Strain identifier
BacDive ID: 13734
Type strain:
Species: Leisingera caerulea
Strain history: <- CCUG <- LMG
NCBI tax ID(s): 999549 (strain), 506591 (species)
General
@ref: 17696
BacDive-ID: 13734
DSM-Number: 24564
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Leisingera caerulea DSM 24564 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine biofilm on stainless steel electrode.
NCBI tax id
NCBI tax id | Matching level |
---|---|
506591 | species |
999549 | strain |
strain history
- @ref: 17696
- history: <- CCUG <- LMG
doi: 10.13145/bacdive13734.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Leisingera
- species: Leisingera caerulea
- full scientific name: Leisingera caerulea (Vandecandelaere et al. 2009) Breider et al. 2014
synonyms
- @ref: 20215
- synonym: Phaeobacter caeruleus
@ref: 17696
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Leisingera
species: Leisingera caerulea
full scientific name: Leisingera caerulea (Vandecandelaere et al. 2009) Breider et al. 2014
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
28960 | negative | 1.8 µm | 0.9 µm | rod-shaped | yes | |
69480 | negative | 99.999 |
colony morphology
@ref | incubation period |
---|---|
17696 | 3-7 days |
60763 | 2-3 days |
pigmentation
- @ref: 28960
- production: yes
multimedia
- @ref: 66793
- multimedia content: EM_DSM_24564_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 17696
- 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 |
---|---|---|---|---|
17696 | positive | growth | 20 | psychrophilic |
28960 | positive | growth | 04-45 | |
28960 | positive | optimum | 24 | psychrophilic |
60763 | positive | growth | 20 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
28960 | positive | growth | 06-09 | alkaliphile |
28960 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
28960 | aerobe |
60763 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
28960 | NaCl | positive | growth | 02-05 % |
28960 | NaCl | positive | optimum | 3.5 % |
observation
- @ref: 28960
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
28960 | 53426 | tween 80 | + | carbon source |
28960 | 4853 | esculin | + | hydrolysis |
28960 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
17696 | catalase | + | 1.11.1.6 |
17696 | cytochrome-c oxidase | + | 1.9.3.1 |
28960 | acid phosphatase | + | 3.1.3.2 |
28960 | alkaline phosphatase | + | 3.1.3.1 |
28960 | catalase | + | 1.11.1.6 |
28960 | gelatinase | + | |
28960 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
17696 | marine biofilm on stainless steel electrode | Genoa, harbour | Italy | ITA | Europe | |
60763 | Marine biofilm on stainless steel electrode | Genoa,the harbour | Italy | ITA | Europe | 2004-10-01 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Engineered product |
#Environmental | #Aquatic | #Marine |
#Environmental | #Biofilm |
taxonmaps
- @ref: 69479
- File name: preview.99_7841.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_800;98_5730;99_7841&stattab=map
- Last taxonomy: Leisingera caerulea subclade
- 16S sequence: AM943630
- Sequence Identity:
- Total samples: 72
- soil counts: 6
- aquatic counts: 57
- animal counts: 8
- plant counts: 1
Safety information
risk assessment
- @ref: 17696
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
17696 | Phaeobacter caeruleus partial 16S rRNA gene, type strain LMG 24369T | AM943630 | 1422 | ena | 999549 |
17696 | Phaeobacter caeruleus strain DSM 24564 16S ribosomal RNA gene, partial sequence | KC176242 | 1402 | ena | 999549 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Leisingera caerulea DSM 24564 | GCA_000473325 | scaffold | ncbi | 999549 |
66792 | Phaeobacter caeruleus DSM 24564 | 999549.4 | wgs | patric | 999549 |
66792 | Leisingera caerulea DSM 24564 | 2512047087 | draft | img | 999549 |
GC content
- @ref: 17696
- GC-content: 63.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 82.788 | no |
flagellated | no | 74.124 | no |
gram-positive | no | 98.393 | yes |
anaerobic | no | 98.814 | yes |
aerobic | yes | 93.421 | yes |
halophile | yes | 86.112 | no |
spore-forming | no | 94.764 | no |
thermophile | no | 96.693 | no |
glucose-util | yes | 58.254 | no |
glucose-ferment | no | 90.205 | no |
External links
@ref: 17696
culture collection no.: DSM 24564, CCUG 55859, LMG 24369
straininfo link
- @ref: 82916
- straininfo: 359367
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19406821 | Phaeobacter caeruleus sp. nov., a blue-coloured, colony-forming bacterium isolated from a marine electroactive biofilm. | Vandecandelaere I, Segaert E, Mollica A, Faimali M, Vandamme P | Int J Syst Evol Microbiol | 10.1099/ijs.0.002642-0 | 2009 | Bacterial Typing Techniques, Base Composition, Biofilms/*growth & development, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Electrodes/*microbiology, Fatty Acids/analysis, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*growth & development/isolation & purification, *Seawater, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 24425741 | Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system. | Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.059576-0 | 2014 | *Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Genetics |
Phylogeny | 24449788 | Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. | Park S, Park DS, Bae KS, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.057646-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistry, *Water Microbiology | Genetics |
Genetics | 24501626 | Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade. | Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Goker M, Klenk HP, Brinkhoff T | Stand Genomic Sci | 10.4056/sigs.3927623 | 2013 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17696 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24564) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24564 | ||||
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 | ||||
28960 | 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 | 25397 | 28776041 | ||
60763 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55859) | https://www.ccug.se/strain?id=55859 | ||||
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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
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 | ||||
82916 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID359367.1 | StrainInfo: A central database for resolving microbial strain identifiers |