Showing papers by "Helmholtz Centre for Environmental Research - UFZ published in 2012"
University of Göttingen1, University of Canterbury2, Agricultural Research Service3, University of Western Australia4, Commonwealth Scientific and Industrial Research Organisation5, Carleton University6, Eötvös Loránd University7, Swedish University of Agricultural Sciences8, Miami University9, Helmholtz Centre for Environmental Research - UFZ10, Imperial College London11, University of Florida12, University of Würzburg13, Lüneburg University14, University of California, Berkeley15, Great Lakes Bioenergy Research Center16, James Cook University17, Australian National University18, National University of Singapore19, Wageningen University and Research Centre20
TL;DR: This review uses knowledge gained from human‐modified landscapes to suggest eight hypotheses, which it hopes will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services.
Abstract: Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on
1,513 citations
TL;DR: It is proposed that cell wall envelopes of bacteria and fungi are stabilised in soil and contribute significantly to small-particulate SOM formation and the related macromolecular architecture of SOM are consistent with most observations on SOM.
Abstract: Proper management of soil organic matter (SOM) is needed for maintaining soil fertility and for mitigation of the global increase in atmospheric CO2 concentrations and should be informed by knowledge about the sources, spatial organisation and stabilisation processes of SOM. Recently, microbial biomass residues (i.e. necromass) have been identified as a significant source of SOM. Here, we propose that cell wall envelopes of bacteria and fungi are stabilised in soil and contribute significantly to small-particulate SOM formation. This hypothesis is based on the mass balance of a soil incubation experiment with 13C-labelled bacterial cells and on the visualisation of the microbial residues by means of scanning electron microscopy (SEM). At the end of a 224-day incubation, 50% of the biomass-derived C remained in the soil, mainly in the non-living part of SOM (40% of the added biomass C). SEM micrographs only rarely showed intact cells. Instead, organic patchy fragments of 200–500 nm size were abundant and these fragments were associated with all stages of cell envelope decay and fragmentation. Similar fragments, developed on initially clean and sterile in situ microcosms during exposure to groundwater, provide clear evidence for their formation during microbial growth and surface colonisation. Microbial cell envelope fragments thus contribute significantly to SOM formation. This origin and the related macromolecular architecture of SOM are consistent with most observations on SOM, including the abundance of microbial-derived biomarkers, the low C/N ratio, the water repellency and the stabilisation of biomolecules, which in theory should be easily degradable.
776 citations
Centre national de la recherche scientifique1, Butterfly Conservation2, Catalan Ornithological Institute3, British Trust for Ornithology4, Finnish Environment Institute5, Lund University6, Charles University in Prague7, Helmholtz Centre for Environmental Research - UFZ8, Statistics Netherlands9, Radboud University Nijmegen10, Wageningen University and Research Centre11
TL;DR: In this article, the authors quantified the yearly change in community composition in response to climate change for 9,490 bird and 2,130 butterfly communities distributed across Europe and found that changes in community compositions are rapid but different between birds and butterflies and equivalent to a 37 and 114 km northward shift in bird and butterfly communities, respectively.
Abstract: Climate changes have profound effects on the distribution of numerous plant and animal species(1-3). However, whether and how different taxonomic groups are able to track climate changes at large spatial scales is still unclear. Here, we measure and compare the climatic debt accumulated by bird and butterfly communities at a European scale over two decades (1990-2008). We quantified the yearly change in community composition in response to climate change for 9,490 bird and 2,130 butterfly communities distributed across Europe(4). We show that changes in community composition are rapid but different between birds and butterflies and equivalent to a 37 and 114 km northward shift in bird and butterfly communities, respectively. We further found that, during the same period, the northward shift in temperature in Europe was even faster, so that the climatic debts of birds and butterflies correspond to a 212 and 135 km lag behind climate. Our results indicate both that birds and butterflies do not keep up with temperature increase and the accumulation of different climatic debts for these groups at national and continental scales.
