The biodiversity crisis demands computational tools to integrate and analyse complex, disparate data and models. This paper presents the concept of FAIR Digital Twins (FDTs) and, drawing on the work of the Biodiversity Digital Twin (BioDT) project (2022–2025), demonstrates how combining Digital Twins with FAIR principles (Findable, Accessible, Interoperable, and Reusable) can transform biodiversity research and decision-making. We show strategies for integrating heterogeneous data, models, and computational workflows within a FAIR framework, paving the way for operational FDTs. The BioDT project developed ten prototype digital twins addressing a critical range of challenges, including grassland and forest dynamics, bird monitoring, ecosystem services, and crop wild relative genetic resources. We discuss implementation challenges such as data fragmentation, semantic interoperability, and operational complexity. Critically, we highlight the opportunities for dynamic adaptation, modular workflows, and cross-domain collaboration, detailing how tools like Research Object Crate (RO-Crate) operationalise FAIR principles for metadata packaging and standardisation. This convergence of Digital Twins with FAIR principles offers a scalable and reusable approach to advancing biodiversity modeling and simulation, providing a robust foundation for evidence-based policy decisions.

The complexity of social-ecological systems poses significant challenges to achieving global sustainability goals. Decision-makers can develop management interventions acting across political, economic, social, technological, legal, and environmental domains, but these interventions have the potential to interact and conflict in complex ways. Importantly, worldviews have the potential to influence how we perceive these interactions will occur and alter our engagement with them. This can lead to paralysis in deliberations about intervention implementation. By taking a coupled sociological-mathematical approach, we demonstrate that integrating qualitative socio-ecological system maps with quantitative analyses of the relationships within these maps can be useful to identify points of leverage to achieve sustainability. Using fuzzy cognitive mapping, we capture perspectives regarding the relatonships between political, economic, social, technological, and environmental (PESTLE) elements of a social-ecological system both now and into the future, from people with different worldviews. Qualitative Boolean analysis of the fuzzy cognitive maps showed that sustainability can be achieved for all worldviews when considering the presence of positive and negative interactions among the PESTLE elements of social-ecological systems. In contrast, using quantitative projections of the PESTLE networks that bring in data on the strengths of the relationships between the PESTLE elements, we show that not all worldviews expect sustainable outcomes, under which circumstances achieving sustainability could be challenging. However, simulating changes to the strengths of the relationships between a few of the PESTLE elements can lead to a sustainable transition in those failing cases, signalling that interventions in key parts of the system can allow the whole social-ecological system to approach a sustainable future with engagement across worldviews. We show that a pluralistic approach, increasing the positive influence of economies on environmental outcomes, can offer viable pathways to sustainability for people coming from different worldviews. This is particularly important in marine systems that, by their nature, are cross-boundary and require inter-cultural solutions.

The Gulf of Heraklion is one of the most well-studied coastal marine ecosystems in the eastern Mediterranean. It is an oligotrophic area, exposed to wave action where muddy sediments prevail and its coastal zone is relatively unaffected by major riverine inputs. However, it faces pressures deriving from urbanisation, tourism, small-scale fisheries and climate change. Amongst its biological components, macrobenthos is an important component of soft-bottom habitats of the continental shelf and considered to be an indicator of environmental and human-induced disturbance. Nevertheless, long-term data are limited, thus restricting our understanding of their temporal trends. This is of particular importance for the Mediterranean Sea which is characterised as a hot spot of biodiversity and climate change impacts on its biota.The macrοbenthic faunal communities were investigated in the continental shelf of Heraklion Bay within the framework of the European funded project entitled MARine Biodiversity and Ecosystem Functioning leading to Ecosystem Services (MARBEFES), with the objective to enhance the understanding of marine biodiversity, ecosystem functioning and the ecosystem services they provide. Additional studies, with the same objectives, were carried under national and local monitoring programmes. Samples were collected from a specific transect of stations, named H2 (10, 20, 30, 40, 50, 100 and 200 m depth), located in the wider marine area of the wastewater treatment plant of Heraklion City. The transect was sampled during three different sampling surveys and periods: June 2010, June 2015 and August 2024.A total of 30,280 individuals were examined belonging to the taxonomic groups of Annelida, Crustacea, Mollusca, Echinodermata, Nemertea and varia. The identification of the key taxonomic classes (Polychaeta, Bivalvia, Gastropoda, Scaphopoda and Malacostraca) revealed 231 macrobenthic taxa. Out of the 231 taxa, only 30 were common amongst all the three sampling periods, while Polychaeta was the most abundant macrobenthic group in all sampling periods.

