New study in Metabarcoding and Metagenomics shares results from FRESHBAR, the first large-scale barcode reference for Nordic benthic freshwater diatoms.
Diatom DNA metabarcoding holds great potential for biodiversity monitoring and ecological assessment, particularly within the EU Water Framework Directive (WFD) and the recently introduced EU Nature Restoration Law (NRL). However, several challenges remain, among which gaps in reference databases have been identified as a major obstacle, especially for understudied habitats and ecoregions.
Ribbon-shaped chains representing colony formation of Eunotia implicata Nörpel, Lange-Bertalot & Alles. Credit to Maria Kahlert.
Stacked chain colonies of Eunotia incisa W.Smith ex W.Gregory. Credit to Maria Kahlert.
In this context, we present results from the national barcoding project (FRESHBAR), conducted between 2019 and 2023 and focusing on benthic freshwater diatoms of Sweden, a key organism group for both ecology and environmental assessment. The study was recently published in the open-accessMetabarcoding and Metagenomics journal. A primary goal of the project was the publication and vouchering of all data, materials, and results to support further research.
Pin-cushion-like colonies (tufts of upright cells sharing a common pad of mucilage at the base) of Eunotia cf. seminulum Nörpel-Schempp & Lange-Bertalot. Credit to Maria Kahlert.
Pin-cushion-like colonies of cells of the Eunotia flexuosa/ pseudoflexuosa/ latitaenia – group. Credit to Maria Kahlert.
The project established a total of 312 diatom cultures, with a focus on oligotrophic and acidic habitats. The cultures were sequenced for two barcodes (rbcL and 18SV4) and identified using light microscopy, while selected strains were additionally examined by scanning electron microscopy. All data, including sampling metadata, barcode sequences, images, and voucher material, were published in accordance with the FAIR principles, and a subset of cultures was archived in diatom culture collections.
Chain-forming colonies in bracelet form of the Eunotia flexuosa/ pseudoflexuosa/ latitaenia – group. Credit to Maria Kahlert.
Nearly all strains were successfully sequenced, identifying 51 taxa across 17 genera. A notable highlight was the relatively high proportion of Eunotia taxa, a genus poorly represented in diatom databases yet frequently encountered in Swedish freshwaters. Beyond molecular and morphological data, we also captured images of colony formation and sexual reproduction stages from living cultures, information that is only rarely documented.
Sexual reproduction (auxospore formation) and ribbon-shaped chains representing colony formation of Eunotia sp. Credit to Maria Kahlert.
Sexual reproduction (auxospore formation) and ribbon-shaped chains representing colony formation of E. myrmica Lange-Bertalot. Credit to Maria Kahlert.
FRESHBAR represents the first large-scale effort to generate barcode reference sequences for Nordic benthic freshwater diatoms. As all data are publicly available, we are confident that the added sequences and morphological information will contribute to more accurate species-level identification, help resolve taxonomic relationships within diatoms, and improve reference databases for environmental monitoring and research.
Original source:
Kahlert M, Mora D, Kusber W-H, Abarca N, Zimmermann J (2026) New DNA barcode reference data of freshwater diatoms (Bacillariophyceae) from Sweden: old acquaintances and new taxa. Metabarcoding and Metagenomics 10: e186778. https://doi.org/10.3897/mbmg.10.186778
Aligning with the International Day for Biological Diversity‘s theme of “Acting locally for global impact,” researchers have released a comprehensive blueprint for building a robust, globally adaptable network of DNA barcoding practitioners.
Heat map illustrating the heterogeneity in the number of available DNA barcode records with species assignment. Data were retrieved from the BOLD Systems data portal in November 2025. Credit to Kaitetzidou et al., 2026.
DNA barcoding has become a cornerstone for modern species identification and biodiversity monitoring, proving vital for applications ranging from ecological research to conservation and environmental policy. Since its inception, the DNA barcoding community worldwide has been convening under the aegis of the International Barcode of Life (iBOL), which provides necessary global coordination. To implement barcoding at scale, build local capacity, and translate scientific advances into actionable practice, iBOL national nodes have been established since the 2010s
Drawing on a survey and workshop conducted under the Horizon Europe Biodiversity Genomics Europe project, this research synthesises experiences from 20 countries, including 17 in Europe, and examines how national nodes are initiated, governed, and sustained. Common challenges included defining scope, securing sustainable funding, harmonising methodologies, and engaging stakeholders. For example, a particularly striking finding was how rarely node coordinators sought guidance from established networks before setting up their own.