623 citations
University of Copenhagen1, University of Maryland, College Park2, Council for Scientific and Industrial Research3, ETH Zurich4, University of Bonn5, Potsdam Institute for Climate Impact Research6, Centre national de la recherche scientifique7, Clark University8, University of Virginia9, University of Florida10, Lund University11, Cheikh Anta Diop University12, University of Buenos Aires13, Helmholtz Centre for Environmental Research - UFZ14
TL;DR: In this paper, the authors provided an analysis of trends in vegetation greenness of semi-arid areas using AVHRR GIMMS from 1981 to 2007, and found that greenness increases are found both in semi-arsid areas where precipitation is the dominating limiting factor for plant production (0.019 NDVI units) and in semiarid regions where air temperature is the primarily growth constraint (0.,013 NDVI Units).
594 citations
Helmholtz Centre for Environmental Research - UFZ1, University of Freiburg2, Max Planck Society3, Centre national de la recherche scientifique4, Stony Brook University5, University of Melbourne6, ETH Zurich7, Goethe University Frankfurt8, University of Regensburg9, Technische Universität München10, University of Potsdam11
TL;DR: In this paper, the authors contrast the extremes of the correlative-process spectrum of species distribution models with respect to core assumptions, model building and selection strategies, validation, uncertainties, common errors and the questions they are most suited to answer.
Abstract: Within the field of species distribution modelling an apparent dichotomy exists between process-based and correlative approaches, where the processes are explicit in the former and implicit in the latter. However, these intuitive distinctions can become blurred when comparing species distribution modelling approaches in more detail. In this review article, we contrast the extremes of the correlative–process spectrum of species distribution models with respect to core assumptions, model building and selection strategies, validation, uncertainties, common errors and the questions they are most suited to answer. The extremes of such approaches differ clearly in many aspects, such as model building approaches, parameter estimation strategies and transferability. However, they also share strengths and weaknesses. We show that claims of one approach being intrinsically superior to the other are misguided and that they ignore the process–correlation continuum as well as the domains of questions that each approach is addressing. Nonetheless, the application of process-based approaches to species distribution modelling lags far behind more correlative (process-implicit) methods and more research is required to explore their potential benefits. Critical issues for the employment of species distribution modelling approaches are given, together with a guideline for appropriate usage. We close with challenges for future development of process-explicit species distribution models and how they may complement current approaches to study species distributions.
572 citations
TL;DR: It is concluded that zebrafish larvae can indeed be regarded as independently feeding from 120 h after fertilization, and should thus be subject to regulations for animal experiments from 120H after fertilized onwards.
491 citations
TL;DR: The OpenGeoSys (OGS) project as discussed by the authors is a scientific open-source initiative for numerical simulation of thermo-hydro-mechanical chemical processes in porous media.
Abstract: In this paper we describe the OpenGeoSys (OGS) project, which is a scientific open-source initiative for numerical simulation of thermo-hydro-mechanical-chemical processes in porous media. The basic concept is to provide a flexible numerical framework (using primarily the Finite Element Method (FEM)) for solving multifield problems in porous and fractured media for applications in geoscience and hydrology. To this purpose OGS is based on an object-oriented FEM concept including a broad spectrum of interfaces for pre- and postprocessing. The OGS idea has been in development since the mid-eighties. We provide a short historical note about the continuous process of concept and software development having evolved through Fortran, C, and C++ implementations. The idea behind OGS is to provide an open platform to the community, outfitted with professional software-engineering tools such as platform-independent compiling and automated benchmarking. A comprehensive benchmarking book has been prepared for publication. Benchmarking has been proven to be a valuable tool for cooperation between different developer teams, for example, for code comparison and validation purposes (DEVOVALEX and CO2 BENCH projects). On one hand, object-orientation (OO) provides a suitable framework for distributed code development; however, the parallelization of OO codes still lacks efficiency. High-performance-computing efficiency of OO codes is subject to future research.
488 citations
TL;DR: In this article, the authors present a method to quantify and map the supply and demand of three essential provisioning services (energy, food, and water) along the rural-urban gradient of the eastern German region Leipzig-Halle.
392 citations
TL;DR: This synthesis outlines the development of ‘species interaction distribution models’ (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices using error matrices in multivariate regression models.
Abstract: Aim Biotic interactions – within guilds or across trophic levels – have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of ‘species interaction distribution models’ (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices.
Location Local to global.
Methods We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions.
Results Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co-occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non-stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio-temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species’ effect and response traits.
