Showing papers by "Helmholtz Centre for Environmental Research - UFZ published in 2014"

Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales

Abstract: Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.

A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers

Abstract: Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km2) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.

A Quantitative Review of Urban Ecosystem Service Assessments: Concepts, Models, and Implementation

Abstract: Although a number of comprehensive reviewshave examined global ecosystem services (ES), few havefocused on studies that assess urban ecosystem services(UES). Given that more than half of the world’ ...

Choosing and using diversity indices: Insights for ecological applications from the German Biodiversity Exploratories

Abstract: Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D-1), Simpson's dominance (D-2), Simpson's evenness (E), and Berger-Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P.lanceolata molecular and chemical diversity. Including these trait-based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system.

Organic chemicals jeopardize the health of freshwater ecosystems on the continental scale

Abstract: Organic chemicals can contribute to local and regional losses of freshwater biodiversity and ecosystem services. However, their overall relevance regarding larger spatial scales remains unknown. Here, we present, to our knowledge, the first risk assessment of organic chemicals on the continental scale comprising 4,000 European monitoring sites. Organic chemicals were likely to exert acute lethal and chronic long-term effects on sensitive fish, invertebrate, or algae species in 14% and 42% of the sites, respectively. Of the 223 chemicals monitored, pesticides, tributyltin, polycyclic aromatic hydrocarbons, and brominated flame retardants were the major contributors to the chemical risk. Their presence was related to agricultural and urban areas in the upstream catchment. The risk of potential acute lethal and chronic long-term effects increased with the number of ecotoxicologically relevant chemicals analyzed at each site. As most monitoring programs considered in this study only included a subset of these chemicals, our assessment likely underestimates the actual risk. Increasing chemical risk was associated with deterioration in the quality status of fish and invertebrate communities. Our results clearly indicate that chemical pollution is a large-scale environmental problem and requires far-reaching, holistic mitigation measures to preserve and restore ecosystem health.

A Unified Classification of Alien Species Based on the Magnitude of their Environmental Impacts

Abstract: Species moved by human activities beyond the limits of their native geographic ranges into areas in which they do not naturally occur (termed aliens) can cause a broad range of significant changes to recipient ecosystems; however, their impacts vary greatly across species and the ecosystems into which they are introduced. There is therefore a critical need for a standardised method to evaluate, compare, and eventually predict the magnitudes of these different impacts. Here, we propose a straightforward system for classifying alien species according to the magnitude of their environmental impacts, based on the mechanisms of impact used to code species in the International Union for Conservation of Nature (IUCN) Global Invasive Species Database, which are presented here for the first time. The classification system uses five semi-quantitative scenarios describing impacts under each mechanism to assign species to different levels of impact-ranging from Minimal to Massive-with assignment corresponding to the highest level of deleterious impact associated with any of the mechanisms. The scheme also includes categories for species that are Not Evaluated, have No Alien Population, or are Data Deficient, and a method for assigning uncertainty to all the classifications. We show how this classification system is applicable at different levels of ecological complexity and different spatial and temporal scales, and embraces existing impact metrics. In fact, the scheme is analogous to the already widely adopted and accepted Red List approach to categorising extinction risk, and so could conceivably be readily integrated with existing practices and policies in many regions.

Understanding Flood Regime Changes in Europe: A state of the art assessment

Abstract: There is growing concern that flooding is becoming more frequent and severe in Europe. A better understanding of flood regime changes and their drivers is therefore needed. The paper reviews the current knowledge on flood regime changes in European rivers that has traditionally been obtained through two alternative research approaches. The first approach is the data-based detection of changes in observed flood events. Current methods are reviewed together with their challenges and opportunities. For example, observation biases, the merging of different data sources and accounting for nonlinear drivers and responses. The second approach consists of modelled scenarios of future floods. Challenges and opportunities associated with flood change scenarios are discussed such as fully accounting for uncertainties in the modelling cascade and feedbacks. To make progress in flood change research, we suggest that a synthesis of these two approaches is needed. This can be achieved by focusing on long duration records and flood-rich and flood-poor periods rather than on short duration flood trends only, by formally attributing causes of observed flood changes, by validating scenarios against observed flood regime dynamics, and by developing low-dimensional models of flood changes and feedbacks. The paper finishes with a call for a joint European flood change research network.

