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.
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.
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.
