LifeWatch Italy - Activitis Report

I t a l i a

Activities Report

Printed in October 2014, this report describes research activities conducted by LifeWatch Italy in the period 2011-2014. The General Assembly of LifeWatch Italy is responsible for its content. Graphics & layout by the LifeWatch Service Centre.

With more than 57,400 animal species and 6,500 plant species, Italy is one of the biggest biodiversity hotspots in Europe. The variety of organisms found in Italy represents a priceless asset in the pursuit of greater scientific understanding: the challenge is to fully grasp the organisation of life in the various ecosystems, starting with the natural and environmental heritage of Italy.

LifeWatch represents an advanced model of research infrastructure for studies of both biodiversity and ecosystems, which are seen as common-pool resources held by citizens for the benefit of citizens. LifeWatch seeks to strengthen ecological awareness and introduce young people to research right from the start of their education.

The broad, interdisciplinary involvement of the Italian scientific community in the construction of LifeWatch in Italy is an indicator of the capacity of our research system to move effectively on the most advanced frontiers of the science of sustainability. This is crucial for generating new development that provides genuine prospects in terms of employment for young people. The fruits of scientific innovation generate knowledge that can open up new fields of application and thus new opportunities for the Italian economy, guaranteeing the well-being of all its citizens.

This report describes the research conducted by LifeWatch Italy in the first three years of its life. It is an initiative that the Ministry of Schools, Universities and Research has supported with conviction from the very beginning, and for which an even stronger and more flexible commitment on the part of Italian institutions is required.

Professor Stefania GianniniMinistry of Schools, Universities and Research (Miur)

LifeWatch Italia Activities Report 5

LifeWatch Italy

Biodiversity is a top priority on the political agenda at all levels because we are starting to realise the societal benefits of clean air and water, uncontaminated foods, a stable climate, natural medicines and a safe environment, all of which depend on the self-organisation of biodiversity.

Italy is a biodiversity hotspot and this issue is a high political priority. Indeed, Italy has played a key role in the construction and transition of LifeWatch, the European Research Infrastructure on Biodiversity. The commitment of the Italian Ministry for Education, Universities and Research (MIUR) and the National Research Council (CNR) resulted in the setting up of the LifeWatch Italy Joint Research Unit (JRU).

By supporting scientific research the JRU aims to:

»Strengthen our knowledge of biodiversity;


» Enhance our current understanding of biodiversity and its relations with ecosystem services and societal benefits;

» Optimise the use of public research funding and increase Italy’s competitiveness in obtaining EU and other international research funds;

» Identify knowledge gaps in the IT platforms currently used for biodiversity, integrating the knowledge arising from focused research programmes;

» Support biodiversity and ecosystem health management with science-based programmes, strategies and realistic problem-solving approaches;

» Support crucial sectors of the national economy and social security system, such as agriculture and fisheries, tourism and human healthcare;

» Raise awareness of the importance of preserving biodiversity, even when the scale of biodiversity organisation requires investment outside national territory [e.g. migratory birds; large pelagic fish (tuna fish or sword fish); shared ecosystems];

» Support environmental policy in terms of both legislation and governance;

» Provide support at the political and institutional level for the development of national strategies to cope with climate change, energy generation and waste management.

The JRU coordinates the Italian contribution to LifeWatch and the national activities of the LifeWatch Service Centre and the e-Biodiversity Research Institute of LifeWatch-ITA. These activities include the work of specific Working Groups responsible for ICT, Modelling, Citizen Science and Showcases (e.g. the Alien species showcase).


The Service Centre is part of the Common Facilities of European LifeWatch, and is responsible for the communication activities of the LifeWatch infrastructure in general, as well as the active involvement of the European scientific community in LifeWatch and the provision of services to users. At the national level, it plays the same role, as it is a core component of the e–Biodiversity Research Institute of LifeWatch-ITA.