This white paper represents the collective perspectives of a network of legal entities based in Europe and with global interests, which includes biodiversity, ecology, and engineering communities, aiming to strengthen Science, Technology, and Innovation (STI) efforts toward achieving the United Nations (UN) Sustainable Development Goals (SDGs). With their combined expertise and through European initiatives such as the Research Infrastructures, the e-Infrastructures, the European Open Science Cloud (EOSC), the Digital Twin projects and academic publishers, these communities provide a base for collaboration in strategically contributing to the implementation of the Kunming-Montreal Global Biodiversity Framework targets. Furthermore, these communities seek to forge an international alliance to further integrate biodiversity conservation into the UN Summit of the Future priorities and the post-SDG agenda.

Anthropogenic light at night (ALAN) can have serious impacts on marine environments. Several studies have demonstrated that ALAN disrupts melatonin production, a hormone critical for regulating circadian rhythm. In this study, the effects of ALAN on melatonin and two of its related indolamines were investigated in the annelid Hermodice carunculata. Specifically, melatonin, serotonin and tryptamine levels were measured every three hours over a 24 h period in the heads of the annelids maintained under constant light and a 12 h light/12 h dark photoperiod, representing control conditions. Melatonin concentration was quantified using an enzyme immunoassay, while serotonin and tryptamine were analyzed by liquid chromatography–tandem mass spectrometry. Melatonin levels in annelid heads remained relatively constant with a pronounced peak at 11:00. A similar pattern was observed under constant light, but the melatonin peak shifted to 14:00. However, serotonin and tryptamine did not exhibit any significant diurnal variations due to constant light exposure. These findings suggest that melatonin secretion in H. carunculata is sensitive to ALAN, whereas its related indolamines are potentially not. The disruption of H. carunculata's melatonin secretion pattern may affect its night-time behavior and reproduction, highlighting the need for further studies to assess the ecological effects of ALAN on various marine invertebrates.

LifeWatch ERIC’s Gender Equality Plan (2025–2027) sets out a clear roadmap for promoting gender equality and equity throughout the organisation. As a continuation of the first plan published in 2022, this updated version introduces more focused and ambitious measures. It reflects LifeWatch ERIC's ongoing commitment to creating a fair, inclusive and respectful working environment for everyone, regardless of gender identity, sexual orientation, age, ethnicity, disability or other personal characteristics.The plan is aligned with the European Commission's requirements for Horizon Europe and aims to make gender aspects an integral part of our internal policies, decision-making, human resources and research activities. Rather than introducing separate or additional measures or programme, the GEP aims to reinforce the LifeWatch ERIC Culture Principle by integrating new measures with existing policies, procedures and best practices that have an impact on equality and diversity in the organisation. Ultimately, this plan goes beyond compliance and represents a broader commitment to organisational excellence, fairness and responsibility, recognising that true innovation can only occur when diversity is fully embraced and supported at all levels.

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 industrialisation 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 raised to level 9. 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 not of a confidential nature and are developed in the form of a standard, structured template.

