Pensoft blog - Part 10

Dead Fish Shed More Intact Cells Into The Environment: A Promising Source For High-Resolution Genomic Analysis From Water

Study in Metabarcoding and Metagenomics investigated the availability of intact fish cells in water as a source of high-quality eDNA, using live and dead Rainbow Trout.

Guest blog post by Hiroki Yamanaka

Fish naturally release their DNA into surrounding waters, a phenomenon that has long powered environmental DNA (eDNA) analysis for detecting species without direct observation. Now, we are aiming for a leap beyond simple species identification toward fine-scale genomic analysis – a frontier that demands much higher-quality DNA samples.

Environmental DNA analysis as a biodiversity assessment tool

Environmental DNA (eDNA) analysis is a non-invasive technique that extracts and detects the genetic material of target species from environmental samples such as water and soil, and it has rapidly transformed biodiversity monitoring. Compared to traditional tools, like catch-and-release or visual surveys, this technique possesses remarkably higher sensitivity, demonstrating unparalleled utility in detecting rare, elusive, or invasive species. Because it is cost-effective and highly efficient, eDNA analysis has become a new biodiversity assessment tool for mapping species distribution on a broad scale.

However, the current primary objective of eDNA analysis largely remains at qualitative species identification – simply asking “what species are here?” – making it an urgent priority to advance the technique toward extracting detailed and much deeper ecological information.

The importance of the “individuality” of cells for further development

The next great frontier for eDNA analysis is its application to population genetics. To understand the health, evolutionary history, genetic diversity, inbreeding, or to identify hybrid individuals within specific populations, extracting high-quality genomic information across multiple genes (multilocus) is essential.

Chum salmon. Photo credit to Jeff Duda, one of the co-authors of the study.

However, free-floating DNA in the environment (bulk eDNA) is rapidly degraded by microbial activity and environmental factors, leaving it highly fragmented. Furthermore, because it is a “genetic soup” mixed with shredded DNA from hundreds of different individuals, the loss of physical linkage – the “individuality” of the genetic material – remains the greatest roadblock.

To solve this, we focused on capturing “intact cells.” A physically undamaged cell membrane acts like a biological shield, protecting the fragile DNA inside from the harsh, degrading environment outside. By isolating these intact cells from environmental water and performing single-cell analysis, it would make it possible to read the complete, uncorrupted genetic fingerprint of a single individual. The study is now available in the open-access journal Metabarcoding & Metagenomics.

eDNA from dead fish is not just noise

To establish a method to specifically detect and quantify intact cells from environmental samples, we conducted a five-day laboratory experiment using live and dead Rainbow Trout (Oncorhynchus mykiss).

Experimental tanks used in the study. Photo by Hiroki Yamanaka, Ryukoku University.
Experimental tanks used in the study. Photo by Hiroki Yamanaka, Ryukoku University.

To distinguish the DNA inside intact cells from the free-floating, degraded DNA in the environment, we utilized propidium monoazide (PMA), a photoreactive DNA intercalating dye. PMA permeates into broken cell membrane and binds the DNA inside off the cell as well as the free-floating DNA outside of the cells; when exposed to strong visible light, it forms cross-links with DNA molecules that physically block subsequent PCR amplification. This effectively silences the “noise,” allowing us to selectively quantify only the pristine DNA protected inside intact cells with healthy membranes.

Rainbow Trout waiting for the introduction to the experimental tanks. Photo by Hiroki Yamanaka, Ryukoku University.

The results of this experiment were a revelation that flips conventional understanding in eDNA analysis. Historically, fish carcasses were viewed as a significant nuisance-biological noise that sheds massive amounts of DNA, causing false-positive detections or distorting biomass estimates.

But, this study demonstrated that carcasses release significantly higher concentrations of both total eDNA and PMA-resistant (intact-cell) eDNA compared to living fish. Particularly on Day 2 and Day 3 of the experiment, tanks containing carcasses yielded roughly 30 times more intact-cell DNA than tanks with live fish. In short, carcasses proved to be a promising source for the high-integrity cells that researchers desperately need.

Cell-by-cell analysis opens the door for the future

Counting and measuring Rainbow Trout used in the study. Photo by Hiroki Yamanaka, Ryukoku University.

This discovery presents a paradigm shift in our understanding of environmental sampling strategies for advanced genomic analysis. To acquire pristine genetic data, sampling waters during or immediately after known mass mortality events in nature-such as the natural die-offs after Pacific salmon migrate and spawn-could be a highly effective approach.

