cobalt, nickel, iron and sulfur were translocated from the residual to the organic/sulfide fraction during the pH shock in R2, increasing 34, 47, 109 and 41% in the organic/sulfide fraction, respectively. This is likely due to the modification of the iron sulfide precipitate stability, which influences the extractability of iron and trace metals. Such a translocation was not observed for the R1 sludge during the first 30h pH shock, but a second 4day pH shock induced significant losses of cobalt (18%), iron (29%) and sulfur (29%) from the organic/sulfide fraction, likely due to iron sulfide dissolution and concomitant release of cobalt. After the 30h pH shock, VFA accumulated in the R2 effluent, whereas both VFA and methanol accumulated in R1 after the 4day pH shock. The formed VFA, mainly acetate, were not converted to methane due to the loss of methanogenic activity of the sludge on acetate. The VFA accumulation gradually disappeared, which is likely to be related to out-competition of acetogens by methanogens. Zinc, copper and manganese supply did not have a clear effect on the acetate removal and methanol conversion, but zinc may have induced the onset of methanol degradation after day 152 in R1.
    Lacustrine spawning: is this a new reproductive strategy among 'large' African cyprinid fishes?
    Graaf, M. de; Nentwich, E.D. ; Osse, J.W.M. ; Sibbing, F.A. - \ 2005
    Journal of Fish Biology 66 (2005)5. - ISSN 0022-1112 - p. 1214 - 1236.
    barbus-intermedius complex - lake tana ethiopia - species flock - adaptive radiation - speciation - evolution - divergence - salmon - diversification - segregation
    Changes in the gonadosomatic index and abundance of the different Labeobarbus species in the mouths of four major afferent rivers of Lake Tana, Ethiopia, were monitored monthly during 1999 and 2000. Riverine spawning was characteristic for seven of Lake Tana's 15 contemporary Labeobarbus species. These seven did not show spatial segregation among afferent rivers but significant temporal segregation occurred in aggregating in the river mouths and migrating towards the upstream spawning areas during the breeding season (June¿October). Among the eight other species, peak gonad development occurred generally in the same period as in the riverine spawners. These species, however, did not aggregate in the river mouths during the breeding period and were absent from the upstream spawning areas. A derived, novel strategy, lacustrine spawning was hypothesized for these eight Labeobarbus species. This hypothesis was further supported by observations of running female fishes in the littoral zones distant from any of the afferent rivers. This derived strategy is only common among the littoraldwelling Labeobarbus species with restricted distribution patterns. At present it is thought that sequential waves of speciation and habitat divergence followed by trophic specialization, shaped the diversity of Lake Tana labeobarbs.
    Copper and trace element fractionation in electrokinetically treated methanogenic anaerobic granular sludge
    Virkutyte, J. ; Hullebusch, E.D. van; Sillanpaa, M. ; Lens, P.N.L. - \ 2005
    Environmental Pollution 138 (2005)3. - ISSN 0269-7491 - p. 517 - 529.
    metal-contaminated soils - heavy-metals - sewage-sludge - sequential extraction - pilot-scale - removal - remediation - speciation - zinc - sediments
    The effect of electrokinetic treatment (0.15 mA cm(-2)) on the metal fractionation in anaerobic granular sludge artificially contaminated with copper (initial copper concentration 1000 mg kg(-1) wet sludge) was studied. Acidification of the sludge (final pH 4.2 in the sludge bed) with the intention to desorb the copper species bound to the organic/sulfides and residual fractions did not result in an increased mobility, despite the fact that a higher quantity of copper was measured in the more mobile (i.e. exchangeable/carbonate) fractions at final pH 4.2 compared to circum-neutral pH conditions. Also addition of the chelating agent EDTA (Cu2+:EDTA4- ratio 1.2:1) did not enhance the mobility of copper from the organic/sulfides and residual fractions, despite the fact that it induced a reduction of the total copper content of the sludge. The presence of sulfide precipitates likely influences the copper mobilisation from these less mobile fractions, and thus makes EDTA addition ineffective to solubilise copper from the granules
    Comparison of three sequential extraction procedures to describe metal fractionation in anaerobic granular sludges
    Hullebusch, E.D. van; Sudarno, S. ; Zandvoort, M.H. ; Lens, P.N.L. - \ 2005
    Talanta 65 (2005)2. - ISSN 0039-9140 - p. 549 - 558.