BiCIKL ( Bi odiversity C ommunity I ntegrated K nowledge L ibrary) is a European Union (EU) Horizon 2020 project (2021–2024) building a new community of research infrastructures (RIs), researchers and other stakeholders, through improved access to interlinked, open and FAIR ( F indable, A ccessible, I nteroperable, R eusable) biodiversity data along the biodiversity research cycle (specimens, sequences, taxon names, publications) (Penev et al. 2022). The project’s 14 partners developed or substantially improved 16 tools and services currently in process of onboarding to the European Open Science Cloud (EOSC), presented in the FAIR Data Place (FDP) of BiCIKL’s flagship product, the Biodiversity Knowledge Hub (BKH). The tools and data were used in Open Call projects, performed by research groups worldwide. A key achievement of BiCIKL is the establishment of several new bi-directional links between the participating RIs through shared and interoperable data standards and web services. The sustainability of the BiCIKL services and especially of the strong collaborative spirit developed through the project will be ensured by a membership agreement for the BKH maintenance and further development. The results of BiCIKL are diverse and tackle various aspects of the implementation of open science practices in biodiversity research. The project partners and external collaborators from the Open Call projects published more than 80 papers and conference abstracts (see the article collections in Penev et al. 2022a and Thessen et al. 2023), two policy briefs (Penev et al. 2024, Agosti et al. 2024), three Biodiversity Information Science (TDWG) symposia (2021, 2023, 2024), several videos and factsheets and other training materials, guidelines and best practice recommendations, and so on. In the special focus of BiCIKL was the extraction and liberation of data from the PDFs of several thousands of published biodiversity articles making it accessible and re-usable. The new BiCIKL community proved to be successful in both technological innovation and long-lasting spirit of collaboration between biodiversity and genomics researchers, data repositories, RIs, publishers and other stakeholders. Beyond BiCIKL, we envisage our work towards further integration and interoperability between data domains by embracing human-in-the-loop collaborations, enhanced by Artificial Intelligence (AI). The implementation of AI and Large Language Models (LLM) should be possible when considering an important condition: to understand the complexity of past, recent and future changes in biodiversity and natural environments the use of AI tools should be based on аdequately curated, semantically structured and interlinked biodiversity data. We see this radical new step as a concerted community effort towards building a “Biodiversity Supergraph” (Fig. 1), understood here as a two-component ecosystem consisting of: centrally orchestrated system of tools and services, and distributed sources of transformed, semantically enhanced FAIR Linked Open Data, supplied by the partnering RIs. centrally orchestrated system of tools and services, and distributed sources of transformed, semantically enhanced FAIR Linked Open Data, supplied by the partnering RIs. The “Biodiversity Supergraph'' will provide integration of the biodiversity data on a scale and operational level that has never been attempted before. It is key for the next decade, to enable a baseline of global, biodiversity-related information serving organisations, academia, industry and society.

Papers including articles that are produced because of the activities of LifeWatch ERIC, in the context of its second implementation period (2022 - 2026) and through the implementation of its new Strategic Working Plan, are published in this special collection. The articles include data papers, papers describing the development and functioning of analytical services and papers describing any other research outcome, produced either by LifeWatch ERIC or by any collaboration with any other ERIC, Research Infrastructure, global aggregator or other legal entity.

Knowledge about biodiversity is largely embedded in a daily growing corpus of over 500 million pages of biodiversity literature that is not machine-actionable. It is thus not open to building a biodiversity knowledge graph, or facilitating the use of artificial intelligence tools. This hinders the completion of a much-needed taxonomic name reference system, prevents the discovery of the biotic interactions underpinning the prediction and understanding of global change trends and consequences, viral spillovers, annotation of genes with their respective phenotypes, and their citations in various domains dealing with biological species such as conservation, agriculture, medicine, life sciences and industry, necessary to achieve the objectives of the Green Deal and address the targets identified in the Global Biodiversity Framework. This Policy Brief highlights key actions that can liberate the scientific data published, exploit their use , promote an enhanced way to publish, and ultimately foster excellence and innovation in biodiversity science, monitoring and conservation.

The ocean takes up approximately 25% of the carbon dioxide that humans emit to the atmosphere, it absorbs most of the excess heat trapped in the Earth system by greenhouse gas emissions, thus regulating climate and life on Earth, and also provides a remarkable number of resources for humanity. Most geo-hazards occur in oceanic areas. High-quality systematic ocean observations are necessary to improvour knowledge and understanding of the complex environmental processes and to serve as early warning systems of great socio-economic impact. Research Infrastructures (RIs) are large- scale facilities that provide resources and services for scientific communities to conduct high-level research and foster innovation. RIs promote knowledge, outreach and education to public, private, and policy stakeholders, as well as providing crucial information to operational services such as Copernicus. In Europe several marine RIs have been established, which are maintained by national and European Union (EU) resources. This paper describes the significance of the marine RIs in the European Marine Observation Landscape, their status in terms of cooperation, coordination and integration. It highlights the socio-economic benefits for this integration process, being a significant pillar of the European Ocean Observing System (EOOS).

LifeWatch ERIC, the e-Science European infrastructure for biodiversity and ecosystem research, launched an Internal Joint Initiative on Non-indigenous Species and Invasive Alien Species (NIS-IAS) as they are considered one of the major drivers of biodiversity and ecosystem change. Here, the case study focused on the trophic biogeography of invasive crustaceans is presented, describing the procedures, resources, and analytical web services implemented to investigate the trophic habits of these 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 of the Louisiana crayfish Procambarus clarkii have been used to evaluate the functionalities and outcomes of the workflow . The Tesseract Virtual Research Environment integrates all the analytical services offered by LifeWatch ERIC, including the ones developed for this case study, by means of a user-friendly interface. The analytical functions implemented for the crustacean workflow provide a proof of concept for future open e-science platforms focusing on NIS-IAS. The workflow conceptual structure can be adapted to a wide range of species, and can be further improved to support researchers in monitoring and predicting trophic-related impacts of NIS-IAS. In addition, it can support policymakers and stakeholders in the implementation of effective management and control measures to limit the negative effects of bioinvaders in recipient environments.