Access to perfectly preserved intact cells paves the way for a revolution in environmental monitoring. By integrating single-cell genomics with eDNA technology, we can overcome the loss of physical linkage that has plagued population genetics. Instead of looking at a mixed picture of DNA from multiple individuals, isolating individual cells for analysis makes it possible to compute exact inbreeding coefficients, map out local population structures, and identify hybrid species. This effectively bridges the gap between basic species detection and highly advanced ecological tracking, providing a technological foundation to deeply monitor the genetic health of entire ecosystems from just a few liters of water.

Limitations and further efforts required

Illustration of Double Helix DNA Structure. Credit to Sumali Ibnu Chamid via Canva.

While this research provides pioneering insights, vital challenges requiring further validation remain. First, because this was a carefully controlled laboratory experiment using a single species (Rainbow Trout), further empirical studies involving a diverse array of taxa in complex, unpredictable natural environments are needed to ensure universal application.

Second, the technological tools – specifically the PMA dye method – require fine-tuning. Our observations confirmed that it sometimes struggles to fully suppress the PCR amplification of extracellular DNA, particularly when targeting the very short DNA fragments (short amplicons) often used in fish eDNA assays. Additionally, as a biological reality, DNA self-degradation by internal cellular enzymes continues even inside the cell. Thus, scientists still need to quantitatively evaluate and model the exact decay rates of DNA housed inside these protective cell membranes.

Despite these technical hurdles, the approach of harnessing the intact cells shed by organisms after they die brightly illuminates a highly promising path toward unlocking the full, high-resolution genetic story of our natural world with parallel development of single cell analysis on the cells from water shed by multicellular organisms.

Note: single cell analysis is commonly conducted on microbes which are unicellular organisms. However, single cell analysis on environment-medium derived multicellular organisms is very scarce for now. The main purpose of the current work was to determine a good timing / good location for cell collection to assure higher concentration of cells with high quality DNA to make the technical tests easier for the single cell analysis development on environmental samples.

Original source:

Yamanaka H, Hirohara T, Hoy MS, Chase DM, Duda JJ, Ostberg CO (2026) Live and dead fish shed different amounts of intact cells: Implications for advancing environmental DNA methodologies. Metabarcoding and Metagenomics 10: e177451. https://doi.org/10.3897/mbmg.10.177451

Giant ichthyosaur with injuries discovered in Northern Bavaria, Germany

Based on its skull length of 1.5 meters, the animal is estimated to have been about 6.6 meters long.

The Mistelgau clay pit near Bayreuth, Germany, is known for its well-preserved marine fossils, particularly its abundance of ichthyosaurs. These large marine reptiles resembled modern dolphins in appearance and lived worldwide during the Early Jurassic period, around 180 million years ago.

The ichthyosaur from Mistelgau now under investigation belongs to the genus Temnodontosaurus. Several parts of its skeleton have been preserved: fragments of the skull and lower jaw, the shoulder girdle, forefins, the spine, and over 100 teeth. The exceptional three-dimensional preservation allows researchers detailed insights into anatomical structures that have rarely been documented before, such as those in the palate, orbital region, and the fins.

Comparisons reveal clear similarities, but also differences to Temnodontosaurus trigonodon—animals of this species are among the largest known ichthyosaurs. Based on its skull length of 1.5 meters, the animal is estimated to have been about 6.6 meters long. These findings are published in the open-access journal Zitteliana.

Fossil *Temnodontosaurus* cf. *trigonodon* (UMO BT 011237.00), viewed from below, showing the skull and body plate, including all isolated bones and teeth recovered from the surrounding sediment. Image credit: Urwelt-Museum Oberfranken.

“Our Temnodontosaurus fossil is one of the youngest finds of this ichthyosaur genus to date. Until now, representatives of this genus have mainly been known from older geological layers, such as the Posidonia Shale of Holzmaden. The discovery from Mistelgau now shows that these large marine reptiles survived longer in the Southwest German Basin than previously documented.”
Dr. Ulrike Albert, SNSB paleontologist

Albert conducts research at the Urwelt-Museum Oberfranken in Bayreuth, one of ten museums belonging to the Bavarian State Collections of Natural History. The team at the Urwelt-Museum Oberfranken has been conducting regular excavations in Mistelgau since 1998. The fossils recovered there are prepared at the Urwelt-Museum and subsequently subjected to scientific analysis.

