LifeWatch ERIC just launched an Internal Joint Initiative (IJI) focusing on the topic of Non-indigenous and Invasive Species (NIS) with the aim of developing new dedicated Virtual Research Environments. The IJI kicked off with the organization of the LifeWatch ERIC First Dahlem-type Workshop: Current and future challenges of NIS in Europe, which took place from 14th to 18th October, in the Casa de la Ciencia, and the V. De Madariaga Foundation, in Seville, Spain.
Dahlem-Type workshop
A Dahlem-type Workshop is defined as a quest for knowledge through an interdisciplinary communication process aimed at expanding the boundaries of current knowledge, addressing high-priority problems, identifying gaps in knowledge, posing questions aimed at directing future inquiries, and suggesting innovative approaches for solutions.
The choice of the Dahlem-type workshop stems from the desire of the infrastructure to use the most participative interdisciplinary approach in the search for new perspectives to drive the international research agenda on NIS and to involve relevant communities in the development of validation cases. For this reason, experts from different domains – from scientists working in the field of NIS, to ICT specialists and bio-informaticians – gathered to select the most promising research and management questions, identify the resources and tools available and specify those to be developed.
LifeWatch ERIC organised two Dahlem-type Workshops in the framework of the Internal Joint Initiative:
NIS IJI Workflows Technical Meeting
Ostend, 16-17/03/2020 *Meeting has been moved online due to Covid-19 pandemic, new arrengements were communicated to participants.
Registration is free of charge and compulsory, please click here.
Scope Completing final scientific & users’ requirements to advance in the ICT developments for Workflows on Non indigenous-Invasive (Alien) Species -NIS- of the Internal Joint Initiative (IJI).
The purpose of this 2-day meeting is:
1) To go over IJI Workflow #1 ARMS+ ASSEMBLE final version review & approval.
2) To discuss other issues: Tesseracto_VRE & rest of workflows (#2 to #6) developments progress, etc.
When
16-17/03/2020
Where
Flanders Marine Institute (VLIZ)
Spuikom & De Noordzee conference rooms – InnovOcean site (entrance: warehouse 61)
Wanderlaarkaai 7
8400 Ostend
Belgium
How to reach us? Click here
Agenda
Coming soon!
More info
https://www.lifewatch.eu/web/guest/iji-workflows-technical-meeting
NIS IJI Workflows Technical Meeting
*Meeting has been moved online due to Covid-19 pandemic, new arrengements were communicated to participants.
Registration is free of charge and compulsory, please scroll down to fill in the form.
Scope
The purpose of this 2-day meeting is:
- To go over IJI Workflow #1 ARMS+ ASSEMBLE final version review & approval.
- To discuss other issues: Tesseracto_VRE & rest of workflows (#2 to #6) developments progress, etc.
- Explore synrgies with ongoing projects.
When
16-17/03/2020
Flanders Marine Institute (VLIZ)
Spuikom & De Noordzee conference rooms – InnovOcean site (entrance: warehouse 61)
Wanderlaarkaai 7
8400 Ostend
Belgium
Where
How to reach us? Click here
Agenda
Coming soon!
Registration is closed.
First Dahlem-type Workshop
LifeWatch ERIC just launched an Internal Joint Initiative (IJI) focusing on the topic of Non-indigenous and Invasive Species (NIS) with the aim of developing new dedicated Virtual Research Environments. The IJI kicked off with the organization of the LifeWatch ERIC First Dahlem-type Workshop: Current and future challenges of NIS in Europe, which took place from 14th to 18th October, in the Casa de la Ciencia, and the V. De Madariaga Foundation, in Seville, Spain.
The choice of the Dahlem-type1 workshop stems from the desire of the infrastructure to use the most participative interdisciplinary approach in the search for new perspectives to drive the international research agenda on NIS and to involve relevant communities in the development of validation cases. For this reason, experts from different domains – from scientists working in the field of NIS, to ICT specialists and bio-informaticians – gathered in Seville to select the most promising research and management questions, identify the resources and tools available and specify those to be developed.
