The research team, working with samples from Polish lakes and from the Mediterranean water column, compared the two sequencing strategies head to head. On the short-read side, they used Illumina MiSeq to sequence the V4 region of the 18S ribosomal RNA gene, the roughly 380-base-pair fragment that has become the de facto standard for protist metabarcoding. On the long-read side, they turned to Oxford Nanopore’s MinION platform, sequencing an amplicon of about 3,200 base pairs that spans the entire 18S gene, the internal transcribed spacers, the 5.8S gene and the beginning of the 28S gene. The comparison included a defined mock community of seven cultured protist species and complex environmental communities from ten freshwater and twelve marine samples.

Nanopore sequencing has long been viewed with caution in biodiversity research because of its higher error rate, which produces a substantial number of insertions and deletions that complicate the construction of clean taxonomic units. Denoising pipelines such as DADA2, which reliably separate biological signal from sequencing error in Illumina data, cannot model Nanopore’s less predictable error profile. The team’s answer is BaNaNA — the Barcoding Nanopore Neat Annotator — a Snakemake-based pipeline that clusters Nanopore reads into Operational Taxonomic Units rather than trying to denoise them. The pipeline basecalls reads with Dorado’s duplex super-accurate model, filters them for length and quality, extracts rDNA fragments with Barrnap, verifies the correct 18S-5.8S-28S structure with a custom Python script, and adjusts the clustering threshold to the average error rate of each sample. Consensus sequences are built with MAFFT alignments within clusters, polished with Minimap2 and Racon, screened for chimeras against the PR2 reference database and de novo, and finally clustered at 99 percent identity to produce the finished OTUs.

The mock community provided the clearest test of what each technology gets right and wrong. Illumina sequencing of the V4 region produced 268 ASVs with an average length of 379 base pairs, while Nanopore sequencing, processed through BaNaNA, yielded 147 OTUs averaging 1,843 base pairs. The Illumina ASVs gave a taxonomic composition that diverged substantially from the known community structure: dinoflagellates appeared most abundant even though they were added at low concentration, while Euglena gracilis, which made up nearly a third of the cells by count, was underestimated by three orders of magnitude. The full-length Nanopore OTUs tracked the expected composition far more closely, with haptophytes and euglenozoans appearing at roughly the right proportions. Crucially, the Illumina data also contained the highest number of false positives — sequences assigned to genera that were never part of the mock community — suggesting that the short-read denoising approach inflates apparent diversity with background noise.

Species-level identification told a similar story. Neither technology detected all seven mock species perfectly, but the full-length Nanopore OTUs achieved the highest number of species-level classifications. The advantage of sequence length became especially evident when the researchers extracted the V4 region from their Nanopore OTUs — creating so-called V4-tags — and compared species assignments. For Paramecium bursaria, the full-length OTUs placed the sequence correctly at species level, while many V4-tags could only be assigned to the genus level, causing the species’ apparent abundance to drop dramatically. The lesson is that longer fragments carry enough information for accurate species-level annotation, provided the reference database is adequate, while shorter fragments lose that resolution even when amplified with the same primers.

Environmental samples from the Masurian lakes and the Gulf of Lion confirmed the pattern in complex natural communities. Illumina sequencing recovered 1,668 ASVs from freshwater and 2,716 from marine samples, while BaNaNA processing of Nanopore data produced 1,068 freshwater and 1,230 marine OTUs averaging nearly 1,800 base pairs. At higher taxonomic levels, both technologies painted very similar pictures of community composition. In the lakes, dinoflagellates and perkinseans dominated, followed by ciliates, cryptophytes and chlorophytes, with little difference between sunlit and dark zones. In the marine samples, dinoflagellates and radiolarians prevailed, and the parasitic diplonemids were detected exclusively by Nanopore sequencing. Bray-Curtis beta diversity analysis grouped samples from both platforms into three distinct clusters corresponding to freshwater, marine photic and marine deep environments, indicating that the ecological patterns were robust regardless of which technology generated the data.