Particularly striking are several modifications to the skeleton, presumably caused by injuries, including those affecting the reptile’s shoulder and jaw joints.

“The injuries likely significantly limited the animal’s ability to catch prey. The fact that it nevertheless survived is evidenced, among other things, by its heavily worn teeth and gastroliths, which we were able to identify in the abdominal region.”
Stefan Eggmaier, preparator at the Urwelt-Museum

Ulrike Albert and Stefan Eggmaier from the Urwelt-Museum Oberfranken at the excavation site in Mistelgau. Image credit: Mathias Orgeldinger.

Gastroliths are extremely rare in ichthyosaurs such as Temnodontosaurus. Eggmaier speculates that the animal may have had to change its diet in order to survive its injuries.

The current findings are part of ongoing research into the ecology of the Jurassic Sea in Upper Franconia. Analyses of teeth and bone structures are planned, with the aim of better understanding the ecology of these animals and their habitat.

Original study:

Eggmaier SA, Albert UEG (2026) A partial skeleton of Temnodontosaurus cf. trigonodon in three-dimensional bone preservation from the upper Toarcian of Mistelgau, Germany. Zitteliana 100: 39-80. https://doi.org/10.3897/zitteliana.100.172724

For more interesting articles about palaeontology, follow Zitteliana on Bluesky and Facebook.

A “Balrog” in the Tunnels: Scientists discover a new cave cricket species on the tiny island of Kastellorizo, Greece

This previously unknown species of cave cricket was found thriving within a network of man-made tunnels.

Despite the intensity of modern exploration, the eastern Mediterranean continues to yield unexpected discoveries. On the small Greek island of Kastellorizo, researchers have documented a previously unknown cave cricket thriving within a network of man-made tunnels.

The species, named Dolichopoda balrogi, was described by researchers from Greece and published in the open-access Journal of Orthoptera Research. This discovery highlights how even small and seemingly ordinary habitats can shelter unique and previously unknown life.

Individuals of the newly discovered Dolichopoda balrogi sp. nov. in the artificial tunnel of Kastellorizo on 17 October 2025 – Male individual. Photo credit: Konstantinos Kalaentzis.
Juvenile. Photo credit: Konstantinos Kalaentzis.

A mysterious cricket in underground tunnels

The new species belongs to the genus Dolichopoda, a group of cave crickets that inhabit dark, humid environments such as caves, crevices, and underground spaces across southern Europe and the eastern Mediterranean. These insects are well known to evolutionary biologists because their isolated populations often evolve into distinct species on islands or in separate cave systems.

On the easternmost Greek island of Kastellorizo, researchers surveyed an artificial tunnel that serves as the island’s sole accessible land cave. To their surprise, they encountered a population of cave crickets bearing characteristics of the cave-dwelling genus Dolichopoda.

Detailed morphological and molecular study confirmed that the specimens represented a species new to science.

Artificial tunnel of Kastellorizo. Photo credit: Konstantinos Kalaentzis.

Why “balrogi”?

The species name balrogi was inspired by the Balrog, a legendary fire-demon from J.R.R. Tolkien’s The Lord of the Rings. In Tolkien’s story, the Balrog is an ancient creature hidden deep beneath the mountains, emerging from darkness. Its discovery is a fitting parallel; the cricket’s preference for deep, dark tunnel systems kept it outside the known record for decades.

The name also alludes to the circumstances of discovery of the species, which was found exclusively in a man-made tunnel. In Tolkien’s narrative, the Balrog is revealed only after the Dwarves “delved too deep”; similarly, Dolichopoda balrogi was discovered on Kastellorizo due to anthropogenic excavation on Mount Vigla, as the island lacks accessible caves. The epithet thus symbolically links deep excavation with the revelation of hidden subterranean fauna.

*Dolichopoda* *balrogi* sp. nov. Image credit: Konstantinos Kalaentzis.

Fortunately, unlike Tolkien’s fearsome creature, Dolichopoda balrogi is harmless – although equally well adapted to life in darkness.

Hidden biodiversity in unexpected places

Kastellorizo is a very small island, covering only about 9 square kilometers. Yet its position in the eastern Mediterranean between Asia and Europe makes it an important biogeographic hotspot.

Geographic distribution of Eastern Mediterranean *Dolichopoda* species. Image credit: © Environmental Systems Research Institute, Inc., CC BY 3.0.

