Strain identifier
BacDive ID: 11284
Type strain:
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)
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
@ref | name | growth | link | composition |
---|---|---|---|---|
6362 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
6362 | NITRINCOLA MEDIUM (DSMZ Medium 1174) | yes | https://mediadive.dsmz.de/medium/1174 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
6362 | positive | growth | 28 | mesophilic |
6362 | positive | growth | 37 | mesophilic |
31482 | positive | optimum | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31482 | positive | growth | 7.5-11.0 | alkaliphile |
31482 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
- @ref: 31482
- oxygen tolerance: aerobe
spore formation
- @ref: 31482
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31482 | NaCl | positive | growth | 1.16-7.54 % |
31482 | NaCl | positive | optimum | 4.64 % |
observation
- @ref: 31482
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31482 | 30089 | acetate | + | carbon source |
31482 | 24996 | lactate | + | carbon source |
31482 | 25115 | malate | + | carbon source |
31482 | 15361 | pyruvate | + | carbon source |
31482 | 30031 | succinate | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31482 | catalase | + | 1.11.1.6 |
31482 | cytochrome 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nitrincola lacisaponensis 4CA | GCA_000691225 | contig | ncbi | 267850 |
66792 | Nitrincola lacisaponensis 4CA | 2576861796 | draft | img | 267850 |
GC content
@ref | GC-content | method |
---|---|---|
6362 | 47.4 | thermal denaturation, midpoint method (Tm) |
31482 | 47.4 |
External links
@ref: 6362
culture collection no.: DSM 16316, ATCC BAA 920
straininfo link
- @ref: 80517
- straininfo: 405043
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16280482 | Nitrincola 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 MR | Int J Syst Evol Microbiol | 10.1099/ijs.0.63647-0 | 2005 | Base 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/pharmacology | Genetics |
Phylogeny | 26481633 | Nitrincola nitratireducens sp. nov. isolated from a haloalkaline crater lake. | Singh A, Vaidya B, Tanuku NR, Pinnaka AK | Syst Appl Microbiol | 10.1016/j.syapm.2015.09.002 | 2015 | Bacterial 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, DNA | Genetics |
Phylogeny | 26705145 | Nitrincola 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 Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000868 | 2015 | Alkalies, 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, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
6362 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16316) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16316 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
31482 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27780 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
69479 | João 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 | ||||
80517 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405043.1 | StrainInfo: A central database for resolving microbial strain identifiers |