The European Marine Biological Resource Centre 

In short: the European Marine Biological Resource Centre (EMBRC) is a Distributed Research Infrastructure providing services to support research on marine biological resources. Its end users are researchers and technological engineers from academia, universities, and from the private sector.

The European Marine Biological Resource Centre (EMBRC) is a distributed Research Infrastructure (RI) composed of marine biological stations and institutes across the European Research Area (ERA). Teams of scientists in EMBRC engage in interdisciplinary research and technological development in marine biology and ecology. The RI is equipped with state-of-the-art research platforms and instruments organized into scientific services. External users from academia and industry can access this stimulating scientific ecosystem to pursue fundamental and applied research on marine bioresources. In particular, EMBRC aims to drive forward the development of blue biotechnologies.

The distributed nature of EMBRC enables it to provide access to the entire marine biodiversity along the European coast, far beyond what each station in isolation can offer. Each of the stations specializes in particular sets of model species, permitting EMBRC as a whole to offer a broad array of models for innovative scientific and technological applications. EMBRC gives its users unprecedented access not only to its interconnected research infrastructure but also to its background knowledge and expertise, thereby greatly facilitating the research endeavors of its external users. The integration of resources and knowledge on such a large scale over the decades to come will enhance the efficiency of training, knowledge transfer, international collaboration and EU global positioning in marine biological sciences. It will foster the development of key enabling technologies, in particular blue biotechnologies. Developments in these fields will, in their turn, stimulate blue growth, economic development and human wellbeing across the ERA. In conclusion, the RI will have an enormous potential in fostering research, education and innovation in marine biology. It will contribute to creation of excellence needed to achieve the goals established in the "Europe 2020 Strategy" and the "2010 ESFRI Roadmap".

EMBRC constitutes one of thirteen Research Infrastructures (RI) on the Biological and Medical Sciences (BMS) group and it forms a bridge towards the Environmental Sciences RIs.

EMBRC obtained three years funding from the European Commission to prepare itself. At the close of this preparatory phase, January 2014, an EMBRC Business Plan and a ready-to-sign Memorandum of Understanding was delivered, inviting countries to express their willingness to set up the EMBRC as a European Research Infrastructure Consortium (ERIC). The signatories, France, Norway, the UK, Belgium, Spain, Portugal, Italy, Greece and Israel, established an EMBRC Implementation Board with the overarching tasks to set up EMBRC and apply for the ERIC status. The Board appointed a General Director, which has commenced her work for EMBRC. France was selected by the partners to host the statutory seat and therefore, the EMBRC core office is located at the UPMC in Paris. Each of the signatory countries has established a national node staffed by a node director and a liaison officer to guarantee optimal collaboration with the core office.

Central Core Office: UPMC, Paris, France
Executive Director: Nicolas Pade
Web: www.EMBRC.eu
Head Quarter secretariat: This email address is being protected from spambots. You need JavaScript enabled to view it. - This email address is being protected from spambots. You need JavaScript enabled to view it.

The Italian Node of the European Marine Biological Resource Centre (EMBRC-IT) was constituted on 05/10/2021 as a JRU (Joint Research Unit), including a total of 16 partners (SZN, CONISMA, CNR, OGS, CTN-BIG, IZSPLV, ENEA, ISPRA, UNITUS, UNICA, UNIFE, UNIME UNIMIB UNINA UNITO, UNIVPM) with SZN as its coordinator and representative institute in EMBRC-ERIC.

The Italian JRU was established according to the principles of complementarity and synergy of the partners regarding the development of new collaborative research projects and research services and in order to strengthen scientific research and foster human and infrastructure resources exchange in the field of blue growth.

The JRU agreement has set itself the following objectives:

Strategic Agenda

• Valorisation of the resources and skills of each of the Parties through their coordinated organization and best practices sharing;
• Coordination of national activities within EMBRC–ERIC and provide support to the MUR and other Ministries in organizing the Italian membership in EMBRC–ERIC and in defining strategic research agendas and roadmaps related to sustainable blue growth;
• Strengthening of Italian scientific research in the field of marine biology and promote training, scientific dissemination and communication in this area;
• Promotion of technology transfer and new relationships with national companies;
• Design and organization of pilot actions and projects, demonstrating the peculiarity and value of the Italian contribution to EMBRC–ERIC;
• Conduction of joint activities aimed at consolidating, strengthening and expanding the EMBRC-ERIC Research Infrastructure and its impact in terms of science and innovation, with particular attention to the spill overs at the national level, also by participating jointly or individually in funding programs of the Research.