The latter has branches distributed throughout Italy, focusing on the construction of a functional backbone, and seeks to reinforce integrated scientific research into biodiversity. The e-Biodiversity Research Institute of LifeWatch-ITA is organised into four thematic centres: Biomolecular, Collections, Interactions and Mediterranean, focusing on species, their genetic and phenotypic traits (including behavioural traits), their niches and their interactions.

e-Biodiversity research institute

Collectionsspecies & traits

Interactionsniches & food webs

Mediterraneanfunctional nodes/showcases

» Interface with users

» Training and capacity building

» Networking and liaison

» Coordination, management & fundraising

» Communication

Species Functions Cadastre

Thematic Centres

Biomolecular »Data Providers

»Data users

Stakeholder Community Service Centre


The Service CentreMission

MissionThe main purpose of LifeWatch is to serve the biodiversity and ecosystem research community in its efforts to improve the understanding and rational management of our ecosystems by policy makers, resource managers, the private sector and the general public. At the European Level the Service Centre acts as LifeWatch ’s interface with all the e-Infrastructure stakeholders, including data users and data providers, administrators, environmental managers and policy makers. It will plan the strategic development and delivery of LifeWatch services, linking the most advanced ICT technologies with the needs of biodiversity science in order to address emerging issues and open up new perspectives for a better understanding and wiser conservation and management of biodiversity and ecosystem services. At the national level the Service Centre is a core component of the e-Biodiversity Research Institute of LifeWatch-ITA, supporting the Thematic Virtual Centres, the Working Groups and all activities pertaining to Italy’s contribution to LifeWatch-EU.


Long-terM goaLs The Service Centre will provide services to the user community so as to facilitate the use of the infrastructure and provide information and support with a particular focus on young scientists. It will also foster user involvement in the development of services and encourage the participation of new communities of interest. The Service Centre will offer a multiple set of services and online tools to a wide community of researchers and other users (policy-makers, managers, administrators, industrial & other enterprises, citizens). It will create and manage Virtual Laboratories and Temporary Cooperation Networks – ad hoc, multi-centre projects, drawing expertise from Europe and beyond to work efficiently and quickly – enabling researchers to meet face-to-face and advance their collaborative work.

Specifically, this entails:

»Optimising access and use of the facility as a whole, with special attention to research opportunities for young scientists via the fellowship programme, in order to foster original and innovative use of the infrastructure;

»Providing special support for European and national policies;

» Increasing the awareness of users, stakeholders and the public, and the visibility of LifeWatch outcomes, providing publicity and other dissemination services to users;

»Providing user access, user support, training and public services and identifying priorities and opportunities for business ventures;

»Promoting the involvement of scientific communities and the identification of potential new data resources.


The Service Centre has developed services and tools for both LifeWatch-EU and LifeWatch-ITA. Services include the LifeWatch Community, as a virtual space, LifeWatch Communication services, available on the Infrastructure webportal, and back-office networking activities. Tools include the interoperability and virtual laboratory facilities developed in collaboration with the staff of the LifeWatch ICT Working Group.

The Service Centre promotes LifeWatch’s contribution to the European Biodiversity Research Space via:

1) participation in drawing up the European Roadmap for e-Biodiversity Infrastructure;

2) organisation of networking activities as part of European and other International e-Biodiversity Initiatives;

3) promotion of scientific debate on research priorities through its active LINCC community;

4) the active involvement of the Italian scientific community in the implementation of the national network, formalised as the LifeWatch-ITA JRU.

Participation

ICT Tools & Services

Products


structure & governance

The structure of the LifeWatch Service Centre has two key functional components:

a Back Office dealing with the coordination of all Service Centre activities, the identification of user demands in terms of emerging scientific questions and the related planning of strategic services deployment, the communication strategy, the coordination of distributed services and the legal and financial issues linked to the Service Centre’s activities;

a Front Office dealing with: 1) all direct interaction with the user community via a user interface and helpdesk, partnerships and networking services; 2) e-training and capacity building; and, 3) funding opportunities. The Front Office will be in charge of providing tools and services for data mining, integration and presentation. Within LifeWatch-ITA the governance of the Service Centre will follow the governance structure of the thematic centres.

service centre structure

Strategic Development of LW Services

LSC Management, Coordination & Contact Development and Management

Coordination of Distributed Services

User Platform & Interface

Partnership & Networking Services

Communication

HelpdeskFunding

OpportunitiesMultimedia

SupportExpert

Consultation

Distributed Services

Training & Capacity Building

Po

rtal Interface

Communication

Front Office

Back Office


service centre structureAchievements

»» Setting»up»the»management»office»of»the»Central»Service»Centre;

»» Organisation»of»a»broad»community»of»experts;

»» Launch»of»the»Lifewatch»portal»and»communication»services;

»» Development»and»implementation»of»initial»LifeWatch»communication»initiatives;

»» Development»of»communities»of»interest»and»collaborative»networks»with»the»support»of»the»Lifewatch»Community»social»space»(user»platform);

»»Design»of»the»data»discovery»infrastructure»so»as»to»allow»access»to»all»worldwide»biological»data»resources»and»accelerate»data»generation.

start-up pLanning

The initial activities of the start-up phase focused on setting up the management office of the main Service Centre and on coordinating local and central services, crucial to building an efficient network of service centres.