As a first step, participants identified and clustered the main issues related to NIS and discussed two macro topics, 1) risks and impacts of NIS, and 2) long-term responses of both the NIS and the native communities after invasion. Participants agreed on the development of a general framework to describe and estimate both risks and impacts of NIS (Topic one) and responses from the perspective of both NIS and native communities (Topic two) in the context of climate change. Several validation cases were proposed for each topic to apply this new framework.
On topic one, the suggested validation cases focus on the EU-scale assessment of ecosystem and habitat-type vulnerability to NIS in the context of climate change, including an assessment of sink source dynamics for specific, model, ecosystem types such as harbour ecosystems. On topic two, the chosen validation cases are based on the availability of long-term data series on a number of relevant invaders: (1) Caulerpa taxifolia and racemose; (2) Callinectes sapidus & other Crustaceans; (3) freshwater fishes at a global scale; (4) Mnemiopsis; (5) Rugulopteryx; (6) Ailanthus invasion and response monitoring with satellite images; (7) Metagenomics for invasive species; and (8) early detection of NIS with the metagenomic approach. An additional validation case was also proposed for later collaboration dealing with the risk for human health of NIS as vectors of pathogens.
The LifeWatch ERIC ICT team’s contribution was to highlight those data resources and services required for the development of the validation cases and to suggest the implementation of an innovative approach, LifeBlock, a LifeWatch ERIC service that for the first time ever applies blockchain technology to biodiversity science.
As an immediate result of this collaboration, scientists and ICT experts jointly outlined a conceptual paper and designed a workflow that will serve as an organised timeline along which different e-tools have to be developed to help address relevant issues related to NIS for scientists, managers, decision-makers and society.
The next Dahlem-type workshop will take place in Rome from 2nd to 6th December 2019, this time driven and coordinated by the ICT community, to produce a second technical paper and pave the way towards developing the required Virtual Research Environments.
1 A Dahlem-type Workshop is defined as a quest for knowledge through an interdisciplinary communication process aimed at expanding the boundaries of current knowledge, addressing high-priority problems, identifying gaps in knowledge, posing questions aimed at directing future inquiries, and suggesting innovative approaches for solutions.
LifeWatch ERIC Internal Joint Initiative
Non-indigenous and Invasive species (NIS) are considered a major threat to biodiversity around the globe: they can impact ecosystems in many ways by outcompeting or predating on native species. Who has not heard of the Burmese pythons in Florida that eat alligators? The negative impact of imported rats and cats that have decimated island fauna populations? However, the long-term impacts of NIS on ecosystem integrity are poorly explored, and policy-makers are often left without sufficient information to make wise management decisions.
In the belief that the first steps in tackling biodiversity loss must be to improve our knowledge by developing better inter-disciplinary paradigms, LifeWatch ERIC is launching an exciting new Internal Joint Initiative (IJI), involving the scientific communities of National Nodes and other European Research Infrastructures, that will thoroughly describe the issues involved in ecosystem and habitat type vulnerability, and produce future scenarios under changing vectors to help decision-makers combat the impacts of climate change.
The LifeWatch ERIC Internal Joint Initiative will combine data, semantic resources, data management services, and data analysis and modelling from its seven member countries – Belgium, Greece, Italy, the Netherlands, Portugal, Slovenia and Spain – to bring together national assets on a scale never attempted before. This integration of Common Facilities and National Nodes will provide the comprehensive and synthetic knowledge so much needed by institutions and administrators.
By deploying and publishing on the LifeWatch ERIC web portal the federated resources and e-Tools and e-Resources, the Internal Joint Initiative will also define the requirements and architecture of the LifeWatch ERIC virtual research environments, and provide a clear demonstration of the Infrastructure’s added value for researchers in addressing specific biodiversity and ecosystem management issues.
Non-indigenous and Invasive Species are a global problem. They are distributed among most plant and animal taxa, and present a number of key issues that remain challenging for both researchers and policy-makers. The knowledge produced by the Internal Joint Initiative will thus be of global significance. It is to be hoped that this demonstration case will be seen to have scientific and socio-economic implications for many different fields of investigation over the coming decades.
