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.     

A comparative review of recovery processes in rivers, lakes, estuarine and coastal waters

The European Water Framework Directive aims to improve ecological status within river basins. This requires knowledge of responses of aquatic assemblages to recovery processes that occur after measures have been taken to reduce major stressors. A systematic literature review comparatively assesses recovery measures across the four major water categories. The main drivers of degradation stem primarily from human population growth and increases in land use and water use changes. These drivers and pressures are the same in all four water categories: rivers, lakes, transitional and coastal waters. Few studies provide evidence of how ecological knowledge might enhance restoration success. Other major bottlenecks are the lack of data, effects mostly occur only in short-term and at local scale, the organism group(s) selected to assess recovery does not always provide the most appropriate response, the time lags of recovery are highly variable, and most restoration projects incorporate restoration of abiotic conditions and do not include abiotic extremes and biological processes. Restoration ecology is just emerging as a field in aquatic ecology and is a site, time and organism group-specific activity. It is therefore difficult to generalise. Despite the many studies only few provide evidence of how ecological knowledge might enhance restoration success.     

Transitional and coastal waters ecological status assessment: advances and challenges resulting from implementing the European Water Framework Directive

The derivation, performance, sensitivity and inherent uncertainty of ecological quality indicators have become major topics in developing tools for the management of marine, transitional and coastal waters. In reviewing the advances in these waters, related to an ecological status assessment, we show the future challenges to be addressed within the European Water Framework Directive (WFD). Using new analyses carried out under the research project ‘Water Bodies in Europe: Integrative Systems to Assess Ecological status and Recovery’, we provide a complete set of assessments for the biological quality elements (BQEs) (phytoplankton, macroalgae-seagrasses, macroinvertebrates and fish) to be assessed, as well as the validation of existing indicators and multimetric indices and, in some cases, the development of new assessment indices. We show that these indices respond differently to different human pressures and they each have challenges in defining reference conditions against which future changes are judged. In investigating good ecological potential, as the response to heavily modified water bodies, we show that there are flaws in the Directive, not least in its definitions. Our analyses have also focussed on uncertainty in using the indices and we emphasise the problems of defining ecological class boundaries based on indices which themselves may be combined indices (multimetrics). The analysis shows that some of those multimetrics are redundant and/or are inter-correlated and thus may reduce the sensitivity in defining ecological class boundaries. If this is related to the drivers-pressures-state change-impacts-response approach then there are lessons for management measures aimed at achieving good ecological status and even the potential for legal challenges to decisions based on uncertain indices under the WFD. Hence, we conclude the continued need for advances in assessing pressures and gradients, and defining reference conditions for state change, index development, impact assessment and the validation of indices for each BQE.     

GEM: a generic ecological model for estuaries and coastal waters

The set-up, application and validation of a generic ecological model (GEM) for estuaries and coastal waters is presented. This model is a comprehensive ecological model of the bottom of the foodweb, consisting of a set of modules, representing specific water quality processes and primary production that can be combined with any transport model to create a dedicated model for a specific ecosystem. GEM links different physical, chemical and ecological model components into one generic and flexible modelling tool that allows for variable sized, curvilinear grids to accomodate both the requirements for local accuracy while maintaining a relatively short model run-time. The GEM model describes the behaviour of nutrients, organic matter and primary producers in estuaries and coastal waters, incorporating dynamic process modules for dissolved oxygen, nutrients and phytoplankton. GEM integrates the best aspects of existing Dutch estuarine models that were mostly dedicated to only one type of ecosystem, geographic area or subset of processes. Particular strengths of GEM include its generic applicability and the integration and interaction of biological, chemical and physical processes into one predictive tool. The model offers flexibility in choosing which processes to include, and the ability to integrate results from different processes modelled simultaneously with different temporal resolutions. The generic applicability of the model is illustrated using a number of representative examples from case studies in which the GEM model was successfully applied. Validation of these examples was carried out using the ‘cost function’ to compare model results with field observations. The validation results demonstrated consistent accuracy of the GEM model for various key parameters in both spatial dimensions (horizontally and vertically) as well as temporal dimensions (seasonally and across years) for a variety of water systems without the need for major reparameterisation.