The Service Centre has begun to implement the first communication initiatives and will draw up a plan taking into account all aspects of communication. In parallel, it will monitor users’ responses and involvement

levels through the user platform. The start-up activities have also involved the facilitation of access to services through the establishment of a helpdesk, coordinating the development and availability of e-learning facilities to support the initial services.


Mission

The Biomolecular Thematic Centre (MoBiLab – Molecular Biodiversity Laboratory) integrates expertise and advanced infrastructure for molecular and bioinformatic analyses with the aim of providing the scientific community with services and support for the study of biodiversity data. Specifically, the Centre provides access to tools for analysing genomic, metagenomic, phylogenetic, phylogeographic and DNA barcoding data, and to databases specifically structured to allow integrated access to molecular information and associated metadata.

The Biomolecular Thematic Centre


Long-terM goaLs

The long-term objectives of MoBiLab include the establishment of consolidated services for the analysis of Molecular Biodiversity data and support for their production. These services will provide valuable tools for the assessment of phenomena concerning entire ecosystems or individual populations which will be useful for drawing up monitoring and management strategies. We plan to make the following services available:

1. Design and application of meta-barcoding and shotgun protocols based on high-throughput sequencing (HTS) technologies;2. Tools for comparative analyses of metagenomes and metatranscriptomes associated with different environments and conditions;3. Tools for molecular and bioinformatic analyses of free-living and symbiotic prokaryotic communities;4. Tools for molecular and bioinformatic analyses of eukaryotic communities;

5. Tools for molecular and bioinformatic analyses of genomes and transcriptomes from prokaryotes and eukaryotes;6. Access to specialised Molecular Biodiversity databases.

A bioinformatics infrastructure for storing and analysing molecular data, produced by LifeWatch and collected from public databases, is currently under construction on the basis of a specific case study of alien species in terrestrial and aquatic sites in Italy. In the near future, this resource will be made available for more general use.


Reference databases for taxonomic assignment in metagenomics. Brief Bioinform. 2012 Nov; 13(6):682-95. Review.

The influence of invasive jellyfish blooms on the aquatic microbiome detected by an Illumina-based deep sequencing strategy. Biological invasions (2014, submitted).

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinformatics (2014, submitted).

Scientific Results

BioMaS: a pipeline for Bioinformatic analysis of Metagenomic AmpliconS (https://recasgateway.ba.infn.it/ , http://galaxy.cloud.ba.infn.it:8080 ).ITSoneDB: a comprehensive collection of ribosomal RNA cluster Internal Transcribed Spacer 1 (ITS1) sequences aimed at supporting metagenomic surveys of fungal environmental communities (http://itsonedb.ba.itb.cnr.it).

MoBiLab participates in the international Ocean Sampling Day (OSD) initiative launched by the MicroB3 EU project (http://www.microb3.eu/osd), providing expertise on sampling and HTS sequencing of the eukaryotic planktonic component at marine sites.

Participation

ICT Tools & Services

Products


governance

The governance structure of the Biomolecular Thematic Centre will consist of a Steering and Scientific Committee composed of representatives of each of the institutions contributing to the Thematic Centre. The Steering and Scientific Committee will elect a coordinator in charge of directing the Centre for a two-year period. Every year, the Coordinator, together with the Scientific Committee, will present the activities report and the Thematic Centre’s strategic plan to the JRU Board.Together with the other LifeWatch Thematic Centres, the Biomolecular Thematic Centre is supported by the Service Centre, which is responsible for public relations, networking and fundraising.


