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
Invisible to the naked eye, phytoplankton play a critically important role at the base of marine food webs, yet their diversity continues to be underestimated. Recently, the UN Global Compact released “The Plankton Manifesto,” highlighting how these microscopic organisms are crucial for addressing the “triple planetary crisis” of climate change, biodiversity loss, and pollution. Diatoms, a major group of photosynthetic microalgae, are particularly powerful in driving roughly 20% of global photosynthesis and forming the very base of marine food webs.
Yet despite their monumental importance, microalgal ecosystems remain largely unexplored and poorly mapped. That is why a recent major scientific undertaking in the Northeast Pacific is so significant.
A First-of-its-Kind Baseline in the Salish Sea
Map of sampling locations. A Distribution of sampling sites throughout the Salish Sea (green markers).Red frame: area of enlargement around Galiano Island (1B); B Sampling sites around Galiano Island (green markers). Map credit to Webber et al., 2026.
Diatom records of the Salish Sea bioregion have historically been fragmentary, dating back to early inventories in the 1800s, and with only scattered surveys filling the gap across the 20th and 21st centuries. As Andrew Simon, PhD student at the University of Alberta, president of IMERSS, and one of the study’s researchers, puts it:
The Salish Sea has long been studied for its rich marine biodiversity. Yet, until now, the history of research on its primary producers has been fragmented, and we have lacked a consolidated baseline record.
Now, for the first time, researchers have taken a significant step toward closing that gap. A team of Canadian researchers — Mark Webber (University of Victoria; IMERSS), Elaine Humphrey (UVic; IMERSS), Arjan van Asselt (IMERSS), Alice Chang (UBC), Evan Morian (Hakai Institute; UBC), and Andrew Simon (IMERSS; University of Alberta) — has published anew checklist of 924 diatom taxa alongside a curated dataset of 11,469 records in the open-access journal Biodiversity Data Journal, providing a long-needed foundation for environmental monitoring across this region of the northeast Pacific Ocean.
Trigonium quinquelobatum, external valve view. SEM. Scale bar: 20 µm, Credit to Webber et al., 2026.
Cocconeis kerguelensis, SV. LM. Scale bar: 5 µm. Photo credit to Webber et al., 2026
Neocalyptrella robusta, live, girdle view. LM. Scale bar: 50 µm, Credit to Webber et al., 2026
The findings include some curious discoveries. Several taxa are reported for the first time on the Pacific coast of North America, including Trigonium quinquelobatum, while others, such as Cocconeis kerguelensis (previously known only from the Indian Ocean) and Neocalyptrella robusta (previously confined to California), suggest a range expansion into cooler waters.
Ecologically, the genus Tabularia stands out as a dominant presence on eelgrass and macroalgae, despite having few species. In contrast, genera like Auliscus, Biddulphia, and Mastogloia are surprisingly scarce in the Salish Sea compared to other regions, leaving open questions about what limits their occurrence there.
This dataset also directly answers a key recommendation from the UN Plankton Manifesto, which urges the scientific community to strengthen plankton research and develop comprehensive plankton atlases to biomonitor the health of marine ecosystems.
Bacteriastrumhyalinium, valve view. LM. Scale bar 20 µm. Credit to Webber et al., 2026.
The Salish Sea — the traditional territory of the Coast Salish peoples — is home to roughly nine million people and is experiencing rapid growth in urbanization, industrial activity, and marine shipping.
Because diatom populations respond quickly to changes in water quality and environmental conditions, they serve as highly effective early-warning bioindicators for shifts in ecosystem health and pollution levels.
Without a clear picture of what the base of the food web looks like today, it is impossible to understand the impact of tomorrow’s environmental changes.
Attheyalongicornis, girdle view. SEM. Scale bar: 10 µm. Credit to Webber et al., 2026.
“We are fortunate to have had a dedicated group of academic researchers and community scientists contribute to this work over many years,” says Mark Webber, IMERSS’ resident diatomist. “Drawing from the literature, microscope analysis, and molecular sequencing, we now have a better picture of the diatoms present in the Salish Sea. Diatoms are vital to the health of countless organisms — from shorebirds and shellfish to fish and mammals. This baseline provides a reference point for understanding changes that could ripple across the entire web of life.“
Local Research for Global Solutions
Actinoptychusadriaticus var. pumila, exterior valve view. SEM. Scale bar: 5 µm. Credit to Webber et al., 2026.