One of the study’s most striking findings concerns the sheer amount of undocumented protist diversity revealed by the long reads. The researchers identified 747 full-length 18S rDNA OTUs whose sequence identity to their closest PR2 reference fell between 80 and 97 percent — a range suggesting they represent taxa not yet in the database. Freshwater environments yielded 513 of these novel OTUs, representing 48 percent of all freshwater OTUs obtained, while marine samples contributed 234, or 19 percent of the marine total. Together, the novel sequences amount to 7.6 percent of all eukaryotic sequences currently in PR2 for freshwater and 3.5 percent for marine environments. Because the OTUs are full-length, they can be aligned and used to reconstruct phylogenetic trees. The resulting tree, built from 721 novel OTUs with IQ-TREE, grouped the sequences into clades spanning six supergroups and fifteen divisions, with most novel taxa belonging to perkinseans and dinoflagellates. The authors note that some of these sequences may represent entirely new clades, something impossible to detect with short amplicons that lack sufficient phylogenetic signal.

The study also highlights a persistent imbalance in protist reference databases. Freshwater samples showed roughly twice the proportion of low-identity sequences compared with marine samples — 41 percent versus 14 percent in the Nanopore data — a discrepancy the authors attribute directly to the underrepresentation of freshwater protists in PR2. Marine ecosystems have historically received more molecular attention, and the gap is visible at every taxonomic level. The researchers argue that filling this gap is essential for the future of long-read metabarcoding, since accurate annotation of full-length sequences requires databases with longer reference sequences. They also point out that Nanopore’s ability to sequence the entire rDNA operon will demand operon-spanning databases that are only now beginning to emerge.

Perhaps the most practically important result is the demonstration that short- and long-read data can be integrated. Because Nanopore OTUs cover the whole 18S gene, researchers can extract any primer-defined fragment — such as the V4 region — in silico and compare it directly with Illumina datasets generated years earlier with different primers. The V4-tags extracted from Nanopore OTUs proved highly comparable to Illumina V4 ASVs, opening the door to long-term biodiversity studies that combine vast archives of legacy Illumina data with new Nanopore surveys. The authors recommend retaining the taxonomic assignment from the full-length 18S rDNA before extracting any specific region, to fully exploit the resolution that long reads provide.

Taken together, the findings position Nanopore metabarcoding not merely as a cheaper complement to Illumina but as a reliable replacement for protist diversity studies. The full-length OTUs offer greater taxonomic resolution, richer phylogenetic information, fewer false positives and direct compatibility with existing short-read datasets. With BaNaNA freely available on GitHub and benchmarked on both mock and environmental communities, the study removes a key bioinformatic barrier that has kept long-read approaches on the margins of protist ecology. As Nanopore chemistry continues to improve — accuracy has risen from 97.6 percent with R9.4.1 flow cells to 99.1 percent with R10.4 — and as reference databases grow to match, the era of reading protist genes in full may finally be at hand.

Subject of Research: A new pipeline called BaNaNA shows that Nanopore long-read sequencing can match Illumina metabarcoding for protist diversity surveys while offering better species resolution, fewer false positives and phylogenetic power that short reads cannot deliver.

Article Title: From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding

Article References: Chwalińska, M., Karlicki, M., Romac, S., Not, F., & Karnkowska, A. (2025). From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding. Metabarcoding and Metagenomics, 9, Article e163750. https://doi.org/10.3897/mbmg.9.163750

Image Credits: AI Generated

DOI: 10.3897/mbmg.9.163750

Keywords: protists, Nanopore sequencing, metabarcoding, 18S rDNA, biodiversity, BaNaNA, long-read sequencing, microbial ecology, eDNA, reference databases, short, long

The research team collected 107 samples at the end of August or the beginning of September over seven years — 2013, 2014, 2018, 2019, 2021, 2023 and 2024 — as part of the International Caving Expedition Ponor Kovači–Izvor Ričine. Sampling sites spanned the Outer Dinarides, a landscape underlain predominantly by Jurassic and Cretaceous limestones and dolomites at elevations between 716 and 1414 metres above sea level. The surveyed network included ten caves, three springs, two lakes, the Šuica River and the sinkhole-type cave Ponor Kovači into which it disappears, together with soil locations across the karst poljes of Hercegbosanska and Zapadnohercegovačka counties.

