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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Exploring variability in environmental impact risk from human activities across aquatic ecosystems
Borgwardt, Florian ; Robinson, Leonie ; Trauner, Daniel ; Teixeira, Heliana ; Nogueira, Antonio J.A. ; Lillebø, Ana I. ; Piet, Gerjan ; Kuemmerlen, Mathias ; O'Higgins, Tim ; McDonald, Hugh ; Arevalo-Torres, Juan ; Barbosa, Ana Luisa ; Iglesias-Campos, Alejandro ; Hein, Thomas ; Culhane, Fiona - \ 2019
Science of the Total Environment 652 (2019). - ISSN 0048-9697 - p. 1396 - 1408.
Aquatic ecosystem - Freshwater - Marine - Coastal - Biodiversity - Drivers
Aquatic ecosystems are under severe pressure. Human activities introduce an array of pressures that impact ecosystems and their components. In this study we focus on the aquatic domains of fresh, coastal and marine waters, including rivers, lakes and riparian habitats to transitional, coastal as well as shelf and oceanic habitats. In an environmental risk assessment approach, we identified impact chains that link 45 human activities through 31 pressures to 82 ecosystem components. In this linkage framework >22,000 activity-pressure-ecosystem component interactions were found across seven European case studies. We identified the environmental impact risk posed by each impact chain by first categorically weighting the interactions according to five criteria: spatial extent, dispersal potential, frequency of interaction, persistence of pressure and severity of the interaction, where extent, dispersal, frequency and persistence account for the exposure to risk (spatial and temporal), and the severity accounts for the consequence of the risk. After assigning a numerical score to each risk criterion, we came up with an overall environmental impact risk score for each impact chain. This risk score was analysed in terms of (1) the activities and pressures that introduce the greatest risk to European aquatic domains, and (2) the aquatic ecosystem components and realms that are at greatest risk from human activities. Activities related to energy production were relevant across the aquatic domains. Fishing was highly relevant in marine and environmental engineering in fresh waters. Chemical and physical pressures introduced the greatest risk to the aquatic realms. Ecosystem components that can be seen as ecotones between different ecosystems had high impact risk. We show how this information can be used in informing management on trade-offs in freshwater, coastal and marine resource use and aid decision-making
Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
Warmerdam, Sonja ; Sterken, Mark G. ; Schaik, Casper van; Oortwijn, Marian E.P. ; Lozano-Torres, Jose L. ; Bakker, Jaap ; Goverse, Aska ; Smant, Geert - \ 2018
Molecular Plant Pathology (2018). - ISSN 1464-6722
abiotic stress - Arabidopsis thaliana - ERF6 - genome-wide association mapping - Meloidogyne incognita - root-knot nematodes - transcription factor

Root-knot nematodes transform vascular host cells into permanent feeding structures to selectively withdraw their nutrients from host plants during the course of several weeks. The susceptibility of host plants to root-knot nematode infections is thought to be a complex trait involving many genetic loci. However, genome-wide association (GWA) analysis has so far revealed only four quantitative trait loci (QTLs) linked to the reproductive success of the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana, which suggests that the genetic architecture underlying host susceptibility could be much simpler than previously thought. Here, we report that, by using a relaxed stringency approach in a GWA analysis, we could identify 15 additional loci linked to quantitative variation in the reproductive success of M. incognita in Arabidopsis. To test the robustness of our analysis, we functionally characterized six genes located in a QTL with the lowest acceptable statistical support and smallest effect size. This led us to identify ETHYLENE RESPONSE FACTOR 6 (ERF6) as a novel susceptibility gene for M. incognita in Arabidopsis. ERF6 functions as a transcriptional activator and suppressor of genes in response to various abiotic stresses independent of ethylene signalling. However, whole-transcriptome analysis of nematode-infected roots of the Arabidopsis erf6-1 knockout mutant line showed that allelic variation at this locus may regulate the conversion of aminocyclopropane-1-carboxylate (ACC) into ethylene by altering the expression of 1-aminocyclopropane-1-carboxylate oxidase 3 (ACO3). Our data further suggest that tolerance to abiotic stress mediated by ERF6 forms a novel layer of control in the susceptibility of Arabidopsis to M. incognita.