The Special Collection of articles on the Science Projects of the EOSC Future project, funded by the European Commission, refers to one of the essential components of the project. This editorial article explains how the Science Projects fit to the EOSC Future, the way their concept has been developed and evolved during the preparation and the implementation of the project and it also makes an introduction to the templates developed by the Science Projects as a plan to carry out their activities.

The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serves the entire biodiversity research cycle, from specimens and observations to sequences, taxon names and finally to scientific publications. The strategic aim of the BKH is to support a functional and integrated biodiversity knowledge graph and an emerging new community of users. The BKH is aimed at biodiversity researchers in the widest sense, research infrastructures and publishers (Fig. 1). The BKH is the key product of the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project (Penev et al. 2022). The four goals of BiCIKL and the BKH are: Improved access to open and FAIR biodiversity data; Establishing of bi-directional data linkages between infrastructures; Development of new methods and workflows for semantic publishing, harvesting, liberating, linking, accessing and re-using of data in literature (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables); Testing and implementation of services through use cases and open call projects for researchers outside the project. Improved access to open and FAIR biodiversity data; Establishing of bi-directional data linkages between infrastructures; Development of new methods and workflows for semantic publishing, harvesting, liberating, linking, accessing and re-using of data in literature (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables); Testing and implementation of services through use cases and open call projects for researchers outside the project. The BKH consists of several modules, such as the Home page that presents the main user groups and the benefits that the BKH provides to them. It has guidelines and protocols, such as various documents on the policies, functions, and recommendations for the users. And it has relevant projects, that use linked FAIR biodiversity data. In the core of the BKH is the FAIR Data Place (FDP), which presents novel services and tools developed over the course of BiCIKL. In the future, the FDP will also accept services for linked data provided by new contributors. The FDP consists of three sub-modules: Infrastructures and organisations: Lists the contributing organisations and research infrastructures with short descriptions and links to their data, tools and services. Research infrastructures are sorted by the main type of biodiversity data they aggregate and serve: specimens, sequences, taxon names and literature. Linked data services: A catalogue of novel services that deliver FAIR data linked between the participating research infrastructures. Examples of such services are: ChecklistBank, LifeBlock, OpenBiodiv, TreatmentBank, SIBiLS “BiodiversityPMC”, eBioDiv, SynoSpecies, PlutoF Curation Tool and others. Become a contributor application form: A formal questionnaire which serves as a basis to check the suitability of an organisation or research infrastructure to join the BKH. Part of the application form is a FAIR data checklist. Infrastructures and organisations: Lists the contributing organisations and research infrastructures with short descriptions and links to their data, tools and services. Research infrastructures are sorted by the main type of biodiversity data they aggregate and serve: specimens, sequences, taxon names and literature. Linked data services: A catalogue of novel services that deliver FAIR data linked between the participating research infrastructures. Examples of such services are: ChecklistBank, LifeBlock, OpenBiodiv, TreatmentBank, SIBiLS “BiodiversityPMC”, eBioDiv, SynoSpecies, PlutoF Curation Tool and others. Become a contributor application form: A formal questionnaire which serves as a basis to check the suitability of an organisation or research infrastructure to join the BKH. Part of the application form is a FAIR data checklist. The BKH serves as a navigation system in a universe of interconnected biodiversity research infrastructures and is open to new contributors and collaborators in accessing open data and knowledge by anybody, anywhere, at any time.

