Diving for Microbes

Sixteen panels of four different clumps of marine microorganisms collected from a methane seep off the coast of northern California. Each clump, called an aggregate, is about 10 microns (millionths of a meter) across. The microbes have been tagged with fluorescent markers. DNA glows blue.

On the ocean floor, a thousand meters under the sea, there's no light and little oxygen. Without conventional sources of food, a group of mysterious microbes have evolved to eat methane, forming the base of an ecosystem that abounds with crabs, tube worms, and shrimp. By consuming this greenhouse gas, these bugs prevent further warming of the planet, showing that despite their itty-bitty size, their importance to the world is not to be overlooked. "They are an integral part of almost every facet of our planet," says Assistant Professor of Geobiology Victoria Orphan, whose team of researchers dive into the ocean to uncover whatever secrets these critters may hold. This group of bugs consists of bacteria and archaea—another type of microscopic life—and Orphan's lab is learning how these two types of microbes work together to harness the energy locked in methane.

Orphan's team explores the sea floor in the waters off the coasts of such places as Costa Rica and the Eel River Basin in northern California, steering robotic submarines equipped with arms that dig for gray mud teeming with the microbes. Sometimes the researchers venture into the murky deep themselves, aboard the Alvin, the sub famous for exploring the wreck of the Titanic.

Back at the lab, they analyze the mud samples with a series of techniques pulled from geochemistry and microbiology. Applying a method called magneto fluorescence in situ hybridization (magnetoFISH), Orphan and her colleagues can pick out the bugs and identify them. The bacteria glow green, while the archaea glow red. The team also uses another technique called nanoscale secondary ion mass spectrometry (nanoSIMS), blasting the microbial cells with a beam of cesium ions and analyzing whatever particles ricochet back out. With nanoSIMS, the researchers discovered that the microbes play a surprisingly big role in the world's nitrogen cycle. Besides eating methane, the bugs apparently can break down gaseous nitrogen into forms that they—and other organisms—can use. Nitrogen is an essential nutrient that makes up 78 percent of our atmosphere, but in its gaseous state it assumes a chemical form that life cannot use.

These bacteria and archaea flourish in harsh, oxygenless environments akin to those on Earth during the first couple billion years of the planet's existence. As organisms that also share DNA with the first-known lifeforms, these methane-munching microbes are living fossils, telling us something about our planet's history. And if life can take hold in such unforgiving conditions on Earth, perhaps it can take hold in extraterrestrial environments. These underwater bugs, then, may be our connection to life in the distant past and on other worlds.

At the very least, these microbes are crucial for life on this planet. "If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt," says Anne Dekas, one of Orphan's graduate students. "I can't think of anything as important as that."

To read more and watch videos from the dives, see the E&S Zmag. Or listen to our audio podcast.