The decision-making process and steps taken were almost entirely based on intuition and the experience from other within-country activities, as well as their perceptions of the activities of other nations’ barcoding nodes,
the researchers note.
Countries are highlighted whose representatives of a national initiative responded to the questionnaire (yellow), attended the workshop (green) or both (yellow–green stripes). Peru and South Africa are not displayed on the map; however, representatives of their national nodes took part in the survey and the workshop, respectively. Credit to Kaitetzidou et al., 2026.
Central to the paper are ten practical recommendations to ensure the establishment and long-term success of national DNA barcoding nodes. The authors emphasise several key priorities, primarily the construction of comprehensive DNA barcode reference libraries and the critical need to align scientific activities with practical biomonitoring requirements.
Furthermore, they strongly advocate for promoting FAIR (Findable, Accessible, Interoperable, and Reusable) and CARE data principles, alongside implementing focused strategies for capacity building, methodological standardisation, communication, and diverse stakeholder engagement.
Stronger national infrastructures will enhance Europe’s capacity for DNA-based biodiversity monitoring and support metabarcoding and metagenomic research. Building on milestones such as the establishment of iBOL Europe in 2022, these local efforts add up to real progress on species discovery, conservation, and environmental management worldwide.
This paper has been published with the support of the Biodiversity Genomics Europe project, funded through Horizon Europe, the UK Research & Innovation Fund and the Swiss Confederation (https://biodiversitygenomics.eu/).
Original source:
Kaitetzidou E, Gadawski P, Goodall-Copestake WP, Dankova G, Gkagkavouzis K, Holak S, Rewicz T, Bącela-Spychalska K, Mamos T, Fantoni K, Jabłońska A, Tończyk G, Trębicki Ł, Aravanopoulos FA, Bruschini C, Bonchev G, Dagher Kharrat MB, Čiampor F, Costa FO, Dapporto L, Ekrem T, Ferreira S, Geiger M, Hausmann A, Hebert PDN, Kalamujić Stroil B, Kamenova S, Kautmanova I, Keskin E, Kučinić M, Lipinskaya T, Mutanen M, Papakostas S, Price B, Ramírez R, Rougerie R, Rulik B, Szucsich N, Van Der Bank M, Triantafyllidis A, Hollingsworth PM, Grabowski M (2026) Empowering national capacity for DNA-based approach to species identification and biodiversity monitoring. Metabarcoding and Metagenomics 10: e183268. https://doi.org/10.3897/mbmg.10.183268
Over the past two decades, environmental DNA (eDNA) analysis has become a crucial tool for monitoring aquatic ecosystems. The most common method, metabarcoding, relies on PCR amplification of a smaller genetic region to identify specific taxa. However, PCR can lead to “significant taxonomic bias” because it often amplifies the DNA of different organisms unequally, making quantitative estimates difficult.
To avoid this, scientists have increasingly explored “shotgun sequencing“- an approach that sequences the DNA in a sample much more broadly – across the entire tree of life and across the genome. Unfortunately, in marine environments, shotgun sequencingis typically overwhelmed by microbial DNA, burying the genetic traces of less abundant macro-organisms such as animals.
Bigger Pores, Better Animal DNA Capture?
In a new study published in Metabarcoding and Metagenomics, researchers investigated if they could capture a higher proportion of eukaryotic (animal and plant) DNA simply by using filters with larger pore sizes.
Filter pore sizes are expected to influence results, since eDNA may be present in many different states, including but not limited to complete organisms, sloughed tissue, feces, free DNA, or gametes.
commented Dr. Adrián Gómez-Repollés, the lead author of the study.
To test this, the team collected 15 seawater samples from Skovshoved Harbour in Denmark and filtered them using pore sizes ranging from 0.2 µm to 8.0 µm. The results showed a stark contrast in the type of DNA captured based on the filter size.
