Strain identifier

BacDive ID: 17835

Type strain: Yes

Species: Celerinatantimonas diazotrophica

Strain Designation: S-G2-2

Strain history: <- C. R. Lovell, Dept. Biological Sciences. University of South Carolina; S-G2-2 <- C. E. Bagwell and A. A. Lucas, Dept. Biological Sciences. University of South Carolina

NCBI tax ID(s): 412034 (species)

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General

@ref: 7536

BacDive-ID: 17835

DSM-Number: 18577

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

description: Celerinatantimonas diazotrophica S-G2-2 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from root of the smooth cordgrass Spartina alterniflora.

NCBI tax id

  • NCBI tax id: 412034
  • Matching level: species

strain history

  • @ref: 7536
  • history: <- C. R. Lovell, Dept. Biological Sciences. University of South Carolina; S-G2-2 <- C. E. Bagwell and A. A. Lucas, Dept. Biological Sciences. University of South Carolina

doi: 10.13145/bacdive17835.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Celerinatantimonadaceae
  • genus: Celerinatantimonas
  • species: Celerinatantimonas diazotrophica
  • full scientific name: Celerinatantimonas diazotrophica Cramer et al. 2011

@ref: 7536

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Celerinatantimonadaceae

genus: Celerinatantimonas

species: Celerinatantimonas diazotrophica

full scientific name: Celerinatantimonas diazotrophica Cramer et al. 2011

strain designation: S-G2-2

type strain: yes

Morphology

cell morphology

  • @ref: 29651
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 7536
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7536positivegrowth28mesophilic
29651positivegrowth17-49
29651positiveoptimum31mesophilic

culture pH

@refabilitytypepHPH range
29651positivegrowth3.5-8.0acidophile
29651positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 29651
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
29651NaClpositivegrowth2.5-8.0 %
29651NaClpositiveoptimum7.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2965115963ribitol+carbon source
2965122599arabinose+carbon source
2965118403L-arabitol+carbon source
2965117057cellobiose+carbon source
2965116947citrate+carbon source
2965123652dextrin+carbon source
2965128757fructose+carbon source
2965128260galactose+carbon source
2965124175galacturonate+carbon source
2965124265gluconate+carbon source
2965117234glucose+carbon source
2965132323glucuronamide+carbon source
2965129987glutamate+carbon source
2965117754glycerol+carbon source
2965128087glycogen+carbon source
2965117716lactose+carbon source
2965125115malate+carbon source
2965117306maltose+carbon source
2965129864mannitol+carbon source
2965137684mannose+carbon source
2965128053melibiose+carbon source
2965137657methyl D-glucoside+carbon source
2965117268myo-inositol+carbon source
29651506227N-acetylglucosamine+carbon source
2965126271proline+carbon source
2965115361pyruvate+carbon source
2965116634raffinose+carbon source
2965126546rhamnose+carbon source
2965130911sorbitol+carbon source
2965130031succinate+carbon source
2965117992sucrose+carbon source
2965127082trehalose+carbon source

enzymes

@refvalueactivityec
29651acid phosphatase+3.1.3.2
29651alkaline phosphatase+3.1.3.1
29651alpha-galactosidase+3.2.1.22
29651catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 7536
  • sample type: root of the smooth cordgrass Spartina alterniflora
  • host species: Spartina alterniflora
  • geographic location: South Carolina, North Inlet salt marsh near Georgetown, Goat Island (33° 20' N 79° 12' W)
  • country: USA
  • origin.country: USA
  • continent: North America
  • latitude: 33.3333
  • longitude: -79.2

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_131812.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_361;96_51269;97_66035;98_88180;99_131812&stattab=map
  • Last taxonomy: Celerinatantimonas diazotrophica subclade
  • 16S sequence: DQ913890
  • Sequence Identity:
  • Total samples: 245
  • soil counts: 15
  • aquatic counts: 187
  • animal counts: 42
  • plant counts: 1

Safety information

risk assessment

  • @ref: 7536
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7536
  • description: Celerinatantimonas diazotrophica strain S-G2-2 16S ribosomal RNA gene, partial sequence
  • accession: DQ913890
  • length: 1493
  • database: ena
  • NCBI tax ID: 412034

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Celerinatantimonas diazotrophica DSM 18577GCA_004339545scaffoldncbi412034
66792Celerinatantimonas diazotrophica strain DSM 18577412034.4wgspatric412034
66792Celerinatantimonas diazotrophica DSM 185772802428811draftimg412034

GC content

@refGC-contentmethod
753641.5high performance liquid chromatography (HPLC)
2965141.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.504yes
flagellatedyes67.32no
gram-positiveno98.856no
anaerobicno94.379yes
aerobicno72.303no
halophileyes60.981yes
spore-formingno94.1no
thermophileno97.341no
glucose-utilyes93.141yes
glucose-fermentyes83.634no

External links

@ref: 7536

culture collection no.: DSM 18577, ATCC BAA 1368

straininfo link

  • @ref: 86826
  • straininfo: 406483

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20511455Celerinatantimonas diazotrophica gen. nov., sp. nov., a nitrogen-fixing bacterium representing a new family in the Gammaproteobacteria, Celerinatantimonadaceae fam. nov.Cramer MJ, Haghshenas N, Bagwell CE, Matsui GY, Lovell CRInt J Syst Evol Microbiol10.1099/ijs.0.017905-02010DNA, Bacterial/genetics, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, *Nitrogen Fixation, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny23852153Celerinatantimonas yamalensis sp. nov., a cold-adapted diazotrophic bacterium from a cold permafrost brine.Shcherbakova V, Chuvilskaya N, Rivkina E, Demidov N, Uchaeva V, Suetin S, Suzina N, Gilichinsky DInt J Syst Evol Microbiol10.1099/ijs.0.045997-02013Bacterial Typing Techniques, Base Composition, Cold Temperature, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Glycolipids/chemistry, Molecular Sequence Data, *Nitrogen Fixation, Oxidoreductases/genetics, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, *Salts, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7536Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18577)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18577
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29651Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2604028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86826Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406483.1StrainInfo: A central database for resolving microbial strain identifiers