When the water flea senses predators in its environment, it suits up, growing tail spines, a pointy helmet and other armor. Now, researchers have sequenced the genome of the water flea, providing hints about its shape-shifting ability and opening the door for environmental research using the crustacean as a model.
The project was 10 years in the making and involved the efforts of 67 researchers, plus at least 200 more who have conducted companion studies using the water flea genome data. The results, reported today (Feb. 3) in the journal Science, reveal that the minute creatures boasts the largest genome of any animal studied. The findings could make the near-microscopic water flea a "modern, high-tech version" of a canary in a coal mine, said study author John Colbourne of Indiana University.
With the information provided by the water flea's genome, "you don't have to wait for the whole ecosystem to show that there's something wrong," Colbourne told LiveScience. "You simply ask a vitally important component of that ecosystem, 'Hey, how are you doing?'"
Many genes, many shapes
The water flea (also known by its scientific name, Daphnia pulex) got its moniker because early observers kept running across blood-red versions, Colbourne said. The color, combined with a pointy snout, made the water flea look like a bloodsucking flea. In fact, D. pulex is a filter feeder and a crustacean, not a flea, Colbourne said. The early specimens were red because of the animal's amazing ability to alter its body in response to its environment. The red water fleas weren't bloodsuckers; they were producing more hemoglobin, the protein that binds oxygen and turns blood red, because they lived in low-oxygen ponds.
D. pulex can also switch back and forth between sexual and asexual reproduction, and when reproducing asexually, it can decide whether to have all-male or all-female offspring. But perhaps the most impressive example of the water flea's adaptability is its armor. When D. pulex senses chemicals in the water given off by predators such as fish, it starts growing defenses, including long tail spines, a pointy helmet, and tooth-like neck spikes.
This adaptability is part of what makes the water flea so intriguing as a research animal, Colbourne said. He and his team sequenced the water flea genome and found that is has at least 30,907 genes – more than any animal examined so far. (Humans have about 23,000 to 25,000 genes.)
This gene overload is caused by two factors, Colbourne said. First, many are duplicates, and D. pulex seems to duplicate its genes at about three times the rate of other invertebrate animals. Second, D. pulex doesn't dump old genes. It keeps them around three times longer than other invertebrates.
Complicating matters, about a third of the animal's genes are unique to the Daphnia lineage, said study co-author Michael Pfrender, who researches ecological genomics at the University of Notre Dame. And for many of these exclusive genes, the water flea carries two copies.
"We don't know what their function is," Pfrender told LiveScience. "Many of the genes that are the most highly duplicated tend to be the genes that fall into the class of unknown genes. So the puzzle for us then is, 'How do we assign function to those genes?'"
The Swiss Army knife of crustaceans
Not satisfied with simply sequencing the genome, the researchers decided to crack that gene-function puzzle. Using cutting-edge techniques, they were able to find out how the water flea genome reacts to various environmental stresses. The major discovery, Colbourne said, was that the unknown genes are the most eco-responsive. That means they change their activity in response to outside influences.
In a second breakthrough, the researchers found that the duplicated genes are what Pfrender called "born-to-be-different" genes. The assumption, Colbourne said, is that duplicated genes only become useful when a lucky mutation makes them that way, a process that's hit-or-miss. But the water flea's duplicated genes can take on new functions much quicker than previously thought. That gives D. pulex a big toolbox to pull from when something in the environment changes.
"It's almost as if the Daphnia genome is like a Swiss Army knife," Colbourne said. "They're all knives, they all cut, but each is a particular shape well-suited for the task."
Testing the waters
Because of this adaptability, the researchers hope to use D. pulex to test water quality and measure environmental change.
"Consider the basic fact that there are roughly 80,000 man-made chemicals in our environment right now," Colbourne said. Less than 10 percent are subject to toxicological testing, he said: "That means for the vast majority of our chemical environment we have no idea what it's doing to animal populations, and we have no idea what happens to human health."
Water fleas have another trick up their exoskeletons that make them good toxicology testers, Colbourne said. When they reproduce sexually, embryos go into a state of arrested development and can stay dormant in lake sediment for decades before waking up and developing. That means 20-year-old Daphnia populations can be resurrected and compared with modern hatchlings. Even after the dormant eggs are no longer viable, Colbourne said, their DNA remains for hundreds or thousands of years. By linking genetic changes over time with environmental changes, researchers would have a picture of what Colbourne called "the ghost of the lake."
"If we could identify those genes in the genome that are linked to the ecological success of this organism, we would have this incredible resource of seeing evolution take place," Colbourne said.
In an op-ed piece published alongside the article in Science, Dieter Ebert of the University of Basel in Switzerland shared Colbourne's optimism.
"With the D. pulex genome, environmental health has found its genomic model," wrote Ebert, who was not involved in the study.
The next five years will likely see a host of research dedicated to uncovering the "Rosetta Stone" of the Daphnia genome, Pfrender said – that is, linking genomic changes to environmental influences. From there, the researchers envision using lab populations of D. pulex to test environmental chemicals. Wild D. pulex populations could be monitored for large-scale genomic change.
"If we wanted to be bold, if we just wanted to stick our necks out and aspire to something, I think that it would be to modernize environmental toxicology," Colbourne said.
You can followSenior Writer Stephanie Pappas on Twitter @sipappas.