    heavy-metals - sewage-sludge - chemical fractionation - sample pretreatment - potential mobility - molasses stillage - trace-metals - sediments - speciation - acid
    In the last few decades. several sequential extraction procedures have been developed to quantify the chemical status of metals in the solid phase. In this study. three extraction techniques (modified [A. Tessier, P.G.C. Campbell, M. Bisson, Anal. Chem. 51 (1979) 844]: [R.C. Stover. L.E. Sommers, D.J. Silvera, J. Water Pollut. Con. F. 48 (1976) 2165]; and the Bureau Communautaire de Reference (BCR) [K.F. Mossop. C.M. Davidson. Anal. Chim. Acta 478 (2003) 111]) were applied to study the distribution of trace (Co, Ni, Zn and Cu) and major (Mn and Fe) elements in two different anaerobic granular sludges from full-scale methanogenic wastewater treatment plants. The Stover scheme displayed a higher number of fractions that induces a poor recovery compared to the other schemes. The sequential extraction scheme recommended by BCR and the modified Tessier scheme gave similar trends and are sufficiently repeatable and reproducible for application in fractionation studies. However, the BCR scheme seems to be of limited utilisation to study anaerobic matrixes because the extraction stage for its reducible fraction may release substantial amounts of trace elements bound to the organic/sulfides fraction, and consequently, the recovery of trace elements in the oxide fraction may be overestimated at the expense of the oxidisable fraction. As a final conclusion. the modified Tessier scheme seems to be the most suitable scheme to study the metal partitioning in anaerobic granular sludges. (C) 2004 Elsevier B.V. All rights reserved.
    Copper toxicity in relation to surface water-dissolved organic matter: biological effects to Daphnia magna
    Kramer, K.J.M. ; Jak, R.G. ; Hattum, B. van; Hooftman, R.N. ; Zwolsman, J.J.G. - \ 2004
    Environmental Toxicology and Chemistry 23 (2004)12. - ISSN 0730-7268 - p. 2971 - 2980.
    koper - toxiciteit - organische stof - waterverontreiniging - daphnia magna - biologische beschikbaarheid - nederland - waterbodems - copper - toxicity - organic matter - water pollution - daphnia magna - bioavailability - netherlands - water bottoms - biotic ligand model - humic-acid - ceriodaphnia-dubia - ion activity - metals - hardness - bioaccumulation - complexation - cadmium - speciation
    Water quality standards for copper are usually stated in total element concentrations. It is known, however, that a major part of the copper can be bound in complexes that are biologically not available. Natural organic matter, such as humic and fulvic acids, are strong complexing agents that may affect the bioavailable copper (Cu2+) concentration. The aim of this study was to quantify the relation between the concentration of dissolved natural organic matter and free Cu2+ in surface waters, and the biological effect, as measured in a standardized ecotoxicological test (48 h¿median effective concentration [EC50] Daphnia magna, mobility). Six typical Dutch surface waters and an artificial water, ranging from 0.1 to 22 mg/L dissolved organic carbon (DOC), were collected and analyzed quarterly. Chemical speciation modeling was used as supporting evidence to assess bioavailability. The results show clear evidence of a linear relation between the concentration of dissolved organic carbon (in milligrams DOC/L) and the ecotoxicological effect (as effect concentration, EC50, expressed as micrograms Cu/L): 48-h EC50 (Daphnia, mobility) = 17.2 × DOC + 30.2 (r2 = 0.80, n = 22). Except for a brook with atypical water quality characteristics, no differences were observed among water type or season. When ultraviolet (UV)-absorption (380 nm) was used to characterize the dissolved organic carbon, a linear correlation was found as well. The importance of the free copper concentration was demonstrated by speciation calculations: In humic-rich waters the free Cu2+ concentration was estimated at ¿10¿11 M, whereas in medium to low dissolved organic carbon waters the [Cu2+] was ¿10¿10 M. Speciation calculations performed for copper concentrations at the effective concentration level (where the biological effect is considered the same) resulted in very similar free copper concentrations (¿10¿8 M Cu) in these surface waters with different characteristics. These observations consistently show that the presence of organic matter decreases the bioavailability, uptake, and ecotoxicity of copper in the aquatic environment. It demonstrates that the DOC content must be included in site-specific environmental risk assessment for trace metals (at least for copper). It is the quantification of the effects described that allows policy makers to review the criteria for copper in surface waters.