The discovery of D. balrogi demonstrates that even small islands can host unique endemic species. It also suggests that artificial underground environments, such as tunnels and abandoned infrastructure, can function as refuges for specialised cave-dwelling organisms.

“These findings remind us that biodiversity discoveries are not limited to remote tropical forests or deep oceans. Even familiar landscapes and human-made structures can harbour species that have remained unnoticed.”
Konstantinos Kalaentzis

Protecting small and fragile ecosystems

Cave-adapted organisms like Dolichopoda crickets often have very restricted distributions, sometimes occurring in only a single cave or underground system. Because of this, they can be particularly vulnerable to habitat disturbance. The authors suggest that documenting and understanding these hidden species is an important first step toward their conservation.

Bayesian inference phylogenetic tree based on mitochondrial COI sequences of *Dolichopoda* species. Image credit: Konstantinos Kalaentzis.

As research continues across the Mediterranean, the researchers note that the countless Greek islands – many still poorly explored biologically – are likely to hold many more hidden biodiversity treasures awaiting discovery.

Cover image:

Newly discovered Dolichopoda balrogi sp. nov. in the artificial tunnel of Kastellorizo on 17 October 2025 – Female individual. Photo credit: Konstantinos Kalaentzis.

Original source:

Kalaentzis K, Alexiou S, Christopoulos A, Minoudi S, Koutsogiannopoulos D, Kotselis C, Triantafyllidis A (2026) Delving too deep: Morphological and molecular description of the cave-dwelling Dolichopoda balrogi sp. nov. (Orthoptera, Rhaphidophoridae) from Kastellorizo Island, Greece. Journal of Orthoptera Research 35(2): 259-266. https://doi.org/10.3897/jor.35.187943

For more interesting articles on orthoptera, visit the Journal of Orthoptera Research website and follow us on Bluesky and Facebook.

New DNA Barcode Reference Data For Freshwater Diatoms (Bacillariophyceae) From Sweden

New study in Metabarcoding and Metagenomics shares results from FRESHBAR, the first large-scale barcode reference for Nordic benthic freshwater diatoms.

Guest blog by Maria Kahlert

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-access Metabarcoding 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. — 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

Pensoft Welcomes Endocrinologia Journal to its Open-Access Journal Portfolio

The peer-reviewed, open-access Endocrinologia Journal, published by the Bulgarian Society of Endocrinology is moving to ARPHA, the publishing platform developed by Pensoft.

Launched by the Bulgarian Society of Endocrinology back in 1996, the open-access, peer-reviewed Endocrinologia Journal is now moving to the publishing platform ARPHA, developed by the scholarly publisher and technology provider Pensoft.

Focusing on research in basic and clinical endocrinology and metabolic disorders, the journal publishes review articles in Bulgarian, alongside original papers and case reports available in both English and Bulgarian. The paper issues of the journal are published quarterly while the electronic online versions of the papers are published as soon as final approval is granted and formatting is completed.

Due to the generous support of the Bulgarian Society of Endocrinology, publication in the journal is free to all authors.

In addition to a refreshed, user-friendly design, the Pensoft-developed publishing platform ARPHA provides its signature fast-track, end-to-end publishing system to the benefit of its users: authors, reviewers and editors alike.

Each submitted manuscript is carried through the review, editing, publication, dissemination and archiving stages without leaving ARPHA’s collaboration-focused online environment. The articles are available in PDF and machine-readable XML formats, so that they are easy to discover, access, cite and reuse. Endocrinologia Journal is indexed in Scopus, CrossRef, EMBASE, and the Bulgarian Citation Index, and archived through CLOCKSS and Zenodo.

The introduction of an online platform for submitting manuscripts will contribute to improved management of the publishing activities of the journal Endocrinology and will help the journal, as the official publication of the Bulgarian Society of Endocrinology, meet current standards for full integration into international scientific databases,
commented Prof. Maria Orbetzova, the journal’s Editor-in-Chief.

Endocrinologia Journal brings a rich legacy of peer-reviewed endocrinology research to our portfolio, and we are excited to support its next chapter. Through ARPHA, we hope to give the journal’s authors, reviewers and editors the tools they need to publish faster, reach further, and make a greater impact,
added Prof. Lyubomir Penev, founder and CEO of Pensoft and ARPHA.