The hydrological architecture of the study area is what makes it scientifically compelling. The Šuica River, with a total length of 48.5 kilometres, emerges from the Veliki Stražanj spring-cave on an elevated plateau between the karst fields Kupreško Polje and Šuičko Polje. It flows through Šuičko Polje, partly within canyons, and then enters Duvanjsko Polje, a 112-square-kilometre karst field subject to periodic flooding. There the river sinks into Ponor Kovači and continues underground toward the Vrilo Spring at the southeastern margin of Livanjsko Polje — a connection confirmed decades ago by dye tracing across an aerial distance of 5150 metres. During active periods, the Vrilo Spring forms a short surface stream, the Ričina, which flows into the artificial Buško Blato Lake, a reservoir covering 55.92 square kilometres with a maximum depth of 17 metres.

In total, the survey identified 45 taxa of testate amoebae to the species level, along with more than 10 additional taxa identified only at the genus level — more than 50 taxa overall. The highest overall biodiversity was recorded in cave habitats, with 33 identified species, followed by soil with 26 species and spring habitats with 23. Caves also yielded the greatest number of unique species, 11 in total, ahead of soil with 7 and lakes with 6. A notable similarity in species composition emerged among soil, spring and cave habitats, which shared six species. Site-level richness peaked at Ponor Kovači and the Vrilo Spring, each with 23 species, followed by soil above Ponor Kovači with 18 species and the Šuica River with 17.

Among the most striking findings was the detection of Psammonobiotus dinarica, a species originally described from caves, in live preparations from the upper course of the Šuica River — a pristine surface karst river roughly 200 metres downstream of its source. This represents the first reliable record of the species outside a cave environment. Its sister discovery, Centropyxis bipilata, another cave-described species, was found exclusively in caves during this study, supporting the hypothesis that it may be a true troglobiont — a cave-adapted organism, a status so far attributed mainly to cave metazoans. The absence of P. dinarica from the middle and lower sections of the Šuica River, which are impacted by municipal wastewaters and agrochemicals and characterized by higher water temperatures and conductivity, hints at a possible sensitivity to environmental stressors and raises the question of whether the species could serve as a bioindicator of good ecological conditions in karst waters.

Statistical analysis revealed a pattern that surprised the researchers. A hierarchical cluster analysis based on Jaccard similarity produced a clear separation of lake assemblages from all others, with the remaining cluster dividing into two subclusters: one containing cave and soil assemblages, the other containing spring and river assemblages. A more detailed site-level analysis based on Bray-Curtis similarity, tested with the SIMPROF routine at the 5% significance level, confirmed four statistically significant clusters grouping lakes, caves and soil by habitat type. Non-metric multidimensional scaling, with a two-dimensional stress value of 0.13, reinforced the same picture. The literature had long suggested that cave assemblages are composed of aquatic and soil species — but the new results show that this composition does not include lake assemblages, at least in this system.

The most notable result of the entire study, however, was the statistically significant linkage of the hydrologically connected trio: the Šuica River, the sinkhole cave Ponor Kovači, and the Vrilo Spring. These three sites are bound by water — the river sinks into the cave and reappears after approximately 5.2 kilometres at the resurgence spring — and the testate amoebae assemblages reflect that connection. At Ponor Kovači, the studied habitat was a small lateral channel that had remained hydrologically disconnected from the river for several months before sampling. The community there had undergone a transformation: imported phototrophs passively introduced during flood events gradually disappeared, dissolved and particulate organic carbon was consumed, and conditions shifted toward oligotrophy. The data from this channel therefore approximate the processes occurring in the deeper sections of the cave.