    Salinity and zinc application effects on phytoavailability of cadmium and zinc
    Khoshgoftar, A.H. ; Shariatmadari, H. ; Karimian, N. ; Kalbasi, M. ; Zee, S.E.A.T.M. van der; Parker, D.R. - \ 2004
    Soil Science Society of America Journal 68 (2004)6. - ISSN 0361-5995 - p. 1885 - 1889.
    swiss-chard - potato-tubers - soil chloride - durum-wheat - availability - speciation - grain
    Salinity and Zn deficiency in soils are two factors that may change the phytoavailability of Zn and Cd. The aim of this study was to determine the effects of salinity and Zn application on soil Cd and Zn solubility and their concentration in wheat shoots. A greenhouse experiment with wheat (Triticum aestivum L. cv. Rushan) consisting of two levels of Zn (0 and 15 mg Zn kg¿1, in the form of ZnSO4), and five salinity levels of irrigation water (0, 60, 120, and 180 mM NaCl, and 120 mM NaNO3) in triplicate was conducted. Wheat was seeded in pots. After 45 d of growth, the shoots were harvested, and Zn and Cd concentrations were determined. After harvesting, electrical conductivity (EC), pH, and concentrations of anions and cations were determined in soil saturation extracts. Concentrations of Cd and Zn species in soil solution were predicted using the speciation program MINTEQA2. Increasing salinity increased total Cd (CdT), Cd2+, CdCl+, CdHCO3+, and CdCl20 concentrations in the soil solution, whereas no such effect was found for the NaNO3 treatment. Higher salinity decreased the total Zn (ZnT) and free Zn2+ concentrations in the soil solution and decreased Zn concentrations in the wheat shoots. With application of Zn fertilizer, shoot Cd concentrations decreased by 11 to 90%, whereas Zn concentration increased by 75 to 103%. Increasing salinity of irrigation water decreased shoot dry matter, especially if no ZnSO4 was applied. Application of Zn had a positive effect on salt tolerance of plant and increased dry matter of shoot
    Leaching of heavy metals from contaminated soils: An experimental and modeling study
    Dijkstra, J.J. ; Meeussen, J.C.L. ; Comans, R.N.J. - \ 2004
    Environmental Science and Technology 38 (2004)16. - ISSN 0013-936X - p. 4390 - 4395.