Filters with smaller pore sizes (0.2 µm and 1.2 µm) retained a significantly greater proportion of bacterial reads than eukaryotic reads (63% vs. 28%); conversely, filters with larger pore sizes (5.0 µm and 8.0 µm) retained a significantly greater proportion of eukaryotic reads than bacterial reads (49% vs. 31%).
By switching to 5.0 µm or 8.0 µm filters, the researchers successfully reduced the dominance of bacteria. Of the 19 metazoan (animal) phyla detected using shotgun sequencing, all but one were found to be more abundant when using the larger pore sizes.
Looking to the Future of Biomonitoring
Taxonomic comparison at the kingdom and phylum levels of eukaryotes detected with shotgun sequencing and metabarcoding. A. Number and relative abundance (percentages) of taxonomically classified reads after rarefaction per sample and kingdom for shotgun sequencing; B. Number and relative abundance of taxonomically classified reads after rarefaction per sample and kingdom for metabarcoding. For both heatmaps, sample replicates are ordered along the y-axis by increasing pore size, starting with the enclosed filter type (EN) and continuing with the open pore filter type (OP). Pore sizes are in µm; C. Cladogram of the full set of eukaryotic phyla identified by shotgun sequencing and metabarcoding. Branch colors represent kingdoms (blue, Metazoa; red, Fungi; green, Viridiplantae; pink, other eukaryotes). Three surrounding rings indicate phyla shared between shotgun sequencing and metabarcoding (gray), phyla uniquely detected with metabarcoding (yellow), and phyla uniquely detected with shotgun sequencing (blue). Information in the rings is summarized in a Venn diagram in the upper left corner. Taxa marked with an asterisk are no longer categorized as a phylum. Credit to Gómez-Repollés et al., 2026
When compared alongside traditional 18S rDNA metabarcoding, the shotgun sequencing method successfully shared 39 of the 54 detected eukaryotic phyla, indicating a similar performance in detecting the presence of high-level taxonomic groups.
To test the potential of shotgun sequencing in applied biomonitoring even further, the researchers examined the results at genus-level for a number of well known marine animals such as fish, mussels, crustaceans and bristle worms. Here, they found both DNA matches to native Danish species but also to exotic taxa that were highly unlikely and probably due to the low level of resolution in shotgun sequencing, where genetic regions of low variation and coverage are sequenced.
Water sample collection. Photo by David Stanciu.
But, when they looked further into the results they observed that the local taxa consistently comprised a higher number of reads. The number of reads could thus be a simple way to initially separate authentic taxa from erroneous matches in eDNA studies based on shotgun sequencing, although the approach needs further testing.
However, the authors note current limitations with the technology, primarily driven by incomplete public DNA reference databases. In the study, only 0.78% of the total shotgun reads could be definitively assigned to a superkingdom level. Another drawback was the lack of field controls to rule out cross-contamination or input from airborne DNA, coupled with a limited spatiotemporal design involving only a single sampling location.
Despite these hurdles, shotgun sequencing and filters with larger pore sizes could potentially be a significant step forward for eDNA in marine biology. As global genomic databases continue to expand, “the taxonomic coverage and resolution of shotgun sequencing should improve, likely enhancing the potential of shotgun sequencing for future eDNA research“, says Philip Francis Thomsen, professor and senior author on the study.
Original study:
Gómez-Repollés A, Sigsgaard EE, Jensen MR, Thomsen PF (2026) Filter pore size influences taxonomic composition of retained eDNA from seawater samples—evidence from shotgun sequencing. Metabarcoding and Metagenomics 10: e164232. https://doi.org/10.3897/mbmg.10.164232
Students at the forefront of conservation or how community science helps gather data on cavity-nesting bees and wasps, enhancing our understanding of ecosystem interactions.
Can students be the front lines of conservation? A new Canada-wide study, published in Metabarcoding and Metagenomics, suggests they can. The efforts of some 5000 students produced data detailed enough to reveal complex ecological networks hidden inside a small PVC and cardboard tube home.
A trap nest installed at a Bees@Schools community science location. Multiple tubes nested in are visible. Photo credit to Sage Handler.
They invited schools to volunteer across Canada to install standardised ‘trap nests’ – simple PVC pipe and cardboard tube homes that mimic natural cavities where bees and wasps build nests.
Cavity-nesting bees and wasps play key roles in pollination and pest control, yet their distributions and feeding relationships are often poorly known because they can be small, secretive and difficult to observe directly.
