The WISER way of organising ecological data from European rivers, lakes, transitional and coastal waters

The implementation of the Water Framework Directive has required intense research in applied aquatic ecology in Europe, and thus created challenges for data management in international research projects. In the project Waterbodies in Europe: Integrative Systems to assess Ecological status and Recovery (WISER), biological and environmental data from rivers, lakes, transitional and coastal waters in 26 European countries were collated. More than one million records of biological observations were stored in the project’s central database, representing phytoplankton, macrophytes, macroalgae, angiosperms, phytobenthos, invertebrates and fish. The central database includes new data from the WISER field campaign in lakes and transitional/coastal waters during 2009–2010 (more than 6,000 biological samples from 58 waterbodies in 14 countries). The purpose of this paper is to provide an overview of the data collated within WISER, in order to facilitate future re-use of these data by other scientists. More specifically, the objectives are to (1) describe the data management in WISER, (2) describe the structure and content of the WISER central database and (3) share experiences and give recommendations for data management in large ecological research projects.     

Uncertainty in ecological status assessments of lakes and rivers using diatoms

The EU’s Water Framework Directive requires all surface water bodies to be classified according to their ecological status. As biological communities show both spatial and temporal heterogeneity, expressions of ecological status will, inevitably, have an element of uncertainty associated with them. A consequence of this environmental heterogeneity is that there is a risk that status inferred from one or more samples is different to the true status of that water body. In order to quantify the scale of temporal uncertainty associated with benthic diatoms, replicate samples were collected from sites across the ecological status gradient in lakes and rivers in the UK. Variability (expressed as standard deviation of temporal replicate samples from a single site) could be described using a polynomial function and this was then used to calculate the risk of placing a water body in the wrong ecological status class. This risk varied depending on the distance from the class boundaries and the number of replicates. Based on these data, we recommend that ecological status is determined from a number of samples collected from a site over a period of time.     

The WISER metadatabase: the key to more than 100 ecological datasets from European rivers, lakes and coastal waters

In ecological sciences, the role of metadata (i.e. key information about a dataset) to make existing datasets visible and discoverable has become increasingly important. Within the EU-funded WISER project (Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery), we designed a metadatabase to allow scientists to find the optimal data for their analyses. An online questionnaire helped to collect metadata from the data providers and an online query tool (http://www.wiser.eu/results/meta-database/) facilitated data evaluation. The WISER metadatabase currently holds information on 114 datasets (22 river, 71 lake, 1 general freshwater and 20 coastal/transitional datasets), which also can be accessed by external scientists. We evaluate if generally used metadata standards (e.g. Darwin Core, ISO 19115, CSDGM, EML) are suitable for such specific purposes as WISER and suggest at least the linkage with standard metadata fields. Furthermore, we discuss whether the simple metadata documentation is enough for others to reuse a dataset and why there is still reluctance to publish both metadata and primary research data (i.e. time and financial constraints, misuse of data, abandoning intellectual property rights). We emphasise that metadata publication has major advantages as it makes datasets detectable by other scientists and generally makes a scientist’s work more visible.     

Remote European mountain lake ecosystems: regionalisation and ecological status

1. A survey of c. 350 remote high altitude and high latitude lakes from 12 different mountain regions across Europe was undertaken to explore ecosystem variability, climate forcing, environmental conditions and pollution threats at a scale not previously attempted.
2. Lakes were sampled for a range of contemporary and sub-fossil organisms including planktonic crustaceans, rotifers, littoral invertebrates, chironomids, diatoms and cladocerans. Survey and cartographic data were used to determine environmental characteristics at each site. Organic pollutants and trace metal concentrations were measured in the lake sediment.
3. A number of separate studies were undertaken which examined the environmental characteristics of the surveyed lakes (climate forcing and chemical composition), distribution of biota relative to local, regional and biogeographical factors and pollution threats (acidification, heavy metals and persistent organic pollutants) to these sensitive ecosystems.
4. There is a strong regional element to the way that environmental factors combine (including climate and pollution threats) and the biota responds in mountain lakes across Europe. From a management perspective it is clear that lake classification and the development of useful typologies and assessments of reference conditions should be undertaken at regional rather than pan-European scales.
5. There are some common features across lake districts related to the timing of industrialisation, but the studies carried out on metals, organic pollutants and nitrate deposition indicate that each lake district has distinct pollution threats. Climate warming already affects most of the lake districts and there are considerable uncertainties as to how this will modify conditions in remote European mountain systems.
6. The lake district concept goes beyond a geographical construct and merits further theoretical and experimental development as an ecological concept.     

