Strain identifier
BacDive ID: 14297
Type strain: 
Species: Stakelama pacifica
Strain history: <- LMG <- C. Chen, State Key Lab. for Marine Environmental Science, Xiamen University
NCBI tax ID(s): 517720 (species)
version 8.1 (current version)
General
@ref: 17829
BacDive-ID: 14297
DSM-Number: 25059
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Stakelama pacifica DSM 25059 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface water.
NCBI tax id
- NCBI tax id: 517720
- Matching level: species
strain history
- @ref: 17829
- history: <- LMG <- C. Chen, State Key Lab. for Marine Environmental Science, Xiamen University
doi: 10.13145/bacdive14297.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Stakelama
- species: Stakelama pacifica
- full scientific name: Stakelama pacifica Chen et al. 2010
@ref: 17829
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Stakelama
species: Stakelama pacifica
full scientific name: Stakelama pacifica Chen et al. 2010
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29698 | negative | 1.5-2 µm | 0.5-0.8 µm | rod-shaped | yes | |
| 69480 | yes | 92.818 | ||||
| 69480 | negative | 99.986 |
pigmentation
- @ref: 29698
- production: yes
Culture and growth conditions
culture medium
- @ref: 17829
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17829 | positive | growth | 28 | mesophilic |
| 29698 | positive | growth | 05-37 | |
| 29698 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29698 | positive | growth | 06-09 | alkaliphile |
| 29698 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 29698
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29698 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.974 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29698 | NaCl | positive | growth | 0-5 % |
| 29698 | NaCl | positive | optimum | 2 % |
observation
- @ref: 29698
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29698 | 30089 | acetate | + | carbon source |
| 29698 | 28260 | galactose | + | carbon source |
| 29698 | 24265 | gluconate | + | carbon source |
| 29698 | 17234 | glucose | + | carbon source |
| 29698 | 17754 | glycerol | + | carbon source |
| 29698 | 17716 | lactose | + | carbon source |
| 29698 | 25115 | malate | + | carbon source |
| 29698 | 15792 | malonate | + | carbon source |
| 29698 | 17306 | maltose | + | carbon source |
| 29698 | 29864 | mannitol | + | carbon source |
| 29698 | 26271 | proline | + | carbon source |
| 29698 | 30911 | sorbitol | + | carbon source |
| 29698 | 17992 | sucrose | + | carbon source |
| 29698 | 27082 | trehalose | + | carbon source |
| 29698 | 18222 | xylose | + | carbon source |
| 29698 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 29698
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
- @ref: 29698
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 17829
- sample type: surface water
- geographic location: central Pacific Ocean
- latitude: 20.5739
- longitude: 174.362
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Surface water
taxonmaps
- @ref: 69479
- File name: preview.99_43329.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_20001;97_24846;98_31470;99_43329&stattab=map
- Last taxonomy: Stakelama pacifica
- 16S sequence: EU581829
- Sequence Identity:
- Total samples: 753
- soil counts: 162
- aquatic counts: 472
- animal counts: 101
- plant counts: 18
Safety information
risk assessment
- @ref: 17829
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17829
- description: Stakelama pacifica strain JLT832 16S ribosomal RNA gene, partial sequence
- accession: EU581829
- length: 1412
- database: ena
- NCBI tax ID: 517720
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Stakelama pacifica DSM 25059 | GCA_004361835 | contig | ncbi | 517720 |
| 66792 | Stakelama pacifica CGMCC 1.7294 | GCA_014645395 | contig | ncbi | 517720 |
| 66792 | Stakelama pacifica strain CGMCC 1.7294 | 517720.11 | wgs | patric | 517720 |
| 66792 | Stakelama pacifica strain DSM 25059 | 517720.7 | wgs | patric | 517720 |
| 66792 | Stakelama pacifica DSM 25059 | 2795385468 | draft | img | 517720 |
GC content
- @ref: 29698
- GC-content: 66
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.256 | yes |
| anaerobic | no | 98.132 | yes |
| halophile | no | 91.954 | no |
| spore-forming | no | 93.891 | yes |
| glucose-util | yes | 92.36 | yes |
| aerobic | yes | 88.551 | no |
| thermophile | no | 98.763 | yes |
| motile | yes | 78.007 | no |
| flagellated | no | 88.591 | no |
| glucose-ferment | no | 91.097 | no |
External links
@ref: 17829
culture collection no.: DSM 25059, CGMCC 1.7294, LMG 24686, JLT 832
straininfo link
- @ref: 83450
- straininfo: 358563
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20081013 | Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean. | Chen C, Zheng Q, Wang YN, Yan XJ, Hao LK, Du X, Jiao N | Int J Syst Evol Microbiol | 10.1099/ijs.0.018945-0 | 2010 | Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
| Phylogeny | 22523167 | Stakelama sediminis sp. nov., isolated from tidal flat sediment. | Thawng CN, Park SJ, Cha JH, Cha CJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.039743-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis | Genetics |
| Phylogeny | 24198054 | Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge. | Felfoldi T, Vengring A, Marialigeti K, Andras J, Schumann P, Toth EM | Int J Syst Evol Microbiol | 10.1099/ijs.0.053736-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, Molecular Sequence Data, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
| Phylogeny | 29205132 | Stakelama algicida sp. nov., novel algicidal species of the family Sphingomonadaceae isolated from seawater. | Kristyanto S, Chaudhary DK, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002506 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
| Phylogeny | 35060848 | Stakelama flava sp. nov., a novel endophytic bacterium isolated from a branch of Kandelia candel. | Chen XH, Chen MS, Li FN, Tuo L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005198 | 2022 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae/microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/isolation & purification | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 17829 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25059) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25059 | ||||
| 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 | ||||
| 29698 | 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 | 26082 | 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 | ||||
| 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 | ||||
| 83450 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID358563.1 | StrainInfo: A central database for resolving microbial strain identifiers |