About the Bulgarian Society of Endocrinology:

Founded in 1958, the Bulgarian Society of Endocrinology (BSE) is a professional medical organization dedicated to advancing endocrinology in Bulgaria. Its core mission encompasses the continuous education of endocrinologists, trainees, GPs, and other specialists, alongside the development of national screening programmes for diabetes, obesity, hypertension, and dyslipidaemia, and the establishment of Bulgarian clinical guidelines on diabetes management. The BSE supports both healthcare professionals, through Schools of Endocrinology and specialist symposia, and patients, via public education courses and media outreach. It hosts annual scientific congresses and publishes the peer-reviewed journal Endocrinologia.

About ARPHA:

ARPHA is a full-featured, end-to-end publishing platform for journals, books, conference materials and preprints. ARPHA offers flexible operating and business models, and a wide-range of automated and human-provided services. The ARPHA team places a special focus on its scholarly communication solutions designed to leverage the visibility and outreach of academic output, while promoting inclusivity and engagement.

About Pensoft Publishers:

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. Back in 2010, Pensoft became the first scientific publisher to introduce semantic enrichments in scholarly publications. Through its Research and Technical Development department, the company is involved in various research and technology projects.

Tiny sesame sea slug species discovered in the waters of northern Taiwan

This tiny nudibranch, which measures less than three millimetres in length, was first spotted by lead author Ho-Yeung Chan during a recreational dive in 2019.

Translucent, speckled, and barely the size of a grain of rice, a new species of sea slug has been identified in the coastal waters of Keelung, Taiwan. Because of its minute size and distinctive black and yellow markings, researchers from National Taiwan Ocean University, National Museum of Natural Science and National Taipei University of Education have named the creature Thecacera sesama.

“Taiwanese divers call it ‘sesame’ in Chinese and it is also small like a sesame seed, hence the name,” the research team explained regarding their decision to honour the local nickname in the scientific nomenclature. This tiny nudibranch, which measures less than three millimetres in length, was first spotted by lead author Ho-Yeung Chan during a recreational dive in 2019.

*Thecacera* *sesama* sp. nov. Details of appearance and morphological features, hand-drawn on a tablet PC by Chen-Lu Lee.

The discovery was a stroke of luck that began during Chan’s undergraduate studies:

“During a recreational dive in the summer during the undergraduate study of HY Chan in 2019, he accidentally discovered Thecacera sesama sp. nov. in northern Taiwan waters.”
The Research Team

Despite its unique appearance, the importance of the find was not immediately obvious. In a modern twist on traditional taxonomy, Chan “never realised Thecacera sesama was a new species until he consulted the sea slug expert ‘Hsini Lin teacher’ on Facebook.”

Living specimens of *Thecacera* *sesama* sp. nov. Image credit: Ho-Yeung Chan et al.

Documenting the species proved to be a significant logistical feat due to the volatile environment of the Keelung coast. The research team noted that the most challenging part of the study was the unique weather conditions of the region.

Taiwan experiences frequent typhoons in the summer and large waves during the winter monsoon season, with sea temperatures often dropping below 16 degrees Celsius. These factors mean that diving for nudibranch research is only possible for about four months of the year, making sightings of such tiny creatures entirely a matter of chance.

Living specimens of bryozoan with *Thecacera* species. Image credit: Ho-Yeung Chan et al.

The life of T. sesama is remarkably focused, as the researchers observed that the species exhibits only four primary behaviours: feeding, searching, mating, and laying eggs on bryozoans, which are tiny aquatic invertebrates often called “moss animals”. Interestingly, the specific bryozoan that T. sesama calls home may itself be a species new to science.

From a broader ecological perspective, these vibrant molluscs play a vital role in the marine environment:

“Nudibranchs are one of the key players in the marine food web. They are extremely colourful and can be spotted on coral reef ecosystems. However, many nudibranchs are very small in size and are extremely difficult to spot underwater with the naked eye.”
The Research Team

The researchers believe that the discovery of T. sesama is just the tip of the iceberg for Taiwanese marine biology. Because many species are so small, many more are likely awaiting discovery and formal study. The full research on Thecacera sesama was published in the open-access journal ZooKeys on 11 May 2026.

Original source:

Chan H-Y, Lee C-L, Chen W-C, Chang C-H, Shao Y-T, Pang K-L (2026) Thecacera sesama sp. nov. (Nudibranchia, Polyceridae) from Taiwan, evident from morphology and phylogenetic analyses of the 16S rDNA and cytochrome c oxidase I gene. ZooKeys 1279: 269-284. https://doi.org/10.3897/zookeys.1279.184298

Cover image:

Two individuals of Thecacera sesama sp. nov. feeding on a bryozoan. Image credit: Ho-Yeung Chan et al.

