REBECCA databases: experiences from compilation and analyses of monitoring data from 5,000 lakes in 20 European countries

Chemical and biological data from more than 5,000 lakes in 20 European countries have been compiled into databases within the EU project REBECCA. The project’s purpose was to provide scientific support for implementation of the EU Water Framework Directive (WFD). The databases contain the biological elements phytoplankton, macrophytes, macroinvertebrates and fish, together with relevant chemistry data and station information. The common database strategy has enabled project partners to perform analyses of chemical–biological relationships and to describe reference conditions for large geographic regions in Europe. This strategy has obvious benefits compared with single-country analyses: results will be more representative for larger European regions, and the statistical power and precision will be larger. The high number of samples within some regions has also enabled analysis of type-specific relationships for several lake types. These results are essential for the intercalibration of ecological assessment systems for lakes, as required by the WFD. However, the common database approach has also involved costs and limitations. The data process has been resource-demanding, and the requirements for a flexible database structure have made it less user-friendly for project partners. Moreover, there are considerable heterogeneities among datasets from different countries regarding sampling methods and taxonomic precision; this may reduce comparability of the data and increase the uncertainty of the results. This article gives an overview of the contents and functions of the REBECCA Lakes databases, and of our experiences from constructing and using the databases. We conclude with recommendations for compilation of environmental data for future international projects.     

Defining types of running waters in Germany using benthic algae: A prerequisite for monitoring according to the Water Framework Directive

The Water Framework Directive of the European Union (EU-WFD) requires the definition of different types of running water which are of relevance when assessing their ecological status. In Germany, 25 close to natural, pristine sampling sites in the Central Highlands and the Central Plains were selected which were considered to represent best conditions available at present. The abundance of benthic algae other than diatoms or Charales was investigated. Sampling was repeated in two different seasons (summer and winter). In total, 107 taxa from 12 classes could be found, of which 70 taxa from eight classes were used for statistical analysis. Multivariate statistical analysis showed that the distribution of the algae was influenced mainly by the acid capacity and hardness of water. Based on the species composition and the abundances of the species, three groups of sampling sites could be distinguished leading to the definition of three types of running water: a. siliceous sites in the Central Highlands, b. organic sites (influenced by peat) in the Central Plains, c. calcareous sites in the Central Highlands and the Central Plains. These types show a specific species composition under reference conditions and differ significantly in terms of species richness and diversity. The results presented here are fundamental for the development of a routine for monitoring the ecological status according to EU-WFD.     

The markup is the model: reasoning about systems biology models in the Semantic Web era

Metabolic control analysis, co-invented by Reinhart Heinrich, is a formalism for the analysis of biochemical networks, and is a highly important intellectual forerunner of modern systems biology. Exchanging ideas and exchanging models are part of the international activities of science and scientists, and the Systems Biology Markup Language (SBML) allows one to perform the latter with great facility. Encoding such models in SBML allows their distributed analysis using loosely coupled workflows, and with the advent of the Internet the various software modules that one might use to analyze biochemical models can reside on entirely different computers and even on different continents. Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization.     

用离散量预测蛋白质的结构型

基于蛋白质的结构类型决定了它的二级结构序列的概念,用二级结构序列参数Nα,Nβ,Nβaβ,N(βαβ）构成离散源,并计算离散量D（Xα）,D（Xβ）,D（Xα＋β）,利用离散增量预测蛋白质的结构类型,它是由这个蛋白质的离散量D（Xn）与四个标准离散D（Xα）,D（Xβ）,D（Xα／β）,D（Xα＋β）之间离散增量的最小值所决定的,预测结果表明,准确率分别达到84．8％（标准集）和83．3％（检验集）。     