Secreted venom allergen-like proteins of helminths: Conserved modulators of host responses in animals and plants
Wilbers, R.H.P. ; Schneiter, Roger ; Holterman, M.H.M. ; Drurey, Claire ; Smant, G. ; Asojo, Oluwatoyin A. ; Maizels, Rick M. ; Lozano Torres, J.L. - \ 2018
PLoS Pathogens 14 (2018)10. - ISSN 1553-7366
Despite causing considerable damage to host tissue at the onset of parasitism, invasive helminths establish remarkably persistent infections in both animals and plants. Secretions released by these obligate parasites during host invasion are thought to be crucial for their persistence in infection. Helminth secretions are complex mixtures of molecules, most of which have unknown molecular targets and functions in host cells or tissues. Although the habitats of animal- and plant-parasitic helminths are very distinct, their secretions share the presence of a structurally conserved group of proteins called venom allergen-like proteins (VALs). Helminths abundantly secrete VALs during several stages of parasitism while inflicting extensive damage to host tissue. The tight association between the secretion of VALs and the onset of parasitism has triggered a particular interest in this group of proteins, as improved knowledge on their biological functions may assist in designing novel protection strategies against parasites in humans, livestock, and important food crops.
Apoplastic venom allergen-like proteins of plant-parasitic nematodes modulate the activation of plant innate immunity by cell surface receptors
Lozano Torres, Jose - \ 2018
Despite causing considerable damage to host tissue during parasitism, nematodes establish persistent infections in both animals and plants. An elaborate repertoire of nematode effectors modulates damage-triggered immune responses of the host. However, the nature and mode of action of most of nematode immunomodulatory compounds is not well understood. We discovered that the nematode effectors named the venom allergen-like proteins (VAPs) selectively suppress host immunity during the onset of parasitism in plants. VAPs are uniquely conserved in secretions of all animal- and plant-parasitic nematodes, but their role in parasitism has remained elusive. Knocking-down the expression of Gr-VAP1 hampered the infectivity of the potato cyst nematode Globodera rostochiensis. By contrast, heterologous expression of Gr-VAP1 and VAPs from the beet cyst nematode Heterodera schachtii, in Arabidopsis, resulted in the loss of basal immunity to multiple pathogens. Surprisingly, VAPs only affect the defence responses mediated by surface-localised immune receptors. The modulation of basal immunity by ectopic expression of VAPs involves extracellular protease-based host defences and jasmonic acid responses. Crystal structures of VAPs revealed lipid binding motifs. In these cavities VAPs can bind palmitate and sterol both in vitro and in vivo. The delivery of VAPs into host tissue coincides with large modifications in the extracellular matrix by migratory nematodes. We, therefore, conclude that parasitic nematodes most likely utilise VAPs to suppress the activation of defences by immunogenic breakdown products in damaged host tissue.
Changes in root architecture of Arabidopsis thaliana induced by the cyst nematode Heterodera schachtii
Willig, J. ; Sonneveld, Devon ; Sterken, M.G. ; Lozano Torres, J.L. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
Low levels of infection by cyst nematodes on some resistant crop varieties result in significant loss in yield, while other heavily infected varieties show hardly any symptoms at all. This difference in responses suggests that some plants tolerate biotic stress by plant parasitic nematodes better than others. The objective of our current research is to investigate whether Arabidopsis thaliana can be used to unravel the genetic architecture and molecular mechanisms underlying differences in tolerance to plant parasitic nematodes in plants. To this end we first looked at changes in root architecture upon inoculation with increasing numbers of the beet cyst nematode Heterodera schachtii. This revealed how plants could compensate for damage induced by cyst nematodes in roots at low inoculation densities. Altogether, our data may demonstrate if Arabidopsis can be used as a model to study tolerance to cyst nematodes in plants.
