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Applied and Environmental Microbiology, June 2008, p. 3559-3572, Vol. 74, No. 11
0099-2240/08/$08.00+0     doi:10.1128/AEM.02722-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Complete Genome Sequence of Nitrosospira multiformis, an Ammonia-Oxidizing Bacterium from the Soil Environment ^,

Department of Plants, Soils, and Climate, Utah State University, Logan, Utah 84322,¹ Departments of Biology and Microbiology and Immunology, University of Louisville, Louisville, Kentucky 40292,² Department of Environmental Sciences, University of California, Riverside, California 92521,³ Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331,⁴ Chemistry, Materials, and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550,⁵ Microbial Program, Joint Genome Institute, Walnut Creek, California 94598,⁶ Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824,⁷ Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831⁸

Received 3 December 2007/ Accepted 7 March 2008

The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196^T) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

Published ahead of print on 4 April 2008.

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