One result defied expectation. The Vrilo Spring, which is actually the entrance to a 2.3-kilometre-long cave system, showed greater similarity to the Šuica River than to Ponor Kovači. The researchers had anticipated the opposite, given the spring’s subterranean provenance. The key difference, they argue, lies in light. The studied habitats at Vrilo Spring sit under diffuse daylight, while Ponor Kovači’s channel is entirely aphotic. Fully illuminated rivers and lakes, and habitats with diffuse light such as springs, allow the development of phototrophic organisms — algae, cyanobacteria and plants — that contribute to the overall availability of organic matter. Microphototrophs serve as food for predatory testate amoebae such as Arcellinida, and the entire ecosystem is shaped by the presence of this organic matter. Light conditions, running from photic through aphotic to diffuse light and back, may thus represent one of the important ecological factors structuring testate amoebae assemblages in karst landscapes.

The study also documented two geographically distant caves — Bilobrkova Cave on the border of Viničko Polje and Velika Bukovačka on the border of Duvanjsko Polje — that formed a distinct subcluster despite being exclusively aphotic habitats during prolonged dry periods. Both lack concentrated surface inflows, yet their assemblages resembled those of the Šuica–Ponor Kovači–Vrilo Spring system in the ordination, suggesting that the lotic, flowing-water character during hydrologically active periods leaves a specific imprint on the microbial community. Meanwhile, repeated detections of testate amoebae with distinct, well-visible morphological features that could not be assigned to any known species suggest that the Dinaric karst may still conceal protist species unknown to science — a region where several new protist species have recently been described and where caves, with their considerable evolutionary potential for speciation driven by strong natural selection, remain highly promising habitats.

The authors emphasize that the total biodiversity of testate amoebae in these habitats is almost certainly greater than documented, given the small sample volumes processed and the exclusive focus on the summer season. Methods that process large volumes of sediment work well for surface habitats but cannot be applied to caves, which are often extremely poor in suitable sediment. Future research, they argue, should include monitoring of abundance and more detailed environmental parameters — substrate structure, microhabitat characteristics, light and hydrology — to enable parametric analyses that would clarify the role of these factors in shaping microbial communities. Because every ecosystem rests on its microbial base, understanding trophic interactions in caves and across karst gradients will be essential for the holistic, science-based protection of both surface and subterranean karst ecosystems in the Dinarides and beyond.

Subject of Research: Biodiversity and community structure of testate amoebae across surface and subterranean karst habitats in the Dinaric karst of Bosnia and Herzegovina

Article Title: Comparative study of testate amoebae biodiversity in surface and subterranean karst habitats – example from Dinaric karst (South-Eastern Europe)

Article References: Baković, N., Baković, R., Siemensma, F., & Pipan, T. (2026). Comparative study of testate amoebae biodiversity in surface and subterranean karst habitats – example from Dinaric karst (South-Eastern Europe). Subterranean Biology, 56, 29-49. https://doi.org/10.3897/subtbiol.56.189049

Image Credits: AI Generated

DOI: 10.3897/subtbiol.56.189049

Keywords: testate amoebae, karst habitats, Dinaric karst, Bosnia and Herzegovina, subterranean biology, cave ecosystems, protists, hydrology, biodiversity, bioindicators, Šuica River, karst springs

The research team, led by Huan Li and Lei Ma of Hebei Normal University together with Jing Huang of Hebei Children’s Hospital, assembled an unusually large sample set for this kind of survey: 2,448 human fecal specimens and 215 ticks of the species Haemaphysalis longicornis, an aggressive, wide-ranging biting tick common across East Asia. Using polymerase chain reaction assays designed to amplify the 18S rRNA gene, a standard molecular marker for identifying eukaryotic microorganisms, the researchers screened every sample for Colpodella DNA. The 18S rRNA gene is favored in studies of protist diversity because it is present in all eukaryotes, contains both conserved and variable regions, and allows newly recovered sequences to be compared against a deep archive of reference sequences from known organisms.

