Collections

One of the grand challenges in ecology is to understand and predict how ecosystems are impacted by changes in environmental conditions and external pressures. The urgency of this challenge is high given the unprecedented rate of global change in climate, land use, and urbanisation. To do so, we need to transform ecology into a predictive science. Scenarios can be used to explore how complex ecosystems could behave under different external pressures. Developing scenarios requires combining knowledge and data. This is analogous to global climate models, which also integrate fundamental knowledge and empirical data on climate processes to forecast consequences of different global emission scenarios. Key for developing high-quality scenarios is the availability of long-term environmental and ecological datasets. 

A Digital Twin is a digital replica of a living or non-living physical entity. Digital Twins allow advanced data-driven modelling and simulation, using Big Data tools to generate novel insights that cannot be obtained with traditional observation models. Building Digital Twins of ecosystems has only recently became possible as Big Data, artificial intelligence (AI) applications and analytics, advanced computing infrastructure, and the FAIR principles have been developed and made available for ecology, ecosystem restoration, and biodiversity science. A Digital Twin of an ecosystem also provides tools to integrate data on abiotic factors (e.g., nutrient deposition, temperature, droughts), biotic factors (e.g., long-term occurrence data on animals and plants, life history data), and human activities (e.g., tourism, agriculture, fishery). Digital Twins consist of diagnostic (data-driven) and dynamic (process-based) models and couples ‘‘Big Data’’ on ecosystems with well-developed process-based models on the relationships between species and their environment. 

This collection hosts the outcomes of the LTER-LIFE project. LTER-LIFE develops an infrastructure that includes a Virtual Research Environment (VRE) and services (e.g., catalogues and repositories that contain FAIR data, models, and software tools) that together can instantiate custom Virtual Laboratories to build Digital Twins of specific ecosystems. 

One of the grand challenges in ecology is to understand and predict how ecosystems are impacted by changes in environmental conditions and external pressures. The urgency of this challenge is high given the unprecedented rate of global change in climate, land use, and urbanisation. To do so, we need ...

This collection hosts the outcomes from the European Union's Horizon Europe project IP4OS under grant agreement No. 101188026 (2025-2026). The main aim of IP4OS is social innovation: to empower multi-professional teams and their organisations in each of the 27 European countries with knowledge, skills, awareness and advocacy to boost the valorisation of scientific knowledge in the ERA to a new level by promoting a concerted approach to agile IP management and OS practices. IP4OS will

(1) describe a concerted IP-OS approach in the Synergy Framework with best practices on agile IP management to support OS practices,

(2) inform the Community of practice about the Synergy Framework with a Role-Model Campaign using advocates, facts and figures,

(3) train multi-professionals in agile IP Management with the Synergy Core Curriculum,

(4) empower multi-professional teams in HEIs and RPOs to use agile IP management to support OS.
As the IP4OS project progresses, the RIO Collection will continue to expand, offering a diverse array of reports, protocols, methodologies, and research papers.

This collection hosts the outcomes from the European Union's Horizon Europe project IP4OS under grant agreement No. 101188026 (2025-2026). The main aim of IP4OS is social innovation: to empower multi-professional teams and their organisations in each of the 27 European countries with knowledge, skil ...

Critical environmental challenges affect aquatic ecosystems worldwide, and the need to coordinate research efforts is increasingly urgent. Mesocosms are key Research Infrastructures (RIs) allowing the study of highly complex environments comparable to natural ecosystems. Mesocosm experiments, which offer controlled yet realistic settings, are crucial for understanding and mitigating the impact of various stressors and their combinations on aquatic ecosystems. The AQUACOSM-RI consortium, comprising over 60 individual state-of-the-art mesocosm facilities at 28 host institutions across Europe, has therefore been instrumental in advancing aquatic environmental research across climate zones including marine, brackish and freshwater ecosystems.

The AQUANAVI project (Navigating Grand Challenges and their Mitigation using Aquatic Experimental RIs) aims to create an interactive atlas of aquatic mesocosm-based experimental research. Data, publications, reports and information generated by the AQUACOSM consortium and other mesocosm facilities worldwide will be integrated into a single, accessible platform incorporating Open Knowledge Maps' AI-driven visual discovery tools. The project will foster collaborations and, by enhancing data FAIRness, it will facilitate fast discovery and efficient use of aquatic RIs globally, accelerating the development of environmental mitigation strategies.

Critical environmental challenges affect aquatic ecosystems worldwide, and the need to coordinate research efforts is increasingly urgent. Mesocosms are key Research Infrastructures (RIs) allowing the study of highly complex environments comparable to natural ecosystems. Mesocosm experiments, which  ...

