Assemble+

EMBRC to continue the work of ASSEMBLE Plus: Stimulating European excellence in marine biology and ecology research.

avril@aquatt.ie — Thu, 13 Oct 2022 09:24:02 +0000

After five successful years, the EU Horizon 2020-funded project, ASSEMBLE Plus (Association of European Marine Biological Laboratories Expanded) has closed and the European Marine Biological Resource Centre (EMBRC) will ensure the continuation of its legacy.

Launched in 2017, ASSEMBLE Plus provided scientists from academia, industry and policy with access to over 30 marine installations in 16 countries. Through specific initiatives such as the Transnational Access Programme, Networking Activities and Joint Research Activities (JRAs), ASSEMBLE Plus stimulated European excellence in fundamental and applied research in marine biology and ecology. Research outputs supported by ASSEMBLE Plus have improved European knowledge and technology bases for applications in blue economy, policy and education.

Key achievements of ASSEMBLE Plus include:

Supporting over 500 international researchers from 46 different countries with their projects, while also enabling new strands of research by funding pilot projects.
Introducing scientists to new facilities as well as offering training, networking and collaboration opportunities for hundreds of early career scientists.
Supporting two initiatives for genomic observations: Ocean Sampling Day (OSD) and Autonomous Reef Monitoring Structures - Marine Biodiversity Observation Network (ARMS-MBON).
Developing open access protocols for genetic manipulation and cryopreservation of marine organisms, camera-based underwater surveying techniques, and novel experimental platforms.
Producing open access data to support further research and advocating for the importance of applying FAIR data principles to all marine research.

In parallel to ASSEMBLE Plus (2017-2022) and the previous, FP7-funded ASSEMBLE project (2009-2014), EMBRC was developed as a long-term research infrastructure to support marine biological research. Today, EMBRC is Europe’s leading research infrastructure for marine biological resources with a mission to support marine biological and ecological research as well as innovation. EMBRC also works to raise awareness of marine biological research, its application, and relevance for society and policy. EMBRC will ensure that the legacy of ASSEMBLE Plus will continue beyond the project, specifically:

Researchers will still be able to access ASSEMBLE Plus facilities via the EMBRC network.
Platforms and protocols developed during ASSEMBLE Plus are available on the EMBRC’s Service Catalogue.
Genomic observation initiatives will continue: ARMS-MBON will be included in the European Marine Omics Biodiversity Observation Network (EMO BON) and OSD will become All Atlantic Sampling Day as part of the AtlantEco project.

Dr Nicolas Pade, ASSEMBLE Plus Scientific Coordinator and Executive Director of EMBRC said,

“I am delighted that EMBRC will be able to continue the important work that ASSEMBLE Plus has started. Collaboration is the key to successful research. Sharing ideas, working with people from different disciplines and visiting other institutions and facilities are all vital tools that will help us to understand and tackle the problems facing our marine environments. We look forward to working with the ASSEMBLE Plus alumni and community for many years to come!”

For more information about the outputs and legacy of ASSEMBLE Plus, please visit assembleplus.eu or download the final project newsletter. For information about EMBRC, visit embrc.eu.

Notes for Editors

About ASSEMBLE Plus

For more information about the project, please visit assembleplus.eu or email assembleplus_ta@embrc.eu. Follow @ASSEMBLE_Plus on Twitter for regular updates from the project.

For ASSEMBLE Plus queries, please contact Mercedes Arjona mercedes.arjona@sorbonne-universite.fr.

For EMBRC queries, please contact the EMBRC Secretariat at secretariat@embrc.eu.

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement no. 730984 (ASSEMBLE PLUS). This output reflects only the author’s view and the European Commission cannot be held responsible for any use that may be made of the information contained therein.

About EMBRC

EMBRC (European Marine Biological Resource Centre) enables researchers to better understand the ocean's biodiversity by facilitating access to marine organisms and their ecosystems, while providing the necessary services, facilities and other resources to support innovative research. Services are provided by more than 70 sites in ten member countries: Belgium, France, Greece, Israel, Italy, Norway, Portugal, Spain, Sweden and the United Kingdom. Read more about how to access EMBRC services or watch the ABCs of using EMBRC video.