A review of dystrophic lake and pool habitat in Europe: An Irish perspective

Freshwater lakes and pools contained within peatlands are unique habitats that support rare and specialised species. Despite this, these ecosystems have been overlooked in conservation and management practices. One of these habitats, ‘3160 Natural dystrophic lakes and ponds’, is protected under the European Union (EU) Habitats Directive with a concerning proportion of these habitats having an “unfavourable-bad” or an “unfavourable-inadequate” conservation status across Europe. Our current understanding of the key physico-chemical and ecological features of this habitat is inadequate which is hindering the implementation of effective conservation measures. This review summarises the current knowledge of this protected lake habitat as defined under the EU Habitats Directive. With a focus on Ireland, we demonstrate how the current monitoring and assessment methods used to characterise and assess the structure and function and conservation status of this habitat, which relies largely on the use of macrophyte community composition and surrogate physico-chemical data collected under the EU Water Framework Directive, is ineffective. We propose the incorporation of further or alternative ecological metrics including, but not limited to, algae and macroinvertebrates which are needed to improve our understanding of the structure and function of this priority lake habitat. In addition, application of such data via ecological metrics would allow for the quantification of biodiversity and species rarity metrics which would aid in identifying sites of conservation importance.     

Determining tipping points in aquatic ecosystems: The case of biodiversity and chlorophyll α relations in fish pond systems

The management of biodiversity in aquatic ecosystems requires knowing the state of water quality linked to regime shifts in various taxonomic groups. We examine this question by studying the fish ponds in the Dombes region, France. These waterbodies are characterized by a high diversity of species. High levels of nutrients due to certain fish farming practices may cause significant eutrophication leading to loss in biodiversity and a shift from high coverage of aquatic vegetation to phytoplankton dominance may also be observed. The aim of this study is to assess tipping points, thresholds for effect, along a gradient of chlorophyll α in different taxonomic groups: aquatic vascular plants, phytoplankton, dragonflies and aquatic macro-invertebrates. Tipping points are analyzed with three different statistical methods: a method which evaluates tipping points with a difference in the mean (TMEAN), a second method which evaluates tipping point by comparing the mean and linear regressions before and after the tipping point (FSTAT) and third a method which evaluates linear regressions with a pivotal tipping point (SEGMENTED). We also compare tipping points for the different taxonomic groups using five different diversity indices: Observed richness, Jackknife first order, Fisher's alpha, Simpson index and Evenness.Our results show that there is an important variation in tipping points following the three statistical methods, but the SEGMENTED is the best method for evaluating tipping points. We observe a high difference of tipping point values for the different taxonomic groups depending on the diversity indices used. Jackknife first order has a better performance to evaluate a eutrophic change according to the diversity than the other indices.In all taxonomic groups, aquatic vascular plants are the most impacted by the chlorophyll α and almost all their tipping points are observed around 60 μg/L chlorophyll α concentrations. No significant relationship is found between chlorophyll α and phytoplankton diversity, while the two other groups, dragonflies and macro-invertebrates, are both impacted by the chlorophyll α but their relevant tipping points are situated in higher values than aquatic vascular plants.     

Lake depth and geographical position modify lake fish assemblages of the European 'Central Plains' ecoregion

1. Classification of European lake fish assemblages can be based on fish‐assemblage structure or morphological, geographical, physical and chemical lake attributes. However, substantial gaps in knowledge exist with respect to the correspondence between both classification approaches. 2. Here, we compiled fish assemblage data from 165 lakes situated in the European ‘Central Plains’ ecoregion. Cluster analysis of fish abundances was performed to compare fish assemblage types of the entire ecoregion with those from previous country‐specific studies. Nonparametric group comparisons, classification trees and partial canonical ordinations were used to infer the correspondence between fish assemblage types and morphology, geographical position and nutrient concentration of the lakes. 3. Three distinct fish assemblages were revealed: vendace (Coregonus albula), ruffe (Gymnocephalus cernuus) and roach (Rutilus rutilus) lake types. Both latitude and lake depth were the best determinants of lake type, but total phosphorus (TP) concentrations were also important. Vendace lakes were deep and had low TP concentrations, whereas the shallower ruffe and roach lakes had higher TP values. Roach lakes were more frequent in the north‐west area of the ecoregion, whereas ruffe lakes were more often found south of the Baltic Sea. 4. Controlling for the influence of nutrient concentration showed that lake morphology and geographical position were important determinants of fish assemblages. However, the variance explained was low (<20%), implying that biological interactions may also be important in forming the lake‐specific fish assemblages. 5. The results suggest that fish assemblages differ between deep and shallow lakes, and between the north‐west and south‐east locations within the Central Plains ecoregion. Accordingly, establishment of depth‐related lake morphotypes is needed, and the European ecoregions recommended to be used in evaluation systems according to the Water Framework Directive seem to be too coarse to reflect the subtle differences of fish species richness along geographical gradients.     