The results were striking in their consistency across the two very different sample types. Colpodella DNA was detected in 136 of the human fecal samples, a detection rate of 5.56 percent, and in 11 of the tick samples, a rate of 5.12 percent. The near-identical prevalence in feces and ticks is one of the more intriguing aspects of the study, hinting at some shared route of exposure or a common environmental reservoir linking the human and tick samples, though the design of the study cannot distinguish among the many possible explanations, including ingestion of contaminated food or water, environmental pass-through, or a genuine biological association with the tick vector.

Every PCR-positive sample yielded a high-quality 18S rRNA sequence when the amplified DNA was read by Sanger sequencing, a validation step that strengthens confidence in the specificity of the detection. Because some of the tick-derived sequences were identical to one another, the researchers collapsed the data into representative sequence types, ultimately selecting one tick-derived sequence and 21 distinct human-derived sequence types for deeper analysis. These 22 representative sequences were deposited in GenBank under accession numbers QB017305 through QB017326, making them available to other researchers for comparison and future surveillance work.

Phylogenetic analysis, the technique biologists use to place newly recovered gene sequences on the tree of life, showed that all 22 representative sequences from the study clustered within previously reported Colpodella lineages. In other words, the DNA found in human stool and ticks belongs to the same evolutionary neighborhood as Colpodella species that have been described from aquatic and terrestrial habitats around the world. The sequences did not branch off into entirely novel territory, which suggests that the organisms detected in Hebei are related to known forms rather than representing a radically divergent new lineage, although species-level identification in this group remains difficult because morphology and molecular data do not always align neatly.

To probe the genetic variation within their dataset, the team performed a haplotype analysis, a method that groups sequences by their shared sets of variable sites. Among the analyzed sequences, they identified three haplotypes, indicating a modest but real degree of genetic diversity among the Colpodella organisms whose DNA was recovered from the samples. Haplotype networks and diversity statistics are standard tools in population genetics, and applying them to environmental protist DNA can reveal whether a detection reflects a single widespread genotype or a mixture of related strains circulating in the environment. In this case, the limited number of haplotypes suggests relatively constrained diversity in the sampled region, though the authors caution that broader sampling would be needed to draw firmer conclusions.

Understanding why this matters requires a short detour into evolutionary biology. Colpodella species are predatory flagellates that feed by a process called myzocytosis, in which they attach to another microbe, puncture its membrane, and suck out its cytoplasmic contents. This dramatic feeding strategy has fascinated cell biologists in part because it may resemble the evolutionary steps that gave rise to intracellular parasitism. Colpodellids are considered the free-living sister group to the Apicomplexa, the phylum that includes Plasmodium, the malaria parasite, and Toxoplasma gondii. Studying Colpodella therefore offers a window into how some of humanity’s most burdensome parasites may have evolved from free-living ancestors that once hunted their prey from the outside.

The new study also fits into a rapidly expanding literature on where Colpodella DNA shows up outside of ponds and soil. Recent surveys have reported the organism’s genetic traces in goats, foxes, and birds; in Hyalomma ticks infesting camels in Egypt; in ticks feeding on ruminants in Italy; in horses; in zoo animals; and even in the urine of a human patient. Clinically, isolated case reports have described Colpodella-like parasites in a woman in China and in a patient with neurological symptoms whose infection was linked to a potential novel tick-borne Colpodella species. A 2025 scoping review of the genus’s biological characteristics and zoonotic potential underscored how much remains unknown about whether these detections represent transient environmental exposure, colonization, or true infection.

That uncertainty is central to how the Hebei findings should be interpreted, and the authors are explicit about the limits of their method. PCR-based detection confirms only that Colpodella DNA was present in the sample; it cannot determine whether live organisms were present, whether they were actively replicating, whether they colonized the human gut or the tick, or whether they caused any disease. DNA can persist after an organism has died, and environmental contamination or passive passage through the body can both produce positive signals. Distinguishing among these possibilities will require complementary approaches, including attempts to culture the organisms, sequencing of additional genetic markers beyond the 18S rRNA gene, and biological studies of how Colpodella interacts with animal hosts.