Achievements

»» Protocols»for»target-oriented»metagenomic»analysis»through»HTS»technologies»have»been»developed»and»applied»to»environmental»issues;

»» Protocols»for»genomic»and»transcriptomic»sequencing»by»HTS»technologies»have»been»made»operational;

»» The»ITSoneDB»database»(http://itsonedb.ba.itb.cnr.it:8080/ITS1/),»a»reference»resource»for»target-oriented»Metagenomic»analysis»of»fungal»communities,»and»the»BioMaS»target-oriented»Metagenomic»analysis»pipeline»(https://recasgateway.ba.infn.it/,»http://galaxy.cloud.ba.infn.it:8080»)»have»been»developed»and»implemented»as»web»services;

»» A»bioinformatic»analysis»pipeline,»called»SARMA»(Species»Assignment»of»high-throughput»sequencing»Reads»from»Metagenomic»Analyses),»has»been»designed»and»is»currently»under»construction»in»order»to»study»the»taxonomical»and»functional»composition»of»microbial»communities»based»on»HTS»data»produced»by»means»of»shotgun»protocols;

»» Molecular»data»and»associated»metadata»concerning»approximately»370»alien»organisms,»available»as»a»public»resource,»have»been»explored»as»a»case»study»to»structure»and»populate»the»laboratory»database.

start-up pLanning

1. Cooperation with the ICT Working Group in structuring and maintaining the infrastructure for storing and providing Molecular Biodiversity data and associated metadata.

2. Exploration of additional data and resources arising from new case studies in the field of Molecular Biodiversity, progressive and continuous integration of such data and updating of the infrastructure.

3. Feedback and data collection from stakeholders in order to optimise the infrastructure based on their needs.


The Collections Thematic Centre

Mission

The Collections Thematic Centre aims to support the creation of the taxonomic backbone (taxonomic hierarchy, names, synonyms, etc.) of the LifeWatch-ITA infrastructure.

The Thematic Centre will contribute to the updating, standardisation and refinement of the data hosted by the infrastructure, making the already existing databases and sources interoperable and accessible through the portal. The Thematic Centre aims to increase and ensure online availability of biodiversity data from collections held by Natural History Museums, Research Institutes, National Parks and private collections.

Photograph: Saulo Bambi - Museo di Storia Naturale Università di Firenze


Long-terM goaLs

1. The Collections Thematic Centre will develop its activities in line with the National Biodiversity Network (NNB) of the Italian Ministry of the Environment (MATTM) and its components.

2. The Thematic Centre will coordinate its activities and efforts with the other Thematic Centres of the e–Biodiversity Research Institute in the development of the Italian Species Cadastre, contributing to the components dealing with systematics and nomenclature.

3. The Thematic Centre will focus on the screening and selection of the available high-quality digital sources containing georeferenced and chrono-georeferenced data, filling the gaps in terms of geographical coverage, taxonomic groups, time series, etc. It will also organise and select the taxonomic databases, giving priority to those with large geographic coverage (preferably worldwide: Global Species Databases – GSDs) and to those recognised as nomenclatural authorities (e.g. AlgaeBase).

4. The Thematic Centre will continue the updating, standardisation, refinement, maintenance and implementation of the data hosted by the LifeWatch-ITA infrastructure (including those pertaining to the Alien species showcase).



The Collections Thematic Centre has participated in several initiatives and developed networking activities with national and international institutions, research groups and project consortia dealing with e-biodivesity taxonomic facilities. These include the Global Biodiversity Information Facility (GBIF), the Pan-European Species directories Infrastructure (PESI) and the Italian Strategy for Biodiversity. The Collections Thematic Centre has organised and participated in a number of scientific expeditions and Bio-Blitzes both in Italy and abroad (e.g. Vietnam and other South-Eastern Asian countries).

The Collections Thematic Centre is currently participating in projects including: NNB (National Biodiversity Network) - implementing datasets with DNA barcode sequences of the Italian fauna included in the Habitats Directive (92/43/EEC) CSMON-LIFE (Monitoring biodiversity by a Citizen Science approach for solving

environmental problems)MIPP LIFE+ Nature (Monitoring of insects with public participation).

The Collections Thematic Centre participates in CETAF (Consortium of European Taxonomy Facilities) and organises taxonomic courses for:DEST (Distributed European School of Taxonomy)ANMS (Italian Association of Scientific Museums) - CollMap national project.

