Strain identifier

BacDive ID: 11284

Type strain: Yes

Species: Nitrincola lacisaponensis

Strain Designation: 4CA

Strain history: <- P. A. Dimitriu, Dept. Biolog. Sci., Univ. Missouri-Rolla, USA; 4CA

NCBI tax ID(s): 267850 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6362

BacDive-ID: 11284

DSM-Number: 16316

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

description: Nitrincola lacisaponensis 4CA is an aerobe, mesophilic, Gram-negative bacterium that was isolated from decomposing wood taken from the shore of Soap Lake, a meromictic, saline, alkaline lake.

NCBI tax id

  • NCBI tax id: 267850
  • Matching level: species

strain history

  • @ref: 6362
  • history: <- P. A. Dimitriu, Dept. Biolog. Sci., Univ. Missouri-Rolla, USA; 4CA

doi: 10.13145/bacdive11284.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oceanospirillaceae
  • genus: Nitrincola
  • species: Nitrincola lacisaponensis
  • full scientific name: Nitrincola lacisaponensis Dimitriu et al. 2005

@ref: 6362

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Nitrincola

species: Nitrincola lacisaponensis

full scientific name: Nitrincola lacisaponensis Dimitriu et al. 2005

strain designation: 4CA

type strain: yes

Morphology

cell morphology

  • @ref: 31482
  • gram stain: negative
  • cell length: 1.4 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31482
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6362BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
6362NITRINCOLA MEDIUM (DSMZ Medium 1174)yeshttps://mediadive.dsmz.de/medium/1174Name: NITRINCOLA MEDIUM (DSMZ Medium 1174) Composition: NaCl 17.5 g/l Na acetate 10.0 g/l Na2B4O7 4.0 g/l NH4Cl 0.5 g/l K2HPO4 0.25 g/l Yeast extract 0.1 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6362positivegrowth28mesophilic
6362positivegrowth37mesophilic
31482positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
31482positivegrowth7.5-11.0alkaliphile
31482positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 31482
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31482
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31482NaClpositivegrowth1.16-7.54 %
31482NaClpositiveoptimum4.64 %

observation

  • @ref: 31482
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3148230089acetate+carbon source
3148224996lactate+carbon source
3148225115malate+carbon source
3148215361pyruvate+carbon source
3148230031succinate+carbon source

enzymes

@refvalueactivityec
31482catalase+1.11.1.6
31482cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 6362
  • sample type: decomposing wood taken from the shore of Soap Lake, a meromictic, saline, alkaline lake
  • geographic location: Washington State, Grant County
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host Body Product#Plant#Timber
#Condition#Alkaline
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_7341.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_2070;97_2495;98_5384;99_7341&stattab=map
  • Last taxonomy: Nitrincola lacisaponensis subclade
  • 16S sequence: AY567473
  • Sequence Identity:
  • Total samples: 358
  • soil counts: 18
  • aquatic counts: 138
  • animal counts: 185
  • plant counts: 17

Safety information

risk assessment

  • @ref: 6362
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6362
  • description: Nitrincola lacisaponensis strain 4CA 16S ribosomal RNA gene, partial sequence
  • accession: AY567473
  • length: 1432
  • database: ena
  • NCBI tax ID: 267850

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitrincola lacisaponensis 4CAGCA_000691225contigncbi267850
66792Nitrincola lacisaponensis 4CA2576861796draftimg267850

GC content

@refGC-contentmethod
636247.4thermal denaturation, midpoint method (Tm)
3148247.4

External links

@ref: 6362

culture collection no.: DSM 16316, ATCC BAA 920

straininfo link

  • @ref: 80517
  • straininfo: 405043

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280482Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake.Dimitriu PA, Shukla SK, Conradt J, Marquez MC, Ventosa A, Maglia A, Peyton BM, Pinkart HC, Mormile MRInt J Syst Evol Microbiol10.1099/ijs.0.63647-02005Base Composition, DNA, Bacterial/analysis/chemistry/genetics, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/*growth & development/isolation & purification, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/chemistry/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism/pharmacologyGenetics
Phylogeny26481633Nitrincola nitratireducens sp. nov. isolated from a haloalkaline crater lake.Singh A, Vaidya B, Tanuku NR, Pinnaka AKSyst Appl Microbiol10.1016/j.syapm.2015.09.0022015Bacterial Typing Techniques, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genome, Bacterial, Geologic Sediments/microbiology, India, Lakes/*microbiology, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26705145Nitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake.Joshi A, Thite S, Kulkarni G, Dhotre D, Joseph N, Venkata Ramana V, Polkade A, Shouche YInt J Syst Evol Microbiol10.1099/ijsem.0.0008682015Alkalies, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Lakes/*microbiology, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6362Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16316)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16316
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
31482Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2778028776041
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
80517Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405043.1StrainInfo: A central database for resolving microbial strain identifiers