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LifeWatch ERIC, the e-Science European infrastructure for biodiversity and ecosystem research, launched an Internal Joint Initiative on Non-indigenous Species and Invasive Alien Species (NIS-IAS) as they are considered one of the major drivers of biodiversity and ecosystem change. Here, the case study focused on the trophic biogeography of invasive crustaceans is presented, describing the procedures, resources, and analytical web services implemented to investigate the trophic habits of these taxa by using carbon and nitrogen stable isotope data. The case study offers a number of analytical tools to determine the variability of the trophic position of invasive crustaceans in a spatially-explicit context and to model it as a function of relevant environmental predictors. Literature-based stable isotope data of the Atlantic blue crab Callinectes sapidus and of the Louisiana crayfish Procambarus clarkii have been used to evaluate the functionalities and outcomes of the workflow. The Tesseract Virtual Research Environment integrates all the analytical services offered by LifeWatch ERIC, including the ones developed for this case study, by means of a user-friendly interface. The analytical functions implemented for the crustacean workflow provide a proof of concept for future open e-science platforms focusing on NIS-IAS. The workflow conceptual structure can be adapted to a wide range of species, and can be further improved to support researchers in monitoring and predicting trophic-related impacts of NIS-IAS. In addition, it can support policymakers and stakeholders in the implementation of effective management and control measures to limit the negative effects of bioinvaders in recipient environments.

The concept of essential biodiversity variables (EBVs) was proposed in 2013 to improve harmonization of biodiversity data into meaningful metrics. EBVs were conceived as a small set of variables which collectively capture biodiversity change at multiple spatial scales and within time intervals that are of scientific and management interest. Despite the apparent simplicity of the concept, a plethora of variables that describes not only biodiversity but also any environmental features have been proposed as potential EBV (i.e. candidate EBV). The proliferation of candidates reflects a lack of clarity on what may constitute a variable that is essential to track biodiversity change, which hampers the operationalization of EBVs and therefore needs to be urgently addressed. Here, we propose that an EBV should be defined as a biological state variable in three key dimensions (time, space, and biological organization) that is critical to accurately document biodiversity change.

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as highquality and complete taxonomic data sets, but these are generally lacking for nonspecialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs., PESI was funded by the European Commission under the Seventh Framework Program (project reference: RI-223806), contributing to the FP7-INFRASTRUCTURES 'Capacities' sub-program under the Coordination and Support Actions (CSA) funding scheme (call: FP7-INFRASTRUCTURES-2007-2).

Assessing ‘natural’ variability of structural and functional components of ecosystems is a main target of MSFD, responding to the need of disentangling biological responses to anthropogenic stresses from those on which human impact is minimal. The scale and the extent of ecosystem components variability are main determinants of ecological patterns and process. Moreover, variability within ecosystems depends on both internal ecosystem dynamics and larger scale drivers and processes. Here we focus specifically on natural variability of biotic ecosystem components and ecosystem processes, which are either descriptors or parameters of relevance in the MSFD monitoring scheme. Metabolic theories have highlighted how the individual body size can be considered as a main, intrinsic driver of variation in populations and communities functional properties. Indeed, individual energetic and behaviour show body size dependent variation according to an x/4 rule. Cascading deterministic effects of individual level size-dependencies have been demonstrated on both population and community levels as well as on functional properties. In the presentation: i. We develop a conceptual analysis of the implication of body size dependencies of individual energetic and behaviour on scale and extent of natural variability in the individual, population and community parameters considered in the MSFD; ii. We present an example of phytoplankton parameter assessments with changing temporal scales of assessment in order to account for the natural variability of cell densities in the phytoplankton guilds; and iii. We infer from implications of biological parameter size dependencies on MSFD monitoring plan accounting for natural variability and derive operational proposals for adaptive monitoring plans.

The Marine Framework Strategy Directive (MFSD, 2008/56/EC) aims for clean, healthy and productive marine ecosystems within all the EU Members states. The MFSD promotes an holistic, ecosystem based approach to marine conservation and monitoring (Art. 13) Monitoring strategies should: 1) focus on the potential of scale dependence in the observed dynamics and 2) be able to integrate the effect of mediating factors operating at different scale levels. However, present knowledge on spatial and temporal fluctuations in marine ecosystems is scarce. The boundaries of natural variation of several important marine ecosystem processes are still undefined. A major source of complexity is the fact that ecosystem processes are occurred across different spatial as well as temporal scales. The present knowledge gap results in uncertainty on the selection of measured parameters and the definition of sampling frequency and sites. Hereby, we discuss theoretical and applied issues related to definition of optimal cross-scale monitoring strategies. Literature data and existing databases were analyzed, to define the connectivity across nested scales of principal D1 (Biodiversity), D5 (Eutrophication), D6 (Seabed habitat integrity) MFSD descriptors. We conclude that present monitoring strategy does not completely fulfil the scaling issues due to lack of theoretical knowledge on cross-scale processes and poor coordination across monitoring operators. A stronger cooperation among member states and regional environmental agencies is needed to implement efficient cross-scale environmental monitoring. This research was developed by partners of the Integrated Regional monitoring Implementation Strategy in the South European Seas (IRIS-SES, http://iris-ses.eu) Project, a pilot project on new knowledge for an integrated management of human activities in the sea (PP/ENV D2/SEA 2012), funded by the European Union.

