Strain identifier
BacDive ID: 5876
Type strain: 
Species: Haloplanus natans
Strain Designation: RE-101
Strain history: R. E. Bardavid RE-101.
NCBI tax ID(s): 926690 (strain), 376171 (species)
version 8.1 (current version)
General
@ref: 7315
BacDive-ID: 5876
DSM-Number: 17983
keywords: genome sequence, 16S sequence, Archaea, aerobe, mesophilic, Gram-negative
description: Haloplanus natans RE-101 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from experimental mesocosm filled with a mixture of water from the Dead Sea and the Red Sea.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 376171 | species |
| 926690 | strain |
strain history
| @ref | history |
|---|---|
| 7315 | <- A. Oren, Hebrew Univ. Jerusalem, Israel; RE-101 <- R. E. Bardavid |
| 67770 | R. E. Bardavid RE-101. |
doi: 10.13145/bacdive5876.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Haloferacales
- family: Haloferacaceae
- genus: Haloplanus
- species: Haloplanus natans
- full scientific name: Haloplanus natans Bardavid et al. 2007
@ref: 7315
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Haloferacaceae
genus: Haloplanus
species: Haloplanus natans
full scientific name: Haloplanus natans Bardavid et al. 2007
strain designation: RE-101
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | confidence |
|---|---|---|---|
| 31916 | negative | 2.5-8 µm | |
| 69480 | negative | 99.991 |
pigmentation
- @ref: 31916
- production: no
Culture and growth conditions
culture medium
- @ref: 7315
- name: RE-101 MEDIUM (DSMZ Medium 1130)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1130
- composition: Name: RE-101/102 MEDIUM (DSMZ Medium 1130) Composition: NaCl 175.0 g/l MgCl2 x 6 H2O 20.0 g/l Agar 15.0 g/l (optional) Yeast extract 5.0 g/l K2SO4 5.0 g/l CaCl2 x 2 H2O 0.1 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7315 | positive | growth | 37 | mesophilic |
| 31916 | positive | growth | 37-52 | |
| 31916 | positive | optimum | 40 | thermophilic |
| 67770 | positive | growth | 37 | mesophilic |
culture pH
- @ref: 31916
- ability: positive
- type: growth
- pH: 6.5-8
Physiology and metabolism
oxygen tolerance
- @ref: 31916
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 96 |
| 69480 | no | 99.975 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31916 | NaCl | positive | growth | 15.08-24.94 % |
| 31916 | NaCl | positive | optimum | 17.4 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31916 | 30089 | acetate | + | carbon source |
| 31916 | 17234 | glucose | + | carbon source |
| 31916 | 33942 | ribose | + | carbon source |
| 31916 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31916 | catalase | + | 1.11.1.6 |
| 31916 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7315 | experimental mesocosm filled with a mixture of water from the Dead Sea and the Red Sea | Sedom | Israel | ISR | Asia |
| 67770 | Experimental mesocosm filled with a mixture of water from the Dead Sea and the Red Sea | Israel | ISR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
Safety information
risk assessment
- @ref: 7315
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Haloplanus natans gene for 16S ribosomal RNA, partial sequence, strain: JCM 14081 | AB477975 | 1431 | ena | 376171 |
| 20218 | Haloplanus natans gene for 16S rRNA, complete sequence, strain: JCM 14081 | AB663396 | 1471 | ena | 376171 |
| 20218 | Haloplanus natans strain JCM 14081 16S ribosomal RNA gene, partial sequence | JN206648 | 1471 | ena | 376171 |
| 7315 | Haloplanus natans strain RE 101 16S ribosomal RNA gene, complete sequence | DQ417339 | 1393 | ena | 376171 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Haloplanus natans DSM 17983 | 2517287030 | draft | img | 926690 |
| 67770 | Haloplanus natans DSM 17983 | GCA_000427685 | scaffold | ncbi | 926690 |
| 66792 | Haloplanus natans DSM 17983 | 926690.3 | wgs | patric | 926690 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 31916 | 66.2 | |
| 67770 | 66.2 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
- trait: spore-forming
- prediction: no
- confidence: 96
- training_data: no
External links
@ref: 7315
culture collection no.: DSM 17983, JCM 14081, CGMCC 1.8972
straininfo link
- @ref: 75355
- straininfo: 302760
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17392206 | Haloplanus natans gen. nov., sp. nov., an extremely halophilic, gas-vacuolate archaeon isolated from Dead Sea-Red Sea water mixtures in experimental outdoor ponds. | Bardavid RE, Mana L, Oren A | Int J Syst Evol Microbiol | 10.1099/ijs.0.64648-0 | 2007 | DNA, Archaeal/genetics, DNA, Ribosomal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification/physiology, Indian Ocean, Israel, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
| Phylogeny | 19767368 | Haloplanus vescus sp. nov., an extremely halophilic archaeon from a marine solar saltern, and emended description of the genus Haloplanus. | Cui HL, Gao X, Li XY, Xu XW, Zhou YG, Liu HC, Zhou PJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.018564-0 | 2009 | DNA, Archaeal/genetics, DNA, Ribosomal/genetics, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/*metabolism | Metabolism |
| Phylogeny | 20511466 | Haloplanus aerogenes sp. nov., an extremely halophilic archaeon from a marine solar saltern. | Cui HL, Gao X, Yang X, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijs.0.025023-0 | 2010 | Base Composition, China, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/*microbiology, Glycolipids/analysis, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Magnesium Chloride/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Metabolism |
| Phylogeny | 24129619 | Haloplanus salinus sp. nov., an extremely halophilic archaeon from a Chinese marine solar saltern. | Qiu XX, Zhao ML, Han D, Zhang WJ, Cui HL | Arch Microbiol | 10.1007/s00203-013-0929-z | 2013 | Bacterial Proteins/genetics, Base Composition, China, DNA, Archaeal/genetics, Glycolipids/metabolism, Halobacteriaceae/*classification/genetics/isolation & purification/*physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Species Specificity | Metabolism |
| Phylogeny | 24488367 | Haloplanus litoreus sp. nov. and Haloplanus ruber sp. nov., from a marine solar saltern and an aquaculture farm, respectively. | Han D, Cui HL | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0123-6 | 2014 | Aquaculture, Base Composition, China, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism | Genetics |
| Phylogeny | 28945530 | Haloplanus salinarum sp. nov., an extremely halophilic archaeon isolated from a solar saltern. | Hwang HB, Kim YE, Koh HW, Song HS, Roh SW, Kim SJ, Nam SW, Park SJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002313 | 2017 | Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Republic of Korea, *Salinity, Sequence Analysis, DNA, *Water Microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
|---|---|---|---|---|---|---|---|
| 7315 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17983) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17983 | ||||
| 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 | ||
| 31916 | 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 | 28173 | ||
| 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) | ||||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 75355 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID302760.1 | StrainInfo: A central database for resolving microbial strain identifiers |