Estimating the ecological status and change of riparian zones in Andalusia assessed by multi-temporal AVHHR datasets

Following the European Commission's Water Framework Directive all surface waters in EU's Member States must reach a good status by 2015. The evaluation of this status will be partly based on ecological criteria, such as the hydro-morphological quality criteria which also evaluate the structure and condition of the riparian zone. Riparian zones with undisturbed or nearly undisturbed condition are given high-ecological status. The agri-environmental measures in the EU promote an extensive use of land to protect the farmed environment and its biodiversity. Recent studies in Andalusia and elsewhere suggest that extensification leads to riparian zones with higher ecological status compared to intensively used areas. We suggest that extensification and thus better ecological status of the riparian zone can be partly approximated by the amount of vegetation permanently present on the area. For this the so-called permanent vegetation fraction was derived from a multi-temporal advanced very high-resolution radiometer (AVHRR) dataset and was used (1) to classify the ecological status of the riparian zone into two classes, favourable and unfavourable, and (2) to assess the effect of agricultural practices on these areas. The classification was validated by field observations in the Guadalquivir river basin while detailed information on farming practices helped to assess the effect of agriculture on the riparian zone. The assessment was carried out in olive land cover because erosion control in olive cultivations is the most widely implemented measure in Andalusia. Results suggest that the remotely sensed permanent vegetation fraction is a good indicator of the favourable and unfavourable ecological status of the riparian zone. Furthermore, extensification of agricultural practices expressed in terms of increasing permanent vegetation cover was shown to have positive effect on the riparian zone as opposed to areas where no measures were implemented.     

Using aquatic macrophyte community indices to define the ecological status of European lakes

Defining the overall ecological status of lakes according to the Water Framework Directive (WFD) is to be partially based on the species composition of the aquatic macrophyte community. We tested three assessment methods to define the ecological status of the macrophyte community in response to a eutrophication pressure as reflected by total phosphorus concentrations in lake water. An absolute species richness, a trophic index (TI) and a lake trophic ranking (LTR) method were tested at Europe-wide, regional and national scales as well as by alkalinity category, using data from 1,147 lakes from 12 European states. Total phosphorus data were used to represent the trophic status of individual samples and were plotted against the calculated TI and LTR values. Additionally, the LTR method was tested in some individual lakes with a relatively long time series of monitoring data. The TI correlated well with total P in the Northern European lake types, whereas the relationship in the Central European lake types was less clear. The relationship between total P and light extinction is often very good in the Northern European lake types compared to the Central European lake types. This can be one of the reasons for a better agreement between the indices and eutrophication pressure in the Northern European lake types. The response of individual lakes to changes in the abiotic environment was sometimes represented incorrectly by the indices used, which is a cause of concern for the use of single indices in status assessments in practice.     

Continental and ecological variance components of European and North American Atlantic salmon (Salmo salar) phenotypes

Juvenile Atlantic salmon ( Salmo salar ) meristic and morphometric characteristics were examined from 47 European and North American river populations. The relative importance of continental origin, stream gradient, overall temperature regime, and seasonal temperatures in explaining the phenotypic variation of these populations was evaluated using multi-way ANOVA. Ecological factors explained a greater percentage of the variance than continental origin for both meristic and morphometric characters. Stream gradient was the most important factor explaining morphometric variation and April-May mean temperature was the most important factor explaining meristic variation.     