This collection is dedicated to assembling significant research outputs that map out the relationships between biodiversity and ecological structure, and their impact on the functioning of coastal and marine ecosystems. It highlights the resultant ecosystem services and societal benefits.

The European Union and its Member States are intensely committed to understanding how the preservation of biodiversity and ecosystem functions can sustain the provision of ecosystem services, goods, and societal benefits. This comprehension is vital for the sustainable use of these resources and for appreciating the natural and social capital aspects of ecosystems, where stakeholder co-creation plays a crucial role.

Open for submissions from the MARBEFES Project consortium (MARine Biodiversity and Ecosystem Functioning leading to Ecosystem Services), this initiative calls for contributions that address significant issues associated with the conceptualization of changes in biodiversity across 12 Broad Belt Transect (BBT) case studies from various regional seas, including the Arctic, Baltic, Northeast Atlantic, and Mediterranean.

These contributions should explore the implications of biodiversity changes for the management and governance of European seas. The BBTs span the entire range of European marine biodiversity, from the frigid Arctic to semi-tropical zones, encompassing dominant habitats and iconic species, and extending from shallow waters to deep-sea environments across diverse socio-economic contexts.

This collection is dedicated to assembling significant research outputs that map out the relationships between biodiversity and ecological structure, and their impact on the functioning of coastal and marine ecosystems. It highlights the resultant ecosystem services and societal benefits.

The Europea ...

The European Reference Genome Atlas (ERGA) is a pan-European initiative that aims to facilitate the generation of high-quality reference genomes for the continent’s biodiversity as part of the global Earth BioGenome Project. Serving as the European node of this worldwide endeavour, ERGA brings together researchers and stakeholders to coordinate standardised sampling, sequencing, data management, assembly, and annotation for reference genomes across diverse groups of eukaryotes. Through projects like the ERGA Pilot Project and the Biodiversity Genomics Europe (BGE) project, as well as contributions from ERGA national nodes and the broader research community, ERGA aims to accelerate the generation and sharing of genomic resources that will contribute to future discoveries and genomics-based applications in ecology, evolution, bioeconomy, and conservation of species in Europe.

An ERGA Genome Report is a technical description that clearly presents the methodologies employed for sequencing and assembling genomes, together with standard quality metrics and relevant metadata, and genome annotation information if available. The ERGA Genome Reports preprinted and/or published through this collection follow a standardised format to ensure consistent quality and facilitate data findability and reuse. Genome Reports published elsewhere will be considered for inclusion in this collection if they (1) align with the ERGA Genome Report standards and (2) clearly acknowledge ERGA in the manuscript. The requirements and recommendations for a Genome Report publication to be included in this collection are detailed here. Through collating Genome Reports from across ERGA affiliated projects and members, this collection provides an open-access resource that promotes high standards, supports comparative analyses, and drives advances in genomics research. Additional information can be obtained from the editors.

The creation of this collection was supported by the Biodiversity Genomics Europe (BGE) project through the Horizon Europe Framework Programme of the European Union under grant agreement No. 101059492, funded by Horizon Europe under the Biodiversity, Circular Economy and Environment (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 22.00173 and 24.00054; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy’s Horizon Europe Guarantee Scheme.

The European Reference Genome Atlas (ERGA) is a pan-European initiative that aims to facilitate the generation of high-quality reference genomes for the continent’s biodiversity as part of the global Earth BioGenome Project. Serving as the European node of this worldwide endeavour, ERGA brings toget ...

This collection hosts the outcomes from the Horizon Europe project PollinERA, grant agreement No. 101135005 (2024-2027), which aims to reverse pollinator population declines and reduce the harmful impacts of pesticides through developing a new systems based environmental risk assessment scheme, tools, and protocols. It includes a broad range of toxicological testing, feeding to in silico models (QSARS, toxicokinetic/toxicodynamic, and ALMaSS agent-based population simulations). Using a strong stakeholder co-development approach, these models will be combined in a One System framework, taking a systems view on risk assessment and policy evaluation, including an international monitoring program developed within the project. The One System framework builds on the recent EFSA Roadmap for action on the environmental risk assessment of chemicals for insect pollinators (IPol‐ERA) project. It expands the environmental risk assessment tools currently used for honey bees to include wild bees, butterflies, moths and hoverflies.  

As the PollinERA project progresses, the RIO Collection will continue to expand, serving as a repository for researchers, policymakers, and practitioners and offering a diverse array of reports, protocols, methodologies, and research papers. 