Benchmarking Organic Micropollutants in Wastewater, Recycled Water and Drinking Water with In Vitro Bioassays

Abstract: Thousands of organic micropollutants and their transformation products occur in water Although often present at low concentrations, individual compounds contribute to mixture effects Cell-based bioassays that target health-relevant biological endpoints may therefore complement chemical analysis for water quality assessment The objective of this study was to evaluate cell-based bioassays for their suitability to benchmark water quality and to assess efficacy of water treatment processes The selected bioassays cover relevant steps in the toxicity pathways including induction of xenobiotic metabolism, specific and reactive modes of toxic action, activation of adaptive stress response pathways and system responses Twenty laboratories applied 103 unique in vitro bioassays to a common set of 10 water samples collected in Australia, including wastewater treatment plant effluent, two types of recycled water (reverse osmosis and ozonation/activated carbon filtration), stormwater, surface water, and drinking water Sixty-five bioassays (63%) showed positive results in at least one sample, typically in wastewater treatment plant effluent, and only five (5%) were positive in the control (ultrapure water) Each water type had a characteristic bioanalytical profile with particular groups of toxicity pathways either consistently responsive or not responsive across test systems The most responsive health-relevant endpoints were related to xenobiotic metabolism (pregnane X and aryl hydrocarbon receptors), hormone-mediated modes of action (mainly related to the estrogen, glucocorticoid, and antiandrogen activities), reactive modes of action (genotoxicity) and adaptive stress response pathway (oxidative stress response) This study has demonstrated that selected cell-based bioassays are suitable to benchmark water quality and it is recommended to use a purpose-tailored panel of bioassays for routine monitoring

OpenGeoSys: An open-source initiative for numerical simulation of thermo-hydro-mechanical/chemical (THM/C) 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.

Defining the Impact of Non-Native Species

Abstract: Non-native species cause changes in the ecosystems to which they are introduced. These changes, or some of them, are usually termed impacts; they can be manifold and potentially damaging to ecosystems and biodiversity. However, the impacts of most non-native species are poorly understood, and a synthesis of available information is being hindered because authors often do not clearly define impact. We argue that explicitly defining the impact of non-native species will promote progress toward a better understanding of the implications of changes to biodiversity and ecosystems caused by non-native species; help disentangle which aspects of scientific debates about non-native species are due to disparate definitions and which represent true scientific discord; and improve communication between scientists from different research disciplines and between scientists, managers, and policy makers. For these reasons and based on examples from the literature, we devised seven key questions that fall into 4 categories: directionality, classification and measurement, ecological or socio-economic changes, and scale. These questions should help in formulating clear and practical definitions of impact to suit specific scientific, stakeholder, or legislative contexts.

Floods and climate: emerging perspectives for flood risk assessment and management

Abstract: Flood estimation and flood management have traditionally been the domain of hydrologists, water resources engineers and statisticians, and disciplinary approaches abound. Dominant views have been shaped; one example is the catchment perspective: floods are formed and influenced by the interaction of local, catchment-specific characteristics, such as meteorology, topography and geology. These traditional views have been beneficial, but they have a narrow framing. In this paper we contrast traditional views with broader perspectives that are emerging from an improved understanding of the climatic context of floods. We come to the following conclusions: (1) extending the traditional system boundaries (local catchment, recent decades, hydrological/hydraulic processes) opens up exciting possibilities for better understanding and improved tools for flood risk assessment and management. (2) Statistical approaches in flood estimation need to be complemented by the search for the causal mechanisms and dominant processes in the atmosphere, catchment and river system that leave their fingerprints on flood characteristics. (3) Natural climate variability leads to time-varying flood characteristics, and this variation may be partially quantifiable and predictable, with the perspective of dynamic, climate-informed flood risk management. (4) Efforts are needed to fully account for factors that contribute to changes in all three risk components (hazard, exposure, vulnerability) and to better understand the interactions between society and floods. (5) Given the global scale and societal importance, we call for the organization of an international multidisciplinary collaboration and data-sharing initiative to further understand the links between climate and flooding and to advance flood research.

Individual-based models in ecology after four decades

Abstract: Individual-based models simulate populations and communities by following individuals and their properties. They have been used in ecology for more than four decades, with their use and ubiquity in ecology growing rapidly in the last two decades. Individual-based models have been used for many applied or "pragmatic" issues, such as informing the protection and management of particular populations in specific locations, but their use in addressing theoretical questions has also grown rapidly, recently helping us to understand how the sets of traits of individual organisms influence the assembly of communities and food webs. Individual-based models will play an increasingly important role in questions posed by complex ecological systems.