Main conclusions There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co-occurrence datasets across large-scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio-temporal data on biotic interactions in multispecies communities.
382 citations
TL;DR: Data clearly indicated pollution of sediments with ARGs in the vicinity of the WTP outlet and the potential of lakes as reservoirs of MRB and potential risks are discussed.
Abstract: At present, very little is known about the fate and perseverance of multiresistant bacteria and their resistance genes in natural aquatic environments. Treated, but partly also untreated sewage of the city of Lausanne, Switzerland is discharged into Vidy bay (Lake Geneva) resulting in high levels of contamination in this part of the lake. In the present work we have studied the prevalence of multiresistant bacteria and resistance genes in the wastewater stream of Lausanne. Samples from hospital and municipal raw sewage, treated effluent from Lausanne’s wastewater treatment plant (WTP) as well as lake water and sediment samples obtained close to the WTP outlet pipe and a remote site close to a drinking water pump were evaluated for the prevalence of multiresistant bacteria. Selected isolates were identified (16S rRNA gene fragment sequencing) and characterized with regards to further resistances, resistance genes, and plasmids. Mostly, studies investigating this issue have relied on cultivation-based approaches. However, the limitations of these tools are well known, in particular for environmental microbial communities, and cultivation-independent molecular tools should be applied in parallel in order to take non-culturable organisms into account. Here we directly quantified the sulfonamide resistance genes sul1 and sul2 from environmental DNA extracts using TaqMan real-time quantitative PCR. Hospital sewage contained the highest load of multiresistant bacteria and antibiotic resistance genes. Wastewater treatment reduced the total bacterial load but evidence for selection of extremely multiresistant strains and accumulation of resistance genes was observed. Our data clearly indicated pollution of sediments with antibiotic resistance genes in the vicinity of the WTP outlet. The potential of lakes as reservoirs of multiresistant bacteria and potential risks are discussed.
366 citations
TL;DR: A mini-review of applications of POM confirms that making the selection and use of patterns more explicit and rigorous can facilitate the development of models with the right level of complexity to understand ecological systems and predict their response to novel conditions.
Abstract: Modern ecology recognizes that modelling systems across scales and at multiple levels—especially to link population and ecosystem dynamics to individual adaptive behaviour—is essential for making the science predictive. ‘Pattern-oriented modelling’ (POM) is a strategy for doing just this. POM is the multi-criteria design, selection and calibration of models of complex systems. POM starts with identifying a set of patterns observed at multiple scales and levels that characterize a system with respect to the particular problem being modelled; a model from which the patterns emerge should contain the right mechanisms to address the problem. These patterns are then used to (i) determine what scales, entities, variables and processes the model needs, (ii) test and select submodels to represent key low-level processes such as adaptive behaviour, and (iii) find useful parameter values during calibration. Patterns are already often used in these ways, but a mini-review of applications of POM confirms that making the selection and use of patterns more explicit and rigorous can facilitate the development of models with the right level of complexity to understand ecological systems and predict their response to novel conditions.
TL;DR: Using detailed information on global crop yields of 60 pollination dependent or profiting crops, a map of pollination benefits on a 5′ by 5′ latitude-longitude grid is provided to guide political decisions on where to protect pollination services by investing in structural diversity of land use.
Abstract: Pollination is a well-studied and at the same time a threatened ecosystem service. A significant part of global crop production depends on or profits from pollination by animals. Using detailed information on global crop yields of 60 pollination dependent or profiting crops, we provide a map of global pollination benefits on a 5′ by 5′ latitude-longitude grid. The current spatial pattern of pollination benefits is only partly correlated with climate variables and the distribution of cropland. The resulting map of pollination benefits identifies hot spots of pollination benefits at sufficient detail to guide political decisions on where to protect pollination services by investing in structural diversity of land use. Additionally, we investigated the vulnerability of the national economies with respect to potential decline of pollination services as the portion of the (agricultural) economy depending on pollination benefits. While the general dependency of the agricultural economy on pollination seems to be stable from 1993 until 2009, we see increases in producer prices for pollination dependent crops, which we interpret as an early warning signal for a conflict between pollination service and other land uses at the global scale. Our spatially explicit analysis of global pollination benefit points to hot spots for the generation of pollination benefits and can serve as a base for further planning of land use, protection sites and agricultural policies for maintaining pollination services.