In addition to providing various services, EMBRC contributes to European and international projects. Diverse in scope and country involvement, these projects aim to enhance EMBRC activities and/or services, strengthen collaboration with similar European organisations, structure the research community and provide services to support research. You can learn more about the projects EMBRC are involved in by visiting the EMBRC Projects page.

A Window on Science: ARMS hard-bottom communities

avril@aquatt.ie — Fri, 07 Oct 2022 13:18:30 +0000

Marine Biodiversity Observation Networks (MBON) are a growing global initiative consisting of regional networks of scientists, resource managers and end users, working to integrate data from existing long-term programmes. The aim is to improve our understanding of changes and connections between marine biodiversity and ecosystem functions. Within ASSEMBLE Plus’s Joint Research Activity 1 (JRA1) there are two genomic observation networks: Ocean Sampling Day (OSD) and Autonomous Reef Monitoring Structures (ARMS-MBON).

ARMS are placed in European coastal waters and retrieved on a regular basis. The aim is to assess the status of, and changes in, hard-bottom communities of near-coast environments, using genetic methods supplemented with image analysis and visual inspection methods. Hard-bottom communities live on coastal seafloors. Studying them has revealed an unprecedented complexity of organisms, many of which have never been observed before! Listen to ASSEMBLE Plus partners, data manager Katrina Exter (VLIZ) and network coordinator Matthias Orbst (UGOT) feature on the LifeWatch ERIC 'A Window on Science' podcast season 2 episode 2. The second season of the series looks at the research cases that validated the development of Virtual Research Environments – online tools and services that enable biodiversity and ecosystem research at scales never before achieved.

Listen to Season 2 Episode 2: ARMS. Hard-bottom Communities.

ASSEMBLE Plus final newsletter – Out now!

avril@aquatt.ie — Thu, 06 Oct 2022 11:07:12 +0000

We are pleased to announce that the fifth and final issue of the ASSEMBLE Plus newsletter is out now!

In this issue, our coordinator Nicolas Pade focuses on the legacy of ASSEMBLE Plus and how the project will continue to live on and have impact through EMBRC. We also meet four users from our Transnational Access Programme and hear their Success Stories as well as all the latest news and event reports from our consortium.

To receive ASSEMBLE Plus news straight to your mailbox please subscribe here.

Download ASSEMBLE Plus Newsletter Issue 5.

Ocean Sampling Day – Data now available!

avril@aquatt.ie — Fri, 09 Sep 2022 13:06:14 +0000

OSD is a simultaneous worldwide research campaign where marine biologists around the globe participate in sampling of the world’s oceans to produce contextual genomic data. OSD was launched by the MicroB3 project in the summer, on the solstice, 21 June 2014, with ASSEMBLE Plus taking on the OSD coordination in 2018. Through MBONs collecting cumulative samples, related in time, space and environmental parameters, researchers can gain invaluable insights into the marine environment, including insights into the changes in biodiversity as a result of climate change and the introduction of non-native species by shipping, etc. DNA analysis with chosen marker genes allows us to identify all prokaryotic and eukaryotic microbial species in the water samples obtained, while analysis of metagenomic data allows us to assess the functional content and potential of bacterial communities. Among the many questions that the data can answer, the basic ones include ‘’what organisms are found where’’ and ‘’what functions they can fulfil, under the assessed environmental conditions’’. All the samplings were carried out in a standardised way to allow comparability among samples and an accurate tracking of changes in the marine environment over time. The data collected will be a reference data set for generations of experiments to follow in the coming decades. One particular project that has benefitted from OSD data is the European Marine Omics Biodiversity Observation Network (EMO BON), an EMBRC project aiming to enhance the European contribution to global genomic observation efforts.

