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New collection of genetic data on marine microbes fills a gap in our knowledge of ocean life

Researchers have assembled the entire collection of RNA molecules for more than 650 microbial life forms and posted the data freely online as part a project that could enlighten our understanding of ecological processes in the ocean.

The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) is an international collaboration that was conceived of and funded by the Gordon and Betty Moore Foundation and carried out by the National Center for Genome Resources, two culture repositories, and dozens of laboratories around the world. It involves CIFAR Senior Fellow and Program Director Patrick Keeling (University of British Columbia) and CIFAR Senior Fellows Alexandra Worden (Monterey Bay Aquarium Research Institute), John Archibald, Alastair Simpson (both Dalhousie University) and Brian Leander (University of British Columbia), CIFAR Fellow Claudio Slamovits (Dalhousie University), and CIFAR Advisor Virginia Armbrust (University of Washington).

MMETSP delved into the enormous task of sequencing the transcriptome — the collection of RNA molecules found in an organism’s cells — of hundreds of species of eukaryotes, a category that includes any organism whose cells contain a nucleus, from seaweed to humans. Many of the ocean-inhabiting eukaryotes chosen for study are poorly understood, although many play key roles in marine ecosystems.

“Microbial life isn’t just a black box of things that are all the same,” says Patrick Keeling, who first met Worden (with whom he co-led a publication about the project) at a meeting of CIFAR’s program in Integrated Microbial Biodiversity.

“If you take a bacterium and a protist, they’re more different from each other by a lot than, say a human is from a tulip. It’s a big, diverse field and there’s a lot of variation.”

While bacteria and viruses — particularly those that affect humans — are fairly well studied, there is a vast population of other life forms with complex cell structures that have nuclei, called eukaryotes. A huge diversity of organisms, such as land plants and humans, are classified as eukaryotes, but research on them is biased toward the animals we can see and plants that use photosynthesis. We know very little about most microscopic eukaryotic species, and many probably remain undiscovered.

“You can’t really understand an ecosystem without looking at all its components,” Keeling says. “If you wanted to go out to the Serengeti and understand the ecology of gazelles, but you didn’t actually take into account grass or lions, your results would be flawed.”

However, the metaphorical grass and lions of microbiology are often difficult to work with, and for that reason, groups of organisms such as protists remain poorly understood. In part, this is because there is very little comparative data for researchers to draw upon when they are trying to sequence, for example, the genome of every eukaryotic organism they find in a bucket of ocean water.

“Sure, you’ll get genes, but you won’t know where they came from,” Keeling says.

Keeling says the MMETSP project was designed to address this problem. The researchers sought suggestions for which transcriptomes would be most useful to the research community, then began to sequence and post the data to the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database for open access as well as the Short Read Archive (NCBI). The collaborators, led by Senior Fellows Keeling and Worden, published a discussion paper about the new resource in PLOS Biology.

“It’s a community resource. It was, right from the start, meant to be something that everybody got to use,” Keeling says.

Keeling says CIFAR brought several of the collaborators on the project together and their discussions shaped the selection of some of the sequenced organisms.

“Several members of the MMETSP advisory board were people from our program due to their strong expertise in this area,” Keeling says. He says Worden suggested bringing the community together to write a paper announcing the MMETSP database and project goals during a discussion with him and CIFAR advisory board member Armbrust at a European Molecular Biology Organization (EMBO) meeting in Spain that was co-sponsored by CIFAR.

The researchers hope the database of transcriptomes will attract the attention of other researchers, who will use the information to vastly improve our understanding of the most abundant life forms on our planet — microbes.

The Marine Microbial Eukaryotic Transcriptome Sequencing Project was funded by the Gordon and Betty Moore Foundation through grants GBMF2637 and GBMF3111.

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