Technische Universität Darmstadt1, University of Freiburg2, University of Bern3, University of Münster4, University of Tübingen5, University of Jena6, University of Potsdam7, Max Planck Society8, University of Ulm9, University of Giessen10, Leipzig University11, Helmholtz Centre for Environmental Research - UFZ12, University of Göttingen13, University of Würzburg14, Technische Universität München15
TL;DR: In this paper, the authors defined a compound, additive LUI index for managed grasslands including meadows and pastures, which summarizes the standardized intensity of three components of land use, namely fertilization, mowing, and livestock grazing at each site.
TL;DR: The analysis reveals the substantial potential of SES models to address issues that are of utmost importance for managing complex human-environment relationships, such as: the implications of ecological and social structure for resource management, and uncertainty in natural and social systems and ways to address it.
Abstract: Conventional approaches to natural resource management are increasingly challenged by environmental problems that are embedded in highly complex systems with profound uncertainties. These so-called social-ecological systems (SESs) are characterized by strong links between the social and the ecological system and multiple interactions across spatial and temporal scales. New approaches are needed to manage those tightly coupled systems; however, basic understanding of their nonlinear behavior is still missing. Modeling is a traditional tool in natural resource management to study complex, dynamic systems. There is a long tradition of SES modeling, but the approach is now being more widely recognized in other fields, such as ecological and economic modeling, where issues such as nonlinear ecological dynamics and complex human decision making are receiving more attention. SES modeling is maturing as a discipline in its own right, incorporating ideas from other interdisciplinary fields such as resilience or complex systems research. In this paper, we provide an overview of the emergence and state of the art of this cross-cutting field. Our analysis reveals the substantial potential of SES models to address issues that are of utmost importance for managing complex human-environment relationships, such as: (i) the implications of ecological and social structure for resource management, (ii) uncertainty in natural and social systems and ways to address it, (iii) the role of coevolutionary processes in the dynamics of SESs, and (iv) the implications of microscale human decision making for sustainable resource management and conservation. The complexity of SESs and the lack of a common analytical framework, however, also pose significant challenges for this emerging field. There are clear research needs with respect to: (i) approaches that go beyond rather simple specifications of human decision making, (ii) development of coping strategies to deal with (irreducible) uncertainties, (iii) more explicit modeling of feedbacks between the social and ecological systems, and (iv) a conceptual and methodological framework for analyzing and modeling SESs. We provide ideas for tackling some of these challenges and indicate potential key focal areas for SES modeling in the future.
TL;DR: Foraging range in wandering albatrosses has shifted poleward in conjunction with changes in wind pattern, while their rates of travel and flight speeds have increased, and the duration of foraging trips has decreased, breeding success has improved, and birds have increased in mass.
Abstract: Westerly winds in the Southern Ocean have increased in intensity and moved poleward. Using long-term demographic and foraging records, we show that foraging range in wandering albatrosses has shifted poleward in conjunction with these changes in wind pattern, while their rates of travel and flight speeds have increased. Consequently, the duration of foraging trips has decreased, breeding success has improved, and birds have increased in mass by more than 1 kilogram. These positive consequences of climate change may be temporary if patterns of wind in the southern westerlies follow predicted climate change scenarios. This study stresses the importance of foraging performance as the key link between environmental changes and population processes.
TL;DR: How stage of invasion affects the extent to which occurrence data represent the ecological niche of organisms and, in turn, influences spatial prediction of species’ potential distributions is examined.
Abstract: Aim The assumption of equilibrium between organisms and their environment is a standard working postulate in species distribution models (SDMs). However, this assumption is typically violated in models of biological invasions where range expansions are highly constrained by dispersal and colonization processes. Here, we examined how stage of invasion affects the extent to which occurrence data represent the ecological niche of organisms and, in turn, influences spatial prediction of species’ potential distributions.
Location Six ecoregions in western Oregon, USA.
Methods We compiled occurrence data from 697 field plots collected over a 9-year period (2001–09) of monitoring the spread of invasive forest pathogen Phytophthora ramorum. Using these data, we applied ecological-niche factor analysis to calibrate models of potential distribution across different years of colonization. We accounted for natural variation and uncertainties in model evaluation by further investigating three hypothetical scenarios of varying equilibrium in a simulated virtual species, for which the ‘true’ potential distribution was known.
