Single-celled organisms called Archaea live in the world’s most inhospitable places—the Dead Sea, the Great Salt Lake, deep-sea vents. Sometimes Archaea swim in the heavily salted water; sometimes they’re encased in salt crystals (the same crystals you sprinkle on food).
Pigment Quantification Plate

H. volcanii colonies on a petri dish with mutations that affect pigment production. Their color indicates how well they can produce energy from available sources. (Photo courtesy of Serena M. Graham, Colby College.)

When there is no oxygen, the tiny creatures switch on a mechanism that creates a protein that allows them to generate energy from sunlight. It’s one example of their resilience—their kind have survived for hundreds of millions of years. In fact, ancient Archea, millions of years old, have been brought back to life from salt mined from deep inside the earth.

But how do these so-called “extreme-ophiles” do this? What causes the organism to switch from one energy source to another? Does this survival adaptation happen in other organisms? “We’re exploring how the cell makes the decision to do this,” said Assistant Professor of Biology Ron Peck.

The research ongoing in Peck’s Colby lab—and the accompanying striking photographs taken by fellow researcher Biology Laboratory Technician Serena Graham—landed on the cover of the Journal of Bacteriology in November. In addition to Peck and Graham, coauthors include Assistant Professor of Biology Dave Angelini, Alex Plesa ’17, now in a molecular biology graduate program at Harvard, and Emily Shaw ’19.

Absorbing DNA. Reviving after millions of years encased in salt. A creature alive in the time of dinosaurs coming back to life. “They live everywhere you think no thing can possibly live,” said Margot Miranda-Katz ’18, another researcher in the lab.

The team, including Abby Gregory ’19, Samantha Lee ’20, and Erika Smith ’18, is looking at whether the same process happens in other organisms as well, and beginning to investigate how the mechanism may have evolved over tens of millions of years. “We can mimic how we think it happened and see if we get the same results,” Peck said.

The creatures in question are very different from the flora and fauna that are visible to the naked eye. Microbes, for example, don’t always acquire their genes from parent to child, but instead use something called horizontal gene transfer. “Microbes are much more willing to say, ‘Hey, there’s some DNA out in the environment. We’re just going to take that in and see what happens,’” Peck said.

Close up images of salt crystals harboring an Archaeal mutant that lacks the ability to make the pigments studied by the lab

Close-up image of salt crystals harboring an Archaeal mutant that lacks the ability to make the pigments studied by the lab. The original size of the crystals is approximately 1 mm. Some of the species the lab is currently studying were revived after millions of years encased in salt like this. (Photo courtesy of Serena M. Graham, Colby College.)

Absorbing DNA. Reviving after millions of years encased in salt. A creature alive in the time of dinosaurs coming back to life. “They live everywhere you think no thing can possibly live,” said Margot Miranda-Katz ’18, another researcher in the lab. “It’s very science fictiony.”

The research has produced some breakthroughs in methods alone. Graham and Angelini devised a way to use digital analysis (AKA Photoshop and some complex mathematical modeling) to measure the density of pigment, an indicator of the energy production mechanism—and the reason many sea salts are pink. The pink pigment is produced when the organisms are metabolizing food sources. When the food is gone, the switch is thrown. In the lab, the Colby researchers swapped synthetic genes into cell lines, identifying down to the amino acid level the switch that turns the pathway on and off, pigment or the sunlight-accepting protein.

Another branch of the research is looking at how the organisms change the genes that they transcribe based on their environment. The organisms are put in water that is less salty, and then the gene transcripts are examined. “We’re seeing what happens, how they survive,” Miranda-Katz said.

In the process, half the Archaea expire. “There’s a lot of death in the lab,” Graham said, “and a lot of really, really salty water.”