The UN Plankton Manifesto stresses that understanding and managing plankton communities can unlock “Plankton-Based Solutions” to support fisheries, clean waters, and climate change mitigation.
Our work demonstrates how sustained collaboration between community scientists and research institutes can bridge these gaps, through partnering community expertise and observation with access to microscopy and molecular technologies,
the team concludes.
The new checklist and dataset will support researchers and policymakers in environmental assessments of the Salish Sea, as the team continues to refine and analyze the data to support ongoing regional research.
Original source
Webber M, Humphrey E, van Asselt A, Chang A, Morien E, Simon ADF (2026) Diatoms (Bacillariophyta) of the Salish Sea, Northeast Pacific: annotated checklist and new species reports. Biodiversity Data Journal 14: e189060. https://doi.org/10.3897/BDJ.14.e189060
IMERSS, or the Institute for Multidisciplinary Ecological Research in the Salish Sea, is a non-profit society based in Galiano Island, British Columbia, Canada. IMERSS joins scientific researchers, citizen scientists, and Indigenous communities to conduct multidisciplinary ecological research, monitor biodiversity and the environment, and communicate results to better understand and respond to change in the Salish Sea bioregion.
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
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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The first national symposium on DNA barcoding took place on 5 December 2025 at the Headquarters of the Bulgarian Academy of Sciences, where it was attended by renowned Bulgarian scientists in the field, in addition to early-career researchers and PhD students representing different institutions.
The event saw a day-long series of lectures and a poster session, during which the participants had the opportunity to get acquainted with the work of their colleagues in various fields of biology.
Amongst the topics were the development of the Bulgarian molecular laboratory in Antarctica; the study of the invertebrate fauna currently underrepresented in DNA reference libraries; the return of the beaver to Bulgaria; and research on phytopathogenic fungi on agricultural crops.
During the coffee breaks sponsored by the National Museum of Natural History, the delegates had the chance to network and exchange experience between institutions and fields of expertise.
Teodor Georgiev, CTO at Pensoft held a presentation about the 2.0 version of the ARPHA Writing Tool. In its greatly improved version, it will feature many new, refined and elaborated workflows that help and simplify data publishing, discoverability, reusability and overall FAIRness.
🗨️Imagine if ALL these links were provided as hyperlinks within a #scholarly publication!
The event was opened and closed by Prof. Dr. Lyubomir Penev, who was elected as the Chair of the Governing Board at the Bulgarian Barcode of Life last year. He is also the founder and CEO of Pensoft.
In his closing speech, Penev expressed his hopes for the development of BgBOL and confirmed the plans of the consortium to turn the symposium into an annual tradition. Congratulations were extended to BgBOL’s newest member: the Institute of Oceanology “Fridtjof Nansen” at BAS.
He also announced the launch of a new special collection in the Biodiversity Data Journal, which will welcome scientific papers related to the Bulgarian and Balkan biota and using DNA barcoding methods. The authors of the first five papers to be submitted and accepted at the collection will take advantage of free publication.
Finally, he thanked the hosts of the Bulgarian Academy of Sciences Headquarters: Stefania Kamenova and Assoc. Prof. Dr. Georgi Bonchev, who are also Vice-Chair and Chair of the Executive Board at BgBOL, respectively. A special thanks went also to Prof. Pavel Stoev, Director of the National Museum of Natural History.
Guest blog post by Iryna Kapshyna, Gritta Veit-Köhler, Leon Hoffman and Sahar Khodami.
During a relaxing beach vacation, most people probably give little thought to whether the beach would still be there if it was not regularly replenished.
In fact, sand nourishment is a common and frequently used coastal protection measure whereby sand is sucked up from the seabed by a flushing ship, transported to the coast, washed up and spread with bulldozers.