Results We confirm our hypothesis that SDMs calibrated in early stages of invasion are less accurate than models calibrated under scenarios closer to equilibrium. SDMs that are developed in early stages of invasion tend to underpredict the potential range compared to models that are built in later stages of invasion.
Main conclusions A full environmental niche of invasive species cannot be effectively captured with data from a realized distribution that is restricted by processes preventing full occupancy of suitable habitats. If SDMs are to be used effectively in conservation and management, stage of invasion needs to be considered to avoid underestimation of habitats at risk of invasion.
TL;DR: In this paper, the authors combined data on land surface and air temperatures, enriched the debate by suggesting the application of indicators for the two distinct data sets and systematically quantified indicators of all approaches for the city of Leipzig, Germany.
TL;DR: A demographic research agenda is formulated that entails advances in incorporating process-based models of demographic responses and range dynamics into a statistical framework, systematic collection of data on temporal changes in distribution and abundance and on the response of demographic rates to environmental variation, and improved theoretical understanding of the scaling of demographics rates and the dynamics of spatially coupled populations.
Abstract: Range dynamics causes mismatches between a species’ geographical distribution and the set of suitable environments in which population growth is positive (the Hutchinsonian niche). This is because source–sink population dynamics cause species to occupy unsuitable environments, and because environmental change creates non-equilibrium situations in which species may be absent from suitable environments (due to migration limitation) or present in unsuitable environments that were previously suitable (due to time-delayed extinction). Because correlative species distribution models do not account for these processes, they are likely to produce biased niche estimates and biased forecasts of future range dynamics. Recently developed dynamic range models (DRMs) overcome this problem: they statistically estimate both range dynamics and the underlying environmental response of demographic rates from species distribution data. This process-based statistical approach qualitatively advances biogeographical analyses. Yet, the application of DRMs to a broad range of species and study systems requires substantial research efforts in statistical modelling, empirical data collection and ecological theory. Here we review current and potential contributions of these fields to a demographic understanding of niches and range dynamics. Our review serves to formulate a demographic research agenda that entails: (1) advances in incorporating process-based models of demographic responses and range dynamics into a statistical framework, (2) systematic collection of data on temporal changes in distribution and abundance and on the response of demographic rates to environmental variation, and (3) improved theoretical understanding of the scaling of demographic rates and the dynamics of spatially coupled populations. This demographic research agenda is challenging but necessary for improved comprehension and quantification of niches and range dynamics. It also forms the basis for understanding how niches and range dynamics are shaped by evolutionary dynamics and biotic interactions. Ultimately, the demographic research agenda should lead to deeper integration of biogeography with empirical and theoretical ecology.
TL;DR: The results suggest that the identification of relevant traits and the relative impacts of functional identity of dominant species and functional diversity are essential for a mechanistic understanding of the role of plant diversity for ecosystem processes such as aboveground biomass production.
Abstract: Background: The different hypotheses proposed to explain positive species richness–productivity relationships, i.e. selection effect and complementarity effect, imply that plant functional characteristics are at the core of a mechanistic understanding of biodiversity effects.
Methodology/Principal Findings: We used two community-wide measures of plant functional composition, (1) community- weighted means of trait values (CWM) and (2) functional trait diversity based on Rao’s quadratic diversity (FDQ) to predict biomass production and measures of biodiversity effects in experimental grasslands (Jena Experiment) with different species richness (2, 4, 8, 16 and 60) and different functional group number and composition (1 to 4; legumes, grasses, small herbs, tall herbs) four years after establishment. Functional trait composition had a larger predictive power for community biomass and measures of biodiversitity effects (40–82% of explained variation) than species richness per se (,1–13% of explained variation). CWM explained a larger amount of variation in community biomass (80%) and net biodiversity effects (70%) than FDQ (36 and 38% of explained variation respectively). FDQ explained similar proportions of variation in complementarity effects (24%, positive relationship) and selection effects (28%, negative relationship) as CWM (27% of explained variation for both complementarity and selection effects), but for all response variables the combination of CWM and FDQ led to significant model improvement compared to a separate consideration of different components of functional trait composition. Effects of FDQ were mainly attributable to diversity in nutrient acquisition and life-history strategies. The large spectrum of traits contributing to positive effects of CWM on biomass production and net biodiversity effects indicated that effects of dominant species were associated with different trait combinations.