Nesting tubes gathered from one trap nest, ready to be cut open and processed. Photo credit to Sage Handler.
Instead of relying only on traditional identification under a microscope, the researchers used DNA metabarcoding – a method that reads DNA from mixed samples and can detect many species at once.
This allowed the team to identify not only which bee or wasp species built each nest, but also which plant pollen or insect prey were brought back as food. The result was a rich, detailed view of both where cavity-nesting bee and wasp species live and how they interact with plants and other insects.
A rainbow of pollen prepared for DNA metabarcoding. Credit: Sage Handler An intact cavity-nesting bee nest extracted from a nesting tube. Credit: Sage Handler (Hill)
A key outcome of the study was the creation of tripartite networks: maps linking (1) the nesting bee or wasp, (2) its food (pollen or insect prey) and (3) parasites. This kind of network is extremely difficult to build through observation alone, but trap nests can act like tiny ecological time capsules.
Every brood cell contains biological traces and metabarcoding can recover them. Students weren’t just collecting insects, they were collecting entire ecological interaction datasets: the raw material needed to build food-web maps across a whole country!
A lot of people want to contribute to conservation or learn more about biodiversity, but don’t know how. This shows that a small, practical action, like hosting a trap nest, can contribute real data that researchers can use. Community and citizen science is becoming more common, so keep an eye out for research happening in your neighbourhood.
says Handler, the lead author of the study
Original resource:
Handler S, Coveny K, Braukmann TWA, Raine NE, Steinke D (2026) Welcome to Hotel Hymenoptera: monitoring cavity-nesting bee and wasp distribution and their trophic interactions using community science and metabarcoding. Metabarcoding and Metagenomics 10: e139674. https://doi.org/10.3897/mbmg.10.139674
Berlin (Germany) and Sofia (Bulgaria), 10th February, 2026 – ResearchGate, the professional network for researchers, and Pensoft Publishers, an independent open access publisher and provider of high-quality scholarly publishing services, today announced an expansion of their Journal Home partnership. Building on an earlier collaboration announced in 2023, the list now expands to 40 journals, covering the majority of Pensoft’s and partners’ journals using the publisher’s ARPHA Publishing Platform.
With most of Pensoft’s eligible partner journals choosing to participate, the expansion reflects strong demand for greater exposure and engagement opportunities, particularly among smaller and developing journals in niche research areas. Through Journal Home, partner publishers can reach more relevant audiences, improve discoverability, and connect more effectively with researchers worldwide.
Participating Pensoft journals will also benefit from:
Increased usage and readership, with full-text open access journal content seamlessly surfaced to highly relevant researcher communities across the ResearchGate platform.
Stronger engagement from new and returning authors, connecting partner journals, including specialist and emerging titles, with targeted researchers and potential authors throughout the research lifecycle.
Dedicated Journal Profiles and prominent placement of Pensoft journals to enhance visibility and branding, boosting recognition of partner journals with researcher communities around the world.
Improved author experience, with the automatic addition of published articles to author profiles, clearer insight into reader engagement, and greater opportunities for meaningful collaboration.
“Journal Home allows us to provide our partner journals with improved visibility and stronger connections with global researcher communities. Many of these journals serve highly specialised fields, and Journal Home helps make sure their articles reach the right researchers, who will benefit from them most.”
Lyubomir Penev, CEO and founder of Pensoft Publishers
“We’re pleased to expand our Journal Home partnership with Pensoft to support an increasing number of partner journals. By bringing these journals onto the platform, smaller and emerging titles can expand their reach, attract high-quality submissions, and connect with the most relevant researcher communities at key moments in their research journey.”
Robyn Mugridge, Head of Partnership Development at ResearchGate
For more information about Pensoft Publishers, please visit www.pensoft.net.
About ResearchGate
ResearchGate is the professional network for researchers. Over 25 million researchers use researchgate.net to share and discover research, build their networks, and advance their careers. Based in Berlin, ResearchGate was founded in 2008. Its mission is to connect the world of science and make research open to all.
