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Newman stayed in Kolter's lab for two years, though, learning everything she could about genetics before accepting a job at the California Institute of Technology—a joint appointment in geological and planetary sciences and biology.
Today, oxygen makes up a fifth of the atmosphere of the earth and most life forms rely on it. But 3.8 billion years ago—when the earliest evidence of life is recorded in ancient rocks—oxygen was scarce. Nailing down exactly when, and how, the atmosphere transitioned to oxygen requires probing the fossil record for the appearance of microorganisms that produced oxygen. “Dinosaur footprints only go back a short ways,” says Newman. “If you want to understand the evolution of life on earth billions of years before that, you need to understand microbiology.”
Typically, geologists have used molecules called 2-methylhopanoids as markers of oxygen-generating life. They've been found in rocks that some claim are 2.7 billion years old. But other geochemical measurements do not find evidence for appreciable oxygen on the earth at that time. At Caltech, and now at MIT, where she moved her lab in 2007, Newman has probed this discrepancy by investigating the role of 2-methylhopanoids in modern bacteria. Her lab has found that the ability of modern bacteria to make these compounds is not related to their ability to generate oxygen. Although more work needs to be done before ruling out 2-methylhopanoids as oxygen markers, Newman says the “case doesn't look very good.”
The biggest focus in the Newman lab now is one that started as a side project: how the bacteria Pseudomonas aeruginosa metabolizes iron. P. aeruginosa produces colorful phenazines—compounds Newman identified in her search for molecules that shuttle electrons to iron. But P. aeruginosa isn't relevant only to the ancient earth—it's the bacteria that most often infect the lungs of people with cystic fibrosis.
The minuscule cellular brushes that normally sweep the lungs clear of mucus are missing in people with the disease. Their lungs build up layers of mucus, a fertile place for bacteria to thrive. These thick layers of mucus have low concentrations of oxygen, resembling the oxygen-deprived atmosphere of the planet billions of years ago.
“Pseudomonads colonize the lungs just like they colonize other surfaces,” says Newman. “They aggregate into multicellular communities that become increasingly resistant to antibiotics with time.”
Since Newman suspects that phenazines are critical to P. aeruginosa's survival in these deep layers without oxygen, she hopes that blocking phenazine cycling might be a way to combat lung infections.
Thanks to the bright colors of phenazines, it's easy to see whether bacteria are producing them. Newman's postdoctoral fellow Lars Dietrich shows the drastic effect of oxygen on phenazine production by pulling two beakers of murky bacterial soup off a shaking platform that keeps the liquids constantly churned and exposed to oxygen. One beaker, filled with unmodified P. aeruginosa, is the color of green Kool-Aid (other natural P. aeruginosa strains produce blue, orange, red, and yellow phenazines). The other beaker, full of almost transparent fluid, is chock full of bacteria that were modified so they can't produce phenazines. Dietrich sets the beakers on his lab bench and immediately the green in the first sample begins to fade.
“Since it's not being shaken around to get lots of oxygen, it's using up the phenazines,” he explains. “Having phenazines is like having a snorkel to breathe underwater.” The bacteria are dumping extra electrons onto the phenazines, which carry the electrons out of the cells.