Nevertheless, the study marks a meaningful addition to surveillance data on an understudied group of protists. The large number of human samples screened, the near-matching detection rates in feces and ticks, the successful sequencing of every positive sample, and the public deposition of 22 representative sequences collectively provide a foundation for future work. As molecular surveys continue to sweep ever more environments and host species, Colpodella keeps appearing in unexpected places, and each new detection sharpens the questions that make this genus scientifically compelling: how these predatory relatives of apicomplexan parasites move between environmental reservoirs, animals, and occasionally people, and whether any of them pose a genuine health risk. For now, the answer in Hebei Province is a well-documented molecular presence and a clear agenda for the research that must follow.

Subject of Research: Molecular detection and genetic diversity of Colpodella protist DNA in human fecal and tick samples in China

Article Title: Molecular Detection and Genetic Characterization of Colpodella spp. DNA in Human Fecal and Tick Samples from Hebei Province, China

Article References: Li, H., Huang, J., Zhang, M., Zhang, Y., Chen, Y., & Ma, L. (2026). Molecular Detection and Genetic Characterization of Colpodella spp. DNA in Human Fecal and Tick Samples from Hebei Province, China. Acta Parasitologica, 71(5), Article 234. https://doi.org/10.1007/s11686-026-01419-6

Image Credits: AI Generated

DOI: 10.1007/s11686-026-01419-6

Keywords: Colpodella, protists, Apicomplexa, Haemaphysalis longicornis, ticks, 18S rRNA, PCR detection, genetic diversity, haplotypes, Hebei Province, zoonotic potential, myzocytosis

The scale of the challenge is matched by the scale of the opportunity. Photosynthetic protists, particularly algae, are responsible for producing around half of the world’s oxygen, making them foundational to the very habitability of the planet. Other protists graze on diverse microorganisms, regulating microbial communities and supporting ecosystem health in soils, oceans, and freshwater systems alike. Their influence extends into human affairs in less welcome ways as well: certain protists spread devastating diseases such as malaria and sleeping sickness, while harmful algal blooms can damage marine ecosystems and the economies that depend on them. Understanding these organisms at the genomic level is therefore not an esoteric pursuit but a matter of environmental, agricultural, and medical consequence.

Why, then, have protists lagged so far behind bacteria, plants, and animals in genomic research? The answer lies in their extraordinary diversity. Protists deviate from nearly every standard biological assumption that makes working with model organisms straightforward. They exhibit an immense range of cell structures, chemistries, genetic makeups, and evolutionary histories. Some possess genomes of bewildering complexity, others have diverged so far from the canonical genetic code that routine analytical tools fail them entirely. This variety makes culturing, sequencing, and analysing protists inherently difficult, and it means that protocols developed for one lineage often fail spectacularly when applied to another. The result is a vast proportion of biodiversity that continues to be overlooked, simply because the technical machinery of modern genomics was not built with these organisms in mind.

Professor Neil Hall, Director of the Earlham Institute, framed the problem in stark terms. Despite representing the largest share of eukaryotic diversity, protists remain poorly classified and understudied, he noted, with their immense and largely unexplored diversity leaving a significant blind spot in our understanding of life on Earth. He acknowledged that the community has made good progress in addressing some of the technical challenges, but warned that if these bottlenecks are not continually overcome and the solutions scaled up, a vast proportion of biodiversity will continue to be overlooked. The new investment is designed precisely to move from incremental progress to systematic, scalable solutions.

The partnership brings together complementary strengths from across Europe. Alongside the Earlham Institute, the collaboration includes the Scottish Association for Marine Science (SAMS), the Culture Collection of Algae and Protozoa (CCAP), and Aalborg University in Denmark, uniting international expertise in protist culturing, single-cell genomics, and long-read sequencing. The project will address technical challenges and bottlenecks for sequencing protists from two sources: bulk cultures maintained in laboratories, and single cells isolated directly from the environment. This dual approach reflects a recognition that many of the most interesting protists have never been brought into culture at all, and that environmental sampling is the only way to reach them.