An approach to evaluating ecological status of populations in forest-nesting birds (Passeriformes and Piciformes)

A 13-year study of forest-nesting birds (orders Passeriformes and Piciformes) has been conducted at five constant census areas in European Russia, Caucasus, and the mountains of Southern Siberia. The nesting individuals are mapped at each census area for two or more nesting periods. The nesting densities for each species are estimated. Raster maps of spatial allocation (MSA) at the scale of the raster grid of 50 × 50 m are obtained for each species. The degree of spatial conservatism (DSC) for each local population is inferred from the pairwise comparisons of the specific MSAs obtained at the same area in different years with the use of the Gamma rank correlation method. This index characterizes the connection of population with the habitat. Based on 5-year observations at that particular census area, the areas of habitats are estimated (Y) and mean DSC values (X) are obtained for all 18 model species. Using the regression model (Y = 117–103.5X; R = 0.84; p < 0.01), it is demonstrated that, under conditions of almost complete saturation, when a population uses almost the entire area of available habitats and maximum carrying capacity of habitat is almost achieved, the total area occupied by the individual nesting home ranges of the particular species is in an inverse linear relationship with the DSC estimates. Based on this model, it is possible to calculate the maximum carrying capacity of habitat for each species from its DSC value. Maximum nesting density for each species at a particular census area is calculated based on its DSC values and mean size of its nesting home range. The ratio between observed and maximum nesting densities allows estimating the degree of saturation of carrying capacity of habitat and the population status of a particular species under different environmental conditions.     

Evolution of MHC class I genes in the European badger (Meles meles)

The major histocompatibility complex (MHC) plays a central role in the adaptive immune system and provides a good model with which to understand the evolutionary processes underlying functional genes. Trans-species polymorphism and orthology are both commonly found in MHC genes; however, mammalian MHC class I genes tend to cluster by species. Concerted evolution has the potential to homogenize different loci, whereas birth-and-death evolution can lead to the loss of orthologs; both processes result in monophyletic groups within species. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. We present the first study of MHC class I genes in a species from the superfamily Musteloidea. The European badger (Meles meles) exhibits moderate variation in MHC class I sequences when compared to other carnivores. We identified seven putatively functional sequences and nine pseudogenes from genomic (gDNA) and complementary (cDNA) DNA, signifying at least two functional class I loci. We found evidence for separate evolutionary histories of the α1 and α2/α3 domains. In the α1 domain, several sequences from different species were more closely related to each other than to sequences from the same species, resembling orthology or trans-species polymorphism. Balancing selection and probable recombination maintain genetic diversity in the α1 domain, evidenced by the detection of positive selection and a recombination event. By comparison, two recombination breakpoints indicate that the α2/α3 domains have most likely undergone concerted evolution, where recombination has homogenized the α2/α3 domains between genes, leading to species-specific clusters of sequences. Our findings highlight the importance of analyzing MHC domains separately.     

Ecological threshold responses in European lakes and their applicability for the Water Framework Directive (WFD) implementation: synthesis of lakes results from the REBECCA project

The objective of this synthesis is to present the key messages and draw the main conclusions from the work on lakes in the REBECCA project, pointing out their links to theoretical ecology and their applicability for the WFD implementation. Type-specific results were obtained from analyses of large pan-European datasets for phytoplankton, macrophytes, macroinvertebrates and fish, and indicators and relationships showing the impact of eutrophication or acidification on these biological elements were constructed. The thresholds identified in many of the response curves are well suited for setting ecological status class boundaries and can be applied in the intercalibration of classification systems. Good indicators for phytoplankton (chrysophytes, cyanobacteria) and macrophytes (isoetids and charaphytes) responses to eutrophication were identified, and the level of eutrophication pressure needed to reach the thresholds for these indicators was quantified. Several existing metrics developed for macrophytes had low comparability and need further harmonisation to be useful for intercalibration of classification systems. For macroinvertebrates, a number of metrics developed for rivers turned out to be less useful to describe lake responses to eutrophication and acidification, whereas other species based indicators were more promising. All the biological elements showed different responses in different lake types according to alkalinity and humic substances, and also partly according to depth. Better harmonisation of monitoring methods is needed to achieve better precision in the dose–response curves. Future research should include impacts of hydromorphological pressures and climate change, as well as predictions of timelags involved in responses to reduction of pressures.     