The Marine Strategy Framework Directive (2008/56/EC) of the European Parliament and of the Council (17th June 2008) establishes a framework for community action in the field of marine environmental policy. A crucial issue will be to improve the existing marine monitoring programs to cover the MSFD requirements. The comparison and identification of gaps in the existent national monitoring is a first step to include new parameters and frequencies of observation according to all relevant Directives and specially to MSFD. Our report is a first, integrated, cross-state assessment of the present state of Mediterranean monitoring networks. Data on monitoring stations have been provided from all member states of IRIS-SES + Croatia and joint in a unique georeferenced dataset. We used the cross-classification to build contingency tables of the counts at each combination of factor levels. Distances from coastline, densities of sampling stations, spatial overlap across descriptors, were also reported. As main results, we observed a large heterogeneity across MS on the parameters measured for each descriptors, on the density of sampling stations and on the frequency of sampling. Larger gaps have been identified for the descriptors Mammals, Birds, Reptiles (D1, D4, D6), Litter (D10), Energy & Noise (D11). The outputs from this work will be included into a GIS planning tool (Activity 3) including many scales and levels on which the MSFD Directive has been built on, such as the characteristics level (e.g. biological features, physicochemical features), pressure and impact, indicator/threshold, spatial (location of monitoring stations) and temporal (frequency-periodicity) across regions-subregions-countries.

A major source of complexity in marine ecosystem monitoring is represented by the fact that ecosystem processes occurring across different spatial and temporal scales. The implementation of the monitoring strategies applied in accordance to Marine Framework Strategy Directive (MFSD, 2008/56/EC) is a step-by-step process, which should be focus on the potential of scale dependence in the observed dynamics and should be able to integrate the effect of mediating factors operating at different scale levels. Nevertheless, the correct definition of monitoring efforts for each indicator needs to reach a well-defined knowledge on the actual assessment of the “object” of monitoring including ranges of natural variability in terms of spatial and temporal natural fluctuations. Unluckily natural fluctuations are not yet well defined in marine environments for all of the MSFD indicators. For these reasons the achievement of MSFD goals could be severely affected by the lack of knowledge which led to the lack of clear and rationale criteria on the basis of which to align and cope the scale of the assessment with the ecosystem natural fluctuations. Hereby we address the design of monitoring programmes concerning water column and seabed habitats integrity indicators (Descriptors D1, D5, D6) by discussing spatial and temporal extent of monitoring based on their scales of natural variation. The multiple layer approach developed on mesoscales could allow reducing mistakes due to sampling and methodological limits and could allow reducing problems ranging within the comprehension of mechanisms to the anticipation of consequences. The opportune mesoscale is dependent on the indicator considered and range within 0.5 – 100 km for the spatial scale and from 0.2 to 12 months for the temporal scale.

The Greek Taxon Information System is an initiative of the LifeWatchGreece Research Infrastructure (ESFRI) that is resuming efforts to compile a complete checklist of all species reported from the Greek territory. Such an effort is necessary as a requirement for all signatories of the Convention on Biological Diversity (Greece is a signatory since 1994). Over an estimation published in 2004 according to which 50,000 species are present in Greece, belonging to most kingdoms except bacteria and viruses, a list of 35,000 valid species (and subspecies) has been assembled from previous national and European initiatives and specialized databases on various groups. A new database will be progressively set up in the LifeWatchGreece Infrastructure within the near future. Before the dissemination of this dataset, it is important that the checklists will be validated by specialists for each taxonomic group. The first step already accomplished was to build and publish Preliminary Checklists for some taxonomic groups of marine fauna, which have been validated by specialists on the basis of their expertise and secondary literature. The publication of these Preliminary Checklists is expected to increase the visibility and usability of the database in the future not only to the scientific community but also to the broader domain of biodiversity management, especially in cases where no such checklists have been published yet. The guidelines used to test the first taxonomic groups are presented in this paper. © Bailly N et al.