About Pensoft Publishers
Pensoft is an independent, open-access scholarly publisher and technology provider, best known for its 40+ biodiversity journals, including ZooKeys, Biodiversity Data Journal, PhytoKeys, MycoKeys, One Ecosystem, and Metabarcoding and Metagenomics. Ever since becoming the first to introduce semantic enrichments and hyperlinks within a scientific article in the field of biodiversity in 2010, Pensoft has been working on various tools and workflows designed to facilitate data findability, accessibility, discoverability and interoperability.
The agreement encompasses five key research and medical bodies, and allows corresponding authors to publish their findings without individual Article Processing Charges.
Pensoft and the University of Zurichhave signed a comprehensive Open Access (OA) agreement, starting a partnership that enables researchers at participating institutions to publish their findings in Pensoft’s peer-reviewed journals without incurring individual Article Processing Charges (APCs).
Under this new framework, publishing costs for corresponding authors affiliated with the respective institutions are 100% covered by a centralised institutional deposit secured by the University of Zurich. By removing financial barriers, the agreement encourages scientists to disseminate their work to both the academic community and the wider public, making research immediately and freely available upon publication.
This initiative ensures that research is shared under open licences in strict accordance with the FAIR principles—making data Findable, Accessible, Interoperable, and Reusable.
“We are excited to start this partnership with the University of Zurich and sign an agreement that reflects our strong commitment to inclusive and equitable open science. By supporting researcher-driven publishing, we continue to foster a sustainable environment for high-impact scientific communication.”
Prof. Lyubomir Penev, CEO of Pensoft
“We are pleased to extend our portfolio of gold open access journals, in which our researchers can publish their findings without paying individual APCs. We thereby strengthen our commitment to open research information.”
University Library Zurich
Are you affiliated with a research institution operating with OA agreements? Is your institution interested in helping resident researchers navigate the complex processes underpinning academic publishing and knowledge sharing? Reach out to <publishing@pensoft.net> to discuss a potential collaboration.
The agreement covers almost 100 institutions, including Karolinska Institutet, Lund University, Uppsala University, and the Royal Swedish Academy of Sciences.
Pensoft and the Bibsam Consortium, operated by the National Library of Sweden, are pleased to announce the signing of a comprehensive Open Access (OA) agreement, marking a significant step in the transition towards a more transparent and open scholarly publishing landscape in Sweden.
Thanks to this move, researchers at participating institutions will be able to publish their findings in 65 journals published by Pensoft or using its advanced publishing platform ARPHA, including flagship titles such as ZooKeys, PhytoKeys, Biodiversity Data Journal, NeoBiota and IMA Fungus, without incurring individual article processing charges (APCs).
All authors affiliated with participating institutions can benefit from this agreement, with publishing costs 100% covered by an institutional deposit secured by the National Library of Sweden.
Unlike subscription-based systems, an OA framework ensures that scientific findings are immediately and freely available to the global community, supporting the global shift toward accessible science and adhering to the FAIR principles (Findable, Accessible, Interoperable, and Reusable).
OA agreements like this one reduce the financial burden on scientists and encourage them to share their work with both academia and the wider public, ultimately lowering barriers to sharing knowledge in a time when scientific input is key to resolving global challenges.
“We are excited to start this partnership with Bisbam and sign an agreement that reflects our strong commitment to open science. By supporting researcher-driven publishing, we continue to foster a sustainable environment for high-impact scientific communication.”
Prof. Lyubomir Penev, CEO of Pensoft
“We are delighted to announce the addition of Pensoft Publishers to our portfolio of nationally funded agreements for 2026. This represents an important step towards achieving full open access to scientific publications in Sweden.”
Niklas Willén, License Manager at Bibsam Consortium and National Library of Sweden
Are you affiliated with a research institution operating with OA agreements? Is your institution interested in helping resident researchers navigate the complex processes underpinning academic publishing and knowledge sharing? Reach out to <publishing@pensoft.net> to discuss a potential collaboration.
A new white paper delivers a clear message: protecting biodiversity is not just an environmental issue. It is essential for food security, public health, climate stability, and the global economy.
The authors make a call for a decisive shift: from fragmented initiatives to a holistic, global approach to biodiversity research and policy, already demonstrated during a workshop at the 79th United Nations General Assembly and the Science Summit (UNGA79). A key part of this transformation concerns the role of research infrastructures in connecting science, technology, and policy: from vast biodiversity collections and genomic observatories, to ecosystem “digital twins” powered by supercomputers.