Since 2018, the ASSEMBLE Plus partner, the Hellenic Centre for Marine Research (HCMR) in Heraklion, Crete, have coordinated OSD, received and processed all the samples as well as extracted the DNA and sequenced 16S and 18S rRNA. Shotgun metagenomics data have also been produced by GENOSCOPE, France.

An important effort was necessary to find the best ways to make the data open access and FAIR (Findable, Accessible, Interoperable and Reusable), this was achieved by collaboration between the Flanders Marine Institute (VLIZ), the German Federation for Biological Data (GFBio) and HCMR. There is no one best route to data FAIRification, and there is still room for improvement in the interoperability between databases hosting biodiversity and environmental data and databases hosting molecular data. OSD data FAIRification has inspired collaborative projects between the European infrastructures European Marine Biological Resource Centre (EMBRC ERIC), ELIXIR Europe, and LifeWatch ERIC, within the context of the European Open Science Cloud (EOSC).

The cost of sequencing has been covered by EMBRC. The value of FAIR data will increase with time, as any new environmental dataset can be compared to it, to add insights on marine biodiversity structure, function and dynamics. As the quantity of genomic data on single species will increase with time, and high quality genomic and biological annotations will be added, OSD data can be revisited and reanalysed delivering more knowledge.

HCMR has carried out a preliminary analysis on the DNA metabarcoding of the OSD 16S rRNA data, to gain insights into the value of the data. These analysis results (species identifications) and the raw sequence data are published, to be shared for exploration with experts around the world. The OSD 2018 and 2019 sampling, environmental, and raw sequence data are published as a metadata record via VLIZ’s Integrated Marine Information System (IMIS); the OSD 2014 data have long been published on PANGAEA. Species identifications obtained from all three years of OSD will also shortly be submitted to biodiversity archives (OBIS, GBIF).

The datasets and metadata are also available via the OSD GitHub Repository which also provides the data in machine-accessible formats, ensuring the data is in compliance with H2020’s Open Research Data Pilot, following the principles of FAIR (Findable, Interoperable, Accessible and Reusable).

For any questions, information, or assistance, contact the OSD team by sending an email to osd-contact@embrc.eu. For more information, please visit the OSD webpage. You can also watch previous videos at the OSD YouTube channel.

Notes for Editors

ASSEMBLE Plus’s Joint Research Activity 1 (JRA1) Genomics Observatories, fosters the application of genomics technologies at Long Term Ecological Research Network (LTER) sites. Research encompasses populating and verifying databases of taxonomic reference barcodes, harmonisation of metabarcoding standard operating procedures (SOPs) across the consortium so that the resulting data can be compared across the partnership, and inter-calibration of classical biodiversity data and genomics data (metabarcoding, meta-transcriptomics, etc.). The results will be the establishment of a distributed Genomics Observatory across the partnership and beyond of which the data are available for virtual access. The project began in October 2017 and will run until September 2022. The project is coordinated by Sorbonne Université.

New approaches for aquaculture and mollusc research as study shows cryopreserved mussel larvae can survive and develop to adult mussels

avril@aquatt.ie — Tue, 16 Aug 2022 08:57:34 +0000

A long-term study funded by the ASSEMBLE Plus project has shown that adult mussels can grow from cryopreserved larvae without compromising the quality of the next generation’s offspring, neither for cryopreservation nor post-thawing development of them.

The Mediterranean mussel Mytilus galloprovincialis is one of the most farmed molluscs worldwide. This is the first time M. galloprovincialis spat produced from cryopreserved larvae were able to develop into adults at the same growth rates as control individuals, be cultured in a natural environment, and even reach average commercial size at the same time as control mussels obtained from non-cryopreserved larvae. Additionally, the viability of the produced adults is apparently unaffected by the cryopreservation process, with fertility and offspring quality comparable with those of control mussels.

Dr Estefania Paredes, Universidade de Vigo, who led the research team that designed the cryopreservation protocol said,

“Shellfish aquaculture needs the development of new tools such as this to reduce its reliance on natural spat collection whilst improving good practices and efficiently increasing production. The results signify strong evidence for the suitability of this cryopreservation method for use in mussel aquaculture and in research, where animals must be in optimal health.”