II Dahlem-Type Workshop
The LifeWatch ERIC Internal Joint Initiative was launched in October 2019 to design and construct a Virtual Research Environment capable of processing and modelling available data on one of the planet’s most burning biodiversity issues, the proliferation of Non-indigenous and Invasive Species (NIS), in order to help mitigate their impacts.
Development of a new Virtual Research Environment (VRE) is essential to further integrate the tools and services available in the LifeWatch ERIC web portal. The process will allow stakeholders greater ability to develop their research activities within the e-Science Infrastructure, whilst also clearly demonstrating the added value that LifeWatch ERIC’s advanced technologies can bring not only to the biodiversity and ecosystem scientific community, but to policy-making and human wellbeing around the globe.
The conceptual paper and workflow-timeline developed at the first Dahlem-type workshop in Seville, Spain, 14-18 October, formed the basis of this second Dahlem-type Workshop, organised in Rome, Italy, from 2-6 December, this time coordinated by the LifeWatch ERIC CTO, Juan Miguel González-Aranda. This second Dahlem-type workshop delivered the first prototype of the new LifeWatch ERIC Non-indigenous and Invasive Species Virtual Research Environment. The collaborative construction and deployment approach and the intense interaction between ICT and NIS experts made it possible to achieve definition of the requirements and needs of the scientific community and of the main architecture layers (application, e-Services composition, e-infrastructure integration, and resources) that underpin the VRE.
Workshop: Online Bioinformatic Platforms to support Metabarcoding and Metagenomics research and Applications
Porto, Portugal, 26-28 February 2020. The pan-European Workshop, held in the Research Centre in Biodiversity and Genetic Resources (CIBIO-InBIO) at the Vairão campus of the University of Porto, Portugal, boasted a very specific title: ‘Online Bioinformatic Platforms to Support Metabarcoding and Metagenomics Research and Applications’.
The workshop witnessed more than 30 participants from nine European countries (Belgium, Estonia, Germany, Greece, Italy, Norway, Portugal, Slovenia, Spain, Switzerland) with different expertise and backgrounds, ranging from metagenomics and metabarcoding, to ecology and ICT.
The workshop was jointly organised with PORBIOTA/ LifeWatch Portugal, DNAqua-Net (dedicated to the protection, preservation and restoration of aquatic ecosystems and their functions) and the EnvMetaGen project at InBIO (Research Network in Biodiversity and Evolutionary Biology). LifeWatch ERIC supported its organisation as part of its Internal Joint Initiative on Non-indigenous and Invasive Species. The workshop explored the architecture and function of an online bioinformatics platform capable to address as many needs of the scientific community as possible, such as:
- Checking existing distributed Bioinformatics e-Resources within the LifeWatch ERIC communities of practice,
- Reaching a common understanding of users’ requirements and needs in Virtual Research Environments, and
- Proposing an efficient and realistic and engaging mechanism from an ICT perspective, capable of federating those e-Resources within the LifeWatch ERIC VREs.
Examples of evidence-based research were provided by the European Open Science Cloud (EOSC), MIRRI (Microbial Research Resource Infrastructure), ELIXIR (which unites Europe’s leading life science organisations in managing and safeguarding the ever-growing volumes of data generated), other Research Infrastructures and Bioinformatics initiatives.
The outcome of the three days was a plan with well-identified next steps towards the co-construction of the bioinformatic platform.