Public-public and public-private collaborations

• Coordination of an up-to-date National Index of scientific services for the «blue» community
• National services catalogue opened to EU Projects and Transnational Accesses
• Single access point: marketing at national and EU level
• Support to efficient and coordinated technology transfer
• Shared management of orders via the Node capacity
• Improved opportunity for scientific interactions, co-authorship and for interdisciplinary collaborations
• Favourable access conditions for associate partner

Improved fundraising capacity

• HE: Participation in EU projects as individual members of EMBRC-IT that can involve the other members of the JRU and EMBRC-IT itself as Affiliated Entity
• PNRR (NextGenerationEU): Strengthening and improvement of operative units (OU) of EMBRC-IT partners
• H2020: Access to EU-IR grants
• PON 2007-2013: Action on «Potenziamento strutturale»
• POR 2014-20: Action on «access to H2020 EU projects»

EMBRC-IT Partners

• Stazione Zoologica di Napoli Anton Dohrn (SZN) – Italian Node Coordinator
• Cluster Tecnologico Nazionale “Blue Italian Growth”(CTN-BIG)
• Consorzio Interuniversitario per le Scienze del Mare (CoNISMa)
• Istituto Nazionale di Oceanografia e Geofisica Sperimentale (OGS)
• Istituto Zooprofilattico Sperimentale di Piemonte, Liguria e Valle d’Aosta (IZSPLV)
• Università di Cagliari (UNICA)
• Università di Ferrara (UNIFE)
• Università di Messina (UNIME)
• Università di Milano-Bicocca (UNIMIB)
• Università di Napoli Federico II (UNINA)
• Università di Torino (UNITO)
• Università della Tuscia (UNITUS)
• Università Politecnica delle Marche (UNIVPM)
• Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)
• Consiglio Nazionale delle Ricerche (CNR)
• Agenzia nazionale per le nuove tecnologie, l’energia e lo sviluppo economico sostenibile (ENEA)

Summary

EMBRC-IT will offer opportunities for the Italian marine research and technological development community at large because:
• The JRU supports and reinforces the cohesion of the Italian Marine Research Community,
• It fosters a higher visibility of this community at the National (MIUR) and International (EU) level,
• It links marine biological resources to innovation, supporting cooperation with universities, research organizations and industries
• It creates critical mass, capable to interact with, and advise, policy makers

The result of its common effort will be more than the sum of the capacity of each.

Contact information

Node Director: Donatella de Pascale
Liaison Officer: Pasquale De Luca
JRU Manager: Giorgio Maria Vingiani

Pezzotti Maria Rosaria

Pinto Maria Rosaria

Coordinator: Christophe Brunet

Activity

The laboratory of Biogeochemistry and Physiology of Plankton is a multidisciplinary laboratory that uses and develops different approaches dedicated to the study of biogeochemistry and physiology of marine phytoplankton. The laboratory covers research activities related to biological oceanography, biogeochemistry and ecophysiology of marine phytoplankton. Mostly, the laboratory BioFilP implements activities and techniques for the study of the responses of marine microalgae to environmental forcing, with the aim to understand the pelagic ecosystem functioning and the potential use of microalgae in "Blue Growth".

Experimental systems

• Room and cultivation system for microalgae, with development of different types of illumination systems suitable for microalgal growth.
• Pelagic mesocosms for in situ experiments.

Analysis

• Photosynthetic rate and regulation of photosynthesis in microalgae.
• Pigments of photosynthetic organisms.
• Bio-optics of water masses and microalgal cultures.
• Antioxidant activities in microalgae.
• Concentrations of macronutrients in the water masses and in microalgal cultures.
• Spectral light in the water masses.