Participation

Products


governance

The governance structure of the Collections Thematic Centre consists of a Steering Committee coordinated by a Representative elected by a simple majority vote. The Coordinator is supported by a Scientific Committee composed of researchers from Italy or other countries, not necessarily affiliated with the Thematic Centre. The Coordinator, together with the Scientific Committee, sets out the strategic goals of the Thematic Centre. The Scientific Committee closely interacts with the ICT Committee composed of IT engineers and experts. The Collections Thematic Centre, like the other LifeWatch Thematic Centres, is connected to the Service Centre, which provides support on public relations, networking, fundraising and management.



Achievements

»» Initial»selection»of»the»main»sources»(e.g.»PESI»-»Pan-European»Species»directories»Infrastructure;»CoL»-»Catalogue»of»Life)»to»be»used»as»nomenclature»references;

»» Screening»of»online»resources»with»high-quality»occurrence»data»(e.g.»CKmap»-»Checklist»and»distribution»of»Italian»fauna);

»» Updating,»standardisation»and»refinement»of»part»of»the»data»included»in»the»Alien»species»showcase;

»» Refinement,»standardisation,»updating»and»partial»digitisation»of»data»for»the»core»of»the»LifeWatch-ITA»platform,»i.e.»the»main»national»database»on»terrestrial»Isopods»(Crustacea,»Isopoda,»Oniscidea),»created»by»the»National»Research»Council»of»Italy.

start-up pLanning

1. Cooperation with the ICT Working Group in the development of the taxonomic basis of the LifeWatch-ITA infrastructure and the development of automated processing for name verification and data refinement, thereby creating useful tools for stakeholders.2. Continued screening of sources to implement the infrastructure, establishing Memoranda of Understanding and agreements between LifeWatch and the managers of existing datasets to make

them interoperable and easily accessible through the platform.3. Development of standard protocols for the acquisition of primary biodiversity data from “Citizen Science” programmes.4. Digitisation of key data included in scientific studies not available online (e.g. taxonomic revisions), which could be essential for the operation of the platform.


Mission

The Interactions Thematic Centre aims to integrate the data resources required to study the responses of interacting individuals, populations and species and analyse the mechanisms underlying biodiversity organisation. With this aim, the Thematic Centre will produce tools and services to standardise, integrate and analyse data on inter-individual interactions at the scale (grain and extent) required. The Thematic Centre also aims to provide the Stakeholder community with a series of tools focusing on the protection, management and recovery of biodiversity and its ecosystem services.

The Interactions Thematic Centre


Long-terM goaLs

1. The main long-term goal of the Interactions Thematic Centre is to coordinate its activities and efforts with the other Thematic Centres of the e-Biodiversity Research Institute in the development of the Italian Species Cadastre, contributing to the components related to ecological interactions at all levels, from inter-individual to interspecific.

2. The Thematic Centre focuses on the functional backbone, organising and making available data resources on keystone ecological niche dimensions, trophic links and other food web interactions, and related functional traits of individuals. A long-term operational goal of the Centre is thus the development of ontology-based standardisation and interoperability tools, progressively embracing guilds and taxonomic groups colonising ecosystem types in Italy.

In the long term the Thematic Centre will also seek to implement:

3. Interactive Species Catalogues and Case Studies to address emerging and interdisciplinary ecological questions and promote the use of the Thematic Centre’s products by the scientific community,

stakeholders and environmental managers.

4. Web Service and Tool (e.g. niche models and null models) Catalogues related to ecological interactions, to be used by scientists and policy makers interested in exploring and summarising biodiversity data.

5. Integration of its activities with the Service Centre regarding e-training for the services and tools developed by the Thematic Centre itself.


ICT tools and services that are being implemented in collaboration with the ICT Working Group include:

3. Compilation of the European Drupal Ecological Information Management System (DEIMS), developed by the Life+EnvEurope project for the LTER-Europe community, with detailed metadata describing datasets on species’ functional traits and ecological niches.

2. The Circlemednet platform, the largest DataBase on Mediterranean and Black Sea lagoons

with abiotic and biotic data on 635 geo-referenced lagoons in 17 countries.

Finalised ICT tools and services include:

1. The Phyto-Bioimaging portal, containing tools for taxonomic classification and morphometric analysis of phytoplankton.

Finalised ICT tools & Services

ICT Tools & Services under development

Products4. Compilation of a registry on the

model of the BioCatalogue, developed by the project of the same name, with

information on the tools and services provided by existing functional trait

databases in order to access, discover and analyse their content.

