OREGON STATE UNIVERSITY

Bacteria move over; there's a new nitrifier in town

05/10/2010

CORVALLIS, Ore. -- It's too early to call for surrender, but bacteria may have to at least share the honors for a chemical process that is critical for life and goes on right under our feet day in and day out. For a century, scientists thought that bacteria were the only organisms that performed one of the key steps in the nitrogen cycle, the conversion of ammonia to nitrate. Now they have confirmed that another common group of microbes known as crenarchaea does the same thing.

Scientists have isolated and sequenced only one member of this group, Nitrosopumilus maritimus. By publishing its complete genome in the Proceedings of the National Academy of Sciences on April 26, an international group of researchers, including two at Oregon State University, has opened the door to understanding how crenarchaea affect the global nitrogen cycle.

Advancing knowledge of that cycle has become an urgent challenge for scientists. Humans pour far more nitrogen into the terrestrial environment than does nature, and the consequences are showing up in polluted well water, estuaries and some ocean "dead zones."

The National Science Foundation drives research on this issue through support for the Nitrification Network, a collaboration among researchers in North America, Asia and Europe. The network facilitated the N. maritimus genome analysis among scientists who brought experience with both bacterial and archaeal biology. The U.S. Department of Energy funded sequencing of the genome.

"Because of the way we use nitrogen on crops, it leaches into surface waters and flows downstream. That fuels our interest in this process," said Dan Arp, co-author and professor of botany and plant pathology at OSU. Arp, dean of OSU's University Honors College, was a member of the team that analyzed the genome to gain insights into the physiology and metabolism carried out by the microorganism.

In the tree of life, crenarchaea belong to the kingdom of Archaea, which were known as "extremophiles" because they were discovered in hot springs and briny pools. Crenarchaea such as N. maritimus are now commonly found in marine and fresh water and in soils, but how much ammonia they convert to nitrate is unknown. Nitrification influences the availability of nitrogen, which is required for plant productivity and thus plays an important role in the carbon cycle.

"Our challenge now is how to tell what crenarchaea and bacteria are doing in the soil," added Arp. "We can count them. I can tell you how many of each are in the soil. What I can't tell you is which ones are actually doing the nitrification. Somewhere in this genome is a unique gene that will only be found in the nitrifying Archaea. Hopefully we can use that to go into soil and water and tell us which ones are the most active."

A clue to N. maritimus' function is a suite of genes that codes for copper-dependent ammonia oxidation enzymes. Nitrifying bacteria use enzymes that depend primarily on iron, so the discovery of a different system was surprising and could foreshadow a new nitrification pathway.

Since the N. maritimus genome shares many gene sequences with other archaeal species, it may also serve as a useful model for understanding the physiology of these microorganisms.

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