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

Open Knowledge Map

Functional biogeography of invasive species: stable isotope analysis to establish the trophic position of two widely-distributed omnivorous crustaceans

Functional Biogeography of Invasive Species

Background
Biological invasions are acknowledged to be significant environmental and economic threats, yet the identification of key ecological traits determining invasiveness of species has remained elusive. One unappreciated source of variation concerns dietary flexibility of non-native species and their ability to shift trophic position within invaded food webs. Trophic plasticity may greatly influence invasion success as it facilitates colonisation, adaptation, and successful establishment of non-native species into new territories. In addition, having a flexible diet gives the introduced species a better chance to become invasive and, as a consequence, to have a strong impact on food webs, determining secondary disruptions such as trophic cascades and changes in energy fluxes. The deleterious effects can affect multiple trophic levels.

Introduction
Crustaceans are considered the most successful taxonomic group of aquatic invaders worldwide. Their ability to colonise and easily adapt to new ecosystems can be ascribed to a number of ecological features including their omnivorous feeding behaviour. This validation case study focuses on two invasive crustaceans widely distributed in marine and freshwater European waters: the Atlantic blue crab Callinectes sapidus and the Louisiana crayfish or red swamp crayfish Procambarus clarkii.

Callinectes sapidus and Procambarus clarkii are opportunistic omnivores that feed on a variety of food sources from detritus to plants and invertebrates. For this reason, they represent a good model to investigate the variation of trophic niches in invaded food webs and their ecological impact on native communities. The ecological consequences of the invasion and establishment of these invasive crustaceans can vary from modification of carbon cycles in benthic food webs to regulation of prey/predator abundance through bottom-up and top-down interactions. Understanding how the trophic ecology of these invasive crustaceans shapes benthic food webs in invaded ecosystems is crucial for an accurate assessment of their impact.  The analysis of stable isotopes can provide important clues on the trophic effects of invasive species within non-native ecosystems by evaluating changes in their trophic position and characteristics of their trophic niche.

Aims
This validation case uses a collection of stable isotopes (δ13C and δ15N) of C. sapidus and P. clarkii and their potential prey in invaded food webs to quantify changes in the trophic position of the invaders and to assess post-invasion shifts in their dietary habits. This case study additionally evaluates the main environmental drivers involved in trophic niche adaptations and whether such bioclimatic predictors influence broad-scale patterns of variation in the trophic position of the invader. 

The workflow is available on this page

 

Open Knowledge Map

 

Risk assessment of NIS introduction and establishment, habitat vulnerability to NIS and estimation of impacts on European Biotopes

Risk assessment of NIS introduction and establishment, habitat vulnerability to NIS and estimation of impacts on European Biotopes

Background
Information about the incidence and impact of Non-indigenous and Invasive Species (NIS) are often scattered across different spatial, temporal and taxonomic scales and, therefore, it can be difficult to draw any comprehensive conclusion about the most vulnerable ecosystems or map the areas more at risk of biological invasion. Occurrence data are usually collected using a variety of sampling approaches and the impact of NIS can affect ecosystems at any biological scale (e.g., individuals, populations, communities, etc.) and with different degrees of severity. The heterogeneity of species occurrence data and the complexity of multiple effects acting at different biological scales and determining ecosystem-dependent changes make estimations of NIS incidence and impact difficult on large geographical scales.

Introduction
Comprehensive, standardised and modular methods to assess both incidence and impact of NIS at different spatial scale (e.g., continental, regional, local) are required to support management and conservation actions and to prioritise areas of intervention. To achieve this objective, researchers have developed two standardised approaches to quantify the incidence and the impact of NIS on ecosystems respectively by means of: occurrence cubes and analysis of the Cumulative IMPacts of invasive ALien species (CIMPAL). Occurrence cubes consist of species occurrence data aggregated on a three-dimensional space (cube) whereby the three dimensions considered are taxonomic, temporal and spatial. Data cubes allow the homogenisation and aggregation of heterogeneous data collected using different methods and standards. The CIMPAL model allows the mapping of cumulative negative impacts of NIS on different ecosystems (marine, freshwater, terrestrial) on the basis of existing evidence. NIS impacts can be additionally mapped according to the main associated pathways of introduction and the relative importance of species on cumulative impacts can be inferred. Using these two standardised methodologies, vulnerability map of biotopes can be produced in order to identify hot spots particularly threatened by NIS and that, in turn, would require special protection and maintenance.

Aims
This validation case aims at using the occurrence cube approach and the CIMPAL model to map ecosystem and habitat type vulnerability at continental scale, inferring the relevance of key risk factors (e.g. vectors of invasion) and intrinsic resistance/resilience components (e.g. native biodiversity, food web structure, etc.) and design scenarios of change, in the context of expected climate changes, for ecosystem and habitat types found highly vulnerable to NIS.

The workflow developed offers a valuable tool that may assist policy makers and managers in their efforts to develop strategies for mitigating the impacts of invasive species and improving the environmental status of marine waters. The method, although tested on the the marine environment, can easily be transferred to the terrestrial environment as well.