5. Standards and ontologies specifically designed to harmonise and integrate scientific data on phytoplankton functional traits.


governance

The governance structure of the Interactions Thematic Centre consists of a Steering and Scientific Committee, composed of representatives of each of the institutions contributing to the Thematic Centre. The Steering and Scientific Committee will elect a coordinator in charge of directing the Centre for a two-year period. Every year, together with the Scientific Committee, the Coordinator will present the activities report and the Thematic Centre’s strategic plan to the JRU Board.

Together with the other LifeWatch Thematic Centres, the Interactions Thematic Centre is supported by the Service Centre, responsible for public relations, networking and fundraising.

Lake Corn Field


start-up pLanning

1. Establishment of memoranda of understanding between LifeWatch and the managers of the existing functional trait datasets in order to provide them with standardisation tools that will make their data interoperable and easily accessible.

2. Compilation of the European DEIMS and BioCatalogue tools with functional trait and niche datasets for existing species.

3. Finalisation of standards and ontologies for phytoplankton functional traits and their extension to zooplankton and macrozoobenthos guilds.

4. Compilation of the European DEIMS and registry, on the model of the BioCatalogue, to include information on food webs.

5. Creation of standards and ontologies to describe food webs through stable isotopes.

6. Implementation of Case Studies of species’ functional traits and food webs to test and validate the virtual infrastructure created by the Thematic Centre.


Mission

The Mediterranean Thematic Centre (MTC) promotes the study of biodiversity and ecological processes at ecosystem level. It brings together biodiversity data, abiotic data and ecological descriptors at the same spatial and functional scale. The structure of the MTC is based on a network of institutions that make it possible to tackle several topics, a wide range of organisms and long-term data series, focusing on basic questions of biodiversity and ecosystem changes. The sites of the Italian Long-Term Ecological Research network (LTER-Italy) ensure the continuous provision and maintenance of long-term series of field- and nature-based biodiversity and ecosystem data. The MTC will promote tools, services and case studies to investigate the relationship between biodiversity and the environment.

The Mediterranean Thematic Centre


Long-terM goaLs

1. The goal of the Mediterranean Thematic Centre is to propose and coordinate case studies of biodiversity and ecosystems (tackling biodiversity loss, climate change, anthropic pressures, ecosystem protection, changes in ecosystem processes), assessing the interaction between biotic and abiotic data.

2. The Mediterranean Thematic Centre focuses on the implementation of interoperability tools for the consultation of data on abiotic variables at all levels, interacting with the other Thematic Centres and with the ICT Working Group, promoting and supporting services for the study of biodiversity.

3. The Thematic Centre will implement the habitat-oriented species database set up in the framework of the Alien Species Showcase (see below), providing tools for ecological analyses, increasing the homogeneity of the data (distribution, taxonomy, and historical series) and providing new insights for the scientific community interested in the study of biodiversity at all levels.

4. Moreover, the Thematic Centre will implement and update an Alien Species Portal as part of the Showcase, by creating fact sheets on alien species (metadata, distribution, occurrence, invasiveness etc.).

5. In addition, the Thematic Centre will support the ceation of an Abiotic Data Catalogue as an interoperability service supporting the Interactive Species Catalogue.


Development of the Alien Species (AS) showcase – “Patterns of ecosystem fragility to alien and invasive species in Europe” – which uses biodiversity data on species occurrence provided by sites of the LTER-Italy network and LifeWatch partners to investigate the pattern of susceptibility of different EUNIS habitats to invasive ASs.The example of the showcase confirms the true value of the scientific innovations and achievements arising from the Thematic Centre’s activities, offering new knowledge and new ways to address biodiversity conservation and management (e.g. prioritising conservation measures for habitat and ecosystem fragility). The results will also be quantified bibliometrically.

Scientific Results

1. The Alien Species Virtual Lab (AS_lab), developed in cooperation with the LifeWatch Service Centre and all the Thematic Centres to produce a virtual environment for the management and analysis of data. The virtual lab provides a shared resource available to researchers involved in the Alien Species showcase. The data collected within the Virtual Lab has enabled the creation of a database with more than 32,000 records of species occurrence from 334 sites, both aquatic (sea, lagoon and freshwater) and terrestrial (from coastal dunes up to mountain habitats), most of them belonging to the LTER-Italy network.The Virtual Lab has the potential to be further developed within the LTER-Italy network and the the National Biodiversity Network (NBN) into a larger species cadastre, including ecological traits.