Presentations:
Christos Arvanitidis | LifeWatch ERIC – mission and recent developments. Download PDF
Rocío Bautista | Bioinformatic analysis at SCBI. Download PDF
Pedro Beja | Next generation sequencing: Opportunities and challenges of a disruptive techmology for biodiversity assessment and monitoring. Download PDF
Bopco & JEMU | The Barcoding Facility for Organisms and Tissues of Policy Concern & The Joint Experimental Molecular Unit. Download PDF
CIBIO | Research Centre in Biodiversity and Genetic Resources. Download PDF
CNR-IBIOM | Infrastructure, data and analysis resources. Download PDF
Day 2 Session 3 | What should be the characteristics of online bioinformatics platforms in LifeWatch ERIC? Download PDF
Mafalda Galhardo | Metabarcoding and data processing pipelines. Download PDF
Juan Miguel González-Aranda | Towards the establishment of a LifeWatch ERIC bioinformatics platform. Download PDF
Tine Grebenc & Nataša Šibanc | Slovenian Forestry Institute. Download PDF
Matjaž Gregorič | Spider webs as a source of eDNA. Download PDF
Marta Goberna | Spanish Institute for Agricultural Research, Department of Environment and Agronomy. Download PDF
Pascal Hablützel | VLIZ’s ambition for online bioformatic platforms to support metabarcoding and metagenomics research. Download PDF
Florian Leese | DNA-based aquatic bioassessment in Europe and beyond: Chances and challenges. Download PDF
Jennifer Leonard | Conservation and Evolutionary Genetics Group, Doñana. Download PDF
Florian Mauffrey | Development of a molecular diatoms index for water quality assessment of Swiss rivers. Download PDF
Niklas Noll | Going through a metabarcoding workflow – pointing out problems and proposing solutions for a bioinformatics platform. Download PDF
Alberto Pallavicini | Units of the Department of Life Sciences, University of Trieste. Download PDF
Christina Pavloudi & Haris Zafeiropoulos | LifeWatchGreece Hellenic Centre for Marine Research. Download PDF
Sergei Põlme | UNITE: Curated and evolving databases for molecular identification and for communicating fungal species. Download PDF
News & events
An alert model reporting tool that combines e-DNA metabarcoding and molecular ecology to study freshwater fish communities and identify new invasive species
Metabarcoding
Background
Freshwater ecosystems have been profoundly affected by habitat loss, degradation, and overexploitation, leaving them now especially vulnerable to biological invasions. Whether non-indigenous species are the key drivers or mere complementary factors of biodiversity loss is still debated among the scientific community, however biological invasions together with other anthropogenic stressors are determining population declines and homogenisation of biodiversity in freshwater ecosystems worldwide. For example, it has been demonstrated that river basins with greater numbers of non-indigenous species have higher extinction rates of native fish species. Consequently, the application of effective biomonitoring approaches to support protection actions of managers, stakeholders and policy-makers is nowadays essential.
Introduction
Conventional methods of monitoring freshwater fish diversity are based on direct observation of organisms and are therefore costly, labour and resource intensive, require taxonomic expertise, and can be invasive. Obtaining information about species and communities by retrieving DNA from environmental samples has the ability to overcome some of these difficulties. The molecular investigation of environmental samples is known as environmental DNA (eDNA). Environmental DNA can be isolated from water, soil, air or faeces as organisms shed their genetic material in the surroundings through metabolic waste, damaged tissues, sloughed skin cells and decomposition. The analysis of eDNA consists of extracting the genetic material and subjecting it to a Polymerase Chain Reaction (PCR) which amplifies the target DNA. The use of high-throughput sequencing (HTS) allows the simultaneous identification of many species within a certain taxonomic group. This community-wide approach is known as eDNA metabarcoding and involves the use of broad-range primers during PCR that amplify a set of species. In recent years, the cost of this technology has drastically decreased, making it very attractive in conservation management and scientific research. A number of studies have demonstrated that eDNA metabarcoding is more sensitive than conventional biomonitoring methods for freshwater fish as it can detect rare or low-abundance taxa. As a result, eDNA metabarcoding can be used as an early-warning tool to detect new NIS at the initial stages of colonisation, when they are not yet abundant in the ecosystem.
Aims
This validation case regards eDNA metabarcoding fish sequences collected from the Douro Basin in Portugal. DNA sequences are processed through a bioinformatic pipeline wrapped in the first part of the analytical workflow which conducts a quality check and assigns the DNA sequences to produce a list of taxa. The analytical workflow developed can process DNA sequences of different kinds, depending on the genetic markers used for the analysis and so this workflow can be applied to different taxonomic groups and ecosystems. The taxa identified might include indigenous organisms as well as newly identified taxa within a certain geographical region. For that reason, the national checklists of introduced and invasive species (GRISS) from GBIF are consulted to check if the organisms detected are recognised as NIS or if previously unrecorded NIS have been detected through eDNA metabarcoding analysis.
The metabarcoding workflow is available on this page