    nica-donnan model - dissolved organic-matter - incinerator bottom ash - humic substances - ion-binding - sandy soil - solubility control - waste - speciation - sorption
    In this paper, we characterize the leaching of heavy metals (Ni, Cu, Zn, Cd, and Pb) from eight contaminated soils over a wide range of pH (pH 0.4-12) using an original approach based on batch pH-static leaching experiments in combination with selective chemical extractions and geochemical modeling. The leached concentrations of the heavy metals are generally much lower than the total concentrations and show a strong pH dependency, resulting in "V-shaped" leaching curves with orders of magnitude changes in solution concentrations. The "multisurface" model used incorporates adsorption to dissolved and solid organic matter (NICA-Donnan), iron/aluminum (hydr)oxide (generalized two-layer model) and clay (Donnan model). These models were applied without modifications, and only the standard set of binding constants and parameters was used (i.e., without any fitting). The model predictions of heavy metal leaching are generally adequate and sometimes excellent. Results from speciation calculations are consistent with the well-recognized importance of organic matter as the dominant reactive solid phase in soils. The observed differences between soils with respect to element speciation in the solid phase correspond to the relative amounts of the reactive surfaces present in the soils. In the solution phase, complexes with dissolved organic matter (DOM) are predominant over most of the pH range. Free metal ions (Me2+) are generally the dominant species below pH 4. The combination of the experimental and modeling approach as used in this study is shown to be promising because it leads to a more fundamental understanding of the pH-dependent leaching processes in soils. The "multisurface" modeling approach, with the selected sorption models, is shown to be able to adequately predict the leaching of heavy metals from contaminated soils over a wide range of conditions, without any fitting of parameters
    Introduction and synthesis: plant phylogeny and the origin of major biomes
    Pennington, R.T. ; Cronk, Q.C.B. ; Richardson, J.E. - \ 2004
    Philosophical Transactions of the Royal Society B. Biological sciences 359 (2004)1450. - ISSN 0962-8436 - p. 1455 - 1464.
    estimating divergence times - cape-flora - floristic diversity - molecular evolution - south-america - global 200 - forest - biogeography - speciation - africa
    Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale
    Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story
    Brooks, D.R. ; Dowling, A.P.G. ; Veller, M.G.P. van; Hoberg, E.P. - \ 2004
    Cladistics-The International Journal of the Willi Hennig Society 20 (2004)1. - ISSN 0748-3007 - p. 32 - 46.
    brooks parsimony analysis - host-parasite coevolution - a-posteriori methods - historical biogeography - vicariance biogeography - cladistic biogeography - phylogenetic biogeography - associations - assumptions - speciation
    Prior studies involving two methods, Brooks Parsimony Analysis (BPA) and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offered new exemplars to demonstrate flaws in BPA, plus a simple fix to correct the flaws found in TreeMap. A re-evaluation of their exemplars clearly shows that the authors' calculations are incorrect, their understanding of the methods is lacking, and that their simple fix does not work. Additional analyses using TreeMap 2.02 are run to show that TreeMap 2.02, like TreeMap 1.0, cannot adequately deal with widespread parasites, contrary to the claims of its supporters. Furthermore, the exemplars corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographic studies
    A comparison of the application of a biological and morphological species concept in the Hebeloma crustuliniforme complex within a phylogenetic framework
    Aanen, D.K. ; Kuyper, T.W. - \ 2004
    Persoonia 18 (2004)3. - ISSN 0031-5850 - p. 285 - 316.
    ribosomal dna-sequences - northwestern europe - combining data - sensu-lato - speciation - systematics - evolution
    A method is presented to derive an operational phenetic species concept for the Hebeloma crustuliniforme complex in northwestern Europe. The complex was found to consist of at least 22 biological species (intercompatibility groups; ICGs). Almost none of these biological species could be recognised unambiguously by morphological criteria. It is therefore necessary to base a phenetic species concept on combinations of biological species. However, such species delimitation must be performed within an explicitly phylogenetic context. It is crucial therefore to have a reliable estimate of the phylogeny of 22 biological species in that complex. Based on two nuclear sequences, we present a best estimate of the phylogeny of biological species within the complex. Using this phylogeny, on the basis of strict monophyly only two species can be morphologically recognised among 22 biological species. Relaxing the criterion of monophyly and allowing paraphyletic groupings of biological species as phenetic species would result in the recognition of three phenetic species. A tree, with the five ICGs of the previously defined morphospecies H. crustuliniforme (1, 2, 3, 4 and 5) constrained as a monophyletic group, can not be rejected. This constrained tree, together with the relaxed criterioon that allows for paraphyletic groupings of biological species, leads to the recognition of four phenetic species, viz. H. crustuliniforme, H. helodes , H. incarnatulum and H. velutipes. These phenetic species are described and a key is provided. Other taxon names are briefly discussed. The very limited ability to translate a biological species concept into an operational phenetic species concept is explained by the lack of qualitative characters and the plasticity of quantitative characters. Recency of common evolutionary history is also a major factor. Intercompatibility tests and DNA based phylogenies indicate that most biological species are very closely related and hence provide support for the claim that correspondence between a biological species concept and a phenetic species concept in the H. crustuliniforme complex is not likely to be forthcoming. In an Appendix morphological descriptions are provided of the 22 ICGs.
