Banner image: Noriko Okamoto isolating cells on the microscope. (Credit: Patrick Keeling)
A global team of CIFAR researchers has captured the first images of a microbe that is one of the most abundant predators in the ocean, yet has until now remained unseen.
Marine diplonemids are a diverse group of single-celled microbes that were completely unknown until they were discovered in a recent, massive ocean biodiversity survey, which established their abundance, but never actually observed the organisms.
A photo of a diplonemid taken at sea. (Credit: Noriko Okamoto)
“To put this in perspective, it would be like ecologists studying the Serengeti for decades and never seeing a lion or cheetah,” says Patrick Keeling, director of CIFAR’s Integrated Microbial Biodiversity program and a professor of botany at the University of British Columbia.
“You have to look a little harder to see predators because they are not as common as the things they eat, and their interactions with the environment are more complex.”
Keeling and a team of CIFAR and UBC researchers successfully hunted down the ocean predators and have published their findings in Current Biology. The study offers the first glimpse of marine diplonemids — in photos of 10 colourless, flagellate cells of diverse shape and size — and offers clues to their role in the environment.
This paper follows long-term discussions between Keeling and four other members of the Integrated Microbial Biodiversity Program: parasitologist Julius Lukeš (University of South Bohemia), evolutionary biologist Thomas A. Richards (University of Exeter), microbial ecologist and biologist Alexandra Z. Worden (Monterey Bay Aquarium Research Institute)and marine microbiologist Alyson Santoro (University of Maryland). The idea began at a CIFAR meeting and slowly blossomed into a review article, drew in new program members and eventually fed into the marine diplonemid project, a collaboration funded by the Gordon and Betty Moore foundation. This study was also supported by the Tula Foundation.
Marine diplonemids presented a number of challenges to researchers trying to study them.
“They’re colourless, not very big, and always swimming around,” says Keeling. “They’re just not in your face and they’re hard to grow.”
Researchers send a device deep into the ocean to collect samples of water and look for microbes. (Credit: Alyson Santoro)
Researchers decided the best approach was to probe the ocean and process organisms in real time. During two week-long expeditions off the coast of California, the team scoured water samples for cells that resembled what they imagined marine diplonemids probably looked like. Keeling says they conducted “heroic” field work under terrible conditions, including a storm that threw the ship off course.
“Imagine a seasick post-doc staring down a microscope trying to pick up a tiny little cell with a glass pipette,” Keeling says. They repeated this process hundreds of times, photographing cells and then freezing them in test tubes.
Researchers faced a fresh set of hurdles back at the lab. If they’re lucky, scientists can culture an organism to get a large sample of DNA, but they don’t know how to keep most microbes in captivity. As predators, marine diplonemids are even more difficult to grow in the lab. That means researchers have to turn to new technologies in single-cell genomics, in which they break open the cell and make random copies of the DNA. This leads to a very incomplete genome – the most complete model was missing 91 per cent.
(Keeling’s lab is developing a new method that may be more effective: single cell transcriptomics, which allows them to use RNA rather than DNA to sequence genes in microbes like marine diplonemids.)
Researchers retrieve the ocean probe for analysis on board the Western Flyer. (Credit: Alyson Santoro)
The analysis, while incomplete, did offer interesting clues about marine diplonemids’ ecology and evolution. First, it showed remnants of algae and bacteria, indicating what they feed on.
The analysis also revealed marine diplonemid genomes are full of “junk” DNA known as introns, which interrupt genes and are removed during expression. All complex cells have introns in their nucleus, but the diplonemid introns were unique and seem to have evolved independently. One intron included clues as to how the introns copy themselves and spread to new genes, similarly to a virus. Keeling says that what’s hidden inside diplonemid cells could help answer questions about the introns’ origins.
Marine diplomenids are only one example of the ocean’s unexplored biodiversity, Keeling says. The team continues to study other marine predators and the next step also includes looking into parasite samples.
“The deep, deep ocean is a mysterious world,” Keeling says.
“Morphological identification and single-cell genomics of marine diplonemids” was published in Current Biology on Nov. 21.