The Biotope vulnerability workflow is available on this page

 

Open Knowledge Map

 

Autonomous Reef Monitoring Structures (ARMS) programme: long-term monitoring of invasive marine species

ARMS

Background
Monitoring hard-bottom marine biodiversity can be challenging as it often involves non-standardised sampling methods that limit scalability and inter-comparison across different monitoring approaches. Therefore, it is essential to implement standardised techniques when assessing the status of and changes in marine communities, in order to give the correct information to support management policy and decisions, and to ensure the most appropriate level of protection for the biodiversity in each ecosystem. Biomonitoring methods need to comply with a number of criteria including the implementation of broadly accepted standards and protocols and the collection of FAIR data (Findable, Accessible, Interoperable and Reusable).

Introduction
Artificial substrates represent a promising tool for monitoring community assemblages of hard-bottom habitats with a standardised methodology. The European ARMS project is a long-term observatory network in which about 20 institutions distributed across 14 European countries, including Greenland and Antarctica, collaborate. The network consists of Autonomous Reef Monitoring Structures (ARMS) which are deployed in the proximity of marine stations and Long-term Ecological Research sites. ARMS units are passive monitoring systems made of stacked settlement plates that are placed on the sea floor. The three-dimensional structure of the settlement units mimics the complexity of marine substrates and attracts sessile and motile benthic organisms. After a certain period of time these structures are brought up, and visual, photographic, and genetic (DNA metabarcoding) assessments are made of the lifeforms that have colonised them. These data are used to systematically assess the status of, and changes in, the hard-bottom communities of near-coast ecosystems.

Aims
ARMS data are quality controlled and open access, and they are permanently stored (Marine Data Archive) along with their metadata (IMIS, catalogue of VLIZ) ensuring data fairness. Data from ARMS observatories provide a promising early-warning system for marine biological invasions by: i) identifying newly arrived Non-Indigenous Species (NIS) at each ARMS site; ii) tracking the migration of already known NIS in European continental waters; iii) monitoring the composition of hard-bottom communities over longer periods; and iv) identifying the Essential Biodiversity Variables (EBVs) for hard-bottom fauna, including NIS.

The ARMS validation case was conceived to achieve these objectives: a data-analysis workflow was developed to process raw genetic data from ARMS; end-users can select ARMS samples from the ever-growing number available in collection; and raw DNA sequences are analysed using a bioinformatic pipeline (P.E.M.A.) embedded in the workflow for taxonomic identification. In the data-analysis workflow, the correct identification of taxa in each specific location is made with reference to WoRMS and WRiMS, web services that are used to check respectively the identity of the organisms and whether they are introduced. 

The ARMS workflow is available on this page

Combining modelling and remote sensing techniques to monitor and control the spread of invasive species

Ailanthus altissima

Background
Ailanthus altissima is one of the most highly invasive plants in Europe. It reproduces both by seeds and asexually through root sprouting. The winged seeds can be dispersed by wind, water and machinery, while its robust root system can generate numerous suckers and cloned plants. Ailanthus altissima typically occurs in very dense clumps, but can also occasionally grow as widely spaced or single stems. This invasive plant can colonise a wide range of anthropogenic and natural sites, from stony and sterile soils to rich alluvial bottoms. Due to its vigour, rapid growth, tolerance, adaptability and lack of natural enemies, it spreads spontaneously, out-competing other plants and inhibiting their growth

Introduction
Over the last few decades, Ailanthus altissima has quickly spread in the Alta Murgia National Park (southern Italy) which is mostly characterised by dry grassland and pseudo-steppe, wide-open spaces with low vegetation, which are very vulnerable to invasion. Ailanthus altissima causes serious direct and indirect damages to ecosystems, replacing and altering communities that have great conservation value, producing severe ecological, environmental and economic effects, and causing natural habitat loss and degradation. The spread of Ailanthus altissima is likely to increase in the future, unless robust action is taken at all levels to control its expansion. In a recent working document of the European Commission, it was found that the cost of controlling and eliminating invasive species in Europe amounts to €12 billion per year. Two relevant questions then arise: i) whether it is possible or not to fully eradicate or, at least, to reduce the impact of an invasive species and ii) how to achieve this at a minimum cost, in terms of both environmental damage and economic resources.

A Life Programme funded the Life Alta Murgia project (LIFE12BIO/IT/000213) had, as its main objective, the eradication of this invasive exotic tree species from the Alta Murgia National Park. This project provided both the expert knowledge and valuable in-field data for the Ailanthus validation case study, which was conceived and developed within the Internal Joint Initiative of LifeWatch ERIC.

Aims
At the start of the ongoing eradication program a single map of A. altissima was available, dating back to 2012. Due to the lack of data, predicting the extent of invasion and its impacts was extremely difficult, making it impossible to assess the efficacy of control measures. Static models based on statistics cannot predict spatial–temporal dynamics (e.g. where and when A. altissima may repopulate an area), whereas mechanistic models incorporating the growth and spread of a plant would require precise parametrisation, which was extremely difficult with the scarce information available. To overcome these limitations, a relatively simple mechanistic model has been developed, a diffusion model, which is validated against the current spatial distribution of the plant estimated by satellite images. This model accounts for the effect of eradication programs by using a reaction term to estimate the uncertainty of the prediction, also providing an automatic tool to estimate a-priori the effectiveness of a planned control action under temporal and budget constraints.