Species of Anguilla as indicators of mercury in the coastal rivers and lakes of Victoria, Australia

Mercury concentrations in the axial muscle tissue of most (243) of the 254 Anguilla australis and most (20) of the 27 A. reinhardtii collected from 30 sites in coastal rivers and lakes in Victoria, Australia, during 1975–78 were well below the Australian statutory health limit (0.5 μg g⁻¹ wet weight). For A. australis the mean mercury concentration was 0.17 μg g⁻¹ (±0.16 s.d. , range 0.01–1.60 μg g⁻¹); for A. reinhardtii the values were 0.37 ± 0.23 μg g⁻¹ (range 0.12–1.10 μg g⁻¹). Statistical analyses showed that variation in mercury concentration due to total length accounted for only 13% of the total variation in A. australis and 2% in A. reinhardtii whereas locality accounted for 54 and 68%, respectively. Both species are thus considered suitable as indicators of mercury pollution.     

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.     

The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches

Most of the present EU Water Framework Directive (WFD) compliant fish-based assessment methods of European rivers are multi-metric indices computed from traditional electrofishing (TEF) samples, but this method has known shortcomings, especially in large rivers. The probability of detecting rare species remains limited, which can alter the sensitivity of the indices. In recent years, environmental (e)DNA metabarcoding techniques have progressed sufficiently to allow applications in various ecological domains as well as eDNA-based ecological assessment methods. A review of the 25 current WFD-compliant methods for river fish shows that 81% of the metrics used in these methods are expressed in richness or relative abundance and thus compatible with eDNA samples. However, more than half of the member states' methods include at least one metric related to age or size structure and would have to adapt their current fish index if reliant solely on eDNA-derived information. Most trait-based metrics expressed in richness are higher when computed from eDNA than when computed from TEF samples. Comparable values are obtained only when the TEF sampling effort increases. Depending on the species trait considered, most trait-based metrics expressed in relative abundance are significantly higher for eDNA than for TEF samples or vice versa due to over-estimation of sub-surface species or under-estimation of benthic and rare species by TEF sampling, respectively. An existing predictive fish index, adapted to make it compatible with eDNA data, delivers an ecological assessment comparable with the current approved method for 22 of the 25 sites tested. Its associated uncertainty is lower than that of current fish indices. Recommendations for the development of future fish eDNA-based indices and the associated eDNA water sampling strategy are discussed.     

The CARLIT method for the assessment of the ecological quality of European Mediterranean waters: Relevance,robustness and possible improvements

The application of the European Union (EU) Water Framework Directive (WFD) requires the assessment of the ecological status (ES) of coastal waters in order to detect environmental changes and implement management plans to prevent their further deterioration. The ES of a water body (WB) has to be assessed on the basis of the status of several biological indicators, referred to as biological quality elements (BQE), such as phytoplankton, macroalgae, seagrasses, macroinvertebrates and fish. We present the most extensive assessment ever undertaken of the ES of Mediterranean waters, by means of the CARLIT index, the most widely used index for the Mediterranean Sea. This index is based on the Ecological Quality Ratio (EQR) between a measured value of Ecological Quality (EQ) and a value corresponding to a reference site. This assessment is based on an extensive field study, covering the whole of the Mediterranean French coasts (including Corsica), 40 WBs and ∼2 970 kilometres of shore (at a 1/2 500 scale). The original Ballesteros CARLIT method is compared to the Nikolić modified method, and we have undertaken the challenge of developing an alternative new simplified CARLIT method. This simplified method, which requires less expert judgement, is easier to implement by local authorities, and provides results similar overall to those of the original method. Previous attempts, if any, to correlate EQRs with anthropogenic stressors (through pressure indices) were mainly based upon land uses or on comprehensive lists of stressors, some spatially very sporadic, temporally highly variable, non-representative of the WB and with the impact poorly established on species and communities. To date, the LUSI (Land Uses Simplified Index) and the MA-LUSI-WB have been the most widely used pressure indices. Here, we propose a new pressure index (HAPI) taking into consideration the possible shortcomings of previous indices. It takes into account the actual pressures at community levels considered by the CARLIT method. It accounts well for the EQR values of the study area, as evidenced by the high correlation coefficient between EQRs and HAPI, better than that of the other pressure indices. The present study provides a comprehensive view of the ES of the French Mediterranean coasts. Surprisingly, the picture is far less cause for concern than expected, although this could result from an artefact due to the focus on superficial waters and habitats inherent to the CARLIT method. Where two successive assessments were performed (23 WBs, 2007–2010 vs 2012–2015), the results were similar, which stresses the robustness of the method and/or the relative stability over time of the overall ES of the WBs, and suggests that the successive assessments could be carried out at low frequency.     