Conclusions/Significance: Our results suggest that the identification of relevant traits and the relative impacts of functional identity of dominant species and functional diversity are essential for a mechanistic understanding of the role of plant diversity for ecosystem processes such as aboveground biomass production.
TL;DR: In this article, the authors used stratified random sampling across 19 land cover classes using 190 sample plots to measure carbon storage and derived canopy cover from color-infrared orthophotos using an object-oriented approach and Random Forest machine learning.
TL;DR: In this article, the authors compare the performance of five modelling techniques (generalised linear models, generalised additive models, Random Forest, boosted regression trees, and maximum entropy) to predict the distribution of Balearic Shearwaters (Puffinus mauretanicus) along the coast of the western Iberian Peninsula.
TL;DR: Degradation experiments with various structurally distinct compounds were carried out, indicating a similar selectivity of the heterogeneous Fenton-like system to that known for oxidation with ·OH.
TL;DR: In this article, the authors applied the carbon footprint analysis to an urban green space project in Leipzig, Germany and compared it with all related carbon sources, from construction and maintenance over the lifetime of 50 years.
TL;DR: In this paper, the authors provide a review of the FTW concept, structure, function, and treatment efficiency reported to date and discuss the potential advantages of this emerging technology for stormwater applications.
Abstract: The treatment of urban stormwater poses numerous technical and operational challenges, particularly due to the intermittent and highly variable nature of hydrologic and pollutant inputs. Floating emergent macrophyte treatment wetlands (FTWs) are a hybridization of ponds and wetlands that offer potential advantages for treatment of these highly variable flows. FTWs utilize rooted, emergent macrophytes growing on a mat or raft floating on the surface of the water rather than rooted in the sediments. Thus, they can tolerate the widely fluctuating water depths typical of stormwater systems, without the risk of the plants drowning. The roots hang beneath the floating mat and provide a large surface area for biofilm attachment. The authors provide a review of the FTW concept, structure, function, and treatment efficiency reported to date and discuss the potential advantages of this emerging technology for stormwater applications. Although still limited, the available data from mesocosm and pilot studies on remo...
TL;DR: The UP threshold for single pesticides based on D. magna is not protective for field communities subject to multiple stressors, pesticide mixtures, and repeated exposures and that risk mitigation measures, such as forested landscape patches, can alleviate effects of pesticides.
Abstract: We compiled data from eight field studies conducted between 1998 and 2010 in Europe, Siberia, and Australia to derive thresholds for the effects of pesticides on macroinvertebrate communities and the ecosystem function leaf breakdown. Dose–response models for the relationship of pesticide toxicity with the abundance of sensitive macroinvertebrate taxa showed significant differences to reference sites at 1/1000 to 1/10 000 of the median acute effect concentration (EC50) for Daphnia magna, depending on the model specification and whether forested upstream sections were present. Hence, the analysis revealed effects well below the threshold of 1/100 of the EC50 for D. magna incorporated in the European Union Uniform Principles (UP) for registration of single pesticides. Moreover, the abundances of sensitive macroinvertebrates in the communities were reduced by 27% to 61% at concentrations related to 1/100 of the EC50 for D. magna. The invertebrate leaf breakdown rate was positively linearly related to the abu...
TL;DR: This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, The Netherlands, and Switzerland, totaling 4685 species, and provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a la...
Abstract: This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, The Netherlands, and Switzerland, totaling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogentic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a la...
TL;DR: Based on this Capture-SELEX procedure, the successful DNA aptamer selection for the aminoglycoside antibiotic kanamycin A as a small molecule target is described.
