Frontiers Paper on Crustaceans Workflow

Crustaceans Workflow

A scientific paper about the LifeWatch ERIC Crustaceans Workflow was published on 4 January 2023 in Frontiers on Environmental Science, the community-driven and peer-reviewed research journals dedicated to making science open, so that scientists can collaborate better and innovate faster to deliver solutions that enable healthy lives on a healthy planet.

LifeWatch ERIC, the e-Science European infrastructure for biodiversity and ecosystem research, launched the Internal Joint Initiative in October 2019 on Non-indigenous Species and Invasive Alien Species (NIS-IAS) because they are considered one of the major drivers of biodiversity and ecosystem change. In this paper, the case study on the trophic biogeography of invasive crustaceans is presented, describing the procedures, resources, and analytical web services implemented in the Tesseract Virtual Research Environment to investigate the trophic habits of two invasive taxa by using carbon and nitrogen stable isotope data. The case study offers a number of analytical tools to determine the variability of the trophic position of invasive crustaceans in a spatially-explicit context and to model it as a function of relevant environmental predictors.

Literature-based stable isotope data of the Atlantic blue crab Callinectes sapidus and the Louisiana crayfish Procambarus clarkii were used to evaluate the functionalities and outcomes of the workflow. The results of the study reveal, both at population-scale and individual-scale, the existence of significant relationships between temperature related variables and the trophic positions of the two species. At relatively higher temperatures, omnivorous invaders occupy higher trophic levels in food webs and become more carnivorous, which in conditions of climate change is likely to increase their overall impact.

Moreover, the functionalities of the Crustacean Workflow within the Tesseract VRE offered by LifeWatch ERIC can be adapted to a wide range of species, and will be further improved to support researchers in monitoring and predicting trophic-related impacts of NIS-IAS. The VRE will also support policymakers and stakeholders in the implementation of effective management and control measures to limit the negative effects of bioinvaders in recipient environments.

Read or download the whole paper here (Di Muri et al).

Click here for links to two related papers:
“An individual based-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters“
“Individual and population-scale carbon and nitrogen isotopic values of Procambarus clarkii in invaded freshwater systems“

“The Blue Crab” Wins International Prix Italia Festival

Prix Italia

Focused on sustainability, the 74th edition of the international Rai Festival of radio, TV and web productions took place from 4 – 8 October in Bari in southern Italy. The short film, realised by the students of University of Salento DAMS Filmmaking Laboratory in collaboration with LifeWatch ERIC, centres on the Blue Crab, an alien species that is increasingly replacing native species and changing the balance of the marine ecosystems in Europe.

Readers familiar with LifeWatch ERIC’s work will know that it spent its first five years focused on five validation cases on Non-indigenous and Invasive species in the development of its Virtual Research Environment. Students from the University of Salento, host of the LifeWatch Italy node and LifeWatch ERIC Service Centre, chose one of these validation cases as the premise for their submission to the “Sustainability” category of the Prix Italia festival this year: the infamous Blue Crab (Callinectes sapidus).

This year’s theme being sustainability, students of the DAMS course quickly accepted Rai’s invitation to participate in the festival’s YLAB challenge, with a documentary made in collaboration with LifeWatch ERIC, the infrastructure’s Multimedia Production Centre and the Master’s course e-Biodiversity and Ecosystem Sciences (EBES). The short film centres on the Blue Crab, an alien species that is increasingly replacing native species and changing the balance of the marine ecosystem in Europe – a focus for research supported by LifeWatch ERIC. It was produced by the University of Salento DAMS Filmmaking Laboratory under the technical supervision of Emiliano Carico by students Martina Di Noi, Immacolata Parisi, Mirko Clemente, Gaia Pascali, Federica Gianfreda, Alessia Merico, Valentina Capone, Cosimo Micelli, Stefania Bocco and Giorgia Chirico.

The students’ creative efforts paid off during the award ceremony at the Kursaal Theatre on Friday 7 October, where “The Blue Crab” won the YLAB challenge prize! To learn more about the effects of the Blue Crab in Europe, read the paper published in the Biodiversity Data Journal “An individual-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters”.

Following this success, DAMS student Mirko Clemente went to the Italian Alliance for Sustainable Development (ASviS) Festival in Rome on Thursday 20 October to present the winning documentary in the session “Sustainability, Culture and Communication”. The aim of the Festival is to spread awareness about sustainability, make sustainable development a topical issue and draw national and local attention to the problems and opportunities related to the achievement of the SDGs (Sustainable Development Goals of the 2030 Agenda). The videos will soon also be broadcast on Sky.

Watch all the entries now on the LifeWatching Science Channel!