Details of the cryopreservation protocol are published in the open access Scientific Reports (August 2022): Heres, P., Troncoso, J. and Paredes, E. (2022). Long-term study on survival and development of successive generations of Mytilus galloprovincialis cryopreserved larvae. Scientific Reports 12, 13632. https://doi.org/10.1038/s41598-022-17935-0.

Notes for Editors

ASSEMBLE Plus’s Joint Research Activity 2 (JRA2) Cryobanking Marine Organisms, addresses a constraint in the exploitation of marine genetic and biological resources, namely the current paucity of capability for preserving these resources ex-situ with guaranteed genetic, phenotypic and functional stability. JRA2 has developed reproducible cryopreservation methodologies for various life-stages of a range of marine macro-organisms and cryo-recalcitrant microorganisms. The results will improve and expand the availability of biological resources for Transnational Access at significantly reduced costs. ASSEMBLE Plus began in October 2017 and will run until September 2022. The project is coordinated by Sorbonne Université.

Image 1: Jesus Troncoso checking the mussels growing to adults in ropes after cryopreservation of the larvae. © Jesus Troncoso.

Image 2: Juvenile mussels (from cryopreserved larvae) settled in ropes with their growth being checked. © Pablo Heres and Estefania Paredes

About ASSEMBLE Plus

For more information about the project, please visit assembleplus.eu or email . Follow @ASSEMBLE_Plus on Twitter for regular updates from the project.

For press queries, please contact Mercedes Arjona mercedes.arjona@sorbonne-universite.fr.

Research contact from the Universidade de Vigo: Estefania Paredes eparedes@uvigo.es

ASSEMBLE Plus researchers deliver findings and protocols to support future genomics research

avril@aquatt.ie — Thu, 11 Aug 2022 17:04:25 +0000

The Horizon 2020-funded project, ASSEMBLE Plus, has a goal stimulate excellence in European research in marine biology and ecology, thereby improving our knowledge- and technology-base for the blue economy, policy and education. Sitting within ASSEMBLE Plus are five research activities covering both applied and fundamental research. One such research activity is entitled “functional genomics”.

Technology has advanced in recent years to make it is quite easy to obtain whole genome or transcriptome data. Whilst much research is focused on this area, it is also vital to study specific functions of single genes to gain a full understanding of how genomes function. However, it is challenging to perform these kinds of functional studies in non-classical biological model organisms. ASSEMBLE Plus through its “functional genomics” research activity is responding to this call.

ASSEMBLE Plus partners have been performing single-gene function studies using up-to-date approaches such as CRISPR-Cas9. This activity has developed new and built upon existing knowledge relating to both, the genetic transformation and genome editing of selected model marine organisms, ranging from bacteria to metazoans (animals).

Multiple publications and protocols are beginning to be generated by the project ensuring that these results are shared. To provide a broad overview, the findings are summarised below:

Descriptions of the outcomes of the Assemble Plus project that have occurred over the course of the project, including:
- Ectocarpus as a model organism to study diverse aspects of brown algal biology¹
- Light regulation in marine Synechococcus cyanobacteria³
- Tail regeneration in the Bahamas lancelet, Asymmetron lucayanum^4,5
- Development of the nerve cord in the Neptune’s Heart Sea Squirt⁸
- Identification of a new “cryptic species” - an animal that appears identical but differs genetically - Asymmetron rubrum¹¹
Established links between genomic information and phenotypes of marine model species, including:
- Amphioxus, a marine animal representing the earliest diverging evolutionary lineage of all chordates - animals that possess a dorsal notochord in at least some developmental stage, including vertebrates²
Reference sets of carefully phenotyped or genotyped genetic resources of different marine organisms ranging from bacteria to metazoans, including:
- Urochordates, cephalochordates, cnidarians, brown algae, cyanobacterias, etc
The development of specific protocols for generation of genetic resources for a panel of emerging/prospective marine model organisms, including:
- Generation of strains of the jellyfish species Clytia and maintain their whole life cycle in the laboratory⁶
- Manipulation and transformation of amphioxus embryos⁷
- Transformation of marine Synechococcus cyanobacteria strains^9,10
- Transformation protocols for different ascidian species