Apoplastic Venom Allergen-like Proteins of Plant Parasitic Nematodes Modulate the Activation of Damage Triggered Immunity by Cell Surface Receptors
Lozano Torres, Jose - \ 2018
Comparative genomics and genotype-phenotype associations in Bifidobacterium breve
Bottacini, Francesca ; Morrissey, Ruth ; Esteban-Torres, Maria ; James, Kieran ; Breen, Justin van; Dikareva, Evgenia ; Egan, Muireann ; Lambert, Jolanda ; Limpt, Kees van; Knol, Jan ; O'Connell Motherway, Mary ; Sinderen, Douwe van - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Bifidobacteria are common members of the gastro-intestinal microbiota of a broad range of animal hosts. Their successful adaptation to this particular niche is linked to their saccharolytic metabolism, which is supported by a wide range of glycosyl hydrolases. In the current study a large-scale gene-Trait matching (GTM) effort was performed to explore glycan degradation capabilities in B. breve. By correlating the presence/absence of genes and associated genomic clusters with growth/no-growth patterns across a dataset of 20 Bifidobacterium breve strains and nearly 80 different potential growth substrates, we not only validated the approach for a number of previously characterized carbohydrate utilization clusters, but we were also able to discover novel genetic clusters linked to the metabolism of salicin and sucrose. Using GTM, genetic associations were also established for antibiotic resistance and exopolysaccharide production, thereby identifying (novel) bifidobacterial antibiotic resistance markers and showing that the GTM approach is applicable to a variety of phenotypes. Overall, the GTM findings clearly expand our knowledge on members of the B. breve species, in particular how their variable genetic features can be linked to specific phenotypes.

EmiStatR: a simplified and scalable urban water quality model for simulation of combined sewer overflows
Torres-Matallana, Jairo Arturo ; Leopold, Ulrich ; Klepiszewski, Kai ; Heuvelink, Gerard B.M. - \ 2018
Water 10 (2018)6. - ISSN 2073-4441
Fast surrogate model - Parallel computing - Urban water modelling

Many complex urban drainage quality models are computationally expensive. Complexity and computing times may become prohibitive when these models are used in a Monte Carlo (MC) uncertainty analysis of long time series, in particular for practitioners. Computationally scalable and fast "surrogate" models may reduce the overall computation time for practical applications in which often large data sets would be needed otherwise. We developed a simplified semi-distributed urban water quality model, EmiStatR, which brings uncertainty and sensitivity analyses of urban drainage water quality models within reach of practitioners. Its lower demand in input data and its scalability allow for simulating water volume and pollution loads in combined sewer overflows in several catchments fast and efficiently. The scalable code implemented in EmiStatR reduced the computation time significantly (by a factor of around 24 when using 32 cores). EmiStatR can be applied efficiently to test hypotheses by using MC uncertainty studies or long-term simulations.

Changes in shoot and root architecture of Arabidopsis thaliana by increasing inoculum densities of the cyst nematode Heterodera schachtii
Willig, J. ; Sonneveld, Devon ; Sterken, M.G. ; Lozano Torres, J.L. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
Some crop varieties show significant loss in biomass even though these are resistant to cyst nematodes. Interestingly, some non-resistant varieties show no symptoms at all. This phenotypical variation is also known as tolerance. In agronomic context, tolerant crop varieties are able to withstand injury and produce acceptable yields. Because of environmental and practical reasons, it is difficult to eradicate below-ground pathogens. Despite the increasing need for tolerance to below-ground pathogens, breeding for tolerance is not yet applied. This has 4 reasons:
1. Disease tolerance for soil-pathogens is difficult to quantify.
2. Unknown if there is enough useful quantitative variation in disease tolerance to soil-pathogens in different ecotypes.
3. The genetic complexity of disease tolerance is not well understood.
4. It is unclear whether disease tolerance has a negative effect on desirable traits.
This research focusses on investigating whether Arabidopsis thaliana could be used as a model plant to detect polymorphic alleles and the recombination or segregation of these alleles that are coding for tolerance.
stUPscales : An R-package for spatio-temporal uncertainty propagation across multiple scales with examples in urbanwater modelling
Torres-Matallana, Jairo Arturo ; Leopold, Ulrich ; Heuvelink, Gerard B.M. - \ 2018
Water 10 (2018)7. - ISSN 2073-4441
Input uncertainty propagation - Space-time ordinary kriging - Spatio-temporal uncertainty characterisation - Temporal aggregation

Integrated environmental modelling requires coupling sub-models at different spatial and temporal scales, thus accounting for change of support procedures (aggregation and disaggregation). We introduce the R-package spatio-temporal Uncertainty Propagation across multiple scales, stUPscales, which constitutes a contribution to state-of-the-art open source tools that support uncertainty propagation analysis in temporal and spatio-temporal domains. We illustrate the tool with an uncertainty propagation example in environmental modelling, specifically in the urban water domain. The functionalities of the class setup and the methods and functions MC.setup, MC.sim, MC.analysis and Agg.t are explained, which are used for setting up, running and analysing Monte Carlo uncertainty propagation simulations, and for spatio-temporal aggregation. We also show how the package can be used to model and predict variables that vary in space and time by using a spatio-temporal variogram model and space-time ordinary kriging. stUPscales takes uncertainty characterisation and propagation a step further by including temporal and spatio-temporal auto- and cross-correlation, resulting in more realistic (spatio-)temporal series of environmental variables. Due to its modularity, the package allows the implementation of additional methods and functions for spatio-temporal disaggregation of model inputs and outputs, when linking models across multiple space-time scales.