Response of ecological indices to nutrient and chemical contaminant stress factors in Eastern Mediterranean coastal waters

Environmental data produced throughout monitoring activities in the framework of the implementation of Water Framework Directive 2000/60/EC (WFD) in Eastern Mediterranean (Greece) were used to assess the sensitivity and response of ecological indices against trace metals, eutrophication and multiple stress factors. The applied ecological indices include multi-metric eutrophication indices, a physicochemical status index applied for the first time in the Greek marine area, benthic indices, phytoplankton biomass index, and integrated status indices assessed through the application of the decision tree integration scheme. To investigate the exceedances in the eco-stoichiometric relationship between nutrients, considered a stressing factor, all physicochemical elements influenced directly or indirectly by eutrophication, such as nutrient concentrations, water transparency, oxygen saturation, particulates concentration, and sediment organic content, were related to ecological indices. Also, chemical contaminant stress factors represented by heavy metal concentrations in the water, as well as multiple stress factors represented by a pressure index, were related to ecological indices. A graphical visualization multivariate tool and statistical correlations were used to evaluate the sensitivity or explanatory power of the tested ecological indices against single and multiple stress factors. Results showed a strong response of all ecological indices to stress factors, although a diversification of sensitivity was evident. Primary production-related indices, i.e., macroalgae and chlorophyll-a indices, are more sensitive to particulates and nitrogen, while secondary production-related indices, i.e., benthic macroinvertebrates indices and eutrophication indices, including nutrients, are more sensitive to phosphates in the water column. The macroalgae index shows the strongest sensitivity to multiple stress factors. Among metals, mostly cadmium seems to match all indices⿿ performance. Nutrient relationships were shown as critical to eutrophication and ecological status.     

Hierarchical toolbox: Ensuring scientific accuracy of citizen science for tropical coastal ecosystems

Increased human population growth threatens the ecological functioning and goods and services provided by tropical coastal ecosystems. However, a lack of scientific baselines and resources hamper efforts to develop and monitor ecological indicators of environmental change. Citizen science can provide a cost and time effective solution, but needs considerable context specific development to ensure it provides valid information of the quality level required for acceptance by the scientific community. We reviewed the use of sampling methods for shore crabs as an example of an abundant tropical coastal organism with high citizen science suitability and ecological indicator capacity. We propose a hierarchical toolbox based on the distinction between rapid methods, allowing fast, noninvasive sampling by independent citizens, and medium speed methods allowing detailed but more invasive sampling requiring trained citizens working in close interaction with professionals. The hierarchical structure enables full use of the large scale data collection ability of citizen scientists at lower levels, while ensuring validation of errors at higher levels. Additionally, at each level, bias reduction and data validation measures can be employed. We conclude that citizen science methodologies can provide accurate large scale data to develop the ecological baselines urgently needed to monitor and manage environmental change in many tropical coastal ecosystems. We discuss a stepwise implementation of the toolbox leading to accuracy metadata which can be independently reviewed as an ultimate accuracy assessment and data integration mechanism among multiple projects.