Abstract: Small organic molecules are challenging targets for an aptamer selection using the SELEX technology (SELEX—Systematic Evolution of Ligans by EXponential enrichment). Often they are not suitable for immobilization on solid surfaces, which is a common procedure in known aptamer selection methods. The Capture-SELEX procedure allows the selection of DNA aptamers for solute targets. A special SELEX library was constructed with the aim to immobilize this library on magnetic beads or other surfaces. For this purpose a docking sequence was incorporated into the random region of the library enabling hybridization to a complementary oligo fixed on magnetic beads. Oligonucleotides of the library which exhibit high affinity to the target and a secondary structure fitting to the target are released from the beads for binding to the target during the aptamer selection process. The oligonucleotides of these binding complexes were amplified, purified, and immobilized via the docking sequence to the magnetic beads as the starting point of the following selection round. Based on this Capture-SELEX procedure, the successful DNA aptamer selection for the aminoglycoside antibiotic kanamycin A as a small molecule target is described.
TL;DR: The Ecosystem Services Partership (ESP4) has organized a series of workshops on sustainable human well-being as mentioned in this paper, focusing on solutions for the problems identified in the previous workshops.
TL;DR: Phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana is provided, using two complementary approaches because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled.
Abstract: As it develops from a single-celled zygote to a mature plant embryo, the thale cress Arabidopsis thaliana passes through a stage during which phylogenetically very ancient genes are preferentially expressed, showing that animals and plants have independently acquired the developmental hourglass as a similar way of managing gene expression as they pass through embryogenesis, even though their morphological development is very different. As it develops from a single-celled zygote to a mature plant embryo, the thale cress Arabidopsis thaliana passes through a stage during which phylogenetically very ancient genes are preferentially expressed. This corroborates recent work on animals demonstrating a similar period of embryogenesis that coincides with what nineteenth-century zoologists recognized as a phase in development — at least in vertebrates — in which embryos of all species looked very similar. It seems that both animals and plants have independently converged on a similar way of managing gene expression as they transform from a single-celled zygote to a multicellular organism, even though their morphological development is very different. Animal and plant development starts with a constituting phase called embryogenesis, which evolved independently in both lineages1. Comparative anatomy of vertebrate development—based on the Meckel-Serres law2 and von Baer’s laws of embryology3 from the early nineteenth century—shows that embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphogenetic series is known as the embryonic ‘hourglass’4,5, and its bottleneck of high conservation in mid-embryogenesis is referred to as the phylotypic stage6. Recent analyses in zebrafish and Drosophila embryos provided convincing molecular support for the hourglass model, because during the phylotypic stage the transcriptome was dominated by ancient genes7 and global gene expression profiles were reported to be most conserved8. Although extensively explored in animals, an embryonic hourglass has not been reported in plants, which represent the second major kingdom in the tree of life that evolved embryogenesis. Here we provide phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana, using two complementary approaches. This is particularly significant because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled. Together with the reported developmental hourglass patterns in animals, these findings indicate convergent evolution of the molecular hourglass and a conserved logic of embryogenesis across kingdoms.
TL;DR: The results suggest that plant diversity contributes to plant community resistance against pathogens by fostering beneficial bacterial communities, and this indirect soil feedback mechanism may contribute to the positive relationship between plant diversity and productivity.
Abstract: Summary 1. Rhizosphere bacteria antagonistic to fungal pathogens improve plant performance by preventing infection. In temperate grasslands, primary productivity often increases with plant diversity, and we hypothesized that this effect may in part rely on the interactions between plants and antagonistic bacteria. 2. We investigated the impact of plant diversity and functional group composition on soil bacteria producing the antifungal compounds 2,4-diacetylphloroglucinol (DAPG) and pyrrolnitrin (PRN) in a long-term grassland biodiversity experiment, as well as their impact on soil suppressiveness. Soil suppressiveness was investigated in a model infection assay with Beta vulgaris and the pathogen Rhizoctonia solani. 3. The abundance of DAPG and PRN producers increased with plant diversity and that of PRN also increased in the presence of grasses. Moreover, legume species richness and coverage decreased the abundance of DAPG and PRN producers, respectively, contrary to beneficial effects of legumes on soil microorganisms reported previously. In turn, soil suppressiveness was at maximum when DAPG and PRN producer abundance was high. 4. Synthesis. Our results suggest that plant diversity contributes to plant community resistance against pathogens by fostering beneficial bacterial communities. This indirect soil feedback mechanism may contribute to the positive relationship between plant diversity and productivity and could also help the development of more sustainable and environmentally friendly agricultural management strategies.