This collection hosts the outcomes from the Horizon Europe project PollinERA, grant agreement No. 101135005 (2024-2027), which aims to reverse pollinator population declines and reduce the harmful impacts of pesticides through developing a new systems based environmental risk assessment scheme, tool ...

The European Union's 2030 Biodiversity Strategy aims to place species and ecosystems on the recovery path by 2030, preserving and restoring Europe's natural capital, and positioning Europe at the forefront of global biodiversity conservation efforts. These commitments urgently respond to the decline of species and the deterioration of nature. A key component of this Strategy is the development of a Trans-European Nature Network (TEN-N) that protects ecosystems and their contributions to people against threats from climate change and unsustainable land use. The TEN-N is expected to increase the resilience of natural ecosystems, supported by the existing Natura 2000 Network and other nationally designated protected areas. New designations are expected to contribute to achieving protected land, including inland waters, comprising 30% of the territory, increasing the network's ecological representativeness, and incorporating novel strictly protected and ecological connectivity areas. Implementing the TEN-N faces major challenges in defining criteria and planning tools to maximize the network's representativeness and connectivity at the European level.

The TEN-N should create a functionally connected system, assimilating biodiversity conservation goals with nature-based solutions for societal needs, such as green and blue infrastructure. In the face of global change, the Network should also ensure that species communities can adapt, providing sufficient and connected spaces for nature. Achieving these goals requires innovative planning approaches, integrating models of biodiversity and ecosystem change with conservation prioritization tools and participatory processes. The TEN-N must be based on SMART (specific, measurable, attainable, relevant, and time-bound) conservation and management objectives and monitoring methods.

NaturaConnect aims to support the development of the TEN-N through transdisciplinary research. Participatory processes are central to its activities, involving stakeholder engagement at regional, national, and international levels. Predictive biodiversity and ecosystem service models form the backbone for analyzing protected area representativeness and connectivity, taking into account multiple prioritization criteria and the diverse perspectives and needs of nature conservation. NaturaConnect seeks to develop data, analytical tools, and knowledge to support solutions —namely, the blueprint for TEN-N configurations. It also analyses best practices for governance of area-based conservation measures and potential funding mechanisms to provide the European Commission and Member States with a comprehensive set of planning and implementation support tools.

Only publications directly resulting from the NaturaConnect project are accepted in this collection.

The European Union's 2030 Biodiversity Strategy aims to place species and ecosystems on the recovery path by 2030, preserving and restoring Europe's natural capital, and positioning Europe at the forefront of global biodiversity conservation efforts. These commitments urgently respond to the decline ...

LifeWatch ERIC has embarked on its new destination towards upgrading and (co-)constructing its Infrastructure as a response to the needs of its target communities and stakeholders. Through an industrialization process, all independent data, software components, publications and other types of research products contributed by the Member Countries will be consolidated and integrated to enable collaborative development. The Technology Readiness Level of LifeWatch ERIC will be soaring to TRL9. This process is described in its new Strategic Working Plan on its second implementation period (2022-2026). Accordingly, this topical collection of papers includes articles which describe the main outcomes, that is the deliverables of this new Strategic Working Plan. The deliverables published in this topical collection are of not confidential nature and are developed in the form of a standard, structured template.

LifeWatch ERIC has embarked on its new destination towards upgrading and (co-)constructing its Infrastructure as a response to the needs of its target communities and stakeholders. Through an industrialization process, all independent data, software components, publications and other types of resear ...

This collection hosts the outcomes from the Horizon Europe project B-Cubed, grant agreement No 101059592 (2023-2026), which aims to transform biodiversity monitoring from a disconnected, labour-intensive activity into an agile and responsive process, tailored to the needs of decision-makers.

To do that, B-Cubed works closely with existing biodiversity initiatives to identify and address policy needs. It leverages the concept of data cubes to standardise access to biodiversity data using the Essential Biodiversity Variables framework. These cubes are the basis for models and indicators of past, current and future biodiversity. The models will be accessible to users in real-time and on-demand in a cloud computing environment, delivering information on biodiversity status and change. To ensure its results can be reused, the project creates exemplar automated workflows for modelling using biodiversity data cubes and for the calculation of change indicators. The effectiveness of B-Cubed’s solutions is demonstrated in four case studies, varying in geographic extent, biodiversity richness and data availability.

This collection will evolve alongside B-Cubed, providing access to the project’s results and serving as a valuable resource for researchers, policymakers, and practitioners.

This collection hosts the outcomes from the Horizon Europe project B-Cubed, grant agreement No 101059592 (2023-2026), which aims to transform biodiversity monitoring from a disconnected, labour-intensive activity into an agile and responsive process, tailored to the needs of decision-makers.

To d ...