“Developing these techniques for a broad range of organisms might not have an obvious application now; however, they can be expected to have a long or midterm impact on society. We are looking at species that are representative of all different organisms from microorganisms to metazoans and so our findings can be adapted and applied by other labs for any organisms, and for different applications” said Hector Escrivá, the Work Package leader for Functional Genomics who is based at the Observatoire Océanologique de Banyuls-sur-Mer (OOB) in France.

The project anticipates that many more publications, datasets and protocols will be released as the project progresses. The protocols developed are for metazoans, macroalgae and microorganisms that represent strategically important resources for academia and also for industry (e.g. bio-actives for food, feed, pharmaceuticals and cosmetics).

To stay up-to-date on the project’s progress, please join the ASSEMBLE Plus mailing list or contact the Work Package leader, Hector Escrivá (CNRS) for more information. A full list of ASSEMBLE Plus publications can be found at: /projects/assembleplus/results/publications

Funding

This project has received funding from the European Commission’s Horizon 2020 research and innovation programme under grant agreement No 730984 (ASSEMBLE Plus). This output reflects the views only of the author(s), and the European Commission cannot be held responsible for any use which may be made of the information contained therein. The project began in October 2017 and will run until September 2022. The project is coordinated by Sorbonne Université.

About ASSEMBLE Plus

Website: assembleplus.eu

Twitter: @ASSEMBLE_Plus

For press queries, please contact Mercedes Arjona (mercedes.arjona@sorbonne-universite.fr)

References

Badis, Y., Scornet, D., Harada, M., Caillard, C., Godfroy, O., Raphalen, M., Gachon, C.M.M., Coelho, S.M., Motomura, T., Nagasato, C., and J.M. Cock (2021) Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. New Phytologist. doi: 10.1111/nph.17525.
Bertrand, S., Carvalho, J.E., Daug, A D., Matentzoglu, N., Daric, V., Yu, J.-K., Schubert, M., and H. Escrivá (2021) The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). Frontiers in Cell and Developmental Biology, 9(992). doi: 10.3389/fcell.2021.668025.
Grébert, T., Nguyen, A.A., Pokhrel, S., Joseph, K.L, Ratin, M., Dufour, L., Chen, B., Haney, A.M., Karty, J.A., Trinidad, J.C., Garczarek, L., Schluchter, W.M., Kehoe, D.M, and F. Partensky (2021) Molecular bases of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria. Proceedings of the National Academy of Sciences, 118 (9) e2019715118. doi: 10.1073/pnas.2019715118.
Holland, N.D., and I.M.L. Somorjai (2020^a) Tail regeneration in a cephalochordate, the Bahamas lancelet, Asymmetron lucayanum. Journal of Morphology. doi: 10.1002/jmor.21297.
Holland, N.D., and I.M.L. Somorjai (2020^b) Serial blockface SEM suggests that stem cells may participate in adult notochord growth in an invertebrate chordate, the Bahamas lancelet. EvoDevo, 11(1):22. doi: 10.1186/s13227-020-00167-6.
Lechable, M., Jan, A., Duchene, A., Uveira, J., Weissbourd, B., Gissat, L., Collet, S., Gilletta, L., Chevalier, S., Leclère, L., Peron, S., Barreau, C., Lasbleiz, R., Houliston, E., and T. Momose (2020) An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica. Biology Open, 9(11). doi: 10.1242/bio.051268.
Le Petillon, Y., Bertrand, S., and H. Escrivá (2020) Spawning Induction and Embryo Micromanipulation Protocols in the Amphioxus Branchiostoma lanceolatum. In: Sprecher S. (eds) Brain Development. Methods in Molecular Biology, vol 2047. Humana, New York, NY. doi: 10.1007/978-1-4939-9732-9_19
McDougall, A., Hebras, C., Gomes, I., and R. Dumollard (2021) Gene Editing in the Ascidian Phallusia mammillata and Tail Nerve Cord Formation Methods and Protocols. Methods in Molecular Biology, 2219. doi: 10.1007/978-1-0716-0974-3_13.
Ratin, M., Garczarek, L., Grébert, T., and C. Halouze (2019^a) Transformation of marine Synechococcus strains by conjugation [protocol]. ID: 27861.
Ratin, M., Garczarek, L., Grébert, T., and C. Halouze (2019^b) Transformation of marine Synechococcus strains by electroporation [protocol]. ID: 27854.
Subirana, L., Farstey, V., Bertrand, S., and H. Escrivá (2020). Asymmetron lucayanum: How many species are valid? PLOS ONE, 15(3): e0229119. doi: 10.1371/journal.pone.0229119.