An ecological classification of Central European macromoths: habitat associations and conservation status returned from life history attributes

To be used as a predictive conservation tool, classification of animal habitats should rely on actual resource requirements of individual species. Shreeve et al. (J Insect Conserv 5:145–161, 2001) produced a resource-based habitat classification for British butterflies, obtaining habitat association groups, whose constituent species differed in their distribution extent, distribution change and vulnerability in Britain. To test the utility of this approach for a group with a less-known biology, we produced a resource-based classification of habitats of Central European macromoths. We worked with macrolepidopteran moth families, except for the megadiverse Geometridae and Noctuidae. We produced a matrix of 178 life history attributes describing resource use by 164 species, subjected the matrix to ordination analysis, and compared the resulting moths groupings with external ecological information. Five habitat association groups were distinguished: I—close canopy moths, II—open canopy moths, III—grasslands moths, IV—herb-feeding hawk moths, and V—lichen feeders. The classification sustained deleting attributes related to host plants taxonomy. Groups I–III sustained control for taxonomic positions of the moths, whereas IV and V did not. Members of the groups differed in the representation of externally obtained habitat associations, biogeography elements, threat status, and range size. Endangered species were over-represented in groups II and III and underrepresented in group I, in agreement with recent land cover changes across the continent. Species resources can be used to reconstruct their habitat needs, and it is possible to scale up from life histories through habitat use to range structures.     

Evolution and current status of ecological phytochemistry

Phytochemical studies have experienced a great deal of change during the last century, not only regarding the number of compounds described, but also in the concept of phytochemistry itself. This change has mainly been related to two key points: the methodologies used in phytochemical studies and the questions regarding 'why secondary metabolites appeared in plants and in other living organisms?' and 'what is their role?'. This transformation in the field has led to new questions concerning such different subjects as evolution, paleobotany, biochemistry, plant physiology and ethnography. However, the main issue is to clarify the role that secondary metabolites play in the plant (and other organisms) and whether the resources invested in their production (C and N allocation, genes encoding their biogenetic pathways, specific enzymes, energy-rich molecules such as ATP and NADPH) have or lack a reasonable reward in terms of advantages for survival. Consequently, in this review the main emphasis will be placed on two subjects related to the evolution of phytochemical studies. The first aim is to describe briefly the influence that the development of the methodologies needed for compound isolation and structure elucidation have had on the field of phytochemistry. The second area to be covered concerns the new theories addressing the role of secondary metabolites from an ecological point of view: co-evolution of plants and their potential enemies (phytophagous insects, microbes, herbivores and other plants), chemical plant defence, adaptative strategies of phytophagues to plant toxins (among them sequestration will be briefly mentioned), and models and theories for carbon and nitrogen allocation. Some final remarks are made to summarize our opinion about the immediate future of phytochemical ecology and phytochemical studies.     

Plankton and ecological status of watercourses in territories of various types (an example of Voronezh oblast)

The differences in the bacterio- and zooplankton communities of small- and medium-sized watercourses classified on the specifics of natural processes and consequences of anthropogenic activity in the territory of Voronezh oblast are described. Soil erosion, along with contamination of surface waters by industrial and municipal sewage and pesticides, has the greatest impact. The water current velocity, contamination by organic matter and nutrients, and the extent of macrophyte overgrowth affect the quantitative and qualitative composition of plankton in local parts of the studied watercourses.     

Estimating Esox lucius (Esocidae, Esociformes) density and population structure in a large European alluvial river: the Allier (France)

We developed a sampling protocol for pike (Esox lucius L., 1758) in large alluvial rivers in order to estimate adult population density and structure. This species is known as an indicator of lowland river biotic integrity in Europe evidencing the interest to determine population densities to a reliable degree of accuracy. A two occasion mark-recapture experiment based on a combination of net fishing and boat electro-fishing was specifically designed for monitoring of backwaters and channel sectors during the annual high flow level of an alluvial river, the Allier (France). Estimated densities calculated by using Chapman-Petersen and Loglinear models were weak, ranging from 0.68 (±0.16) fish.ha^?1 to 0.71 (±0.20) fish.ha^?1. However, when the densities are divided by the area of potential riverine habitats, pike abundance was calculated as being 15.3 (±3.7) fish.ha^?1 to 15.9 (±3.8) fish.ha^?1. Pike growth was high and 8 to 9 year-old females were captured. Age and sex distribution emerged as unbalanced, highlighting the precarious status of pike in the studied stretch of the river due to very limited recruitment. Pike were mainly captured in parapotamic side arms which underlines the importance of lateral habitats in semi regulated large alluvial rivers with wide riffle-pool-run sequences dominating geomorphological units.     