The icthyofauna of the Mhlathuze coastal lakes: some preliminary results

The fish faunas of the four Mhlathuze coastal lakes and the lower river comprise a diverse assortment of over fifty marine, estuarine and freshwater species. Three freshwater species are endemic to KwaZulu-Natal and nine estuarine species are endemic to southern Africa. Five species are of conservation significance. Species numbers in Lakes Mzingazi and Cubhu are similar historically and both lakes served as secondary nursery habitats for estuarine associated fishes. This role has been impacted by the construction of weirs at their outlets which prevent successful recruitment of estuarine species, especially during drought years when lake water levels are low. The fish faunas of Lakes Nsezi and Mangeza are depauperate and lack marine or estuarine components. In order that these systems fulfil their potential function as secondary nursery habitats to many estuarine fish species, minimum lake water levels must be set to ensure sufficient outflows at proposed fish ladders during critical spawning and migration times.     

A new transparent handy sampler for collecting water from lakes,rivers and seas

A handy sampler for collecting water from lakes, rivers and seas is described. The sampler consists of an exchangeable sample tube and a new sample-holding system. The system comprises an upper disk, a lower disk, a pair of arms with a guide pin and a semicircular arm guide with a groove. The water sample collected into the acryl tube is held without flow by a tight tube-closing system. Contamination of the sample by chemical and biological materials from the sample tube is minimized by exchanging the tube with a clean one at each sampling station. This new sampler is light, simple and useful for sampling of water from surface to bottom.     

上升流和水团对浙江中部近海浮游动物生态类群分布的影响

依据2010年4月、7月和11月对浙江中部近海上升流海域进行的海洋调查资料,运用定量、定性方法,探讨了上升流对该海域浮游动物生态类群分布的影响.结果表明:3个季节共鉴定浮游动物64种,桡足类占主要优势,包括5个生态类群,分别是暖温带近海种、暖温带外海种、亚热带近海种、亚热带外海种和热带大洋种.在种类数组成上,春季以暖温带近海种为主,夏季则是亚热带近海种和亚热带外海种居多,秋季也是亚热带种居多,其中夏季暖温带种种类数要高于春季和秋季,这一现象与同时期东黄海沿海有所不同,主要是由于上升流将一些在海洋底部度夏的暖温种带至海洋表面造成的.此外,3个季节生态类群都是以近海种为主,表明沿岸流是影响这一海域的最主要的水团.在丰度组成上,4月暖温带近海种占总丰度的98.79％,7月暖温带近海种也是组成丰度的重要部分,10月则是亚热带近海种丰度最高.丰度组成所反映的规律与种类数组成规律一致.上升流的存在导致夏季近海暖温带种大量出现,是影响这一海域浮游动物生态类群组成的重要因素;受长江径流和椒江径流的影响,近海种成为主要生态类群,是这一海域浮游动物的一个重要的生态特征.     

www.freshwaterecology.info – An online tool that unifies,standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences

Species’ ecological preferences are progressively important for understanding distribution patterns, for conserving biodiversity or for assessing and evaluating the status of freshwater ecosystems. Comprehensive databases compiling species traits are already established in the terrestrial realm, but widely missing in freshwater science. We established a database for European taxa of five aquatic organism groups by compiling information on taxonomy, ecology and distribution based on extensive literature surveys, which were performed by experts for the targeted organism groups. The database includes fishes (654 taxa/21 ecological preferences), macro-invertebrates (8586/40), macrophytes (1083/5), diatoms (8868/36) and phytoplankton (1976/4). It is available online with various options and tools for finding information and has currently over 800 users. The reviewed literature as well as examples given in this paper, highlight the importance of the general availability of knowledge on ecological preferences for various aspects in ecological assessment. Freshwaterecology.info is considered a service for basic research, applied scientists, water managers or other stakeholders. It serves as base for bioassessment and monitoring.     

