Strain identifier
BacDive ID: 5969
Type strain:
Species: Halostagnicola larsenii
Strain Designation: XH-48
Strain history: A. Ventosa XH-48.
NCBI tax ID(s): 797299 (strain), 353800 (species)
General
@ref: 7132
BacDive-ID: 5969
DSM-Number: 17691
keywords: genome sequence, 16S sequence, Archaea, aerobe, mesophilic, Gram-negative, rod-shaped
description: Halostagnicola larsenii XH-48 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from sediment of saline Lake Xilinhot .
NCBI tax id
NCBI tax id | Matching level |
---|---|
353800 | species |
797299 | strain |
strain history
@ref | history |
---|---|
7132 | <- A. Ventosa, Univ. Seville, Dept. Microbiol. Parasitol., Spain; XH-48 <- A. M. Castillo et al. |
67770 | A. Ventosa XH-48. |
doi: 10.13145/bacdive5969.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Natrialbales
- family: Natrialbaceae
- genus: Halostagnicola
- species: Halostagnicola larsenii
- full scientific name: Halostagnicola larsenii Castillo et al. 2006
@ref: 7132
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Natrialbaceae
genus: Halostagnicola
species: Halostagnicola larsenii
full scientific name: Halostagnicola larsenii Castillo et al. 2006
strain designation: XH-48
type strain: yes
Morphology
cell morphology
- @ref: 31790
- gram stain: negative
- cell length: 01-03 µm
- cell width: 0.5-1 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31790
- production: yes
Culture and growth conditions
culture medium
- @ref: 7132
- name: HALOPIGER MEDIUM (DSMZ Medium 1138)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1138
- composition: Name: HALOPIGER MEDIUM (DSMZ Medium 1138) Composition: NaCl 195.0 g/l MgSO4 x 7 H2O 50.8 g/l MgCl2 x 6 H2O 32.5 g/l Yeast extract 5.0 g/l KCl 5.0 g/l CaCl2 x 2 H2O 0.8 g/l NaBr 0.6 g/l NaHCO3 0.16 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7132 | positive | growth | 37 | mesophilic |
31790 | positive | growth | 25-50 | |
31790 | positive | optimum | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31790 | positive | growth | 06-09 | alkaliphile |
31790 | positive | optimum | 07-08 |
Physiology and metabolism
oxygen tolerance
- @ref: 31790
- oxygen tolerance: aerobe
spore formation
- @ref: 31790
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31790 | NaCl | positive | growth | 15-30 % |
31790 | NaCl | positive | optimum | 20 % |
observation
- @ref: 31790
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31790 | 30089 | acetate | + | carbon source |
31790 | 22599 | arabinose | + | carbon source |
31790 | 28757 | fructose | + | carbon source |
31790 | 28260 | galactose | + | carbon source |
31790 | 17234 | glucose | + | carbon source |
31790 | 29987 | glutamate | + | carbon source |
31790 | 17754 | glycerol | + | carbon source |
31790 | 17716 | lactose | + | carbon source |
31790 | 17306 | maltose | + | carbon source |
31790 | 29864 | mannitol | + | carbon source |
31790 | 17272 | propionate | + | carbon source |
31790 | 33942 | ribose | + | carbon source |
31790 | 27082 | trehalose | + | carbon source |
31790 | 18222 | xylose | + | carbon source |
31790 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31790 | catalase | + | 1.11.1.6 |
31790 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
7132 | sediment of saline Lake Xilinhot (43° 55' N 115° 37' E) | Inner Mongolia | China | CHN | Asia | 43.9167 | 115.617 |
67770 | Sediment of a saline lake (Lake Xilinhot) in Inner Mongolia | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Lake (large) |
#Environmental | #Aquatic | #Sediment |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_187283.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_68906;97_89556;98_121847;99_187283&stattab=map
- Last taxonomy: Halostagnicola larsenii
- 16S sequence: AB663441
- Sequence Identity:
- Total samples: 6
- soil counts: 1
- aquatic counts: 5
Safety information
risk assessment
- @ref: 7132
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Halostagnicola larsenii gene for 16S rRNA, partial sequence | AB301489 | 1433 | ena | 797299 |
