Up to 4% 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 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,” says University of Illinois microbiology and Institute
for Genomic Biology 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 laboratory, 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.
To explain this “methane paradox,” Karl and DeLong noted that many aerobic marine microbes host
an enzyme that can cleave the carbon-phosphorus bond. If that bond were
embedded in a molecule with a single carbon atom, methylphosphonic acid, one of
the byproducts of this cleavage would be methane. Karl and DeLong even showed
that incubation of seawater microbes with methylphosphonic acid led to methane
production.
“There was just
one problem with this theory,” van der Donk says. “Methylphosphonic acid has
never been detected in marine ecosystems. And based on known chemical pathways,
it was difficult to see how this compound could be made without invoking
unusual biochemistry.”
Van der Donk’s
laboratory conducted further experiments that demonstrated that the N. maritimus was actually synthesizing phosphonic acids.
“The chemical
analysis was a Herculean effort,” Metcalf says. The microbe is “one-tenth the
size of the standard laboratory rat microbe, E. coli, and grows at
much lower cell densities,” he says. The team relied on N. maritimus discoverer David Stahl, of the University of
Washington, to grow the microbe in culture for their analysis.
“So we grew 100
liters of culture to get a few, maybe 50 or 100 milligrams of cells, of which
maybe 1% is phosphorus, of which maybe 5% is methylphosphonate,” Metcalf says.
The experiments
indicated that the methylphosphonate was bound to another molecule, likely a
sugar attached to the microbe’s surface, van der Donk says. When N. maritimus dies, other marine microbes break the
carbon-phosphorus bond of the methylphosphonate to gobble up the phosphorus, an
element that is rare in the oceans but essential to life. This encounter
generates methane.
The biochemistry
that allows N. maritimus to produce methylphosphonate is “unprecedented,” Metcalf says.
“Organisms that
make phosphonates tend to use weird chemistry for all kinds of things,” van der
Donk says. “But this is very unusual. One of the carbon atoms of the HEP is
oxidized by four electrons and the other is turned into a methyl group. I’m not
aware of any other cases where that happens.”
The new findings
will help those modeling the geochemistry of the ocean to understand climate
change, Metcalf says.
“We know that
about 20% of the greenhouse effect comes from methane and 4 percent of that
comes from this previously unexplained source,” he says. “You have to know
where the methane comes from and where it goes to understand what will happen
when the system changes.”