The influence of aggregate size fraction and horizon position on microbial community composition
Fox, Aaron ; Ikoyi, Israel ; Torres-Sallan, Gemma ; Lanigan, Gary ; Schmalenberger, Achim ; Wakelin, Steve ; Creamer, Rachel - \ 2018
Applied Soil Ecology 127 (2018). - ISSN 0929-1393 - p. 19 - 29.
Aggregate sized fraction - Bacteria - Community profiling - Fungi - Horizon position - Next generation sequencing
The influence of horizon position and aggregate size on bacterial and fungal community composition was determined. From nine sites, soils were collected from the top three horizon positions (H1, H2 and H3). Physical fractionation separated samples into large macroaggregate (LM, >2000 μm), macroaggregate (MAC, >250 μm), microaggregate (MIC, <250 μm), and silt and clay (SC, 53 μm) fractions. In all samples, the structure of the bacterial and fungal community composition was assessed via restriction fragment length polymorphism (T-RFLP), and for the four aggregate sizes from the top two horizons positions an in-depth analysis of the bacterial community was conducted using next generation sequencing (NGS). Bacterial and fungal communities both differed between aggregate-sizes. Changes in the composition of the bacterial and fungal communities also occurred among horizon positions, with a significant interaction between aggregate size and horizon position evident for the bacterial community. Using NGS, it was shown that aggregate-size had a significant effect on the bacterial community in both horizon positions at both the phyla and family taxonomic levels. MAC and MIC significantly differed in the % relative abundance of bacterial groups, potentially indicating differing predation pressures. These results indicate that both horizon position and aggregate size support distinct microbial communities. Understanding these parameters is critical in our comprehension of the patterns of microbial diversity in soil.
Quantifying in situ phenotypic variability in the hydraulic properties of four tree species across their distribution range in Europe
González-Muñoz, N. ; Sterck, F. ; Torres-Ruiz, J.M. ; Petit, G. ; Cochard, H. ; Arx, G. von; Lintunen, A. ; Caldeira, M.C. ; Capdeville, G. ; Copini, P. ; Gebauer, R. ; Grönlund, L. ; Hölttä, T. ; Lobo-do-Vale, R. ; Peltoniemi, M. ; Stritih, A. ; Urban, J. ; Delzon, S. - \ 2018
PLoS One 13 (2018)5. - ISSN 1932-6203
Many studies have reported that hydraulic properties vary considerably between tree species, but little is known about their intraspecific variation and, therefore, their capacity to adapt to a warmer and drier climate. Here, we quantify phenotypic divergence and clinal variation for embolism resistance, hydraulic conductivity and branch growth, in four tree species, two angiosperms (Betula pendula, Populus tremula) and two conifers (Picea abies, Pinus sylvestris), across their latitudinal distribution in Europe. Growth and hydraulic efficiency varied widely within species and between populations. The variability of embolism resistance was in general weaker than that of growth and hydraulic efficiency, and very low for all species but Populus tremula. In addition, no and weak support for a safety vs. efficiency trade-off was observed for the angiosperm and conifer species, respectively. The limited variability of embolism resistance observed here for all species except Populus tremula, suggests that forest populations will unlikely be able to adapt hydraulically to drier conditions through the evolution of embolism resistance.