Conceptualizing Urban Shrinkage

Abstract: Since the second half of the 20th century, urban shrinkage has become a common pathway of transformation for many large cities across the globe. Although the appearance of shrinkage is fairly unive...

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Abstract: Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool segemehl (http://www.bioinf.uni-leipzig.de/Software/segemehl/).

Large-sample hydrology: a need to balance depth with breadth

Abstract: A holy grail of hydrology is to understand catchment processes well enough that models can provide detailed simulations across a variety of hydrologic settings at multiple spatiotemporal scales, and under changing environmental conditions. Clearly, this cannot be achieved only through intensive place-based investigation at a small number of heavily instrumented catchments, or by empirical methods that do not fully exploit our understanding of hydrology. In this opinion paper, we discuss the need to actively promote and pursue the use of a "large catchment sample" approach to modeling the rainfall–runoff process, thereby balancing depth with breadth. We examine the history of such investigations, discuss the benefits (improved process understanding resulting in robustness of prediction at ungauged locations and under change), examine some practical challenges to implementation and, finally, provide perspectives on issues that need to be taken into account as we move forward. Ultimately, our objective is to provoke further discussion and participation, and to promote a potentially important theme for the upcoming Scientific Decade of the International Association of Hydrological Sciences entitled Panta Rhei.

Surface-subsurface model intercomparison: A first set of benchmark results to diagnose integrated hydrology and feedbacks

Abstract: There are a growing number of large-scale, complex hydrologic models that are capable of simulating integrated surface and subsurface flow. Many are coupled to land-surface energy balance models, biogeochemical and ecological process models, and atmospheric models. Although they are being increasingly applied for hydrologic prediction and environmental understanding, very little formal verification and/or benchmarking of these models has been performed. Here we present the results of an intercomparison study of seven coupled surface-subsurface models based on a series of benchmark problems. All the models simultaneously solve adapted forms of the Richards and shallow water equations, based on fully 3-D or mixed (1-D vadose zone and 2-D groundwater) formulations for subsurface flow and 1-D (rill flow) or 2-D (sheet flow) conceptualizations for surface routing. A range of approaches is used for the solution of the coupled equations, including global implicit, sequential iterative, and asynchronous linking, and various strategies are used to enforce flux and pressure continuity at the surface-subsurface interface. The simulation results show good agreement for the simpler test cases, while the more complicated test cases bring out some of the differences in physical process representations and numerical solution approaches between the models. Benchmarks with more traditional runoff generating mechanisms, such as excess infiltration and saturation, demonstrate more agreement between models, while benchmarks with heterogeneity and complex water table dynamics highlight differences in model formulation. In general, all the models demonstrate the same qualitative behavior, thus building confidence in their use for hydrologic applications.

Interannual variation in land-use intensity enhances grassland multidiversity.

Abstract: Although temporal heterogeneity is a well-accepted driver of biodiversity, effects of interannual variation in land-use intensity (LUI) have not been addressed yet. Additionally, responses to land use can differ greatly among different organisms; therefore, overall effects of land-use on total local biodiversity are hardly known. To test for effects of LUI (quantified as the combined intensity of fertilization, grazing, and mowing) and interannual variation in LUI (SD in LUI across time), we introduce a unique measure of whole-ecosystem biodiversity, multidiversity. This synthesizes individual diversity measures across up to 49 taxonomic groups of plants, animals, fungi, and bacteria from 150 grasslands. Multidiversity declined with increasing LUI among grasslands, particularly for rarer species and aboveground organisms, whereas common species and belowground groups were less sensitive. However, a high level of interannual variation in LUI increased overall multidiversity at low LUI and was even more beneficial for rarer species because it slowed the rate at which the multidiversity of rare species declined with increasing LUI. In more intensively managed grasslands, the diversity of rarer species was, on average, 18% of the maximum diversity across all grasslands when LUI was static over time but increased to 31% of the maximum when LUI changed maximally over time. In addition to decreasing overall LUI, we suggest varying LUI across years as a complementary strategy to promote biodiversity conservation.

Applications of polyparameter linear free energy relationships in environmental chemistry.