Equipment

• HPLC analysis for pigments.
• PAMs: Dual-pam and PSI.
• Autoanalyzer for nutrient concentration analysis.
• Spectrophotometer.
• Spectroradiometer in situ probe.
• Bio-optical in situ probe (AC-9).
• Laminar flow hood.
• Room and cultivation system for microalgae.

Responsible: Maria Cristina Buia

Activities

The activities of this laboratory are characterized by the application of various and integrated approaches, classical and innovative, which are conducted in mesocosm/laboratory and in the field, to study the adaptive responses of benthic organisms (invertebrates and macrophytes), and their trophic interactions in relation with environmental factors and gradients, climate change and anthropogenic disturbances. The approaches used include the physiology of individual species, the structure of populations and the dynamics of benthic communities and coastal ecosystems, to identify early-warning signals/descriptors at different level of biological complexity, and finalized to a correct management and conservation of the coastal systems and their biodiversity.

Systems for laboratory experiments

• System for automatic culturing of model organisms.
• Thermostatic chambers for rearing and experiments of benthic organisms in axenic conditions.
• Tanks for maintenance and experimentation of benthic organisms in sea-water open systems.

Analysis

• Qualitative and quantitative analyses of benthic samples deriving mainly from hard and soft bottom vegetated habitats, and soft sediments within the continental shelf.
• Biometric and biomass analyses.
• Biological assays and test for bioactive substances.
• Sample preparation for elemental analyses, and for observation at the  scanning and transmission electron microscopy.
• Measurements of environmental variables (Temp., pH, irradiance, dissolved oxygen).
• Measurements of photosynthetic efficiency in macrophytes.

Instrumentation

• Stereomicroscopes, optical microscopes, inverted optical microscope.
• Freezer at -20 °C and refrigerators +4 °C.
• Laminar flow flume and chemical flume.
• Thermostatic cells and chambers.
• Autoclave, ovens, muffle.
• Filtration system.
• Spectophotometer.
• Analytical and technical balance, microbalance.
• Deionizer.
• Liofilizer (deep-dryer).
• Laboratory oxymeter and pH-meter, portable pH-meter.

For scientific underwater use and diving:

• Cameras and video-cameras with underwater dedicated casts.
• Diving-PAM, pH-meters, quantameter, multi-parametric probes.
• Grabs, dredges, corers for sediment and benthos, air-lift sampler, hand-towed net and plankton nets.

Responsible: Raffaella Casotti

Activities

The laboratory of Microbial Ecology carries on research on marine microorganisms (mainly diatoms and autotrophic/heterotrophic picoplankton) studying their diversity, activity and metabolic functions as well as their interactions with the environment, both physical-chemical and biological. The activities are held mainly by direct methods, that is, independent from cultivation, but monospecific cultures are also used to test specific hypotheses or further characterize microorganisms. The fields of activity cover the biological oceanography, ecophysiology and marine ecology in general.
The laboratory also implements the technical and instrumental approaches for the study of microorganisms, mainly as regards the use of flow cytometry for the monitoring of marine plankton and for the development of early warning systems for biological environmental risk.

Experimental systems

• Thermostated cabinets for growing microalgae and bacteria under controlled light and temperature conditions.
• Tanks for experiments on board ships or outdoors for incubations and manipulations of natural plankton communities.

Analysis

• Counts and measurements of optical parameters (scatter and fluorescence) on cells and unicellular organisms by flow cytometry and epifluorescence microscopy.
• Estimates of growth rates and grazing of picoplankton.
• In situ hybridization with oligonucleotide probes for the characterization of bacterial communities.
• Estimates of DNA content of algae and cell lines by flow cytometry (including dynamics of the cell cycle).
• DNA and RNA extraction for metagenomics and metatranscriptomics.
• Analysis of cellular concentrations of picophytoplankton with scanning flow cytometers at high frequency in both laboratory and on board boats.
• Analysis of concentrations and cellular properties of marine bacteria with prototype automatic coloring module.

Instrumentation

• Conventional flow cytometry.
• Scanning flow cytometer with automated sampling module.
• Laminar flow hood.
• Thermostated cabinets for algal and bacterial cultures.
• Epifluorescence microscope with camera.
• Basic instrumentation for laboratory (centrifuges, thermostated baths, pHmeter, filtration rigs, sonicators, refrigerators and freezers).