The Ozone Monitoring Instrument : Overview of 14 years in space
Levelt, Pieternel F. ; Joiner, Joanna ; Tamminen, Johanna ; Veefkind, J.P. ; Bhartia, Pawan K. ; Zweers, Deborah C.S. ; Duncan, Bryan N. ; Streets, David G. ; Eskes, Henk ; Der, Ronald A. Van; McLinden, Chris ; Fioletov, Vitali ; Carn, Simon ; Laat, Jos De; Deland, Matthew ; Marchenko, Sergey ; McPeters, Richard ; Ziemke, Jerald ; Fu, Dejian ; Liu, Xiong ; Pickering, Kenneth ; Apituley, Arnoud ; Abad, Gonzalo González ; Arola, Antti ; Boersma, Folkert ; Miller, Christopher Chan ; Chance, Kelly ; Graaf, Martin De; Hakkarainen, Janne ; Hassinen, Seppo ; Ialongo, Iolanda ; Kleipool, Quintus ; Krotkov, Nickolay ; Li, Can ; Lamsal, Lok ; Newman, Paul ; Nowlan, Caroline ; Suleiman, Raid ; Tilstra, Lieuwe Gijsbert ; Torres, Omar ; Wang, Huiqun ; Wargan, Krzysztof - \ 2018
Atmospheric Chemistry and Physics 18 (2018)8. - ISSN 1680-7316 - p. 5699 - 5745.
This overview paper highlights the successes of the Ozone Monitoring Instrument (OMI) on board the Aura satellite spanning a period of nearly 14 years. Data from OMI has been used in a wide range of applications and research resulting in many new findings. Due to its unprecedented spatial resolution, in combination with daily global coverage, OMI plays a unique role in measuring trace gases important for the ozone layer, air quality, and climate change. With the operational very fast delivery (VFD; direct readout) and near real-time (NRT) availability of the data, OMI also plays an important role in the development of operational services in the atmospheric chemistry domain.
Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
Warmerdam, S. ; Sterken, M.G. ; Schaik, C.C. van; Oortwijn, M.E.P. ; Sukarta, O.C.A. ; Lozano Torres, J.L. ; Dicke, M. ; Helder, J. ; Kammenga, J.E. ; Goverse, A. ; Bakker, J. ; Smant, G. - \ 2018
Heligmosomoides polygyrus Venom Allergen-like Protein-4 (HpVAL-4) is a sterol binding protein
Asojo, Oluwatoyin A. ; Darwiche, Rabih ; Gebremedhin, Selam ; Smant, Geert ; Lozano-Torres, Jose L. ; Drurey, Claire ; Pollet, Jeroen ; Maizels, Rick M. ; Schneiter, Roger ; Wilbers, Ruud H.P. - \ 2018
International Journal for Parasitology 48 (2018)5. - ISSN 0020-7519 - p. 359 - 369.
Heligmosomoides polygyrus bakeri is a model parasitic hookworm used to study animal and human helminth diseases. During infection, the parasite releases excretory/secretory products that modulate the immune system of the host. The most abundant protein family in excretory/secretory products comprises the venom allergen-like proteins (VALs), which are members of the SCP/TAPS (sperm-coating protein/ Tpx/antigen 5/pathogenesis related-1/Sc7) superfamily. There are >30 secreted Heligmosomoides polygyrus VAL proteins (HpVALs) and these proteins are characterised by having either one or two 15 kDa CAP (cysteine-rich secretory protein (CRISP)/antigen 5/pathogenesis related-1) domains. The first known HpVAL structure, HpVAL-4, refined to 1.9 Å is reported. HpVAL-4 was produced as a homogeneously glycosylated protein in leaves of Nicotiana benthamiana infiltrated with recombinant plasmids, making this plant expression platform amenable for the production of biological products. The overall topology of HpVAL-4 is a three layered aba sandwich between a short N-terminal loop and a C-terminal cysteine rich extension. The C-terminal cysteine rich extension has two strands stabilized by two disulfide bonds and superposes well with the previously reported extension from the human hookworm Necator americanus Ancylostoma secreted protein-2 (Na-ASP-2). The N-terminal loop is connected to alpha helix 2 via a disulfide bond previously observed in Na-ASP-2. HpVAL-4 has a central cavity that is more similar to the Nterminal CAP domain of the two CAP Na-ASP-1 from Necator americanus. Unlike Na-ASP-2, mammalian CRISP, and the C-terminal CAP domain of Na-ASP-1, the large central cavity of HpVAL-4 lacks the two histidines required to coordinate divalent cations. HpVAL-4 has both palmitate-binding and sterol-binding cavities and is able to complement the in vivo sterol export phenotype of yeast mutants lacking their endogenous CAP proteins. More studies are required to determine endogenous binding partners of HpVAL-4 and unravel the possible impact of sterol binding on immune-modulatory functions.
Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana
Warmerdam, Sonja ; Sterken, Mark G. ; Schaik, Casper van; Oortwijn, Marian E.P. ; Sukarta, Octavina C.A. ; Lozano-Torres, Jose L. ; Dicke, Marcel ; Helder, Johannes ; Kammenga, Jan E. ; Goverse, Aska ; Bakker, Jaap ; Smant, Geert - \ 2018
New Phytologist 218 (2018)2. - ISSN 0028-646X - p. 724 - 737.
Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance. To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed four quantitative trait loci (QTLs) located on chromosomes 1 and 5 of A. thaliana significantly associated with reproductive success of M. incognita, none of which harbours typical resistance gene homologues. Mutant analysis of three genes located in two QTLs showed that the transcription factor BRASSINAZOLE RESISTANT1 and an F-box family protein may function as (co-)regulators of susceptibility to M. incognita in Arabidopsis.
Our data suggest that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.
Fire effects and ecological recovery pathways of tropical montane cloud forests along a time chronosequence
Oliveras, Imma ; Román-Cuesta, Rosa M. ; Urquiaga-Flores, Erickson ; Quintano Loayza, Jose A. ; Kala, Jose ; Huamán, Vicky ; Lizárraga, Nohemi ; Sans, Guissela ; Quispe, Katia ; Lopez, Efrain ; Lopez, David ; Cuba Torres, Israel ; Enquist, Brian J. ; Malhi, Yadvinder - \ 2018
Global Change Biology 24 (2018)2. - ISSN 1354-1013 - p. 758 - 772.
carbon allocation - forest structure - metabolic scaling theory - regeneration - species diversity
Tropical montane cloud forests (TMCFs) harbour high levels of biodiversity and large carbon stocks. Their location at high elevations make them especially sensitive to climate change, because a warming climate is enhancing upslope species migration, but human disturbance (especially fire) may in many cases be pushing the treeline downslope. TMCFs are increasingly being affected by fire, and the long-term effects of fire are still unknown. Here, we present a 28-year chronosequence to assess the effects of fire and recovery pathways of burned TMCFs, with a detailed analysis of carbon stocks, forest structure and diversity. We assessed rates of change of carbon (C) stock pools, forest structure and tree-size distribution pathways and tested several hypotheses regarding metabolic scaling theory (MST), C recovery and biodiversity. We found four different C stock recovery pathways depending on the selected C pool and time since last fire, with a recovery of total C stocks but not of aboveground C stocks. In terms of forest structure, there was an increase in the number of small stems in the burned forests up to 5–9 years after fire because of regeneration patterns, but no differences on larger trees between burned and unburned plots in the long term. In support of MST, after fire, forest structure appears to approximate steady-state size distribution in less than 30 years. However, our results also provide new evidence that the species recovery of TMCF after fire is idiosyncratic and follows multiple pathways. While fire increased species richness, it also enhanced species dissimilarity with geographical distance. This is the first study to report a long-term chronosequence of recovery pathways to fire suggesting faster recovery rates than previously reported, but at the expense of biodiversity and aboveground C stocks.
Effects of soil type and depth on carbon distribution within soil macroaggregates from temperate grassland systems
Torres-Sallan, Gemma ; Creamer, Rachel E. ; Lanigan, Gary J. ; Reidy, Brian ; Byrne, Kenneth A. - \ 2018
Geoderma 313 (2018). - ISSN 0016-7061 - p. 52 - 56.
Grassland - Soil aggregation - Soil organic carbon - Subsoil

Grassland soils have been highlighted as a global soil carbon (C) sink, and have the potential to sequester additional C. Sequestration of C can occur through incorporation of soil organic carbon (SOC) within microaggregates and the silt and clay fractions. The distribution of SOC within macroaggregate fractions gives an insight into both SOC dynamics and its incorporation into the soil. Research to date on soil C has tended to focus on the topsoil (0–30 cm). While many studies have assessed the changes in aggregation and SOC dynamics after land use or management change, this paper assesses aggregation and SOC dynamics in the topsoil and subsoil of twenty-one temperate grassland sites covering four soil types (Haplic Luvisol, Haplic Stagnosol, Haplic Cambisol, Stagnic Cambisol). Results show that there are no differences in SOC between soil types in the surface 0–30 cm, except a decrease in the quantity of microaggregates within macroaggregates in Haplic Stagnosols. In the subsoil, the silt and clay fraction of clay-illuviated soils had a lower percentage of SOC. Soils with clay illuviation and reducing conditions had a decreased proportion of SOC in microaggregates and silt plus clay within small macroaggregates in the subsoil. This could be caused by a combination of (i) reduced incorporation of SOC into smaller fractions, because POM inputs could be limited due to soil saturation limiting root growth, and (ii) reduced mineralisation and subsequent incorporation of POM into microaggregates and silt plus clay within macroaggregates. These results enable elucidation of the mechanisms driving aggregate formation (and thus C sequestration in microaggregates and silt plus clay fractions) in topsoil and subsoil. This study shows that the dynamics of SOC in subsoil horizons is soil-type dependant and that differences between soil types cannot be elucidated when the sampling is limited to 30 cm. This suggests that the IPCC guidelines for SOC measurements should also include the sampling of subsoil horizons in order to get valuable information that allows discerning between soil types.