2. The Abiotic Data Catalogue, containing most of the abiotic data resources available on the web. The catalogue will include analysis tools for the integration of biodiversity data with abiotic data.

Finalised ICT Tools & Services

Products


governance

The governance structure of the Mediterranean Thematic Centre consists of a Steering and Scientific Committee, composed of representatives of each of the institutions contributing to the Thematic Centre. The Steering and Scientific Committee will elect a coordinator in charge of directing the Centre for a two-year period. Every year, together with the Scientific Committee, the Coordinator will present the activities report and the strategic plan to the JRU Board.Together with the other LifeWatch Thematic Centres, the Mediterranean Thematic Centre is supported by the Service Centre, responsible for public relations, networking and fundraising.The Mediterranean Thematic Centre works in synergy with several Institutions including Istituto Agronomico Mediterraneo (CPZ Bari), Agenzia Regionale Protezione dell’Ambiente Puglia (ARPAP), Universities, Consiglio Nazionale delle Ricerche, Stazione Zoologica Anton Dohrn and the LTER-Italy network.


start-up pLanning

The Italian scientific community will be integrated with the LifeWatch Infrastructure by involving it in the construction of the infrastructure itself and by encouraging it to actively take advantage of the tools it provides. To this end, the Mediterranean Thematic Centre will:

» Inform the stakeholders (Scientific Societies, Federations, Associations, Research Councils and Data provider platforms interested in biodiversity and ecosystems) about the availability of biotic and abiotic diversity databases hosted by the LifeWatch infrastructure;

»Test the availability of ontologies and reference standards for data providers, amending and adapting them, developing new ontologies when necessary and supplying services to external data providers;

»Develop and maintain an Abiotic Database Catalogue containing most of the abiotic data resources available on the web. The catalogue will include analysis tools for the integration of biodiversity data with abiotic data;

»Develop connections with the LTER-Italy network, whose sites will contribute to the provision and maintenance of long-term biodiversity and ecosystem data series.


Working Groups

Besides the Thematic Centres, the Joint Research Structure of LifeWatch-ITA benefits from the contribution of four Working Groups.

The Working Groups are flexible transversal structures charged with supporting all Thematic Centres and the Service Centre in their research activities by perfoming short-term tasks or transversal measures on behalf of the JRU.

Currently four Working groups are operational:

» ICT;» Modelling;» Alien Species;» Citizen Science.


ict Working group

ICT is a multidisciplinary working group, comprising computer scientists, engineers, ecologists and biologists, transversally supporting the activities of the e-Biodiversity Research Institute and Service Centre by developing or providing ICT services and tools.Mission - The ICT Working Group is devoted to enhancing the innovation and development of the ICT infrastructure of both the Thematic Centres and the Service Centre in their fields of competence. The development of services and tools for data aggregation, standardisation, discovery and analysis is a central pillar of the ICT working group’s mission.Products - The ICT group is developing the European and Italian LifeWatch portals, supporting all Thematic Centres and the Alien Species’ working group producing geoportals, geographical information systems, services (integration of European DEIMS within the LifeWatch portal) and tools for data interoperability.

ModeLLing Working group

Modelling is a transversal working group supporting the activities of the e-Biodiversity Research Institute by providing services for data analysis and modelling.Mission - The Modelling Working Group is devoted to fostering innovation in data analysis within the LifeWatch Virtual Laboratory, producing web services for the application of powerful modelling tools to address key emerging scientific questions.Products - The Modelling Group has started to produce a catalogue of the available web-based modelling services that will be offered to LifeWatch users in the virtual Lab facilities, and is developing e-training tools dealing with model assumptions, data requirements and the related uncertainties of the resulting model-based scenarios.


aLien species Working group

The purpose of the Alien Species thematic working group is to develop a LifeWatch showcase on a topic of major interest for biodiversity organisation and conservation.Mission - The Alien Species Working Group aims to provide a concrete example of what LifeWatch can offer to users. The Working Group conducts cutting-edge research on ecosystems and habitat vulnerability to alien species invasion, using virtual lab facilities, services and tools supplied by the LifeWatch infrastructure.Products - The Alien Species group has developed a database on Italian ecosystem vulnerability to alien species invasion, covering more than 15% of overall biodiversity in Italy. The Working Group has also produced scientific papers for the biodiversity research community, new knowledge for environmental managers and policy makers, and simple and accessible information for citizens.