    Riverine spawning and reproductive segregation in a lacustrine cyprinid species flock, facilitated by homing?
    Palstra, A.P. ; Graaf, M. de; Sibbing, F.A. - \ 2004
    Animal Biology 54 (2004)4. - ISSN 1570-7555 - p. 393 - 415.
    barbus-intermedius complex - lake tana ethiopia - south-africa - divergence - evolution - speciation - salmon - hybridization - meridionalis - selection
    This paper aims at assessing the reproductive segregation within the endemic Barbus (renamed Labeobarbus) species flock of Lake Tana (Ethiopia). Migration, followed by temporal and spatial reproductive segregation in the upstream tributaries of two inflowing rivers was studied systematically over the 1999 and 2000 spawning seasons. Physical events that may trigger lacustrine migration and characterise suitability of spawning grounds were analysed. Six species migrate 3040 km upstream Gumara River during declining flow, just after the rainy season. Spawning occurs in the well-oxygenated gravel beds of four Gumara tributaries. Eight 'large barb' species were absent from the rivers, or found only incidentally, thus segregating them at a macro-spatial scale from the six river-spawners. The missing species spawn either in the lake or in other rivers not sampled. Long distance migration and species-specific spawning sites suggest that homing may have facilitated reproductive isolation and speciation. A fine-tuning between homing and gonad development is suggested since females reach spawning maturity only as they arrive at the spawning grounds. This study provides convincing evidence for reproductive segregation, and contributes in unravelling the evolution of this unique Labeobarbus species flock. Collective migration and riverine spawning of six Labeobarbus species makes them very vulnerable for overfishing at the spawning areas.
    The evolution of non-reciprocal nuclear exchange in mushrooms as a consequence of genomic conflict
    Aanen, D.K. ; Kuyper, T.W. ; Debets, A.J.M. ; Hoekstra, R.F. - \ 2004
    Proceedings of the Royal Society. B: Biological Sciences 271 (2004)1545. - ISSN 0962-8452 - p. 1235 - 1241.
    basidiomycete coprinus-cinereus - mitochondrial-dna - uniparental inheritance - pleurotus-ostreatus - podospora-anserina - pheromone - specificities - homokaryons - speciation - mechanisms
    Heterothallic mushrooms accomplish sex by exchanging nuclei without cytoplasm. Hyphal fusions occur between haploid mycelia resulting from germinated spores and subsequent reciprocal nuclear exchange without cytoplasmic mixing. The resulting dikaryon is therefore a cytoplasmic mosaic with uniformly distributed nuclei (two in each cell). Cytoplasmic inheritance is doubly uniparental: both mated monokaryons can potentially transmit their cytoplasm to the sexual spores, but normally only a single type per spore is found. Intracellular competition between mitochondria is thus limited, but at the dikaryon level, the two types of mitochondria compete over transmission. This creates the conditions for genomic conflict: within the dikaryon, a selfish mitochondrial mutant with increased relative transmission can be favoured, but selection between dikaryons will act against such a mitochondrial mutant. Moreover, because nuclear fitness is directly dependent on dikaryon fitness, a reduction in dikaryon fitness directly conflicts with nuclear interests. We propose that genomic conflict explains the frequent occurrence of non-reciprocal nuclear exchange in mushrooms. With non-reciprocal exchange, one monokaryon donates a nucleus and the other accepts it, but not vice versa as in the typical life cycle. We propose a model where non-reciprocal nuclear exchange is primarily driven by mitochondria inducing male sterility and the evolution of nuclear suppressors
    Morphology, chemistry and distribution of neoformed spherulites in agricultural land affected by metallurgical point-source pollution
    Leguedois, S. ; Oort, F. van; Jongmans, A.G. ; Chevalier, P. - \ 2004
    Environmental Pollution 130 (2004)2. - ISSN 0269-7491 - p. 135 - 148.