The Culture Collection of Algae and Protozoa, housed at the Scottish Association for Marine Science, manages one of the world’s largest and most taxonomically diverse protist culture collections. Within the project, CCAP will provide researchers with stable cultures of key protist lineages, enabling them to scale up biomass and enrichment, and will contribute expertise in developing ecologically informed cultivation methods. Drawing on existing knowledge and success stories from across the protist community, the researchers will begin with ten major classes of protists before scaling up their efforts, testing existing protocols across species to compare, optimise, and evaluate successes in extraction, cell lysis, and DNA amplification methods. This comparative, systematic approach is intended to replace the ad hoc trial-and-error that has characterised much protist genomics to date.

The SAMS contribution extends well beyond the established collection. Dr David Green, Principal Investigator in Molecular Microbiology at the Scottish Association for Marine Science, explained that SAMS researcher Dr Frederik De Boever has developed a new cultivation approach based on how these organisms live in nature. That ecologically grounded strategy has led to the creation of a unique research collection including more than 50 genera from some of the least understood groups of protists, such as Provora, centrohelids, telonemids, rhodelphids, kathablepharids, and heterotrophic Paulinella. Together, Green noted, the CCAP and SAMS collections cover an exceptionally wide range of evolutionary diversity, giving scientists a powerful resource for exploring how these organisms evolved and function, and one that is likely to lead to many important and exciting discoveries.

The Earlham Institute arrives at the collaboration with a proven track record of extracting genomic surprises from non-model organisms. Its researchers have previously revealed fascinating diversity and evolution among protists, including species harbouring previously unknown Legionella bacteria, and unique divergence in the DNA code itself, findings that underscore just how radically these organisms can depart from biological convention. Through its high-performance sequencing platforms and technical skill in scalable short-read and long-read workflows, together with single-cell sequencing and analysis, Earlham scientists will work with SAMS to optimise cell lysis and DNA extraction methods, identified as one of the major technical bottlenecks in the field. Breaking open protist cells without destroying their genetic material is far harder than it sounds when cell walls, scales, and chemistries vary wildly across lineages.

Meanwhile, the collaboration with Aalborg University targets the frontier of cultivation-independent genomics. Ramunas Stepanauskas, Professor of Single Cell Genomics at Aalborg University, described single-cell genomics as a key technology for recovering the genomic blueprints of these dominant yet elusive eukaryotes, most of which remain uncultured. According to Stepanauskas, the project will advance cultivation-independent genome recovery from unicellular eukaryotes, unlocking the fundamental biology, evolutionary history, and biotechnological potential of this vast and underexplored component of the planet’s biota. The ability to sequence the genome of a single cell plucked directly from seawater or soil, without ever growing it in a laboratory, promises to open windows onto lineages that have never been seen under controlled conditions.

Open science and a collaborative culture sit at the heart of the undertaking. Knowledge and skills exchange across all partners, at all stages of the workflow, is designed to ensure that learnings are shared and that methods and protocols are cross-validated across disciplines. The ambition reaches beyond the four institutions involved: by equipping the wider research and innovation community with improved pipelines, culturing resources, and technical protocols, the project aims to deliver increased reproducibility and to enable successful international protist sequencing projects for years to come. As Professor Hall put it, the partners are excited to be bringing this community together to drive forward improvements in the technical challenges facing the field. If the collaboration succeeds, the invisible majority of eukaryotic life may finally begin to receive the genomic attention its diversity demands, with consequences ranging from new industrial enzymes and sustainable agricultural tools to a fundamentally richer map of the tree of life.

Subject of Research: Protist genomics and single-cell sequencing technology development

Article Title: Major investment to unlock the potential of protist research

Article References: Major investment to unlock the potential of protist research. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: protists, genomics, single-cell sequencing, Earlham Institute, SAMS, CCAP, Aalborg University, Gordon and Betty Moore Foundation, long-read sequencing, algae, eukaryotic diversity, biomanufacturing