Beach extent before and its changes after sand nourishment: Immediately before the sand nourishment (T0, beige); After the sand nourishment the beach reached its maximum extent (T1, burgundy); Two more sampling dates (T2 and T3, dark and light pink).
Due to continuous erosion – the removal of sand by storms, waves and currents – sand nourishment has to be repeated regularly. Otherwise, uncontrolled erosion would mean the loss of beaches, shore areas, coastal cliffs and dunes.
But, while they are important, coastal protection measures such as sand nourishments incur high costs and often lead to the disturbance of ecosystems.
At Ahrenshoop on the Baltic Sea, researchers investigated the effects of sand nourishment on the meiofauna – organisms less than one millimeter in size – and found significant results.
We took a total of 246 sediment samples for the investigation of meiofauna from the beach at Ahrenshoop and analysed them in the laboratory in Wilhelmshaven. Photo: Leon Hoffman
“State-of-the-art genetic methods and the traditional method of identifying and counting the animals under the microscope show the same result. The communities of meiofauna changed drastically after the sand was washed up and slowly recovered over the course of a year.”
Project coordinator, Dr Gritta Veit-Köhler.
Immediately after the impact, mites (Acari) and annelid worms (Annelida) had almost completely disappeared from the swash zone, copepods (Copepoda) declined significantly, while the number of flatworms (Platyhelminthes) increased.
Meiofauna organisms are the most numerous animals on the seabed and play an important role in the food webs there. They are well suited as ‘bioindicators’ to detect and study environmental impacts and various forms of ecosystem disturbance, including those caused by humans. Due to their small body size, ubiquity and large numbers, their communities can be studied with small sample sizes.
Over a period of one and a half years, the researchers took and analysed a total of 246 sand samples from the beach-water interface.
“Using the classic taxonomic method, we identified 27,445 individuals under the microscope, which we assigned to ten higher taxonomic groups such as nematodes and copepods. But it was only the genetic analysis that brought the full diversity of species to light.”
Iryna Kapshyna, doctoral student and first author of the study.
Meiofauna organisms collected on the beach at Ahrenshoop. Top left: Tardigrade, flatworm, top right: copepod, nematode, bottom left to right: marine mite, annelid. Scales 0.1 mm each. Images: Iryna Kapshyna, Olena Uzun, Tobias Fischer
Using the ‘metabarcoding’ method, in which all animals in a sample are analysed together and differences in specific gene segments (here V1&V2) are searched for, a large number of samples can be analysed quickly and reliably.
The researchers were able to identify a total of 843 so-called ‘operational taxonomic units’ (OTUs) – in simple terms, different species.
“843 species sounds like a lot – but in fact, the beach studied had a lower diversity of meiofauna compared to the deep sea or other marine areas.”
Dr Sahar Khodami, Senckenberg am Meer.
The size of the organisms studied means they have previoulsy been difficult to study and have not received as much attention as larger species.
“When considering the effects of coastal protection measures on ecosystems, the smallest marine animals should not be overlooked! Metabarcoding can replace the traditional morphological method, after initial studies using both methods.”
The research team.
Original study:
Kapshyna I, Veit-Köhler G, Hoffman L, Khodami S (2024) Impact of a coastal protection measure on sandy-beach meiofauna at Ahrenshoop (Baltic Sea, Germany): results from metabarcoding and morphological approaches are similar. Metabarcoding and Metagenomics 8: e127688. https://doi.org/10.3897/mbmg.8.127688
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Dr. Paul D. N. Hebert, known as “the father of DNA barcoding,” has been honoured with the prestigious Benjamin Franklin Medal, a testament to his trailblazing contributions to biodiversity science.
Dr. Hebert’s innovative work has advanced our understanding of global biodiversity, making the identification of species easier, which in turn helps support global conservation efforts. By devising a method that allows the quick and efficient discerning of species, he has transformed biodiversity science.
DNA barcoding has many applications in the classification and monitoring of biodiversity. It can help protect endangered species, control agriculture pests, and identify disease vectors.
Dr. Hebert is also chair of the advisory board of Pensoft’s journal Metabarcoding and Metagenomics. He has authored 13 papers in ZooKeys, substantially contributing to untangling the taxonomy of braconid wasps, butterflies, and other insects.
