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Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics

Periodic Reporting for period 1 - EnvMetaGen (Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics)

Reporting period: 2015-09-01 to 2016-11-30

The overall goal of EnvMetaGen project is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, in the area Environmental Metagenomics. It aims to strengthen the research potential of human resources, lab facilities and next-generation genome sequencing equipment (funded by a FP7 CAPACITIES project), addressing and supporting the emerging research line in environmental metagenomics regarding applications in biodiversity conservation, invasive species control, ecosystem services assessment, as well as environmental (bio)monitoring.
EnvMetaGen is important for society as it is predicted to contribute to the regional and national smart specialization strategies, as the overall objectives are to develop tools and approaches to foster environmentally sustainable development, and strengthening innovation and knowledge transfer activities, raising the international and national network of collaborations and partnerships, in close collaboration with local and global industrial partners, as well as with governmental agencies. In addition, the project has the objective to contribute to the advanced training of highly-qualified human resources, and to the communication, dissemination and exploitation of InBIO’s research and innovation in this emerging field.
Summary of work carried out during the reporting period and main results

Recruitment of the ERA Chair Team (WP2)
A nearly complete ERA Chair Team recruitment, consisting of the ERA Chair holder, the ERA Chair Research Team and the ERA Chair Support Team, was accomplished during this reporting period. The only exception was for the for the Knowledge Transfer and Dissemination officer KTDO, who was recruited in mid-December 2016.

Building of partnering Networks (WP3)
The ERA Chair holder, visited the University of St Andrews, Scotland, UK. He gave two presentations related to the research being conducted in the EnvMetaGen project. Collaborative arrangements for diet analysis by DNA metabarcoding were discussed.
The ERA Chair holder also made a visit to Queen Mary University of London to give a departmental seminar on the EnvMetaGen project. Discussions on various possibilities for collaborative projects were held.
A partnership was also established with the DNAqua-Net COST EU Action. This partnership is opening up for new collaborations between the two projects.

H2020 training courses (WP3)
Three training courses were attended by personnel involved in the EnvMetaGen project. Attended courses:
- Horizon 2020 Training course “Developing Winning Proposals”, Cambridge, UK.
- Horizon 2020 Training course “A Practical Approach on Horizon 2020 Grant Writing”, Brussels, Belgium.
- Workshop on “Finance in Horizon 2020” held in Cambridge, United Kingdom.

Deployment of an eDNA laboratory and Building capacity for eDNA analysis (WP4)
Acquisition of the equipment related to the computational activities have largely been concluded and the efforts in implementing capacity building in environmental genomics at InBIO is ongoing regarding: (i) Building and organising reference collections of DNA sequences, (ii) Collecting and conserving eDNA samples, (iii) Lab analysis of eDNA samples, and (iv) Analysing the outputs of next-gen DNA sequencing platforms.

Project Communication and Dissemination Plan (WP6)
A first version of the Communication and Dissemination Plan for EnvMetaGen was elaborated and submitted to the EC project portal.

Newsletters, Website and Social Media (WP6)
The EnvMetaGen project activities, news and events which have been occurring till date of the project have been disseminated and communicated through the Weekly CIBIO-InBIO Newsletter, via Social Media, the CBIO-InBIO website and now more recently via the newly developed and fully EnvMetaGen dedicated website (

Participation in Workshops and Conferences (WP6)

Conference attendance
EnvMetaGen Team members have during the reporting period participated and given both oral and poster presentations at the International Longterm Ecological Research first global Open Science Meeting (South Africa), the XVII Congresso Ibérico de Entomologia (Portugal), the International Bat Research Conference (South Africa), the Congenomics 2016 – Conference on Conservation Genomics (Portugal), and the “Encontro sobre Biodiversidade e Conservação de Invertebrados em Portugal” (Portugal).

Workshop/course attendance and other Communication and Dissemination events
Vanessa Mata, PhD student, attended the Summer school in ecology and integrative biology, part of the TULIP LABoratory of EXcelence (INRA, France).
The post-doctoral researcher Joana Paupério presented EnvMetaGen project activities at the Instituto Politécnico de Bragança (UTAD), Vila Real.
The post-doctoral researcher Joana Paupério, gave a talk to classes of the 10th and 11th grade on the subject of Biodiversity Barcoding in the scope of the Darwin Day.
The EnvMetaGen Project Manager participated in a workshop entitled “Open Access and Open Data in Horizon 2020” (OpenAIRE), Coimbra, Portugal.
Three seminars were organized in the scope of the EnvMetaGen project objectives:
- “Environmental Metagenomics” (Simon Jarman, June 2016).
- “Integrated Analysis of
The societal impact of the project so far has been to introduce a new research group for environmental metagenomics that will act as a focus for this research area within the Portuguese scientific community. This group has had extensive contact with the wider scientific community within Portugal and also with the general community. Recruitment of scientists to work within the group has had a clear local impact on the community as it has allowed two Portuguese nationals to return to their home country; and three other European Community nationals from Sweden, Ireland and the UK are employed there also. This creates integrative links between other EU countries and the community of the North region of Portugal. Steps have been taken to develop the field of environmental metagenomics beyond the state of the art, but this research is still in its early stages as staff have only just been recruited to undertake the work. New developments in this area will become apparent with time.
EnvMetaGen - Water sampling