Abstract: Partitioning behavior of organic chemicals has tremendous influences on their environmental distribution, reaction rates, bioaccumulation, and toxic effects. Polyparameter linear free energy relationships (PP-LFERs) have been proven to be useful to characterize the equilibrium partitioning of organic chemicals in various environmental and technical partitioning systems and predict the respective partition coefficients. Over the past decade, PP-LFER solute descriptors for numerous environmentally relevant organic chemicals and system parameters for environmentally important partitioning systems have been determined, extending substantially the applicability of the PP-LFER approaches. However, the information needed for the use of PP-LFERs including descriptors and parameters is scattered over a large number of publications. In this work, we review the state of the art of the PP-LFER approaches in environmental chemical applications. The solute descriptors and system parameters reported in the literature an...

Designing forest biodiversity experiments : general considerations illustrated by a new large experiment in subtropical China

Abstract: Summary 1. Biodiversity–ecosystem functioning (BEF) experiments address ecosystem-level consequences of species loss by comparing communities of high species richness with communities from which species have been gradually eliminated. BEF experiments originally started with microcosms in the laboratory and with grassland ecosystems. A new frontier in experimental BEF research is manipulating tree diversity in forest ecosystems, compelling researchers to think big and comprehensively. 2. We present and discuss some of the major issues to be considered in the design of BEF experiments with trees and illustrate these with a new forest biodiversity experiment established in subtropical China (Xingangshan, Jiangxi Province) in 2009/2010. Using a pool of 40 tree species, extinction scenarios were simulated with tree richness levels of 1, 2, 4, 8 and 16 species on a total of 566 plots of 25� 8 9 25� 8m each. 3. The goal of this experiment is to estimate effects of tree and shrub species richness on carbon storage and soil erosion; therefore, the experiment was established on sloped terrain. The following important design choices were made: (i) establishing many small rather than fewer larger plots, (ii) using high planting density and random mixing of species rather than lower planting density and patchwise mixing of species, (iii) establishing a map of the initial ‘ecoscape’ to characterize site heterogeneity before the onset of biodiversity effects and (iv) manipulating tree species richness not only in random but also in trait-oriented extinction scenarios. 4. Data management and analysis are particularly challenging in BEF experiments with their hierarchical designs nesting individuals within-species populations within plots within-species compositions. Statistical analysis best proceeds by partitioning these random terms into fixed-term contrasts, for example, species composition into contrasts for species richness and the presence of particular functional groups, which can then be tested against the remaining random variation among compositions. 5. We conclude that forest BEF experiments provide exciting and timely research options. They especially require careful thinking to allow multiple disciplines to measure and analyse data jointly and effectively. Achiev

BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure

Abstract: A notable increase in failure of managed European honeybee Apis mellifera L. colonies has been reported in various regions in recent years. Although the underlying causes remain unclear, it is likely that a combination of stressors act together, particularly varroa mites and other pathogens, forage availability and potentially pesticides. It is experimentally challenging to address causality at the colony scale when multiple factors interact. In silico experiments offer a fast and cost-effective way to begin to address these challenges and inform experiments. However, none of the published bee models combine colony dynamics with foraging patterns and varroa dynamics.We have developed a honeybee model, BEEHAVE, which integrates colony dynamics, population dynamics of the varroa mite, epidemiology of varroa-transmitted viruses and allows foragers in an agent-based foraging model to collect food from a representation of a spatially explicit landscape.We describe the model, which is freely available online (www.beehave-model.net). Extensive sensitivity analyses and tests illustrate the model's robustness and realism. Simulation experiments with various combinations of stressors demonstrate, in simplified landscape settings, the model's potential: predicting colony dynamics and potential losses with and without varroa mites under different foraging conditions and under pesticide application. We also show how mitigation measures can be tested.Synthesis and applications. BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics.

Classification and Modelling of Nonextractable Residue (NER) Formation of Xenobiotics in Soil – A Synthesis

Abstract: This review provides a comprehensive overview about nonextractable residue (NER) formation and attempts to classify the various types. Xenobiotic NER derived from parent pesticides (or other environmental contaminants) and primary metabolites sorbed or entrapped within the soil organic matter (Type I) or covalently bound (Type II) pose a considerably higher risk than those derived from productive biodegradation. However, biogenic nonextractable residues (bioNER) (Type III) resulting from conversion of carbon (or nitrogen) from the compounds into microbial biomass molecules do not pose any risk. Experimental approaches to clearly distinguish between the types are provided, and a model to prospectively estimate bioNER formation in soil is proposed.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Abstract: Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species Existing global databases of species’ threat status or population time series are dominated by charismatic species The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines We describe and assess a new database of more than 16 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – wwwpredictsorguk) We make site-level summary data available alongside this article The full database will be publicly available in 2015