Il granchio blu (in Italian)

Our Earth, Our Home

Sonata breve (in Italian)

About the Prix Italia Festival

The 74th edition of the annual international Festival of radio, TV e web productions took place, organised by the Italian channel Rai, from 4 – 8 October in Bari in southern Italy, with the title “Sustainable Me”. Founded in Capri in 1948, the festival grows in influence each year, with 13 new members participating in the Prix Italia for the first time in 2022, among these Public Service broadcasters of Algeria, Bulgaria, Cameroon, Chile, Cuba, Jordan, Peru and the territory of Kosovo. This time round, the productions entered in the shortlists came from 31 different broadcasters and 23 different countries. Sixty-for competing products were selected by 86 jurors from the 321 works presented: 155 television programmes, 94 radio and 72 web projects. More than just a competition, Prix Italia is a celebration of creativity, with the three days full of conferences, shows, webinars and masterclasses, presented by a variety of international talents and attended by representatives from the UN, the Executive Board EBU (European Broadcasting Union) alongside the most noteworthy European broadcasters.

Second open access data paper published in the Biodiversity Data Journal

procambarus clarkii

The “LifeWatch ERIC Collection of Data and Services Papers” published in the Biodiversity Data Journal is dedicated to the resources and assets developed, upgraded and used during the implementation of the Internal Joint Initiative (IJI), our flagship project focused non-indigenous and invasive species (NIS). Following the debut paper “An individual-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters” (Di Muri et al.) in January, a second open-access data paper in this series was published on 20 October 2022, entitled “Individual and population-scale carbon and nitrogen isotopic values of Procambarus clarkii in invaded freshwater ecosystems” (Di Muri et al.).

Freshwater ecosystems are amongst the most threatened habitats on Earth; nevertheless, they support about 9.5% of known global biodiversity while covering less than 1% of the globe’s surface. One such threat are NIS such as the Louisiana crayfish, Procambarus clarkii. Crayfish species are widely-distributed freshwater invaders and, while alien species introductions occur mostly accidentally, alien crayfish are often released deliberately into new areas for commercial purposes. Native to the south United States and north Mexico, P. clarkii has been introduced in Europe, Asia and Africa, having negative impacts in the majority of invaded habitats where it became dominant, meaning it had become essential to evaluate the ecological consequences and quantify its impact.

The paper presents two geo-referenced datasets of isotopic signatures of the Louisiana crayfish and its animal and vegetable prey in invaded inland and brackish waters. To the best of the authors’ knowledge, this effort represents the first attempt to collate in standardised datasets the sparse isotopic information of P. clarkii available in literature. The datasets provide a spatially explicit resolution of its trophic ecology and can be used to address a variety of ecological questions concerning its ecological impact on recipient aquatic food webs.

The research was carried out within the context of the IJI, more specifically the ‘Crustaceans Workflow’, one of the validation cases used to develop an interdisciplinary Virtual Research Environment that utilises disruptive technologies to deal with the impacts of NIS on native species, genetic diversity, habitats, ecosystem functioning and services, and to inform current practices in environmental management and policy implementation. Stay tuned for the next paper!


ACCESS THE PAPER HERE

“A Window on Science” Renewed for Third Season

AWOS S3

We are back for another season! The first LifeWatch ERIC podcast season focused on the Internal Joint Initiative, the construction of Virtual Research Environments (VREs), and the second drew on the five validation cases used to develop those VREs. Season Three starts up on 20 July 2022, moving a little outside the infrastructure itself into the broader world of Open Science, Invasive Alien Species and practical applications of the LifeWatch ERIC VRE. The first five episodes span the August holiday break:

  • Wednesday 20 July: WoRMS (World Register of Marine Species)
  • Wednesday 3 August: Ocean Optimism
  • Wednesday 7 September: The Critical Zone
  • Wednesday 21 September: Essential Biodiversity Variables, and
  • Wednesday 5 October: The ENVRI Project.

These LifeWatch ERIC podcasts will be embedded in our website portal at the following link (find all of Season 1 here and Season 2 here), and are also available on Spotify, Google Podcasts, Apple Podcasts, and Amazon Music. Our overall purpose is to raise awareness of the good work being done to understand and remedy the damage caused by climate change and anthropogenic pressures. So have a look at the video and take a note of the dates!


A Window on Science Season 3 | Podcast Trailer


Rolling Out Season 2 of the LifeWatch ERIC Podcast “A Window on Science”

LifeWatch ERIC Podcast

While the first LifeWatch ERIC podcast season focused on the Internal Joint Initiative, the construction of Virtual Research Environments, this second season draws on the experiences of the scientists and ICT specialists involved in the five validation cases used to develop said Virtual Research Environments. Five investigations into the impact of Non-indigenous and Invasive Species on a range of environments suffering from climate change and anthropogenic pressures.