Behind the paper are a network of legal entities based in Europe and holding global interests, which includes biodiversity, ecology, and engineering communities, coordinated by the LifeWatch European Research Infrastructure Consortium (ERIC).
With their combined expertise and through European initiatives, such as Research Infrastructures, e-Infrastructures, the European Open Science Cloud (EOSC), the Digital Twin projects and academic publishers, these communities provide a basis for collaboration in strategically contributing to the implementation of the Kunming-Montreal Global Biodiversity Framework (K-M GBF) targets.
Biodiversity needs to be placed at the centre of the upcoming 2026 UN Summit of the Future and become a core pillar of the agenda after the 2030 deadline for the United Nations Sustainable Development Goals (UN SDGs).
The UN Pact for the Future should include biodiversity as a core pillar: “not only of environmental sustainability, but of equity, security, and intergenerational justice”.
urges the team.
To do this, the authors propose the establishment of a global alliance that will strategically integrate biodiversity conservation into the core priorities of the UN Summit of the Future and the post-SDG agenda.
This alliance is meant to join the voices of researchers, policymakers, indigenous knowledge holders, civil society, and industry to ensure that biodiversity underpins peace, prosperity, and justice as a universal enabler.
The white paper also demonstrates how the research infrastructures collectively contribute to the seven Strategic Considerations of the K-M GBF, outlined here in brief and further detailed in the full publication:
Contribution and rights of Indigenous Peoples and local communities: Ensuring fair recognition and sharing of benefits with indigenous peoples and local communities, thus integrating their knowledge into biodiversity science.
Collective efforts towards the targets of the K-M GBF: Coordinating biodiversity monitoring, databases, and digital infrastructures to track progress towards global conservation targets.
Fulfilment of the three principal objectives of the Convention on Biological Diversity (CBD) and its protocols: Studying or supporting the study of all aspects of biodiversity; and providing public and streamlined access to biodiversity information.
Implementation through science, technology, and innovation: Developing and offering technologically advanced and novel solutions for research, data sharing and management to various users; and promoting open science by publishing research findings and increasingly sharing more facets of the research process.
Ecosystem approach: Developing and implementing technologies that enable a cross-domain, multidisciplinary approach to studying biodiversity and ecosystems; and using holistic, cross-disciplinary methods to understand and predict biodiversity and environmental dynamics.
Cooperation synergies: Collaborating with organisations responsible for implementing the CBD, policy agents, international research projects; and participating in international forums and social, scientific and technical initiatives.
Biodiversity and health linkages: Demonstrating how healthy ecosystems support human health, food security, and resilience to pandemics by supporting interdisciplinary research through bringing together knowledge and data and uncovering links and interactions between humans and the environment.
“With the UN’s ‘Pact for the Future’ currently being shaped, we see a unique opportunity to anchor biodiversity as a unifying thread across global goals that will transform how societies respond to the intertwined crises of climate change, nature loss, and pollution,” say the authors.
The white paper is the latest contribution to the LifeWatch ERIC Strategic Working Plan Outcomes open-science collection meant to provide a one-stop access point to the most important deliverables by the European biodiversity and ecosystem research infrastructure, which is currently undergoing a significant upgrade as a response to the needs of its target communities and stakeholders.
***
Original source:
Arvanitidis C, Barov B, Gonzalez Ferreiro M, Zuquim G, Kirrane D, Huertas Olivares C, Drago F, Pade N, Basset A, Deneudt K, Koureas D, Manola N, Mietchen D, Casino A, Penev L, Ioannidis Y (2025) From Knowledge to Solutions: Science, Technology and Innovation in Support of the UN SDGs. Research Ideas and Outcomes 11: e168765. https://doi.org/10.3897/rio.11.e168765
This publication is part of a collection:
LifeWatch ERIC Strategic Working Plan Outcomes Edited by Christos Arvanitidis, Cristina Huertas, Alberto Basset, Peter van Tienderen, Cristina Di Muri, Vasilis Gerovasileiou, Ana Mellado
Europe’s biodiversity and ecosystem research infrastructure. LifeWatch ERIC provides access to biodiversity and ecosystem data, services and other research products: its virtual workbenches and digital twins for biodiversity science enable researchers worldwide to analyse biodiversity patterns, processes, and changes in ecosystems, and derive evidence-based knowledge for science and policy.