Discovery of new marine worm species as part of Horizon 2020 project, ASSEMBLE Plus

avril@aquatt.ie — Thu, 11 Aug 2022 16:24:43 +0000

Researchers from the Swedish Museum of Natural History have identified a new species of marine worm living in the Basque region of Spain. Named Faerlea assembli, the worm is just 0.8mm long and was discovered as part of research conducted at Plentzia Marine Station.

The new species belongs to an important group of worms known as the Acoelomorpha. These small, soft-bodied worms are abundant throughout many different types of marine sediment. They form a key part of marine food chains and studying their populations offers a way for scientists to monitor the overall health of different environments. Acoelomorphs are particularly sensitive to human impact and their diversity is reduced in areas such as beaches that are visited by many tourists.

The new species, Faerlea assembli belongs to the Mecynostomidae family of acoelomorphs. This group is most abundant in shallow, sandy sediments and therefore they are particularly vulnerable to impacts by human activities. It is a fragile species with limited, localised distributions.

Professor Ulf Jondelius led the research team that identified the new species. Commenting on the significance of the finding, he said

“When it comes to understanding the diversity of marine life, we are still only scratching the surface. Small marine species such as this are often over-looked yet they play crucial roles in marine ecosystems. Identifying new species, such as Faerlea assembli, provides a first step in gathering the data needed for wider population studies to monitor environmental status.”

The project was conducted as part of a visit Professor Jondelius made to the Plentzia Marine Station supported by the European-funded, Horizon 2020 project, ASSEMBLE Plus and the new species was named to reflect this support.

The ASSEMBLE Plus Transnational Access Programme provides funding for researchers to carry out their own projects using resources not available in their home institutes. With access to over 30 marine biological stations and installations, the initiative helps participants to enhance their skills, create new collaborations and contribute to scientific understanding.

Details about the new species are published in the Zoological Journal of the Linnean Society (October 2021). Atherton, S. and Jondelius, U. (2021). Phylogenetic assessment and systematic revision of the acoel family Isodiametridae. Zoological Journal of the Linnean Society, zlab050. https://doi.org/10.1093/zoolinnean/zlab050

Notes for Editors

The ASSEMBLE Plus project received funding from the European Commission’s Horizon 2020 research and innovation programme under grant agreement No 730984 (ASSEMBLE Plus). This output reflects the views only of the author(s), and the European Commission cannot be held responsible for any use which may be made of the information contained therein. The project began in October 2017 and will run until September 2022. The project is coordinated by Sorbonne Université.

About ASSEMBLE Plus

Website: assembleplus.eu

Twitter: @ASSEMBLE_Plus

For press queries, please contact Mercedes Arjona (mercedes.arjona@sorbonne-universite.fr)

Research contacts from the Swedish Museum of Natural History:

Dr Sarah Atherton sarah.atherton@nrm.se and Prof Ulf Jondelius ulf.jondelius@nrm.se.

Image is of the newly identified Faerlea assembli worm species (image credit Ulf Jondelius)