20218 | Halostagnicola larsenii gene for 16S rRNA, complete sequence, strain: JCM 13463 | AB663441 | 1473 | ena | 797299 |
7132 | Halostagnicola larsenii partial 16S rRNA gene, type strain XH-48T | AM117571 | 1372 | ena | 797299 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halostagnicola larsenii XH-48 | GCA_000517625 | complete | ncbi | 797299 |
66792 | Halostagnicola larsenii XH-48, DSM 17691 | 2510065051 | complete | img | 797299 |
67770 | Halostagnicola larsenii XH-48, complete genome | CP007055 | ncbi | 797299 | |
66792 | Halostagnicola larsenii XH-48 | 797299.3 | complete | patric | 797299 |
66792 | Halostagnicola larsenii XH-48 | 797299.7 | plasmid | patric | 797299 |
66792 | Halostagnicola larsenii XH-48 | 797299.8 | plasmid | patric | 797299 |
66792 | Halostagnicola larsenii XH-48 | 797299.9 | plasmid | patric | 797299 |
66792 | Halostagnicola larsenii XH-48 | 797299.6 | plasmid | patric | 797299 |
GC content
@ref | GC-content | method |
---|---|---|
7132 | 61.0 | thermal denaturation, midpoint method (Tm) |
31790 | 61 | |
67770 | 61 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 82.818 | yes |
flagellated | no | 96.106 | yes |
gram-positive | no | 95.812 | yes |
anaerobic | no | 97.818 | no |
halophile | yes | 89.495 | yes |
spore-forming | no | 93.431 | yes |
thermophile | no | 81.386 | yes |
glucose-util | yes | 93.869 | no |
aerobic | yes | 93.514 | no |
glucose-ferment | no | 80.471 | no |
External links
@ref: 7132
culture collection no.: DSM 17691, CECT 7116, CGMCC 1.5338, JCM 13463
straininfo link
- @ref: 75458
- straininfo: 297210
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16825623 | Halostagnicola larsenii gen. nov., sp. nov., an extremely halophilic archaeon from a saline lake in Inner Mongolia, China. | Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A | Int J Syst Evol Microbiol | 10.1099/ijs.0.64286-0 | 2006 | Aerobiosis, Anaerobiosis, Base Composition, China, DNA, Archaeal/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Enzymes/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Halobacteriaceae/*classification/cytology/genetics/*isolation & purification/physiology, Lipids/chemistry/isolation & purification, Magnesium Chloride/metabolism, Microscopy, Phase-Contrast, Molecular Sequence Data, Mongolia, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Water Microbiology | Enzymology |
Phylogeny | 20081018 | Halostagnicola kamekurae sp. nov., an extremely halophilic archaeon from solar salt. | Nagaoka S, Minegishi H, Echigo A, Usami R | Int J Syst Evol Microbiol | 10.1099/ijs.0.014449-0 | 2010 | Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification, Lipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA | Genetics |
Phylogeny | 20543148 | Halostagnicola alkaliphila sp. nov., an alkaliphilic haloarchaeon from commercial rock salt. | Nagaoka S, Minegishi H, Echigo A, Shimane Y, Kamekura M, Usami R | Int J Syst Evol Microbiol | 10.1099/ijs.0.023119-0 | 2010 | Alkalies/*metabolism, China, DNA, Archaeal/genetics, Fatty Acids/metabolism, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolism | Metabolism |
Phylogeny | 25479949 | Halostagnicola bangensis sp. nov., an alkaliphilic haloarchaeon from a soda lake. | Corral P, Corcelli A, Ventosa A | Int J Syst Evol Microbiol | 10.1099/ijs.0.000006 | 2014 | Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification, Lakes, Lipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, *Water Microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
7132 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17691) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17691 | ||||
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31790 | 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 | 28776041 | 28061 | ||
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
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 | ||||
75458 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297210.1 | StrainInfo: A central database for resolving microbial strain identifiers |