Strain identifier

BacDive ID: 133633

Type strain: Yes

Species: Nitratireductor indicus

Strain Designation: RC92-7, C115

NCBI tax ID(s): 721133 (species)

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General

@ref: 29861

BacDive-ID: 133633

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, motile, rod-shaped

description: Nitratireductor indicus RC92-7 is a Gram-negative, motile, rod-shaped bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 721133
  • Matching level: species

doi: 10.13145/bacdive133633.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Nitratireductor
  • species: Nitratireductor indicus
  • full scientific name: Nitratireductor indicus Lai et al. 2011

@ref: 29861

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Phyllobacteriaceae

genus: Nitratireductor

species: Nitratireductor indicus

strain designation: RC92-7, C115

type strain: yes

Morphology

cell morphology

  • @ref: 29861
  • gram stain: negative
  • cell length: 3 µm
  • cell width: 1.3 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 29861
  • production: no

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29861positivegrowth10-43
29861positiveoptimum27.5mesophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
29861NaClpositivegrowth<7 %
29861NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2986130089acetate+carbon source
2986117128adipate+carbon source
2986116449alanine+carbon source
2986122653asparagine+carbon source
2986135391aspartate+carbon source
2986116947citrate+carbon source
2986117234glucose+carbon source
2986129987glutamate+carbon source
2986117754glycerol+carbon source
2986128087glycogen+carbon source
2986127570histidine+carbon source
2986124996lactate+carbon source
2986125017leucine+carbon source
2986125115malate+carbon source
2986115792malonate+carbon source
2986117306maltose+carbon source
2986137684mannose+carbon source
2986151850methyl pyruvate+carbon source
2986117268myo-inositol+carbon source
29861506227N-acetylglucosamine+carbon source
2986118257ornithine+carbon source
2986118401phenylacetate+carbon source
2986126271proline+carbon source
2986117272propionate+carbon source
2986130031succinate+carbon source
2986117992sucrose+carbon source
2986126986threonine+carbon source
2986127082trehalose+carbon source
2986153258sodium citrate+carbon source
2986153426tween 80+carbon source
2986117632nitrate+reduction

enzymes

@refvalueactivityec
29861acid phosphatase+3.1.3.2
29861alkaline phosphatase+3.1.3.1
29861catalase+1.11.1.6
29861cytochrome oxidase+1.9.3.1
29861urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 29861
  • sample type: seawater

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_7174.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2450;97_4122;98_5274;99_7174&stattab=map
  • Last taxonomy: Nitratireductor indicus subclade
  • 16S sequence: GU447302
  • Sequence Identity:
  • Total samples: 1569
  • soil counts: 518
  • aquatic counts: 466
  • animal counts: 273
  • plant counts: 312

Sequence information

16S sequences

  • @ref: 29861
  • description: Nitratireductor indicus strain C115 16S ribosomal RNA gene, partial sequence
  • accession: GU447302
  • length: 1448
  • database: nuccore
  • NCBI tax ID: 1231190

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitratireductor indicus C115GCA_000300515contigncbi1231190
66792Nitratireductor indicus C1151231190.3wgspatric1231190
66792Nitratireductor indicus C1152519899619draftimg1231190

GC content

  • @ref: 29861
  • GC-content: 59

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes82.66no
gram-positiveno98.458no
anaerobicno96.934no
aerobicyes89.495no
halophileno66.947no
spore-formingno97.058no
thermophileno94.905yes
glucose-utilyes87.978yes
flagellatedno53.707no
glucose-fermentno92.458no

External links

@ref: 29861

culture collection no.: CCTCC AB 209298, LMG 25540, MCCC 1A01260

straininfo link

  • @ref: 91535
  • straininfo: 368611

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20228212Nitratireductor indicus sp. nov., isolated from deep-sea water.Lai Q, Yu Z, Yuan J, Sun F, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.022962-02010Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Phylogeny27535803Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment.Yuan CG, Jiang Z, Xiao M, Zhou EM, Kim CJ, Hozzein WN, Park DJ, Zhi XY, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0014322016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Mesorhizobium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
29861Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172623528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91535Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID368611.1