Strain identifier
BacDive ID: 13761
Type strain:
Species: Roseivivax sediminis
Strain history: <- X Cui, Yunnan Inst., China
NCBI tax ID(s): 936889 (species)
General
@ref: 16074
BacDive-ID: 13761
DSM-Number: 21977
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped
description: Roseivivax sediminis DSM 21977 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from salt mine sediment from a crystallizer pond.
NCBI tax id
- NCBI tax id: 936889
- Matching level: species
strain history
@ref | history |
---|---|
16074 | <- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang |
67771 | <- X Cui, Yunnan Inst., China |
doi: 10.13145/bacdive13761.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Roseivivax
- species: Roseivivax sediminis
- full scientific name: Roseivivax sediminis Xiao et al. 2012
@ref: 16074
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Roseivivax
species: Roseivivax sediminis
full scientific name: Roseivivax sediminis Xiao et al. 2012
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
30483 | negative | rod-shaped | no | |
67771 | negative | |||
69480 | negative | 99.981 |
pigmentation
- @ref: 30483
- production: yes
Culture and growth conditions
culture medium
- @ref: 16074
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: NaCl 100.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16074 | positive | growth | 28 | mesophilic |
30483 | positive | growth | 15-42 | |
30483 | positive | optimum | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30483 | positive | growth | 6.5-8.5 | alkaliphile |
30483 | positive | optimum | 7.75 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30483 | facultative anaerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.957 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30483 | NaCl | positive | growth | 1-15 % |
30483 | NaCl | positive | optimum | 7.50 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30483 | 22599 | arabinose | + | carbon source |
30483 | 16236 | ethanol | + | carbon source |
30483 | 17234 | glucose | + | carbon source |
30483 | 17754 | glycerol | + | carbon source |
30483 | 17306 | maltose | + | carbon source |
30483 | 37684 | mannose | + | carbon source |
30483 | 15361 | pyruvate | + | carbon source |
30483 | 26546 | rhamnose | + | carbon source |
30483 | 30911 | sorbitol | + | carbon source |
30483 | 4853 | esculin | + | hydrolysis |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
30483 | acid phosphatase | + | 3.1.3.2 |
30483 | alkaline phosphatase | + | 3.1.3.1 |
30483 | alpha-galactosidase | + | 3.2.1.22 |
30483 | catalase | + | 1.11.1.6 |
30483 | cytochrome oxidase | + | 1.9.3.1 |
30483 | urease | + | 3.5.1.5 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16074 | - | - | - | - | - | + | - | +/- | + | + | - | + | - | + | +/- | - | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
16074 | salt mine sediment from a crystallizer pond | Yunnan Province, Fenggang salt mine (23° 28' N 100° 43' E) | China | CHN | Asia | 23.4667 | 100.717 |
67771 | From salt mine sediment, soda lake | Yunnan Province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Other | #Mine |
#Environmental | #Aquatic | #Pond (small) |
#Environmental | #Terrestrial | #Sediment |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_18645.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3750;97_4610;98_5918;99_18645&stattab=map
- Last taxonomy: Roseivivax sediminis
- 16S sequence: HQ615878
- Sequence Identity:
- Total samples: 639
- soil counts: 34
- aquatic counts: 467
- animal counts: 122
- plant counts: 16
Safety information
risk assessment
- @ref: 16074
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16074
- description: Roseivivax sediminis strain YIM D21 16S ribosomal RNA gene, partial sequence
- accession: HQ615878
- length: 1449
- database: ena
- NCBI tax ID: 936889
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710 | GCA_900112685 | scaffold | ncbi | 936889 |
66792 | Roseivivax sediminis strain YIM D21,KCTC 23444,ACCC 10710 | 936889.3 | wgs | patric | 936889 |
GC content
@ref | GC-content | method |
---|---|---|
16074 | 67.7 | high performance liquid chromatography (HPLC) |
30483 | 67.7 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 72.187 | yes |
flagellated | no | 91.23 | yes |
gram-positive | no | 98.413 | no |
anaerobic | no | 96.552 | yes |
aerobic | yes | 87.426 | no |
halophile | yes | 82.494 | yes |
spore-forming | no | 95.423 | no |
glucose-ferment | no | 90.798 | yes |
thermophile | no | 97.27 | yes |
glucose-util | yes | 93.928 | yes |
External links
@ref: 16074
culture collection no.: DSM 21977, ACCC 10710, KCTC 23444, YIM D21, YIM D21(T)
straininfo link
- @ref: 82941
- straininfo: 402709
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21984676 | Roseivivax sediminis sp. nov., a moderately halophilic bacterium isolated from salt mine sediment. | Xiao W, Wang YX, Liu JH, Wang ZG, Zhang XX, Ji KY, Lai YH, Wen ML, Cui XL | Int J Syst Evol Microbiol | 10.1099/ijs.0.037119-0 | 2011 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Mining, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Sodium Chloride, *Soil Microbiology | Genetics |
Phylogeny | 25155864 | Roseivivax jejudonensis sp. nov., isolated from the junction between the ocean and a freshwater spring at Jeju Island, South Korea. | Jung YT, Lee JS, Yoon JH | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0265-6 | 2014 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, *Water Microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16074 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21977) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21977 | |||
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 | |||
30483 | 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 | 26817 | 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) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68369 | Automatically annotated from API 20NE | |||||
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 | |||
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 | |||
82941 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402709.1 | StrainInfo: A central database for resolving microbial strain identifiers |