Cryptic diversity within the harmful dinoflagellate Akashiwo sanguinea in coastal Chinese waters is related to differentiated ecological niches

Blooms of the harmful dinoflagellate Akashiwo sanguinea are responsible for the mass mortality of fish and invertebrates in coastal waters. This cosmopolitan species includes several genetically differentiated clades. Four clonal cultures were established by isolating single cells from Xiamen Harbour (the East China Sea) for morphological and genetic analyses. The cultures displayed identical morphology but were genetically different, thus revealing presence of cryptic diversity in the study area. New details of the apical structure complex of Akashiwo sanguinea were also found. To investigate whether the observed cryptic diversity was related to environmental differentiation, 634 cells were obtained from seasonal water samples collected from 2008 to 2012. These cells were sequenced by single-cell PCR. For comparison with Chinese material, additional large subunit ribosomal DNA sequences were obtained for three established strains from Malaysian and French waters. To examine potential ecological differentiation of the distinct genotypes, growth responses of the studied strains were tested under laboratory conditions at temperatures of 12 °C to 33 °C. These experiments showed four distinct ribotypes of A. sanguinea globally, with the ribotypes A and B co-occuring in Xiamen Harbour. Ribotype A of A. sanguinea was present year-round in Xiamen Harbour, but it only bloomed in the winter and spring, thus corresponding to the winter type. In contrast, A. sanguinea ribotype B bloomed only in the summer, corresponding to the summer type. This differentiation supports the temperature optimum conditions that were established for these two ribotypes in the laboratory. Ribotype A grew better at lower temperatures compared to ribotype B which preferred higher temperatures. These findings support the idea that various ribotypes of A. sanguinea correspond to distinct ecotypes and allopatric speciation occurred in different climatic regions followed by dispersal.     

Description of diatoms from the Southwest to West Greenland coastal and open marine waters

Detailed studies on sub-Arctic and Arctic marine diatom assemblages contribute to the understanding of spatial distribution patterns and their physical drivers. In this study, diatom species were analyzed from water samples collected with a Niskin bottle rosette combined with a CTD along the West Greenland coast (63°58′N–71°08′N and 50°49′W–59°06′W) during summer 2007. Diatom community was represented mainly by three genera Thalassiosira, Fragilariopsis, and Chaetoceros and linked to observed hydrographic and environmental conditions. Thalassiosira spp. were common in coastal waters (particularly Godthåbsfjord) and linked to increased surface water temperature, typical of summer water stratification in West Greenland. Fragilariopsis spp., along with other dominant species associated with higher geographic latitudes, dominated in Arctic fjords (Uummannaq Fjord-Qaumarujuk Fjord). These species generally characterized coastal waters influenced by melting sea ice and/or glacial ice. Chaetoceros spp. were linked to more saline open marine waters, particularly in the Davis Strait south of 70°N, probably corresponding to weaker water stratification and the influence of the West Greenland Current. The present paper provides new knowledge on diatom assemblages along a south–north climate gradient in West Greenland, which is necessary in order to understand how observed ocean-climate changes influence Arctic marine ecosystems. This study provides a reference for palaeoenvironmental reconstructions using diatom microfossils deposited in the West Greenland marine sediments.     

Selective recruitment and resurgence of tropical river phytoplankton: evidence from the Nile system of lakes,rivers, reservoirs and ponds