For more interesting articles on zoology, follow ZooKeys on Facebook and Bluesky.

Four Decades of Overlooked Data Reveal the Hidden Amphipod Diversity of Italian Seas

A new inventory of over 300 amphipod species from Italian seas offers an updated picture of their distribution and biodiversity.

Guest blog post by Prof. Sabrina Lo Brutto

What if some of the most important clues about marine biodiversity were already collected but never fully shared?

That’s the question that motivated this study, published in Biodiversity Data Journal. It brought together over 40 years of unpublished data on marine amphipods – ecologically crucial crustaceans – from across Italian waters. By unifying scattered records and making them openly accessible, researchers have assembled comprehensive and up-to-date inventories of these species for the Mediterranean.

Satellite image of the Mediterranean Sea with Italy and Sicily. Image provided by Prof. Sabrina Lo Brutto.

Researchers analysed 4,344 previously unpublished records spanning from 1980 to 2025, identifying 302 amphipod species across the Adriatic, Tyrrhenian, and Ionian Seas. Interestingly, they found that the Tyrrhenian Sea harbours the highest taxonomic richness (258 species), while the Adriatic Sea accounts for the greatest number of records due to intense historical sampling.

A Number of species per sea; B Venn diagram illustrating the distribution and shared amphipod species across the three areas, Tyrrhenian Sea (light blue), Ionian Sea (red), Adriatic Sea (blue). Credit to Badalucco et al., 2026.

This work not only updates the Italian inventory but also reinforces the country’s central role as a biodiversity hotspot in the Mediterranean.
noted Prof. Sabrina Lo Brutto of the Department of Earth and Sea Sciences (DiSTeM) at the University of Palermo, the coordinator of the study.

Why amphipods matter

A female hyalid amphipod species (Serejohyale sicilia) with eggs — A female hyalid amphipod species (*Serejohyale sicilia*) with eggs. Image credit to Prof. Sabrina Lo Brutto.

Amphipods are small, often just a few millimeters long, but they play an outsized role in marine ecosystems. They recycle nutrients, connect food webs, and serve as prey for fish, birds, and mammals. Because they respond quickly to environmental stress, they are also powerful bioindicators, helping scientists detect pollution and ecological changes.

Yet despite their importance, our knowledge of where these species live has been fragmented. In some cases, outdated or incomplete records have even led to cascading misidentifications in the scientific literature.

A collaborative effort across Italy

Map of Italy with georeferenced species records — Map showing the distribution of the georeferenced species records. Points were differentiated by colours, based on the sea upon which they lie: Tyrrhenian Sea (light blue), Ionian Sea (red) and Adriatic Sea (blue). Credit to Badalucco et al., 2026.

This study represents a collective effort coordinated under the National Biodiversity Future Center (NBFC). Researchers from universities, environmental agencies, and research institutes across Italy contributed data spanning more than four decades.

By harmonizing these datasets under the FAIR principles (Findable, Accessible, Interoperable, Reusable), we ensured that the information was not only scientifically robust but also openly available for future research.
commented the first author of the study, Dr. Antonina Badalucco (Dept. DiSTeM, University of Palermo).

The full dataset is now accessible via the Global Biodiversity Information Facility (GBIF), making it a resource for scientists worldwide.

A changing Mediterranean

Percentage of the amphipod species per substrate/habitat categories.
*The species *Dendropoma petraeum* is now accepted as *Dendropoma cristatum*. Credit to Badalucco et al., 2026.

The presence of non-indigenous species is a reminder that marine ecosystems are rapidly evolving. The study identified 11 alien species primarily concentrated in ports, lagoons such as the Venice Lagoon, and aquaculture facilities. Increased shipping, aquaculture, and global connectivity are allowing these species to travel farther and establish themselves in new environments, sometimes with significant ecological consequences.

At the same time, researchers observed that sampling efforts have intensified dramatically in the last decade, driven in part by European environmental policies such as the Marine Strategy Framework Directive – generating a surge in available data, while also highlighting how much earlier information had remained underused.

Why this matters now

Understanding where species live is the foundation of conservation. Without accurate distribution data, it’s nearly impossible to track biodiversity loss, identify vulnerable habitats, or design effective protection strategies.
Prof. Lo Brutto explained

By filling long-standing gaps in knowledge, this research supports broader efforts – such as the EU’s and National Biodiversity Future Centre’s shared goal to protect 30% of land and sea by 2030 – and provides a baseline for monitoring future environmental change.