ETS2 repressor factor (ERF) insufficiency causes craniosynostosis (CRS4) in humans and mice. ERF is an ETS domain transcriptional repressor regulated by Erk1/2 phosphorylation via nucleo-cytoplasmic shuttling. Here, we analyze the onset and development of the craniosynostosis phenotype in an Erf-insufficient mouse model and evaluate the potential of the residual Erf activity augmented by pharmacological compounds to ameliorate the disease. Erf insufficiency appears to cause an initially compromised frontal bone formation and subsequent multisuture synostosis, reflecting distinct roles of Erf on the cells that give rise to skull and facial bones. We treated animals with Mek1/2 and nuclear export inhibitors, U0126 and KPT-330, respectively, to increase Erf activity by two independent pathways. We implemented both a low dosage locally over the calvaria and a systemic drug administration scheme to evaluate the possible indirect effects from other systems and minimize toxicity. The treatment of mice with either the inhibitors or the administration scheme alleviated the synostosis phenotype with minimal adverse effects. Our data suggest that the ERF level is an important regulator of cranial bone development and that pharmacological modulation of its activity may represent a valid intervention approach both in CRS4 and in other syndromic forms of craniosynostosis mediated by the FGFR-RAS-ERK-ERF pathway.

The current knowledge on the risk of climate change for biodiversity and ecosystems needs to be improved by seeking evidence from cross-domain analyses. As a demonstration case, this study analyses how to investigate and monitor the rapid increase of Non-Indigenous Invasive Species (NIS) in European ecosystems. These species may not only replace indigenous ones but also alter habitats, interacting with the changing environment and eventually severely influence established socio-economic regimes. The challenge is to adopt a comprehensive approach by considering the bulk of the biotic and abiotic variables and their interactions, which may be even more important for the distribution of the NIS than the occurrence of the NIS. Such approaches require access to big datasets (from genomics to in situ and satellite borne environmental data) and high computational power, especially for those models with iterative algorithms. This study aims to: integrate data from different scientific disciplines in the marine subdomain (e.g. chemistry, physics, biodiversity, ecosystems, genomics, socio-economics) into an analytical framework in order to advance our knowledge on the impact of NIS on European marine biodiversity and ecosystems; to connect the analytical framework and federate access to relevant data infrastructures at the EOSC portal in order to mobilise and empower a larger community of researchers and potential data providers; and to demonstrate and promote the benefits and potential of web-based science using EOSC.A break-through Technical Composability Layer (Tesseract, which includes an additional option with Jupyter Notebook) is used in order to achieve the horizontal composability of the services. Only FAIR-compliant datasets are used in this study. However, because the nature of the project is primarily multidisciplinary and cross-domain, the only way to guarantee that the results deriving by the different disciplines/domains are comparable is to FAIR-ify the web services used, too. This way, it is ensured that both the quality and process potential in the different disciplines and domains are comparable and therefore so are their results.This paper brings together scientists making basic research on biodiversity and ecosystems, computer engineers, including software and web developers, in order to create a FAIR-compliant virtual research environment (VRE) to achieve both the scientific goals and the community engaged.

This Science Project (SP) contributes to the estimation of the impacts of the invasive species on the European Biodiversity and Ecosystems. This topic is important for European Green Deal and the new European Biodiversity Strategy. The SP is also linked with the socio-economic issues because of the NIS implications to the local ecosystems and their services, and their societal goods and services. Since many of the above impacts may be of local scale, they may alter common practices in circular economies. The SP is implemented by: (a) Combining different sources of data and information; (b) Using a dual workflow to analyse the data; (c) Integrating its resources with core EOSC services and potentially horizontal services available; (d) Engaging the relevant scientific communities. The users will be able to: (a) Analyse distribution patterns of invasive species from different sources of data; (b) Compare the above patterns; (c) Provide managerial suggestions to relevant authorities; (d) Build on the existing infrastructure to address more complex questions (e.g. future scenarios).

The diversity and distribution of polychaetes in the coastal area and the EEZ of the Republic of Cyprus is presented based on both the literature records and new data acquired in a wide range of environmental monitoring programmes and research projects. A total of 585 polychaete species belonging to 49 families were reported in Cyprus waters; among them, 205 species (34%) were recorded based on the literature only, 149 (26%) were new records based on our own data, and a total of 231 spp. (40%) were recorded from both the literature and new data. A total of 51 polychaete species were identified as non-indigenous; among them, 32 were confirmed as alien species, 4 were considered cryptogenic, and 15 were considered questionable as there were doubts about their identity. The Indo-Pacific Schistomeringos loveni was reported for the first time in the Mediterranean Sea, while four species already reported in the literature, namely, Bispira melanostigma, Fimbriosthenelais longipinnis Leonnates aylaoberi, and Rhodopsis pusilla, were added to the list of non-indigenous polychaetes in the Mediterranean Sea. The current work highlights the importance of implementing environmental monitoring programmes and carrying out research surveys targeting benthic macrofauna assemblages.