Acylomus ergoti, one of the many insect species Dr. Hebert has worked on.
His innovative approach has sparked discussions and debates around the role of novel methodologies in taxonomy.
Dr. Hebert’s recognition with the Benjamin Franklin Medal demonstrates the critical role of biodiversity studies in dealing with global challenges such as the biodiversity crisis. He has inspired a generation of scientists to push the boundaries of knowledge and drive innovation in research technology.
We at Pensoft extend our heartfelt congratulations to Dr. Paul D. N. Hebert on this well-deserved recognition. He continues to lead the way in unravelling the complexities of global biodiversity.
Through the analysis of DNA traces in the droppings of a Leisler’s bat colony, researchers at LIB have now identified over 350 different insect species that were consumed by the bats.
Adequate food supply is a fundamental need and requirement for survival. To protect a species, it is often very helpful to know what that species prefers and frequently consumes. Through the analysis of DNA traces in the droppings of a Leisler’s bat colony, researchers at LIB (Leibniz Institute for the Analysis of Biodiversity Change) have now identified an astonishingly high number —over 350— different insect species that were consumed by the bats.
Especially for small animal species and those that are nocturnal, it can be extremely difficult to determine what they feed on. Identifying small prey insects or their remains is also rarely possible down to the exact species or family. In the case of the studied bat species, there is the additional challenge that it is a forest bat species that needs to be located first. “Following bats equipped with radio transmitters in the forest at night is quite special,” says Martin Koch, co-initiator of the study.
Design and installation of the guano trap (3 m) and roost entrance (9 m).
Fortunately — but also complicating matters — there are about 13 different bat species living in the investigated area near Bonn, in the forests of the Natura 2000 area ‘Waldreservat Kottenforst.’ Initially, as part of an EU Life+ project, roosts — the trees where the bats live — of the Leisler’s bats were identified, from which the study’s starting material was then obtained. This was done using a specially developed “guano trap.” The trap consists of approximately 2.2 square meters of mosquito netting stretched rectangularly.
It was installed about 3 meters high on the tree trunk, below the entrance to the roosting cavity at about 9 meters high. During the so-called “twilight swarming” after the nightly insect hunt, the bats return to the roosting cavity and initially circle the tree. They frequently perch briefly next to the cavity entrance and stick a small guano pellet to the trunk. Regularly, pellets fall and land in the mosquito netting under the cavity entrance. This “bat guano” was collected, fixed, and further processed in the laboratory.
“It’s fascinating how much DNA you can extract from a small amount of droppings and how much information we can draw from the DNA: from which bat species does the droppings come, and what has the bat eaten?” explains Dr. Kathrin Langen. Using the DNA contained in the droppings, our researchers were able to determine nine samples from nine different nights when only the target species swarmed around the roosting tree. On six other nights, other bats and a species of mouse were also active around the roosting tree. From the nine samples containing only the guano of the evening bat, an astonishingly rich menu was then reconstructed: the group consumed at least 126 different species of moths, 86 different species of flies and mosquitoes, 48 species of beetles, and a few dozen other various species of bugs, mayflies, caddisflies, and lacewings. Occasionally, spiders, harvestmen, lice, and other small animals were also consumed.
Timeline showing arthropod community composition at order level in the guano of N. leisleri, all three markers combined (COImldg, COIArt, 16S). With the exception of plots showing RRA assigned to major groups depending on sampling date (4C and 4F), read counts were not taken into account. A, D Number of species of each arthropod order detected at each time point; B, E Relative number of species per arthropod order as a percentage of the diet; C, F Species detected in each arthropod order, based on relative read abundances.
From the results, the team was able to deduce which of the three molecular genetic markers used worked best and provided the most species detections, a total of 358. “It’s incredibly satisfying to see what species lists come out at the end of all the lab work and bioinformatics,” says Dr. Sarah Bourlat, Head of the Metabarcoding Section at LIB, Bonn. However, the temporal course of the composition of the consumed insects was also interesting to observe: from late March to late June, the number of species in the guano steadily increases, only to decrease again by mid-August. This aligns very well with the activity patterns of certain insect groups.
