The Ammonia-Oxidizing Gene
Soil microbes, in a process known as nitrification, combine ammonia with oxygen to form nitrates, which are used as nutrients by plants.
"Ammonia oxidation is an important step in the nitrogen cycle that was believed for the last 100 years to be solely performed by bacteria," said Christa Schleper, full professor of Molecular biology of Archaea at University Bergen, Norway.
The discovery was made possible by a combination of different techniques ranging from molecular biology, biochemistry to metagenomics. Using a novel sequencing technique and bioinformatics tools, Stephan C. Schuster, associate professor of biochemistry and molecular biology at Penn State, and his co-workers accurately measured the quantities of active bacteria and archaea in the complex mixtures of soil organisms. The international research team reported their findings in the Aug. 17 issue of Nature.
Archaea are single-celled microbes that, along with bacteria, comprise a category of small organisms whose genetic material, or DNA, is not stored in a nucleus (as it is in animals and plants). Crenarchaeota, which belong to the archaea, are found in various habitats, including soil.
"We think crenarchaeota in soil gain their energy from oxidizing ammonia," said Schuster. "But we don't know yet if they can also gain energy by other means. The bacterial counterparts can only do ammonia (and urea) oxidation, nothing else."
During a recent study of a collection of genes in microorganisms, researchers had stumbled on a particular gene, which is responsible for the production of a key enzyme used for the oxidation of ammonia.
The gene was subsequently found in a marine strain of archaea that uses ammonia as its sole source of energy. Researchers examined soil samples from 12 pristine and agricultural lands across three climatic zones to see if such ammonia-oxidizing microorganisms were present in terrestrial ecosystems as well.
"We measured the abundance of the particular crenarchaeota gene alongside the same type of gene from bacteria," explained Schleper.
The tally suggested that copies of the archaeal gene in the soil samples were up to 3,000 times more abundant than copies of the bacterial gene. High amounts of lipids specific to crenarchaeota confirmed the organism's presence.