The recruitment of major species-components of phytoplankton is considered with reference to diverse water-bodies—rivers, headwater lakes, reservoirs and lateral waters—of the Nile system. The importance of massive ‘inocula’, carried in flowing and inter-communicating waters, is emphasised; the most direct evidence is from quantitative population dynamics in longitudinally sampled river-reservoir systems. Other indications of extraneous derivation are taken from geographical distribution and apparent invasions of newly recorded species. For five reservoirs, there are records of initial colonisation (in two) and of the annual colonisation of seasonally impounded water (in three). There was a selective recruitment of reservoir/river major species over 1 year to newly created ponds, from a massive inoculum of added river water, studied in relation to the novel and changing physical and chemical environment. Periods of predominant decomposition were there linked with the abundance of other species not observed in the original river water. Reservoir species can be carried to extend abundance far downstream, as observed in the Blue Nile where normal succession was altered by a new reservoir upstream; also in Egypt below the former Aswan Reservoir and the later High Dam Lake. The different and distinctive compositions of the phytoplankton communities in headwater lakes reflect large environmental differences that, with high downstream turbulence, probably make them insignificant for recruitment of most species typical of the downstream waters. There is evidence from hydrology and floristic similarities for recruitment from lateral standing waters along the river, especially those of one major swamp area.     

A new lophiid anglerfish,Lophiodes fimbriatus from the coastal waters of Japan

A new species of lophiid anglerfish,Lophiodes fimbriatus, Is described. The holotype was captured from Wakayama and the paratype from Kuba-jima, Okinawa Prefecture, The present species is distinguished from its congeners by the combinations of the following characters: slender and branched tendrils present on both dorsal and ventral surfaces of the body, lightly pigmented illicium, simple vestigial esca, and paired tendrils on the third dorsal spine.     

The S100B protein in biological fluids: more than a lifelong biomarker of brain distress

S100B is a calcium-binding protein concentrated in glial cells, although it has also been detected in definite extra-neural cell types. Its biological role is still debated. When secreted, S100B is believed to have paracrine/autocrine trophic effects at physiological concentrations, but toxic effects at higher concentrations. Elevated S100B levels in biological fluids (CSF, blood, urine, saliva, amniotic fluid) are thus regarded as a biomarker of pathological conditions, including perinatal brain distress, acute brain injury, brain tumors, neuroinflammatory/neurodegenerative disorders, psychiatric disorders. In the majority of these conditions, high S100B levels offer an indicator of cell damage when standard diagnostic procedures are still silent. The key question remains as to whether S100B is merely leaked from injured cells or is released in concomitance with both physiological and pathological conditions, participating at high concentrations in the events leading to cell injury. In this respect, S100B levels in biological fluids have been shown to increase in physiological conditions characterized by stressful physical and mental activity, suggesting that it may be physiologically regulated and raised during conditions of stress, with a putatively active role. This possibility makes this protein a candidate not only for a biomarker but also for a potential therapeutic target.     

Environmental chemistry of rivers and lakes, part v: a comparative study of the chemical and physicochemical characteristics of organic carbon dissolved in river and lake waters

To determine the chemical and physicochemical characteristics of dissolved organic carbon in the Ado River and the Yasu River, the main rivers flowing into Lake Biwa, the adsorption behavior onto hydrous iron oxide (HIO) and the reactivity to KMnO₄ oxidant were investigated in parallel with measurement of the distribution profiles of dissolved organic carbon (DOC) along the rivers. In one year of observation at the mouths of the two rivers, DOC concentrations were found to vary in the Ado over the range 0.28–1.21 mg C l⁻¹ and in the Yasu over the range 1.01–2.68 mg C l⁻¹. Act-DOC, one of the fractions separated from the total DOC by its adsorption-active character onto HIO at pH 4, was thought primarily to control the variation of total DOC, as in Lake Biwa. The int-DOC, another fraction separated by its adsorption-inert or -inactive character onto HIO, remained at almost a steady value around 0.18 ± 0.07 mg C l⁻¹ in the Ado, which was lower than that (0.35 ± 0.05 mg C l⁻¹) in Lake Biwa. The act-DOC in river waters was reactive to KMnO₄ oxidant, showing a linear relation with the amount of permanganate consumed for the reaction (chemical oxygen demand: COD). In river waters, the relation can be approximated by a straight line expressed as COD (mg O₂ l⁻¹) = 0.64 × act-DOC (mg C l⁻¹) − 0.02. In contrast, in the lake water the relation was COD (mg O₂ l⁻¹) = 0.97 × act-DOC (mg C l⁻¹) − 0.50. Received: March 3, 1999 / Accepted: December 2, 1999