Genes added to this marine protist (left) show up as green dots (right) under a fluorescence microscope.
Yoshihisa Hirakawa/University of Tsukuba
Fifty percent of the oxygen we breathe comes from ocean microbes. Yet these tiny marine organisms have largely remained a mystery to science. Now, thanks to the efforts of more than 100 researchers around the globe, scientists have found a way to unlock the genomes of a handful of these creatures by genetically engineering their DNA.
The study “will propel advances in plankton biology,” says Angela Falciatore, a marine biologist with CNRS, the French national research agency, at Sorbonne University who was not involved with the work. Those advances could shed light on the early evolution of life and potentially even lead to new antibiotics, she says.
Plankton are the invisible life that color our oceans blue, green, and even red at times. Some of these plankton are single-celled organisms called protists that, like plants, use light to transform carbon dioxide into oxygen. Protists don’t just keep us breathing, they also make up the base of the ocean’s “food web.” They serve as meals for larger plankton, which in turn become food for even larger creatures such as invertebrates and fish.
“There is a wealth of unexplored protists with a huge impact on these ecosystems,” says Peter Kroth, an algal biologist at the University of Konstanz who was not involved with the work.
In 2015, the Gordon and Betty Moore Foundation—a philanthropic organization that supports basic research about microbes and the environment—provided $8 million to researchers to close that knowledge gap. Studies of animals, plants, yeast, and bacteria have shown that when scientists modify an organism’s genes, they uncover clues to how those genes—and the organisms themselves—function. The awardees eventually pooled their expertise and insights, picking a range of 39 species to work on. Some species were chosen because of their economic importance—protist-linked red tides and other algal blooms can be catastrophic to fisheries and recreation—and some because they represented different branches of the protist family tree.
“These organisms are as different as humans are to fish, and even more,” says project co-coordinator Thomas Mock, a microbiologist at the University of East Anglia. The teams collected creatures with tongue-twisting names like archaelastid, opisthokont, and coccolithophore primarily from water in coastal environments.
The next step was figuring out how to grow each species in sufficient quantities to work with. The researchers tested different combinations of nutrients and temperatures with each to see what worked best.
Then, to explore the genes, the scientists had to try to get foreign DNA into them—something that had rarely been done before. They discovered that sometimes shooting tiny gold or tungsten particles coated with DNA was most effective at getting the DNA through the cell membrane. Other times, the researchers used electricity to zap cell membranes to make them leaky so DNA could squeeze in. The next step was getting the DNA to be part of the genome, or at least to be translated into a protein.
Sometimes the gene got in and started to make proteins. But sometimes the protist’s defenses destroyed it. In other cases, researchers found that the enzymes they typically use for genetic engineering didn’t work at the low temperatures some of the protists live at, so they had to find new enzymes to do the job. “No single group in the world could have faced these technical challenges alone,” Falciatore says.
All told, the scientists were able to add genes to 13 species. These included a protist that kills fish with its toxins and one that also infects mollusks and amphibians, the group reports today in Nature Methods.
The paper also represents an important first step, Falciatore says, as it’s still very hard to genetically modify some of these species. “A big challenge will be to reproduce these protocols in different laboratories and to make these procedures routine.”
The work should also help reveal how the protists work. By modifying their DNA and monitoring how the protists’ behavior, function, or biochemistry changes, the researchers are beginning to learn what those genes do. Genes that affect the protists’ ability to fight off bacteria, for example, may code for proteins that could lead to new antibiotics for people. And genes that do the same thing in distantly related protists likely represent genes already in existence in an early ancestor, shedding light on protist evolution. Kroth says: “My lab will definitely benefit.”