Lower tier toxicity risk assessment of agriculture pesticides detected on the Río Madre de Dios watershed, Costa Rica
Arias-Andrés, M. ; Rämö, R. ; Mena Torres, F. ; Ugalde, R. ; Grandas, L. ; Ruepert, C. ; Castillo, L.E. ; Den Brink, P.J. van; Gunnarsson, J.S. - \ 2018
Environmental Science and Pollution Research 25 (2018)14. - ISSN 0944-1344 - p. 13312 - 13321.
Ecotoxicology - Pesticides - Risk assessment - Tropics

Costa Rica is a tropical country with one of the highest biodiversity on Earth. It also has an intensive agriculture, and pesticide runoff from banana and pineapple plantations may cause a high toxicity risk to non-target species in rivers downstream the plantations. We performed a first tier risk assessment of the maximum measured concentrations of 32 pesticides detected over 4 years in the River Madre de Dios (RMD) and its coastal lagoon on the Caribbean coast of Costa Rica. Species sensitivity distributions (SSDs) were plotted in order to derive HC5 values for each pesticide, i.e., hazard concentrations for 5 % of the species, often used as environmental criteria values in other countries. We also carried out toxicity tests for selected pesticides with native Costa Rican species in order to calculate risk coefficients according to national guidelines in Costa Rica. The concentrations of herbicides diuron and ametryn and insecticides carbofuran, diazinon, and ethoprophos exceeded either the HC5 value or the lower limit of its 90 % confidence interval suggesting toxic risks above accepted levels. Risk coefficients of diuron and carbofuran derived using local guidelines indicate toxicity risks as well. The assessed fungicides did not present acute toxic risks according to our analysis. Overall, these results show a possible toxicity of detected pesticides to aquatic organisms and provide a comparison of Costa Rican national guidelines with more refined methods for risk assessment based on SSDs. Further higher tier risk assessments of pesticides in this watershed are also necessary in order to consider pesticide water concentrations over time, toxicity from pesticide mixtures, and eventual effects on ecosystem functions.

A new reference genome sequence for genotyping virulence in continental European field populations of Globodera pallida
Holterman, M.H.M. ; Blokhina, T. ; Elsen, S.J.J. van den; Lozano Torres, J.L. ; Smant, G. ; Helder, J. - \ 2017
Plant-parasitic nematodes form an increasingly important problem in agriculture, causing significant crop losses worldwide. The majority of these losses are caused by a small number of species, such as cyst nematodes (e.g., Globodera rostochiensis and G. pallida), root-knot nematodes (Meloidogyne spp.) and stem nematodes (Ditylenchus spp.). With a regulatory ban on most nematicidal agrochemicals, the main method of control at the moment is the use of resistant crop cultivars. However, the current spectrum of nematode resistance genes used in major crops is extremely narrow. Prolonged exposure of field populations to a narrow range of resistance genes can result in the appearance of nematode genotypes with modified virulence characteristics.
To better understand the genetic mechanisms underlying selection for virulence in the potato cyst nematode G. pallida in the Netherlands, we needed to generate a new reference genome. For this, we deliberately chose an old isolate; a population that had not been exposed to potato cultivars harbouring the resistance genes that were most widely used over the past thirty years. We generated a new genome sequence of this G. pallida isolate with PacBio sequencing technology. This resulted in a new genome sequence which consists of significantly fewer and longer contigs than the publicly available genome sequence of this species. An automated procedure was used to create an initial annotation. After a further manual refinement of the annotation with a particular focus on effector families, this genome sequence will serve as a reference for the elucidation of virulence characteristics in G. pallida populations from The Netherlands and surrounding countries.
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