Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

Journal Article · Tue Jan 01 04:00:00 EST 2008 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/AEM.02722-07· OSTI ID:931195

Norton, Jeanette M ^[1]; Klotz, Martin G ^[2]; Stein, Lisa Y ^[3]; Arp, D J ^[4]; Bottomley, Peter J ^[4]; Chain, Patrick S. G. ^[5]; Hauser, Loren John ^[6]; Land, Miriam L ^[6]; Larimer, Frank W ^[6]; Shin, M ^[7]; Starkenburg, Shawn R ^[4]

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1. Utah State University (USU)
2. University of Louisville, Louisville
3. University of California, Riverside
4. Oregon State University
5. Lawrence Livermore National Laboratory (LLNL)
6. ORNL
7. U.S. Department of Energy, Joint Genome Institute

The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), 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.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 931195
• Journal Information: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 11 Vol. 74; ISSN AEMIDF; ISSN 0099-2240
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
CHROMOSOMES
FUNCTIONALS
GENES
GLYCOGEN
HYDROGENASES
LACTONES
MEMBRANES
PLASMIDS
PORINS
PROTEINS
SOILS
STORAGE
SYNTHESIS
UREASE