CSC hosts one of the world’s most powerful supercomputers (LUMI), pioneering biodiversity digital twins and climate models. CSC provides critical support for data-intensive projects that link computing, AI, and environmental science.
A federation of hundreds of data centres providing global-scale computing, AI, and data services. EGI enables large-scale analysis of biodiversity and environmental data from sensors and satellites, supporting international collaboration.
A hub for marine research, coordinating Europe’s Digital Twin of the Ocean and global biodiversity data systems, such as WoRMS (World Register of Marine Species). VLIZ drives blue innovation and ocean data integration.
Europe’s infrastructure for marine biology, offering access to organisms, labs, and genomic observatories. EMBRC connects over 70 institutes across 10 countries, supporting research “from genes to ecosystems.”
The largest initiative to digitise and unify Europe’s natural science collections into a single, FAIR-data-based infrastructure. DiSSCo makes museum collections globally accessible, boosting taxonomic, ecological, and environmental research.
A European e-Infrastructure dedicated to building a globally connected, interoperable, and sustainable open research ecosystem, with Open Science at its core. By offering a suite of services covering the entire research lifecycle, guidelines, and practices that support the adoption of Open Access and FAIR data principles across its network of National Open Access Desks in 34 countries, OpenAIRE supports local researchers, funders, and policymakers in aligning with European and global open science policies.
Founded in 1992 “by scientists, for scientists”, the academic open-access publishing company is well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials. Through its Research and Technical Development department, the company is involved in various research and technology projects. Pensoft coordinated the EU project BiCIKL (2021-2024), which established a new community of Research Infrastructures and users of FAIR and interlinked biodiversity data.
The world’s largest computing society, established to foster ethical and responsible innovation. ACM brings global expertise in computing and AI to biodiversity research and policy.
A leading ICT and AI research institute advancing digital infrastructures and open science platforms. Athena connects computing innovation with biodiversity, humanities, and societal challenges.
That’s not just a question for crime shows. It’s also exactly what we want to ask every pollinating insect we catch. Who are you – which species? And what have you done – which flowers have you visited, carrying pollen from one to the next? And these questions are important!
Do you like chocolate? Or maybe coffee? How about apples, strawberries, or cherries? All of them need insect pollinators. Unfortunately, many insects are in decline, threatening the stability of ecosystems. Studying them is more important than ever. Traditionally, researchers relied on field observations of foraging behaviour. But these are time-consuming and can never capture the full picture. That’s why many groups now use genetic approaches, studying the pollen carried by insects. This method is called pollen-metabarcoding, where a short genetic sequence from a specific region (in our case, ITS2) can identify the plant species that pollen belongs to.
There’s just one catch: collecting pollen often means killing the insect. Lethal sampling does have its merits – the preserved specimen can be used to answer other questions in the future, for example. But in our case, it felt counterintuitive. We want to study species that might already be endangered, and killing them could worsen their situation. So we had to find another way.
In the field, we found queen-marker cages easy to use and really helpful to get the genetic material we need for our analyses. Credit: Willi Müller.
Enter: the queen-marker cage. This tool – borrowed from beekeepers – is a plastic tube with a mesh at one end and a plunger at the other. We used it to capture a bumble bee, immobilize it, and remove its pollen. The mesh is also large enough to clip one of the bee’s feet – in insects, this part is called the tarsus. That may sound harsh, but it doesn’t significantly affect the animal. During our collection, we observed those five-footed bumble bees visiting flowers and gathering pollen in the days after release, with no difference to their six-footed counterparts.
The mesh of the queen-marker cage is just big enough for a fine pair of scissors to fit through the holes and allow for precise clipping of the bumble bee’s tarsus, here Bombus lucorum agg.
But why take a bee’s foot in the first place? Many animal groups include cryptic species – species that look almost identical, even to experts. Bumble bees are no exception. The only reliable way to tell these look-alike species apart is through DNA barcoding, often using the COI gene. A single clipped foot provides just enough tissue to barcode the bee itself, in addition to analyzing the pollen it carried.
