PROJECT INFORMATION
GOLD Project ID
Gp0035725  
Project Name
Nitrospina gracilis 3/211  
Other Names
  
Legacy ER Project ID
41109  
Legacy GOLD ID
Gi39306  
NCBI BioProject Name Nitrospina gracilis 3/211 genome sequence
NCBI BioProject ID 189458
NCBI BioProject Accession PRJEB1269
NCBI Locus Tag
NITGR  
NCBI BioSample Accession SAMEA2272521
PI
Added By JGI automated process on 2013-02-26
Last Modified By Jon Bertsch on 2013-12-23
Project Comments
  
Project Status
Permanent Draft  
Project Relevance
  
Sequencing Center University of Vienna (Austria)
Collaborating Institute
  
Funding Agency
  
Project Description
In marine systems, nitrate is the major reservoir of inorganic fixed nitrogen. The only known biological nitrate-forming reaction is nitrite oxidation, but despite its importance, our knowledge of the organisms catalyzing this key process in the marine N-cycle is very limited. The most frequently encountered marine NOB are related to Nitrospina gracilis, an aerobic chemolithoautotrophic bacterium isolated from ocean surface waters. To date, limited physiological and genomic data for this organism were available and its phylogenetic affiliation was uncertain. In this study, the draft genome sequence of Nitrospina gracilis strain 3/211 was obtained. Unexpectedly for an aerobic organism, N. gracilis lacks classical reactive oxygen defense mechanisms and uses the reductive tricarboxylic acid cycle for carbon fixation. These features indicate microaerophilic ancestry and are consistent with the presence of Nitrospina in marine oxygen minimum zones. Fixed carbon is stored intracellularly as glycogen, but genes for utilizing external organic carbon sources were not identified. N. gracilis also contains a full gene set for oxidative phosphorylation with oxygen as terminal electron acceptor and for reverse electron transport from nitrite to NADH. A novel variation of complex I may catalyze the required reverse electron flow to low-potential ferredoxin. Interestingly, comparative genomics indicated a strong evolutionary link between Nitrospina, the nitrite-oxidizing genus Nitrospira, and anaerobic ammonium oxidizers. This includes the horizontal transfer of a periplasmically oriented nitrite oxidoreductase and other key genes for nitrite oxidation at an early evolutionary stage. Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae.  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications Frontiers in microbiology The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer.
Other Publications
  
PROJECT COMPOSITION
Study Nitrospina gracilis 3/211
Organism Nitrospina gracilis 3/211
Analysis Projects Nitrospina gracilis 3/211
Number of Analysis Projects 1
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31)
Finishing Goal
  
Sequencing Comments
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
56  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0035725
Organism Name
Nitrospina gracilis 3/211  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
NITROSPINAE  
Genus
Nitrospina  
Genus Synonyms
  
Species
Nitrospina gracilis  
Subspecies
  
Species Synonyms
  
Strain
3/211  
Strain Synonyms
  
Serovar-Biovar
  
Culture Collection ID
  
Type Strain
Unknown  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 1266370
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Nitrospinae  
NCBI Class
Nitrospinia  
NCBI Order
Nitrospinales  
NCBI Family
Nitrospinaceae  
NCBI Genus
Nitrospina  
NCBI Species
Nitrospina gracilis  
ISOLATION CLASSIFICATION
Ecosystem
  
Ecosystem Category
  
Ecosystem Type
  
Ecosystem Subtype
  
Specific Ecosystem
  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
  
Temperature Optimum
  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram-  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

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