Up to 4 percent of the methane on Earth comes from the ocean’s oxygen-rich waters, but scientists have been unable to identify the source of this potent greenhouse gas. Now researchers report that they have found the culprit: a bit of “weird chemistry” practiced by the most abundant microbes on the planet.
The findings appear in the journal Science.
The researchers who made the discovery did not set out to explain ocean geochemistry. They were searching for new antibiotics. Their research, funded by the National Institutes of Health, explores an unusual class of potential antibiotic agents, called phosphonates, already in use in agriculture and medicine.
Many microbes produce phosphonates to thwart their competitors. Phosphonates mimic molecules the microbes use, but tend to be more resistant to enzymatic breakdown. The secret of their success is the durability of their carbon-phosphorus bond.
“We’re looking at all kinds of antibiotics that have this carbon-phosphorus bond,” said University of Illinois microbiology and Institute for Genomic Biology (IGB) professor William Metcalf, who led the study with chemistry and IGB professor Wilfred van der Donk. “So we found genes in a microbe that we thought would make an antibiotic. They didn’t. They made something different altogether.”
The microbe was Nitrosopumilus maritimus, one of the most abundant organisms on the planet and a resident of the oxygen-rich regions of the open ocean. When scanning microbial genomes for promising leads, Benjamin Griffin, a postdoctoral researcher in Metcalf’s lab, noticed that N. maritimus had a gene for an enzyme that resembled other enzymes involved in phosphonate biosynthesis. He saw that the microbe also contained genes to make a molecule, called HEP, which is an intermediate in phosphonate biosynthesis.
To determine whether N. maritimus was actually producing a desirable phosphonate antibiotic, chemistry postdoctoral researcher Robert Cicchillo cloned the gene for the mysterious enzyme, expressed it in a bacterium (E. coli), and ramped up production of the enzyme. When the researchers added HEP to the enzyme, the chemical reaction that ensued produced a long sought-after compound, one that could explain the origin of methane in the aerobic ocean.
Scientists had been searching for this compound, methylphosphonic acid, since 2008, when David Karl at the University of Hawaii, Edward DeLong at MIT and their colleagues published an elegant – yet unproven – hypothesis to explain how methane was arising in the aerobic ocean. The only microbes known to produce methane are anaerobes, unable to tolerate oxygen. And yet the aerobic ocean is saturated with methane.
