Surprising metals found in microbes

For first time, organism shown to need rare earth element to survive

HOT DIGS  Methylacidiphilum fumariolicum, the first life form found to rely on a rare earth element for survival, lives in steaming volcanic mud pits like this one outside Naples, Italy.

Paola Marinani, Radboud University Nijmegen

Look out, smartphone users: Bacteria may be after your rare earths. A microbe that lives in one of Earth’s harshest environments, sulfurous volcanic mud pits, needs one of several industrially valuable metals to make a vital enzyme. While rare earth elements have been found previously in plants and microbes, the mud-pit bacterium is the first organism known to need them for survival.

Methylacidiphilum fumariolicum makes its home in volcanic pools outside Naples, Italy, where it endures steaming-hot temperatures and mud as acidic as lemon juice. Scientists led by Huub Op den Camp, a microbiologist from Radboud University Nijmegen in the Netherlands, discovered the bacterium in 2007 and brought it back to the lab, where they had trouble getting it to survive in their standard growth medium. The bacterium thrived only when the scientists added water from its original home.

To better understand the microbe, Thomas Barends, a biochemist at the Max Planck Institute for Medical Research in Heidelberg, Germany, probed the three-dimensional structure of M. fumariolicum‘s version of methanol dehydrogenase, a key enzyme used by the bacterium and many others that harvest energy from methane. Barends found that while previously studied methane-munching species insert a calcium atom into the enzyme, M. fumariolicum uses a different metal. But in computer simulations, he couldn’t find an element that fit into the enzyme’s structure.

Op den Camp’s team, meanwhile, had discovered that the mud pools that M. fumariolicum lives in have far more rare earth elements than do most other places where bacteria live. So they suggested Barends try cerium in his simulation. Cerium is the planet’s most abundant rare earth element but one never previously found in an enzyme. “I thought, ‘no way, that never happens in biology,’” Barends says. But he put it into his model and it worked.

To confirm the simulation results, the scientists grew the microbe with several rare earth elements and found that it thrived equally well on a diet of lanthanum, cerium, praseodymium or neodymium. The researchers also analyzed the bacteria’s methanol dehydrogenase and found traces of whichever element they had added, confirming the enzyme was storing the elements. The scientists report their findings September 12 in Environmental Microbiology.

Op den Camp and Barends now think M. fumariolicum could be just the first of many bacteria found to rely on rare earth elements. “It may be that people simply never looked,” Barends says.

The work will inspire other researchers to revisit data for hints of microbes using rare earth metals, predicts Marina Kalyuzhnaya, a microbiologist at the University of Washington in Seattle. “I’m quite sure we will see more papers in this area,” she says.

Chris Anthony, a retired biochemist from the University of Southampton in England who discovered methanol dehydrogenase 50 years ago, agrees that rare earth elements could be much less rare in microbiology than scientists thought. He says, “If I had a lab now I’d be running around testing everything to see if I could find them.”

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