Looking ahead

This is not the end of the story; it’s a starting point. Our study shows the immense value of unlocking existing data and making it accessible. We hope it will inspire similar efforts across other regions and taxonomic groups, helping to build a more complete picture of life in our oceans.
Prof. Lo Brutto concluded

Original study:

Badalucco A, Auriemma R, Balistreri P, Baratti M, Bonifazi A, Capillo G, Cimmaruta R, Coccia I, D’Amore A, Desiderato A, D’Iglio C, Grech D, Iaciofano D, Lattanzi L, Lezzi M, Lionello M, Macaluso E, Mancini E, Martino C, Marusso V, Mercurio M, Mucciolo S, Prato E, Pulieri M, Puthod P, Scipione MB, Scirocco T, Sirchia B, Specchiulli A, Targusi M, Trabucco B, Vannucci A, Rosati I, Lo Brutto S (2026) A contribution to the inventory of marine amphipod species from Italian waters based on unpublished sources and FAIR principles. Biodiversity Data Journal 14: e189256. https://doi.org/10.3897/BDJ.14.e189256

Remote fieldwork and museum collections reveal hidden pit viper diversity in High Asia

Published in ZooKeys, a recent study revises the Himalayan pit viper group using a combination of fresh and historical DNA, morphology, skeletal anatomy, and ecological observations.

The high mountain ranges of Asia remain among the least biologically explored regions of the continent. Now, an international team of researchers has shown that one of their most elusive venomous snakes, long treated a single species, is in fact a complex of five distinct species, three of which are new to science.

Published in the open-access journal ZooKeys, the study revises the Himalayan pit viper group using a combination of fresh and historical DNA, morphology, skeletal anatomy, and ecological observations. The data reveals that what scientists had long treated as a single widespread species, the Himalayan pit viper first described in 1864, actually consists of multiple deeply distinct evolutionary lineages.

The analyses identified five clearly distinct species-level lineages, i.e. the Himalayan pit viper in the strict sense, Gloydius chambensis described in 2022, and three previously unrecognised species from different parts of Pakistan and Nepal. Alongside genetic divergence, these lineages exhibit distinct morphological and skeletal variations.

Phylogeny and distribution of five pit viper species in the Himalaya and Hindu Kush. Image credit: Dr Daniel Jablonski

“These mountain systems still harbour overlooked vertebrate diversity and hold important clues to the biogeography of Asia,” says Daniel Jablonski of Comenius University Bratislava, who has been conducting extensive research in Pakistan and Afghanistan for many years.

“By combining modern field sampling with data from historical museum specimens, we uncovered evolutionary lineages that had remained hidden for more than a century after the original description of the Himalayan pit viper.”
Daniel Jablonski

A key element of the discovery was the integration of newly collected material with a powerful source of evidence: DNA extracted from museum specimens collected in the 19th and early 20th centuries. This included the original type specimen of the Himalayan pit viper, allowing the researchers to clarify the identity of the species in its strict scientific sense.

The study underscores the enduring scientific value of natural history collections. Indeed, specimens gathered by earlier generations of explorers and preserved in museums are still helping scientists solve modern biological puzzles, especially in regions where fieldwork remains difficult.

Paratype of the newly described species Gloydius hindukushensis from northwestern Pakistan. Image credit: Dr Daniel Jablonski and Dr Frank Tillack.
Paratype of the newly described species Gloydius nepalensis from Nepal. Image credit: Dr Daniel Jablonski and Dr Frank Tillack.

In fact, part of the discovery had been waiting in plain sight. “Museum specimens are not just records of the past. They are active research tools and essential infrastructure for future science,” says Sylvia Hofmann from the Museum Koenig as part of the Leibniz Institute for the Analysis of Biodiversity Change, who has comprehensively worked in the Himalaya and Tibetan Plateau during the past 20 years.

“Some of the key evidence had been sitting in museum collections for more than a hundred years. We just didn’t have the tools to recognise it. As analytical methods continue to improve, the scientific value of these collections will only grow and revealing biodiversity we didn’t even know was there.”
Sylvia Hofmann

Representatives of the herpetofauna play an important role in the ecosystem, particularly as ecological indicators, within the food chain, and as predators in pest control. A group of top predators in the region consist of pit vipers adapted to mountainous environments, which have so far been studied only very inadequately in the Himalayan region.