The beech moth was the most frequently consumed butterfly, and a mayfly known as the transient virgin or ‘Uferaas’, was the most frequently consumed mayfly. The author team has listed the most important ecological parameters for the 18 key prey species in the study to contribute to better protecting the Leisler’s bat and the habitats needed by its prey insects.
Research article: Bourlat SJ, Koch M, Kirse A, Langen K, Espeland M, Giebner H, Decher J, Ssymank A, Fonseca VG (2023) Metabarcoding dietary analysis in the insectivorous bat Nyctalus leisleri and implications for conservation. Biodiversity Data Journal 11: e111146. https://doi.org/10.3897/BDJ.11.e111146
Researchers have found that advanced DNA technologies can get a detailed snapshot of insect diversity within a bird’s nest, showing everything from the bird’s last meal to disease-causing parasites.
“Birds’ nests are fascinating microcosms, but until now, studies have only examined the living insects that can be seen crawling and flying around the nests,” says Valerie Levesque-Beaudin, lead author on the study and a leading expert in Diptera taxonomy at the Centre for Biodiversity Genomics (CBG) at the University of Guelph (U of G).
With newer DNA-based methods, researchers can pick up traces of environmental DNA to get a snapshot of all the species in these tiny ecosystems. “The analysis of nest contents and environmental DNA, or ‘eDNA’ as it’s called, via metabarcoding helps us to gain more insight into a bird’s diet, parasites, and other factors that could impact a bird’s health and breeding success,” says Levesque-Beaudin.
For the study, published in Metabarcoding and Metagenomics, researchers collected 20 birds’ nests from the 162-hectare Arboretum at U of G. They examined the nests using DNA barcoding to identify insects to species and DNA metabarcoding to look at the entire nest ecosystem.
Organisms leave traces of DNA behind as they move through the environment, and researchers can use metabarcoding to build a comprehensive picture of life in the nest. Metabarcoding pulls all DNA traces in a bulk sample – in this case, parts of dead insects, debris, and dust from birds’ nests. This method differs from DNA barcoding, where a single specimen – an insect in this case – is DNA sequenced to identify it to species level.
The CBG team used emergence traps for a first sweep of the nest’s contents followed by a second, deeper probe using DNA metabarcoding to identify all the species encountered in the nest. Researchers passed the nests through a sieve, collecting insect remains and the dust for DNA extraction. “We not only found insects making a living in the nest, but traces of prey, parasites, and many other things,” says Levesque-Beaudin. “The most unexpected was the amount of information gained on other birds’ species whose feathers were either used for nest building or whose nests were essentially overbuilt by the nesting species.”
A tent-like emergence trap is used to contain and collect insects living inside the nest debris. PHOTO: VALERIE LEVESQUE-BEAUDIN
“This approach has the potential to revolutionize how we study bird nests as a micro-ecosystem. It unravels connections between different ecological guilds within the nest and connections of the birds with their environment, which would otherwise remain hidden,” says Dr. Bettina Thalinger, senior author of the study.
The CBG’s Associate Director of Analytics, Dr. Dirk Steinke, says the study has positive implications for bird conservation efforts. He says his students have already begun looking at American Kestrels, a threatened bird of prey, to find out if there are clues in the nest communities via metabarcoding and if DNA can help scientists determine if lack of prey or increased parasitism could be among the causes of nestling mortalities.
Darwin’s finch, also called Galápagos finch. PHOTO BY CHRIS HO, CENTRE FOR BIODIVERSITY GENOMICS.
Galapagos finches are another species threatened by the avian vampire fly – a parasite that attacks nestlings – and treatments include pesticides. Steinke notes that one of his graduate students has begun using DNA metabarcoding in the finches’ nests to understand better the potential impact of pesticide treatment on the entire arthropod nest community.
Research article:
Levesque-Beaudin V, Steinke D, Böcker M, Thalinger B (2023) Unravelling bird nest arthropod community structure using metabarcoding. Metabarcoding and Metagenomics 7: e103279. https://doi.org/10.3897/mbmg.7.103279
News piece originally published by the Centre of Biodiversity Genomics. Republished with permission.