Of course, the work doesn’t end in the field. Once we had the samples, the real detective work started in the lab. And as everyone with hay fever knows: pollen gets everywhere. To avoid contamination, we processed everything in a special clean lab, wearing full-body protective suits. It may seem over the top, but when you’re working with invisible grains of pollen, even the smallest contamination can skew the results.
As pollen is everywhere, we had to use a special clean lab with the corresponding attire.
And in the end, it worked! Our results matched expectations: we detected a cryptic species (fittingly named Bombus cryptarum), we saw that the longest flowers were visited only by bumble bees with the longest tongues, and the pollen we identified came from plants flowering at our study sites during collection.
Now we have a simple and non-lethal way to gather the genetic material needed to identify pollinators and the flowers they visit, answering ‘Who are you, and what have you done?’ – without adding pressure to vulnerable insect populations.
Studying pollination helps us understand and protect ecosystems. Bombus lucorum agg. and Apis mellifera on Phacelia tanacetifolia. Credit: Anna Wurster.
Orignal source
Edwards A, Gemeinholzer B (2025) Case study of non-lethal sampling for plant-pollinator networks via barcoding and metabarcoding on bumble bees in Germany. Metabarcoding and Metagenomics 9: e141904. https://doi.org/10.3897/mbmg.9.141904
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In October 2025, four major institutions in the biodiversity research landscape: TDWG, GBIF, OBIS and GEO BON, will come together as the organisers of the Living Data 2025 conference.
The event is set to be among one of the most crucial international gatherings of the year for experts and stakeholders in the field of biodiversity data. Set to take place in the Colombian capital of Bogotá between 21st and 24th, Living Data 2025 will centre around four core themes:
Open data
Data integration
Biodiversity data application
Community engagement and capacity-building
As an academic publisher with experience and commitment to all these thematic areas, Pensoft will participate in the event in the capacity of an exhibitor and an award sponsor, as well as a symposium host.
The conference delegates will have the chance to learn more about the publisher, its exclusively open-access scholarly portfolio and participation at various international scientific projects when they visit the company’s branded stand.
During the event, the scientific publisher and technology provider will also present the Pensoft Award for the Best Student Oral Presentation, which grants the winner a free publication in an open-access, peer-reviewed journal from our portfolio.
Crucially, Pensoft’s involvement in the Living Data 2025 programme also includes a dedicated four-hour session titled “Long Live Biodiversity Data: Knowledge Transfer and Continuity across Research Projects”.
The symposium will be jointly co-organised by Pensoft, LifeWatch ERIC and the Naturalis Biodiversity Centre. As the title suggests, the session will focus on the longevity of scientific outputs as they are generated, shared and re-used across disciplines, organisations and initiatives. In this context, tools, information hubs and workflows enabling exchanges that truly consolidate the global biodiversity data space over time will be showcased.
In a broader sense, the session will also seek to demonstrate how targeted communication can help transform science results into actionable knowledge by raising awareness among agenda-setters. This will speak to the potential of a multi-level approach to information sharing to bridge the gap between science and policy in relation to increasingly ambitious global environmental objectives.
Multiple projects affiliated with Pensoft will be represented in these deliberations, in order to share a diverse array of relevant insights:
22 October (Wednesday): 10:45 AM – 12:45 PM (UTC/GMT-5)
23 October (Thursday): 10:45 AM to 12:45 PM (UTC/GMT-5)
You can find out more about Living Data, including the details on registering for an in-person or virtual attendance, on the conference’s website. Our session is listed on this page under ID number 6788879.
As an additional note, the organisers of the conference have launched a call for extended abstracts for all speakers at Living Data 2025 that will remain open until 1st October 2025. The participants who opt to publish their conference abstracts in the Biodiversity Information Science and Standards (BISS) journal will enjoy permanent and far-reaching accessibility and discoverability for their conference contributions.
The TDWG network, who launched BISS as their official scholarly outlet in 2017 in collaboration with long-time partner Pensoft, have posted a list of the advantages for submitting an extended abstract, even though they have already had their abstracts accepted by the Living Data 2025 organisers. Amongst the reaslons are many perks typically associated with a conventional research article, such as DOI registration, indexation at dozens of scientific databases, embedded media, tables and supplementary materials, and usage metrics.
