Major investment to unlock the potential of protist research

The project –led by the Earlham Institute in Norwich, in partnership with the Scottish Association for Marine Science (SAMS), the Culture Collection of Algae and Protozoa (CCAP), and Aalborg University in Denmark – brings together international expertise in protist culturing, single-cell genomics, and long-read sequencing.

This ambitious undertaking, funded by the Gordon and Betty Moore Foundation, will address technical challenges and bottlenecks for sequencing protists from bulk cultures and single-cells isolated directly from the environment.

Prof Neil Hall, Director of the Earlham Institute said: "Despite representing the largest share of eukaryotic diversity, protists remain poorly classified and understudied. Their immense and largely unexplored diversity leaves a significant blind spot in our understanding of life on Earth.

"We've made good progress in addressing some of the technical challenges facing the community, but if we don't continue to overcome these bottlenecks and scale these solutions, a vast proportion of biodiversity will continue to be overlooked."

Protists play vital roles in environmental processes. Photosynthetic protists, particularly algae, produce around 50% of the world's oxygen, while other protists graze on diverse microorganisms, regulating microbiomes and supporting ecosystem health. 

However they can also be destructive, spreading diseases such as malaria and sleeping sickness, and damaging marine ecosystems through harmful algal blooms.

Their extraordinary diversity and deviation from standard biological assumptions present significant challenges to the community. Their extensive range of cell structures, chemistries, genetic makeup, and evolutionary histories makes culturing, sequencing, and analysing these organisms inherently difficult. 

The Culture Collection of Algae and Protozoa (CCAP) housed at the Scottish Association for Marine Science manages one of the world’s largest and most taxonomically diverse protist culture collections. This will provide researchers with stable cultures of key protist lineages to scale up biomass and enrichment, and expertise in developing ecologically-informed cultivation methods.

Drawing on existing knowledge and success stories from the protist community, researchers will start working on ten major classes of protists before scaling up, testing existing protocols across species to compare, optimise, and evaluate successes in extraction, cell lysis, and DNA amplification methods.

Dr David Green, Principal Investigator in Molecular Microbiology at the Scottish Association for Marine Science said: "In addition to the protists held in CCAP, SAMS researcher Dr Frederik De Boever has developed a new cultivation approach based on how these organisms live in nature. This has led to the creation of a unique research collection that includes more than 50 genera from some of the least understood groups of protists, such as Provora, centrohelids, telonemids, rhodelphids, kathablepharids and heterotrophic Paulinella.

"Together, the CCAP and SAMS collections cover an exceptionally wide range of evolutionary diversity. This breadth gives scientists a powerful resource for exploring how these organisms evolved and function, and is likely to lead to many important and exciting discoveries."

Meanwhile, the Earlham Institute has developed significant experience working with non-model organisms and protists, revealing fascinating diversity and evolution, including species harboring previously unknown Legionella bacteria, and unique divergence in DNA code. 

Through their platforms and technical skill in scalable short and long-read workflows, and single-cell sequencing and analysis, scientists at Earlham Institute will be working with SAMS to optimise cell lysis and DNA extraction methods – identified as one of the major technical bottlenecks. They’ll also be collaborating with Aarlborg University to develop single-cell sequencing workflows for protists taken directly from their environment.

Ramunas Stepanauskas, Professor of Single Cell Genomics at Aalborg University said: “Single-cell genomics is a key technology for recovering the genomic blueprints of these dominant yet elusive eukaryotes, most of which remain uncultured. Our 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 our planet's biota."