Over the next three months, therefore, you will hear from the terrestrial and marine researchers, ICT technicians and software engineers, molecular geneticists and data managers who worked together in trans-disciplinary teams to construct and test five workflows – pipelines of data sourcing and processing – to make that research possible at scales never achieved before. The LifeWatch ERIC podcast season 2 “A Window on Science” features:

  • Wednesday 11 May: The Atlantic Blue Crab
  • Wednesday 25 May: ARMS. Hard-bottom communities
  • Wednesday 8 June: Metabarcoding
  • Wednesday 22 June: Ailanthus, and
  • Wednesday 6 July: Biotope.

Don’t forget that these LifeWatch ERIC podcasts, as well as being embedded in our website portal (find all of Season 1 here and the live episodes of Season 2 here), are also available on Spotify, Google Podcasts, Apple Podcasts, and Amazon Music.

The Next-Generation Research Infrastructure

A Window on Science S1

As promised in the trailer we released a few weeks ago, Season 1, Episode 1 of our brand new podcast ‘A Window on Science’ is now live!

The first season of the LifeWatch ERIC podcast series ‘A Window on Science’ outlines the  steps forward that the European e-Science infrastructure for biodiversity and ecosystem research has made in the last two years, developing cutting-edge services for researchers. Our CEO, Christos Arvanitidis, opens the series, walking us through terminology that may seem challenging to non-scientific audiences: Research Infrastructures, the Joint Internal Initiative, and virtual servers. The conversation places LifeWatch ERIC clearly in the context of the European Research Area and outlines not only the progress already made, but strategic plans for the next five years – becoming ‘the next-generation Biodiversity and Ecosystem Research Infrastructure’.

If you’re interested in the topics covered in this podcast, and want to find out more, we invite you to visit our dedicated minisite on the Internal Joint Initiative, or to flick through our ‘Alien Alert!’ magazine.

The Window on Science podcasts are available on our website and on the following platforms:

A Window on Science

Podcasts

LifeWatch ERIC, the European e-Science Infrastructure for Biodiversity and Ecosystem Research, is launching a new podcast series. Entitled “LifeWatch ERIC: A Window on Science”, the fortnightly 10-minute broadcast is geared towards the widest possible audience, from researchers to informaticians, and from politicians to ordinary people concerned about climate change and the environment. 

Starting on 16 March 2022, the early episodes will focus on the Internal Joint Initiative, LifeWatch ERIC’s core activity in its first five years: the development of a new, innovative Virtual Research Environment focused on Non-indigenous and Invasive Species. And if that sounds complicated to you, perhaps you would do well to tune into the first few podcasts, designed to demystify some of that science-speak.

As Christos Arvanitidis, CEO of LifeWatch ERIC commented, “The podcasts are offered as an easy-to-digest communication to raise awareness of our work beyond the scientistic communities already involved. We’re hoping they will have a great impact and attract more users to our next-gen Big Data management facilities”.

The Window on Science podcasts are available on our website and on all major podcast platforms:

Series One. Introducing the Internal Joint Initiative:

16 March Trailer

30 March LifeWatch ERIC Chief Executive Officer, Christos Arvanitidis

12 April    Alberto Basset, Director of the LifeWatch ERIC Service Centre, Lecce

27 April    LifeWatch ERIC Chief Technology Officer, Juan Miguel González-Aranda

Stay tuned, more details on Seasons Two and Three coming up soon!

Debut open access paper published in the Biodiversity Data Journal

Biodiversity Data Journal

The “LifeWatch ERIC Collection of Data and Services Papers” published in the Biodiversity Data Journal is dedicated to the resources and assets developed, upgraded and used during the implementation of the Internal Joint Initiative (IJI), our flagship project focused non-indigenous and invasive species (NIS). The first open-access data paper in this series was published on 25 January 2022, entitled “An individual-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters” (Di Muri et al.).

The paper presents compiled datasets of isotopic signatures of the Atlantic blue crab and its prey in invaded coastal and transitional habitats. The analysis of these data can be used to calculate the trophic position of the invader, evaluate its adaptation within new ecosystems and investigate changes in the structure and functioning of invaded food webs.

Having already colonised most of the eastern and central Mediterranean Sea and the Black Sea in recent decades, the Atlantic blue crab is currently widening its distribution towards the western region of the basin. Its impact within invaded habitats was assessed in a number of studies using stable isotope analysis, and Di Muri et al. have combined the results into a geo-referenced dataset.

The research was carried out within the context of the IJI, more specifically the ‘Crustaceans Workflow’, one of the validation cases used to develop an interdisciplinary Virtual Research Environment that utilises disruptive technologies to deal with the impacts of NIS on European native species, genetic diversity, habitats, ecosystem functioning and services, and to inform current practices in environmental management and policy implementation. Read about the second paper in the series here.

