Research Feature: Mapping the Genome of Nitrobacter winogradskyi

Posted: March 10, 2006
Contact: Shawn Starkenburg, 541-737-4214, starkens@onid.orst.edu.

A team from Oregon State University and their colleagues has mapped the genome of a bacterium that plays a role in the global nitrogen cycle. The bacterium, called Nitrobacter winogradskyi, carries out nitrite oxidation – a process important for recycling nitrogen in soils and sewage treatment.

“This step of the nitrogen cycle is understudied at the genetic level,” says OSU microbiology PhD student Shawn Starkenburg. “Sequencing the genome for this bacterium provides a baseline to study this process in more detail.” Starkenburg, OSU faculty, Luis Sayavedra-Soto, Daniel Arp, and Peter Bottomley, and colleagues from the Department of Energy, the University of Louisville, and the University of Wisconsin report on their study in the March 2006 issue of Applied and Environmental Microbiology.

Genome map of Nitrobacter winogradskyi.
Genome map of Nitrobacter winogradskyi.

 

Mapping the genome was a multi-step process. The Department of Energy’s Office of Biological and Environmental Research carried out the initial sequencing at the Joint Genome Institute and provided funding for the project. Starkenburg then traveled to Lawrence Livermore National Labs to edit and fill in missing pieces in the genetic code. The next step was to identify individual genes and, if possible, determine their function. Starkenburg and his co-authors used computer programs to compare the gene sequences in the N. winogradskyi genome to genes with known functions in other organisms. “We tentatively assigned functions to about seventy percent of the bacterium’s 3143 genes,” said Starkenburg. For example, they identified and further characterized the genes that code for enzymes that give the bacterium its unique ability to oxidize nitrite.


Illustration from U.S. EPA.

The nitrogen cycle describes the movement of nitrogen from the atmosphere, into soils and living things, and back into the atmosphere. At many stages in the cycle it must change forms and bacteria mediate many of these transformations. N. winogradskyi is one the nitrifying bacteria – a group of organisms that help convert nitrogen in the form of ammonia into nitrate.

Nitrite oxidation is an important process in both soils and wastewater treatment. It is part of the reaction sequence that converts ammonia, a toxic form of nitrogen produced by decaying plant and animal matter, into nitrate. In soils, this conversion makes nitrogen available to living things – nitrate is more readily taken up by plants than ammonia. In sewage treatment, the removal of ammonia prevents plant effluent from harming fish and other aquatic organisms. The ammonia to nitrate conversion is also a necessary first step for denitrification – a process used at some treatment plants to remove nitrate from plant effluent by converting it into nitrogen gas.

Starkenberg is a PhD candidate in microbiology and the recipient of a Subsurface Biosphere IGERT fellowship. Other authors on the study were Patrick Chain of the Joint Genome Institute and Lawrence Livermore National Laboratory; Luis Sayavedra-Soto, Peter Bottomley, and Daniel Arp of Oregon State University; Loren Hauser, Miriam Land, and Frank Larimer of Oak Ridge National Laboratory; Stephanie Malfatti of Lawrence Livermore National Laboratory; Martin G. Klotz of the University of Louisville; and William Hickey of the University of Wisconsin.

Links:

  • Research article in Applied and Environmental Microbiology (free access available from OSU computers). Full citation: Starkenburg, S., Chain, P., Sayavedra-Soto, L., Hauser, L. Land, M., Larimer, F., Malfatti, S., Klotz, M., Bottomley, P. Arp, D., and Hickey, W., 2006, Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255, Applied and Environmental Microbiology, Vol. 72, No. 3, p. 2050-2063.
  • Faculty web pages for Luis Sayavedra-Soto, Peter Bottomley, and Daniel Arp.