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations,however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. Yes

The loss of species is known to have a negative effect on ecosystem functioning, but detailed mechanisms of this relationship are still far from being fully understood. Several hypotheses have been proposed in the past to explain the functional response of ecosystems to species loss, but many studies still rely on using community structure as a surrogate for ecosystem functioning. This study investigates how the spatio-temporal distribution patterns of polychaetes and their associated functional patterns in six Mediterranean coastal lagoons change under simulated scenarios of species loss. The results show that each lagoon responds differently to potential species loss: in stressed lagoons with few dominating species the change of patterns is extremely variable and unpredictable, whereas lagoons characterised by complementarity seem to be more robust towards changes. The patterns between community structure and functioning in each lagoon show strong similarities in the lagoons dominated by few species, but the patterns diverge in complementary communities. The findings highlight the importance of considering the ideosyncratic effects of species loss on ecosystem function as well as the risk of using structural patterns as surrogates for functional patterns when taking decisions at a managerial level.

The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential. © 2014 Elsevier B.V.

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as highquality and complete taxonomic data sets, but these are generally lacking for nonspecialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. © de Jong Y et al.

Principali risultati del network europeo di eccellenza MARBEF

International audience; The European program CIGESMED addresses the Good Environmental Status of the coralligenous habitats. Its implementation on the field is firstly attempted by 4 protocols to be applied in France, Greece and Turkey. They have been tested in Marseille's region, since early 2014. These protocols are the following: (i) cartography of chosen coralligenous sites, (ii) spatial variability analysis by means of photo-quadrats and image processing, (iii) population genetics study of two common biobuilding species that may be cryptic (the bryozoan Myriapora truncata, and the rhodophyta Lithophyllum cabiochiae), and (iv) metagenomic approach of benthic species. The ultimate aim of these protocols is to link the results from the population genetics analysis and the spatial variability analysis to the sites' features thanks to the cartography. First results suggest that different clades exist for both complex of the previous species. Cartography forshadows models of repartition for species assemblages; they will then be compared between regions in the second part of the project.

The study of ecosystem functioning - the role which organisms play in an ecosystem - is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http:// polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. © Faulwetter S et al.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called "cybertypes", and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information. © 2013 Sarah Faulwetter.

This paper describes a dataset of polychaetes (Annelida) from 14 midlittoral rocky shore sampling sites in Greece and Italy (Mediterranean Sea). The dataset combines the outcome of four different projects studying the hard substrate midlittoral zone in the Mediterranean between 1984 and 2009. Samples were collected by scraping and collecting the organisms from a framed area. The maximal sampling depth was 1.5 m. In total, 123 polychaete species were recorded, five of which are new records for the respective biogeographic sectors of the Mediterranean. The dataset contains 788 occurrence records, fully annotated with all required metadata. These data contribute to the knowledge of a previously very understudied regional habitat, since at present, comprehensive lists of the midlittoral communities in the Mediterranean are provided through only a few, paper-based, studies. This dataset is one of the first electronic data compilations of the Mediterranean midlittoral zone communities and certainly the most comprehensive of its kind, contributing to the ongoing efforts of the Ocean Biogeographic Information System (OBIS) which aims at filling the gaps in our current knowledge of the world's oceans. It is accessible at http://ipt.vliz.be/resource.do? r=mediterraneanpolychaetaintertidal. © Keklikoglou K et al.

For the upcoming calls for Horizon 2020 research funding, the European Commission has said that it would prefer bids from open, collaborative consortia rather than the competitive bids seen in previous funding programmes. To this end, the organizers of 18 European biodiversity informatics projects agreed at a meeting in Rome…

The global NaGISA (Natural Geography in Shore Areas) initiative focusing on long-term monitoring of coastal biodiversity has recently been expanded to the Mediterranean. On the basis of datasets from four Mediterranean hard substrate sites and by using the most abundant polychaete family (Syllidae), two questions are addressed in this study: (a) Is the biodiversity sampled in the two NaGISA sites, based on the family Syllidae, representative of the regional one of the Mediterranean Sea? (b) Are local syllid taxo-communities assembled at random from the regional species pool? Randomisation tests determining to what extent local species lists and their phylogenetic relationships are assembled at random from a regional one showed that at small observational scales (e. g. replicate units, depths) the phylogenetic diversity is assembled at random from the one known to exist locally. It is assumed, therefore, that local processes here have a stronger influence on community assembly than historical-evolutionary processes. The latter is in accordance with previous results derived from using polychaetes to test the same hypotheses at a pan-European level. Local syllid biodiversity in the western Mediterranean is a random subset of the Mediterranean one, whereas that of the NaGISA sites in the eastern Mediterranean is only under certain conditions. Therefore, the currently observed biodiversity of the Mediterranean sites can be considered as representative of that of the entire regional sea only under certain assumptions, as far as the syllid taxo-communities are concerned, demonstrating the potential of the taxon as a surrogate of the polychaete biodiversity. © 2012 Springer Science+Business Media B.V.