    smelter-contaminated soils - sequential extraction - exafs spectroscopy - speciation - lead - microprobe - france - metals - zn - pb
    Metal distribution patterns in superficial soil horizons of agricultural land affected by metallurgical point-source pollution were studied using optical and electron microscopy, synchrotron radiation and spectroscopy analyses. The site is located in northern France, at the center of a former entry lane to a bunker of World War 11, temporarily paved with coarse industrial waste fragments and removed at the end of the war. Thin sections made from undisturbed soil samples from A and B horizons were studied. Optical microscopy revealed the occurrence of yellow micrometer-sizcd (Ap horizon) and red decamicroineter-sized spherulites (AB, B(1)g horizons) as well as distinct distribution patterns. The chemical composition of the spherulites was dominated by Fe, Mn, Zn, Pb, Ca, and P. Comparison of calculated Zn stocks, both in the groundmass and in spherulites, showed a quasi-exclusive Zn accumulation in these neoformed features. Their formation was related to several factors: (i) liberation of metal elements due to weathering of waste products, (ii) Ca and P supply from fertilizing practices, (iii) co-precipitation of metal elements and Ca and P in a Porous soil environment, after slow exudation of a supersaturated soil solution in more confined mineral media. (C) 2004 Elsevier Ltd. All rights reserved.
    Aluminum solubility and mobility in relation to organic carbon in surface soils affected by six tree species of the northeastern United States
    Dijkstra, F.A. ; Fitzhugh, R.D. - \ 2003
    Geoderma 114 (2003)39479. - ISSN 0016-7061 - p. 33 - 47.
    temperate forests - stream water - red spruce - matter - deposition - toxicity - podzolization - speciation - chemistry - horizons
    We compared Al solubility and mobility in surface soils among six tree species (sugar maple [Acer saccharum], white ash [Fraxinus americana], red maple [Acer rubrum, L.], American beech [Fagus grandifolia, Ehrh.], red oak [Quercus rubra, L.], and hemlock [Tsuga canadensis, Carr.]) in a mixed hardwood forest in northwestern Connecticut. We analyzed forest floors and mineral soils at 0¿5- and 10¿20-cm depths for exchangeable cations, pyrophosphate extractable Al (Alpyr; presumably solid organically bound Al), and total carbon, and solutions (from tension lysimeters) at 0- and 20-cm depths for pH, total organic C (TOC), and Al fractions. Forest floors beneath red maple, beech, and red oak had the highest exchangeable and extractable Al contents (0.4¿0.6 and 2.9¿3.2 mol m¿2, respectively), and the forest floor beneath sugar maple the lowest (0.1 and 0.8 mol m¿2, respectively). High concentrations of exchangeable H (under hemlock) and exchangeable Ca (under sugar maple) appear to depress exchangeable Al in forest floors. For soil solutions at 20-cm depth during the spring season, we found a strong and significant relationship between dissolved organic Al complexes (Alorg) and TOC. The TOC under all species appeared to have a similar capacity to bind Alorg. The capacity to bind dissolved Al was not saturated at high TOC concentrations in the forest floors of hemlock and red oak. Particularly under hemlock, low pH (3.5¿3.7) and high concentrations of TOC (40¿70 mg l¿1) percolating from the forest floor helped to dissolve Al from soil minerals, and more Alorg moved to deeper soil layers under hemlock than under the hardwood species. Despite pronounced differences in dissolved Al among tree species, no significant differences were found in the pyrophosphate extractable Al pools in mineral soil among tree species at different depths. The intensity, with which these trees influence Al migration throughout their life span, was probably too small to have caused pronounced effects in Al redistribution in the soil.
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