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Appl. Environ. Microbiol. doi:10.1128/AEM.02722-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. 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; Departments of Biology and Microbiology & Immunology, University of Louisville, Louisville, KY 40292; Department of Environmental Sciences, University of California, Riverside, California 92521; Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331; Chemistry, Materials, and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550; Microbial Program, Joint Genome Institute, Walnut Creek, California 94598; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824; Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831

^* To whom correspondence should be addressed. Email: jennyn{at}cc.usu.edu.

	Abstract

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 2827 putative proteins. Of these, 2026 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 N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presence of gene clusters encoding urease and hydrogenase, a RuBisCO-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 AOB genomes. 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 towards 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.