This robust tool can be easily applied to other geographical areas and, potentially, to different species.

The developed workflow is available on this page

Open Knowledge Map

Validation cases

Validation cases

Five validation cases were agreed on by the scientific community representatives to focus on various aspects of Non-indigenous and Invasive Species (NIS) invasions that satisfied the desire of the infrastructure to engage a range of disciplines in the investigation of this broad and complex topic.

In a succession of collaborative workshops in late 2019, scientists and ICT experts jointly drew up a conceptual paper and agreed on a workflow that would serve as a living timeline, along which different e-tools could be developed to address the data requirements of the NIS scientists, and then serve as a resource for environmental managers, decision-makers and citizens interested in biodiversity and ecosystem research.

Framework and knowledge map

General Framework for the Internal Joint Initiative

Click on the framework to enlarge it.

Open Knowledge Map

Knowledge maps provide an instant overview of a topic by showing the main areas at a glance, and papers related to each area clustering similar open and closed access papers. If you want to know more about Open Knowledge Map tool please visit this link.

Internal Joint Initiative

Rationale for the Internal Joint Initiative

The warnings of 15,000 scientists, of the United Nations Paris Climate Change Conference (COP21) and now of the UN Global Assessment Study clearly demonstrate that humanity is bringing our life support system, the biosphere, to the point of collapse. The effort to counteract this current loss of biodiversity requires concrete actions at all levels. For science, it means improving our current level of knowledge, to move beyond the present fragmentation of science, and to foster greater complementarity and synergy between disciplines, by developing new inter-disciplinary paradigms and starting to build synthetic knowledge, so as to boost innovation and involve more young scientists and civil society.

LifeWatch ERIC is Europe’s first line of response to this emergency, applying and advancing ICT technologies, web networks, interconnecting scientific communities and research centres internationally into its web-based research infrastructure.

Objectives

The Internal Joint and Collaborative Initiative (IJI) was created in order to:

  1. Boost the integration of tools and services into the LifeWatch ERIC web portal
  2. Focus on a major scientific issue in biodiversity and ecosystem research with relevant socio-economic implications in different fields;
  3. Produce new and synthetic knowledge that is needed by institutions, administrations and managers to give solutions to major environmental problems at different scales;
  4. Involve the LifeWatch ERIC National scientific communities, key international research groups and other European research Infrastructures with related interests and running activities; and,
  5. Make this effort an example of the functioning of the LifeWatch ERIC e-Infrastructure through its dissemination and outreach activities.

The topic of non-indigenous and invasive species (NIS) was chosen as the first demonstration case of the functioning of the LifeWatch ERIC e-Infrastructure. This initiative helps addressing some of the main issues on NIS in the field of ecosystem and habitat type vulnerability and in the context of climate change as well as help highlight societal needs and potential solutions to be tested.

ENVRI International Winter School DATA FAIRness

Click here to see the programme.

The Winter School was organised over a two-week period, on average dedicating around 40 hours in total (including preparation). It was structured around daily activities, with scheduled lectures and presentations in the mornings (09-11), followed by associated group and individual work time (11-12).

Target audience:

Since the focus was on supporting end users in how to make the best use of data, understanding the end user perspective was very important to developing good user interfaces and services to interact with data.
The main target groups were the staff at ENVRI data centres, researchers and PhD candidates, with the aim to:

  • present state-of-the-art technologies relevant to FAIRification of services
  • based on real-life use cases, encourage adoption of new technology to enhance data centre functionality
  • enable new knowledge-exchange networks for ENVRI data professionals

For practical reasons, we could only accommodate 30 participants in total. The selection of participants was based on a mix of criteria, including motivation and use case descriptions.

Towards ENVRI Community International Winter School DATA FAIRness

In July-September 2020 we organised a three-day webinar programme, which introduced the main topics of the winter school (the use of FAIR data in ENVRI Community, and for Environmental and Earth sciences research) with theoretical presentations, exercises and discussion. The training materials (slides, presentations, recordings, etc.) are available on the ENVRI-FAIR Training Platform. 

Towards ENVRI Winter School

Towards ENVRI Community International Winter School DATA FAIRness

Webinar Programme July-September 2020

Due to the COVID-19 emergency, our planned summer school, initially scheduled for 10-15 July was postponed to January 2021. The restrictions for travelling to and from Italy, the other safety measures adopted in many countries to contain the virus and the general uncertainty made it impossible for us to confirm the original schedule. The revised website with the updated programme can be found here.

In the meanwhile, we decided to organise a three-day webinar programme, which introduced the main topics of the Winter School (the use of FAIR data in ENVRI Community, and for Environmental and Earth sciences research) with theoretical presentations, exercises and discussion.

Target audience:

The main target group were the ENVRI-FAIR project partners data centre staff, but anyone interested was permitted to attend the webinars.