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David Ewing Duncan

A View from David Ewing Duncan

Extreme Metagenomics: Chasing Bugs in the Bowels of the Earth

Research highlights the lengths that microbiologists are going to to discover bizarre new bacteria.

  • June 27, 2007

As microbiologists scour the earth’s most inaccessible places to find ever more weird–and potentially useful–microbugs, I’m half-expecting a new reality show to pop up on the Sci-Fi Channel, or perhaps ESPN-5: Extreme Microbes!

Scientists studying the tiniest of bugs have long traveled to peculiar locales, but now the entire field has been invigorated afresh by the new age of metagenomics–the study of groupings of bacteria found in, say, a bucket of water, a patch of human skin, or a spade full of muck. Armed with sophisticated new technologies to identify millions of different kinds of bacteria inhabiting a specific mini environment, the new “metageneticists” are deploying to nooks and crannies ranging from acid spills to deep caverns in search of microbial communities.

In News@Nature.com, writer Josie Glausiusz describes a spelunking expedition led by microbiologist Diana Northup a thousand feet below the earth, deep into New Mexico’s Lechuguilla Cave. She and her team from the University of New Mexico hiked through tangled miles of passageways while rappelling down pits, traversing perilous edges of cliffs, and tramping around underground lakes on their way to collect bacteria that deposit manganese crusts and oxidized iron on cavern walls. Northup is also part of a multiple-university consortium appropriately dubbed SLIME–Subsurface Life in Mineral Environments.

A previous attempt by Northup to snatch up a batch of manganese- and iron-dropping critters failed to produce results because she and her team inadvertently contaminated their samples with fungi that they had brought in on their hiking boots. Back in the lab, the fungi had popped up like weeds in the agar plates when Northup tried to grow the bacteria. This time the team brought clean suits–a misnomer for a posse of microbe hunters who were exceptionally filthy with sweat and muck after their subterranean trek.

Northup also decided to take no chances in growing her samples, so she brought in glass tubes to get her bugs started in their own environment of absolute darkness, cool temperatures, and high humidity. Scientists have found that the classic method for growing bacteria–adding samples to agar-rich petri dishes–doesn’t work for an estimated 99.9 percent of microbes, which thrive best in their own ecological soup. This is one reason that metagenomics is taking off. Another is that advances in technology now allow researchers to sequence all DNA in a meta sample to find out how many species and gene variants appear in a given eco niche.

Perhaps the best known metagenomicist is J. Craig Venter, whose Sorcerer II Global Ocean Sampling Expedition announced in March that it had discovered six million new genes and thousands of new protein families, some of which may offer novel solutions for storing and producing energy, among other possibilities. Others are finding microbes that might clean up pollution or produce newfangled antibiotics.

Writer Glausiusz describes the search for antibiotics in her article, as well as a nascent move to commercialize discoveries resulting from the search for slime:

Meanwhile, Kim Lewis and Slava Epstein of Northeastern University in Boston, Massachusetts, are trolling the depths of the uncultured for new antibiotics using a diffusion chamber in which microbes are suffused in the conditions of their natural environment–soil, for example, or sea water plus marine sediments. Lewis and Epstein have founded the company NovoBiotic to capitalize on their cultures. “The practical benefits are enormous,” Lewis says. “If you want to discover new stuff, you want to go to organisms you haven’t seen before. It’s reasonable to assume that 99% of the remaining bacteria will have at least some useful antibiotics.”

The spelunking Northup has begun to find antibiotics in her samples. Initially, though, she strove to grow crust-forming cave bacteria to understand their basic biology. “One of the reasons we culture rather than do DNA sequences is because we want to catch them in the act of precipitating the minerals, so that we can say definitely, ‘These guys can do it,’” she says.

I encourage you to read the entire article on News@Nature.com; it’s creepy-crawly stuff and utterly fascinating. I also suggest that you attend Technology Review’s Emerging Technologies Conference at MIT from September 25 through 27, where I will be moderating a panel on metagenomics.

Glausiusz, Josie, “Extreme culture: From acid mine drainage to the bowels of the Earth,” Josie Glausiusz reports how researchers are taking great pains to grow recalcitrant bacteria, Nature, Published online: 20 June 2007; | doi:10.1038/447905a

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