Researchers grab chance to experiment with LifeWatch ERIC tools at Hands-on Session

Screenshot of Hands-on Session featuring smiling participants

On Friday 4 June 2021, as a follow-up to the successful e-Science for NIS Research Workshop on 20-21 May, LifeWatch ERIC gave researchers the opportunity to try out LifeWatch ERIC-developed software at a Hands-on Session. It marked the debut of key tools built by LifeWatch ERIC as part of its Internal Joint Initiative (IJI) in its quest to facilitate open access data in the domains of biodiversity and ecosystem research.

All training resources, including presentations, demos and manuals are available through the LifeWatch ERIC Training Platform. (Please note, those who missed out on the Session can find the relevant materials simply by following the link to the training programme and creating an account).

After an introduction from CTO and ICT-Core Director Juan Miguel González-Aranda, together with Service Director Alberto Basset, the floor was given to technical staff, Lucia Vaira, Xeni Kechagioglou, Antoni Huguet Vives, Nikos Miandakis and Antonio José Saénz Albanés, to explain and demonstrate the Metadata Catalogue and the Tesseract VRE, which was illustrated using the Crustaceans Workflow (presented at the Workshop on 20 May). After the presentations and demonstrations, participants were given the opportunity to try the services and workflows for themselves, interacting with the trainers who provided guidance and feedback.

The session was brought to a close with input from Juan Miguel González-Aranda, who reiterated the importance of continued feedback and exchange with the scientific community in order for LifeWatch ERIC to refine and improve its services. CEO Christos Arvanitidis then thanked everyone who took part, noting that the Session was just the beginning of the results LifeWatch ERIC has to showcase after its first five years of hard work alongside dedicated collaborators. He also highlighted that LifeWatch ERIC is leading an important Work Package as part of the EOSC Future project, and how the efforts of everyone involved will ensure that LifeWatch ERIC services can be deployed on the EOSC platform, benefiting a wider audience than ever before.

LifeWatch ERIC showcases: new technology for biodiversity researchers

The 20–21 May was an important milestone for the LifeWatch ERIC, as it hosted its long-anticipated e-Science for NIS workshop, albeit in a virtual form due to the ongoing pandemic. The workshop was organised with the support of ENVRI-FAIR, and was hugely successful, attracting over 220 registrations. The aim of the event was to showcase the results of five research endeavours, known as validation cases, into Non-indigenous and Alien Species (NIS) conducted over the last 18 months within the LifeWatch ERIC Internal Joint Initiative.

These validation cases led to the development of five separate workflows, created through the joint effort of scientists and ICT experts, both from LifeWatch ERIC Common Facilities and Distributed Centres, to accommodate the data and analytical processes generally required by the NIS scientific community. In turn, these workflows have been integrated into Tesseract technical composability layer, the new Virtual Research Environment (VRE) platform being developed by LifeWatch ERIC. Both the innovative advances in technology and the associated scientific reports sparked engaged and enthusiastic discussion over the two days. In fact, the workshop proved to be particularly appreciated by attendees, with 85% rating it as “very good” or “excellent”, as well as the web-services presented also considered “very good” or “excellent” by 78% of participants.

LifeWatch ERIC is at the service of the biodiversity and ecosystem research community, and is constantly seeking to create opportunities for mutual exchange. For this reason, the presentations of the validation cases were complemented by a series of round tables, featuring academics and experts from a wide range of fields. The speakers debated the ecological, economic and social impact of NIS, and the need to work across disciplines, combining social and natural sciences. The final consensus was that greater coordination of data collections is required in order to integrate existing data from different sources, and find ways to enable access to such collections.

Non-indigenous Invasive Species have enormous impacts on ecosystem services, human health and on the economy. This is why LifeWatch ERIC was proud to present the results of the validation cases providing powerful and flexible workflows capable of integrating more data and services than has yet been possible. The workflows will be available in the LifeWatch ERIC Tesseract VRE, which among its many innovative functions, enable the import of data from different sources, their exploration in maps for validation, and the use of standard tools to connect data analytics through its HPC and cloud-related technologies. Tesseract is also built around the unique LifeWatch ERIC tool known as LifeBlock, which uses Blockchain technology to ensure the integrity of all data inputs and full recognition for contributors. The VRE is not only an innovative tool that can be customised to other bioregions, but it will continue to evolve in the light of future feedback from scientists. In the long run, the use of Tesseract will contribute to boosting social awareness about biodiversity and help policymakers concerned about habitat conservation to implement sound science-based decisions.

LifeWatch ERIC would like to take this opportunity to acknowledge the superb efforts of all the team members involved, and to thank ENVRI-FAIR Science Cluster for its support during the workshop, as well as all the wonderful speakers and participants who actively contributed to make this 2-day workshop a success and with whom LifeWatch ERIC hopes to continue working in the future.

The recording of the workshop will shortly be made available, in the meantime, you can find the workshop presentations here.