Strain identifier

BacDive ID: 13764

Type strain: Yes

Species: Roseobacter litoralis

Strain history: CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh149

NCBI tax ID(s): 391595 (strain), 42443 (species)

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General

@ref: 2939

BacDive-ID: 13764

DSM-Number: 6996

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, motile, rod-shaped

description: Roseobacter litoralis DSM 6996 is a psychrophilic, Gram-negative, motile bacterium that was isolated from seaweed.

NCBI tax id

NCBI tax idMatching level
391595strain
42443species

strain history

@refhistory
2939<- T. Shiba, Otsuchi Marine Res. Center, Univ. Tokyo, OCh 149
67770IAM 14593 <-- IFO 15278 <-- T. Shiba OCh149.
120634CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh149

doi: 10.13145/bacdive13764.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Roseobacter
  • species: Roseobacter litoralis
  • full scientific name: Roseobacter litoralis Shiba 1991

@ref: 2939

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseobacter

species: Roseobacter litoralis

full scientific name: Roseobacter litoralis Shiba 1991

type strain: yes

Morphology

cell morphology

  • @ref: 120634
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2939MEDIUM FOR ERYTHROBACTER LONGUS (DSMZ Medium 695)yeshttps://mediadive.dsmz.de/medium/695Name: MEDIUM FOR ERYTHROBACTER LONGUS (DSMZ Medium 695) Composition: Peptone 2.0 g/l Proteose peptone no. 3 1.0 g/l Yeast extract 1.0 g/l Soytone 1.0 g/l Fe(III) citrate 0.1 g/l Sea water Distilled water
2939BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
41077Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120634CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2939positivegrowth20psychrophilic
41077positivegrowth22psychrophilic
67770positivegrowth25mesophilic
120634positivegrowth5-30
120634nogrowth37mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12063417632nitrate-reduction
12063416301nitrite-reduction

antibiotic resistance

  • @ref: 120634
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6777030033bacteriochlorophyll ayes
12063435581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120634oxidase+
120634beta-galactosidase+3.2.1.23
120634alcohol dehydrogenase-1.1.1.1
120634gelatinase-
120634amylase-
120634catalase+1.11.1.6
120634tween esterase-
120634lysine decarboxylase-4.1.1.18
120634ornithine decarboxylase-4.1.1.17
120634urease+3.5.1.5

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2939-----+--------------+
2939-----+--------------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2939seaweedJapanJPNAsia
67770SeaweedJapanJPNAsia
120634SeaweedJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Aquatic plant
#Environmental#Aquatic
#Host#Algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_7769.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_252;97_275;98_5681;99_7769&stattab=map
  • Last taxonomy: Sulfitobacter
  • 16S sequence: X78312
  • Sequence Identity:
  • Total samples: 1124
  • soil counts: 18
  • aquatic counts: 1065
  • animal counts: 24
  • plant counts: 17

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29391Risk group (German classification)
1206341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.litoralis (ATCC 49566) gene for 16S ribosomal RNAX783121369ena391595
20218Roseobacter litoralis 16S rRNA gene, 23S rRNA gene and internal transcribed spacer (ITS), strain DSM 6996AJ012707984ena391595
20218Roseobacter litoralis strain NBRC15278 16S ribosomal RNA gene, partial sequenceDQ9156241307ena42443
2939Roseobacter litoralis strain Och 149 16S ribosomal RNA, partial sequenceNR_0275931369nuccore42443
67770Roseobacter litoralis gene for 16S ribosomal RNA, partial sequence, strain: JCM 21268LC0690371386ena42443

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseobacter litoralis Och 149391595.25plasmidpatric391595
66792Roseobacter litoralis Och 149391595.26plasmidpatric391595
66792Roseobacter litoralis Och 149391595.27plasmidpatric391595
67770Roseobacter litoralis Och 149GCA_000154785completencbi391595

GC content

  • @ref: 67770
  • GC-content: 57-57.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 2939

culture collection no.: DSM 6996, ATCC 49566, OCh 149, JCM 21268, CIP 104265, IAM 14593, IFO 15278, NBRC 15278, ATCC 46566

straininfo link

  • @ref: 82943
  • straininfo: 14629

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism15184132Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria.Pradella S, Allgaier M, Hoch C, Pauker O, Stackebrandt E, Wagner-Dobler IAppl Environ Microbiol10.1128/AEM.70.6.3360-3369.20042004Alphaproteobacteria/*genetics/metabolism, Bacterial Proteins/genetics/*metabolism, Chromosome Mapping, Electrophoresis, Gel, Pulsed-Field, *Genome, Bacterial, Light-Harvesting Protein Complexes/genetics/*metabolism, Molecular Sequence Data, Photosynthesis, Photosynthetic Reaction Center Complex Proteins/genetics/*metabolism, Phylogeny, Plasmids/genetics, Restriction Mapping, Rhodobacter sphaeroides, Roseobacter/genetics/metabolism, Sequence Analysis, DNAGenetics
Genetics21693016Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff TBMC Genomics10.1186/1471-2164-12-3242011Genome, Bacterial, Genomic Islands, Glycogen/metabolism, Metals, Heavy/metabolism, Molecular Sequence Data, Photosynthesis/genetics, Plasmids/chemistry/genetics, Roseobacter/*genetics/physiology, Species SpecificityMetabolism
Metabolism21908634Formation of polyhydroxyalkanoate in aerobic anoxygenic phototrophic bacteria and its relationship to carbon source and light availability.Xiao N, Jiao NAppl Environ Microbiol10.1128/AEM.05955-112011Aerobiosis, Bacteria/chemistry/*metabolism/ultrastructure, Carbon/*metabolism, DNA, Bacterial/chemistry/genetics, *Light, Magnetic Resonance Spectroscopy, Microscopy, Electron, Transmission, Molecular Sequence Data, *Photosynthesis, *Phototrophic Processes, Polyhydroxyalkanoates/*metabolism, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Metabolism23047149Proteomic responses of Roseobacter litoralis OCh149 to starvation and light regimen.Zong R, Jiao NMicrobes Environ10.1264/jsme2.me120292012Biological Transport/genetics, Carbohydrate Metabolism/*genetics, Carbon/metabolism, Gene Expression Regulation, Bacterial, Glucose/metabolism, Light, Pentose Phosphate Pathway/genetics, Phototrophic Processes/*genetics, Protein Biosynthesis/genetics, Proteome/*analysis, Proteomics, Roseobacter/*enzymology/*metabolism, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Starvation, Transcription, Genetic/geneticsGenetics
Phylogeny28671525Roseobacter ponti sp. nov., isolated from seawater.Jung YT, Park S, Lee JS, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0019222017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Roseobacter/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny32730197Roseobacter cerasinus sp. nov., isolated from a fish farm.Muramatsu S, Kanamuro M, Sato-Takabe Y, Hirose S, Muramatsu Y, Takaichi S, Hanada SInt J Syst Evol Microbiol10.1099/ijsem.0.0043602020*Aquaculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2939Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6996)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6996
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41077Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16154
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69479João 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
82943Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14629.1StrainInfo: A central database for resolving microbial strain identifiers
120634Curators of the CIPCollection of Institut Pasteur (CIP 104265)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104265