“Our work aims to close these gaps in knowledge and to lay the groundwork and provide inspiration for further, in-depth studies on this ecologically and medically relevant group.”
Frank Tillack of the Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Research

Tillack maintains close ties with Nepalese colleagues and has been collaborating with them for 35 years on projects concerning the biodiversity of herpetofauna in the Himalaya.

An important part of the study is the osteology of these snakes, including the skull anatomy of the lectotype BMNH 1946.1.19.64 of *Gloydius himalayanus*, collected more than 160 years ago.
Image credit: Kristin Mahlow-Tillack.

The study also emphasises how much remains to be discovered in regions that have long been difficult to access for scientific research. “Pakistan’s high mountains are still full of biological surprises,” says Rafaqat Masroor of the Pakistan Museum of Natural History, the country’s leading herpetologists.

“This finding highlights how little we still know about a region long shaped by socio-political instability.”
Rafaqat Masroor

Beyond taxonomy, the findings also carry an important conservation message:

“Each of the newly recognised species seems to occupy a relatively restricted range in fragile mountain environments, highlighting new ecological and evolutionary questions.”
Daniel Jablonski

Without recognising such diversity, it would be impossible to assess it accurately or protect it effectively.

Original study:

Jablonski D, Tillack F, Mahlow-Tillack K, Petzold A, Wilzo M, Das A, Idrees M, Baniya CB, Masroor R, Hofmann S (2026) Integrative taxonomy reveals previously undescribed diversity within the Gloydius himalayanus complex (Squamata, Viperidae, Crotalinae) from the Himalaya and Hindu Kush. ZooKeys 1280: 83-153. https://doi.org/10.3897/zookeys.1280.182768

New Study Outlines How Countries Can Build Effective DNA Barcoding Networks

New research in Metabarcoding and Metagenomics provides a blueprint for building a robust, globally adaptable network of DNA barcoding practitioners.

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

Published in the open-access journal Metabarcoding and Metagenomics, the article “Empowering national capacity for a DNA-based approach to species identification and biodiversity monitoring” by E. Kaitetzidou et al. provides strategic advice on establishing iBOL national nodes.

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

A new PollinERA policy brief proposes regional budget system for pesticide management for Europe

The brief proposes assigning ecological regions an annual toxic-unit (TU) budget linked to environmental carrying capacity.

A new policy brief from the PollinERA project calls for a major shift in EU pesticide regulation, arguing that current assessments of individual substances fail to address the cumulative environmental impacts of pesticide use across landscapes, and that many pesticide bans are unnecessary if the scale of use is managed.

The brief, “A Regional Budget System for Pesticide Management: Systems-first environmental risk assessment: the case for change,” proposes assigning ecological regions an annual toxic-unit (TU) budget linked to environmental carrying capacity. Farmers would register pesticide applications digitally, with approvals dependent on available regional budget capacity.

The authors, Christopher John Topping, Johan Axelman and James Henty Williams, argue that the approach would better align pesticide regulation with EU environmental obligations under the Water Framework Directive, Natura 2000 and the Nature Restoration Law. The brief also outlines key advantages, including environmental protection, regulatory simplification, resistance management, improved farmer access, fair access, and stronger market incentives for lower-impact products.

The brief also proposes implementation through three targeted amendments within the current EU Omnibus process: linking pesticide use conditions under Regulation (EC) 1107/2009 to regional ecological limits; introducing Regional Pesticide Management Plans under the Sustainable Use Directive (2009/128/EC); and aligning regional budget calibration with Water Framework Directive and Nature Restoration Law targets. According to the authors, no new legislative framework would be required.

The policy brief is accompanied with a commentary for further reading, “Pesticide Regulation and the Omnibus Process: A systems-based regional management approach: operational framework, fair access, and market incentives.” Both the policy brief and technical support document are available on the Research Ideas and Outcomes (RIO) journal, in PollinERA’s open-access collection, as well as on PollinERA’s website.

Read the policy brief here.

About PollinERA
PollinERA (Understanding pesticide-Pollinator interactions to support EU Environmental Risk Assessment and policy) is a four-year Horizon Europe project that aims to move the evaluation of the risk and impacts of pesticides and suggestions for mitigation beyond the current situation of assessing single pesticides in isolation on honey bees to an ecologically consistent assessment of effects on insect pollinators.

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