Coordinator: Gabriele Procaccini

Scientific activities

Strumentazione di base per la biologia molecolare (PCR, centrifughe, apparati elettroforetici, transilluminatore, bagni termostatici, spettrofotometro, fluorimetro, pH-metro, bilancia di precisione)
Gene gun (apparecchio per la trasformazione biolistica)
In the laboratory of Molecular Ecology and Functional Genomics we carry out studies addressing ecological questions, using molecular approaches. The laboratory covers research  activities ranging from molecular phylogeny and taxonomy to phylogeography and population genetics, using sequence analysis and analysis of polymorphic markers, such as microsatellites and SNPs. It also deals with the study of gene function through functional genomics approaches and reverse genetics (mainly production of transgenic lines of diatoms). We also makes use of analysis of environmental genomics and comparative transcriptomics, and we carry out gene expression studies in natural and controlled conditions (RNA-Seq, RT-qPCR).

Experimental systems

• Mesocosms for maintaining benthic organisms under controlled conditions.
• Walk-in chamber for microalgal cultures.

Analysis

• DNA extraction, purification and quantification.
• RNA extraction, purification, quantification and reverse transcription.
• Protein extraction and quantification.
• Sample preparation for RT-qPCR in plates.
• Samples preparation for massive sequencing.
• Samples preparation for sequence analysis.
• Samples preparation for fragments analysis.
• single and multiplex PCR.
• Electrophoresis on agarose and acrylamide gel.
• Statistical analysis of population genetics and molecular phylogeny.
• Primers design, analysis of electropherograms.
• Cloning and bacterial transformation.
• Preparation of plasmid DNA (mini and maxi prep).
• Biolistic transformation and cultivation of GM crops.
• Algal cultures.
• Colorimetric assays with fluorescent vital dyes and microscopic analysis.
• Southern blot, Northern blot.
• Western blot and enzyme assays (colorimetric, ELISA).
• Use of specialized software for the analysis of protein and nucleotide databases and for the exploration of genomes.

Equipments

• Basic equipment for molecular biology (PCR, centrifuges, electrophoresis apparatus, transilluminator, thermostatic baths, spectrophotometer, fluorometer, pH meter, balance).
• Gene gun (apparatus for biolistic transformation).
• Hoods for algal cultures.
• Microscopes.
• Mixer Mill (Tissue Lyser).
• PC and software for molecular analysis.
• Fume hood.
• TurboGen (equipment for generating marine turbulence).

Coordinator: Daniele Iudicone

Activities

The aim of the laboratory is to support the study of the ecology of marine plankton and  of the ocean physics that is relevant for the plankton ecology. The laboratory of ecological modeling has as main activity the preparation and realization of numerical simulations of the ocean circulation at microscale (DNS), mesoscale (ROMS) and at global scale (NEMO) and of the associated plankton dynamics. The activities are integrated with statistical analysis of environmental (physicochemical) data, ecological (populations) data and biological (metagenomics, functional parameters) data.

Experimental systems

• In-house configurations of numerical codes for simulating the ocean  circulation, the fluid dynamics at the microscale (turbulence) and the impact on microorganisms.
• In-house configurations of numerical codes for simulating planktonic populations at different levels of complexity.
• Turbulence Profiler.
• Devices for the production of marine turbulence in lab (TurboGen).

Analysis

• Analysis of the variability of the ocean physics (including thermodynamics) and biochemistry at various spatial and temporal scales at basin and sub-basin scales.
• Statistical analysis of environmental data and ecological.
• Water mass thermodynamic budgets.

Instrumentation

• Servers and computers for numerical simulations.
• Software for data analysis.
• Software for the simulation of the physics and biology of marine organisms (produced in-house or by external collaborators).

Head: Marina Montresor

Activities

The lab contains equipment and infrastructure used for the study of the functional and taxonomic diversity of marine plankton. In particular, in this laboratory analyses are carried out on the taxonomic and molecular diversity of plankton samples collected at the Long Term Ecological Research site MareChiara in the Gulf of Naples as well as elsewhere, in the frame of participation in regional and global projects. Experimental approaches focus on the physiology and life cycles of marine microalgae and on the feeding behaviour of zooplankton.

