Major Funding Push Aims to Crack the Genomic Secrets of Earth’s Most Overlooked Life Forms

Protists may be the least celebrated majority on Earth. These single-celled and simple multicellular eukaryotes represent the largest share of eukaryotic diversity on the planet, yet they remain poorly classified, poorly understood, and chronically understudied. Now, a major new international collaboration led by the Earlham Institute in Norwich, and funded by the Gordon and Betty Moore Foundation, sets out to change that. By tackling the deep technical bottlenecks that have long frustrated researchers working on these organisms, the project aims to unlock the potential of protist research for biomanufacturing, sustainable agriculture, and environmental applications, while filling one of the most significant blind spots in our understanding of life on Earth.

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