Estimating European admixture in African Americans by using microsatellites and a microsatellite haplotype (CD4/Alu)

We have analyzed 10 unlinked microsatellites and a linked Alu deletion polymorphism at the CD4 locus in an African American population sample from Chicago (USA). Heterozygosity estimates at the microsatellite loci range from 0.727±0.025 (D3S1358) to 0.873±0.017 (D18S51), with an average of 0.794±0.016. These values are comparable to or higher than those reported for Europeans, with only one exception (D3S1358). The CD4/Alu haplotypic diversity (0.887±0.012) is comparable to diversity levels observed in sub-Saharan African populations and is higher than the diversity levels reported in European populations. No consistent pattern of within, between, or multi-locus deviations from Hardy-Weinberg expectations is observed, suggesting a low sub-heterogeneity within the sampled population. We have applied a maximum likelihood method and estimated the proportion of European admixture to the African American gene pool to be 0.26±0.02. The narrow confidence interval indicates that allele frequency data from multiple microsatellite loci, whether analyzed independently or as haplotypes, are particularly useful for estimating genetic admixture. Received: 9 September 1998 / Accepted: 3 November 1998     

Low major histocompatibility complex class I (MHC I) variation in the European bison (Bison bonasus)

Variation in the major histocompatibility complex (MHC) class I of the European bison was characterized in a sample of 99 individuals using both classical cloning/Sanger sequencing and 454 pyrosequencing. Three common (frequencies: 0.348, 0.328, and 0.283) haplotypes contain 1-3 classical class I loci. A variable and difficult to estimate precisely number of nonclassical transcribed loci, pseudogenes, and/or gene fragments were also found. The presence of additional 2 rare haplotypes (frequency of 0.020 each), observed only in heterozygotes, was inferred. The overall organization of MHC I appears similar to the cattle system, but genetic variation is much lower with only 7 classical class I alleles, approximately one-tenth of the number known in cattle and a quarter known in the American bison. An extensive transspecific polymorphism was found. MHC I is in a strong linkage disequilibrium with previously studied MHC II DRB3 gene. The most likely explanation for the low variation is a drastic bottleneck at the beginning of the 20th century. Genotype frequencies conformed to Hardy-Weinberg expectations, and no signatures of selection in contemporary populations but strong signatures of historical positive selection in sequences of classical alleles were found. A quick and reliable method of MHC I genotyping was developed.     

Macrobenthic invertebrate energy densities and ecological status in freshwater watercourses (Friuli Venezia-Giulia,Northeast Italy)

The present study provides energy density (ED) data and models for four macrobenthic invertebrate genera inhabiting freshwater lotic environments (Baetis, Hydropsyche, Rhyacophila, and Onychogomphus). Samples were collected in the hydrological freshwater network of the Region Friuli Venezia Giulia within different watercourse types (creeks, streams, rivers channels, and ditches), and energy density was directly measured using an adiabatic bomb calorimeter. Measured ED expressed in Joule g^?1 wet weight was strongly and positively correlated with percentage of dry weight (DW%) for all genera investigated (r²?>?0.9504), allowing to obtain genus-specific predictive models based on the relationship between ED and DW%. Models were validated and showed good predictive power, as 90th percentile of observed percentage errors ranged between 4.23% and 5.18% while medians ranged between 1.32% and 2.83%. ANCOVA disclosed significant differences between the models, as those for Rhyacophila and Onychogomphus differed significantly from the others. The empirical models were used to build a dataset of estimated energy density, to assess the relationship between energy density and ecological status of the monitored riverine systems, assessed in compliance with European and Italian law by the application of four different ecological indices (ICMi, RQE_IBMR, STAR_ICMi, and LIMeco). Information regarding ED levels for freshwater macrobenthic invertebrates is still neglected in biomonitoring programs, but it could be useful to interpret some ecological situations in the context of ecological status assessment, especially in relation to the trophic condition of the investigated riverine systems.