Systems for experimentation

• Light- and temperature-controlled walk-in incubator and incubators of different volume for in vivo experiments with phyto- and zooplankton.
• Optical system for video footage of zooplankton organisms.
• Plankton wheel for experimentation with phyto-, micro- and mesozooplankton.

Analysis

• Quantitative analysis of marine phytoplankton and zooplankton.
• Preparation of phytoplankton cultures and their morphological and molecular characterization.
• Phylogenetic analysis.
• "Metabarcode" analysis of marine plankton with Next Generation Sequencing approaches.

Instrumentation

• Stereoscopes and optical microscopes
• Microscope with epifluorescence illumination and digital cameras to take photographs and movies.
• Zooscan with related software.
• Camera System for video-registration of zooplankton movement.
• Area equipped for the isolation of cultures and experimentation (laminar flow hood, microscopes for cell isolation, fluorimeter).
• Molecular Laboratory equipped for DNA extraction, PCR, DNA electrophoresis, preparation for NGS sequencing.

Coordinator: Francesco Paolo Patti

Activities

In the Laboratory of Integrative Taxonomy of Marine Organisms the activities are based on the analysis of classic taxonomy, phylogeny and comparative phylogeography of marine organisms by means of a multidisciplinary integrated approach (morphological, molecular, cellular and ecological). Following the main activities:

• Sample sorting, identification and counting in ecological and monitoring projects (e.g. Marine Strategy).
• Expert identification of organisms using traditional and advanced morphological and molecular methods (including preparation and deposition of genetic and ecological vouchers).
• Extraction and storage of DNA from different organisms (seaweeds and marine invertebrates tissue).
• RNA extraction from different organisms (seaweeds and marine invertebrates tissue).
• Extraction of secondary metabolites.
• Mini-gel electrophoresis and digital documentation.
• PCR amplification of DNA.
• Molecular cloning of target DNA segments (plasmid preps, restriction and PCR analysis).
• Real-Time fluorescent-based polymerase chain reaction.
• DNA barcoding.
• Terminal Restriction Fragment Length Polymorphism.
• DNA sequencing of fragments (in collaboration with SZN Molecular Biology and Bioinformatics Unit).
• Analysis of DNA sequences including the reconstruction of phylogenetic trees.

Systems for the experimentation

• Dedicated lab protocols.
• Bioinformatic systems analysis: 1) study of nucleotide variability (ad-hoc open source software for metadata analysis); 2) decomposing morphotypes forms into size and shape by geometric morphometric methods.

Analysis

• Analysis of DNA sequences including the reconstruction of phylogenetic trees.
• Analysis of the morphological variability and the genetic polymorphism.
• Analysis of allele frequency and genotype distribution.
• Analysis of terminal restriction Fragment Length Polymorphism.
• Preparation of samples for morphological analysis (using dedicated buffer solutions for microscope observations - Stereomicroscope and Scanning Electron Microscope) and molecular analysis (cryopreservation, standards and RNAlater fixatives for tissue preservation).

Equipment

• Stereomicroscope.
• Vibratome.
• Rotavapor.
• Chemical fume hood.
• Laminar flow hood.
• Mini-Gel horizontal electrophoresis systems.
• Refrigerated Bench-top Centrifuge.
• Spectrophotometer "Genequant Pro Classic".
• PCRs (Techne- Euroclone).
• RTPCR BIO RAD Opticon 2.
• Incubator for cell cultures.
• Analytical balance.
• Temperature controlled water bath (5l, +30°C/+120°C).
• Bench-top vortex mixer with general purpose head.
• Vertical laboratory autoclave and steam sterilizer.
• Laboratory Ice Machine.
• Liquid nitrogen dewars (5l+30l).
• Vertical Ultrafreezer -86°C.
• Vertical Freezers -20°C.
• UVP BioDoc imaging workstations for gel documentation and fluorescent imaging.
• Dedicated computer for phylogenetic reconstruction and data mining.