title: Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.
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 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.
authors.affiliation: Department of Plants, Soils, and Climate, Utah State University, Logan, UT 84322-4820, USA. jennyn@cc.usu.edu
authors.forename: Jeanette M
authors.initials: JM
authors.lastname: Norton
authors.forename: Martin G
authors.initials: MG
authors.lastname: Klotz
authors.forename: Lisa Y
authors.initials: LY
authors.lastname: Stein
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Arp
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bottomley
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.forename: Loren J
authors.initials: LJ
authors.lastname: Hauser
authors.forename: Miriam L
authors.initials: ML
authors.lastname: Land
authors.forename: Frank W
authors.initials: FW
authors.lastname: Larimer
authors.forename: Maria W
authors.initials: MW
authors.lastname: Shin
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Starkenburg
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D018628:Gene Dosage; D016680:Genome, Bacterial; D008660:Metabolism / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D043369:Nitrosomonadaceae / Q000235:genetics* / Q000302:isolation & purification; D016366:Open Reading Frames; D010957:Plasmids; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D000641:Ammonia