citizen science Working group

Citizen Science is a thematic working group that aims to raise awareness of the relevance of scientific research into biodiversity.Mission - The Citizen Science Working Group participates in concrete initiatives for citizens’ involvement in research activities concerning various aspects of biodiversity. The Working Group also promotes project opportunities for funding citizen science initiatives in the framework of LifeWatch.Products - The Citizen Science group has contributed to the launch of a European-level NGO on the theme, has applied successfully, together with some of the LifeWatch member institutions, for Life+ project funding, and is presenting new project proposals based on various sources of funding. The group is also very much involved in the educational sector, working to include schools in scientific activities focusing on biodiversity.


LifeWatch Italy JRU organigram

enrico BrugnoLi

JRU coordinator

coordination coMMittee

Enrico Brugnoli - Coordinator

Alberto Basset Alessandra PugnettiValerio SbordoniOliviero Spinelli

ManageMent coMMittee

Alberto Basset - JRU Manager

Luca BartolozziGiuseppe CorrieroGiorgio Matteucci

Graziano PesoleMaurizio Raeli

Adriana Zingone


The Service [email protected]@lifewatchitaly.eu+39 0832 29 42 75

The Biomolecular Thematic [email protected]@[email protected]+39 080 5443588+39 081 5833 295+39 080 5929675

gJ

g

J

service centre

Alberto Basset - CoordinatorChiara Del’Antoglietta - Communication Nicola Fiore - ICTSara Montinaro - Communication Alessandro Oggioni - ICT Stefania Presicce - AdministrationPaolo Tagliolato - ICT

the BioMoLecuLar theMatic centre

Graziano Pesole - CoordinatorAdriana Zingone - CoordinatorMonica Santamaria - Researcher Caterina Manzari - Research AssistantMaria Paola Tomasino - Research Assistant

Thematic Centres contact detaiLs


The Collections Thematic Centre [email protected]

[email protected] +39 055 2755116

The Interactions Thematic Centre [email protected]

[email protected]+39 0832 29 87 22

The Mediterranean Thematic [email protected]

[email protected]+39 0984 84 14 84

gJ

gJ

gJ

the coLLections theMatic centre

Luca Bartolozzi - Coordinator Valerio Sbordoni - Coordinator

Fabio Cianferoni - Research AssistantStefano De Felici - Research Assistant

the interactions theMatic centre

Alberto Basset - CoordinatorAlessandra Pugnetti - Coordinator

Ilaria Rosati - TechnologistCaterina Bergami - Research Assistant

the Mediterranean theMatic centre

Giuseppe Corriero - Coordinator Giorgio Matteucci - CoordinatorAlessandra Pugnetti - Researcher

Marco Bascietto - TechnologistCataldo Pierri - Research Assistant

Paolo Colangelo - ICT


Funding: cash & in-kind contributions

All the activities of the LifeWatch-ITA JRU have been supported in cash from two main sources: an annual grant from the Italian Ministry of Education, Universities and Research (MIUR), which was given to the National Research Council for the development of the LifeWatch infrastructure, and a grant from Puglia Regional Administration, drawn from Structural Funds, to assist in the construction of the LifeWatch Service Centre and related physical infrastructure.

All the activities of the LifeWatch-ITA JRU have been supported in kind by the National Research Council (CNR) and by the other member institutions of the JRU in the form of personnel costs, joint use of funds from LifeWatch spin-off projects, and tools and services in the field of e-Biodiversity produced by the institutional research units contributing to LifeWatch-ITA.

Most of the activities and products described in this report have also been supported in kind by contributions from individuals affiliated with a large number of public and private bodies and companies, who have expressed their belief in LifeWatch’s mission and development and have given their time and energy in planning, designing and implementing the building blocks of the LifeWatch infrastructure described in this report.


Members


www.lifewatchitaly.ithttps://twitter.com/LifeWatchIT http://www.facebook.com/lifewatch.italia

www.lifewatchitaly.it

https://twitter.com/LifeWatchIT

Documents

LifeWatch Italy - Activitis Report