Strain identifier

BacDive ID: 5381

Type strain: Yes

Species: Erythrobacter litoralis

Strain Designation: T4

Strain history: CIP <- 2001, IAM <- DSMZ <- V. Yurkov: strain T4

NCBI tax ID(s): 39960 (species)

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General

@ref: 3290

BacDive-ID: 5381

DSM-Number: 8509

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, mesophilic, Gram-negative, motile, rod-shaped

description: Erythrobacter litoralis T4 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from cyanobacterial mat.

NCBI tax id

  • NCBI tax id: 39960
  • Matching level: species

strain history

@refhistory
3290<- V. Yurkov, T4
120629CIP <- 2001, IAM <- DSMZ <- V. Yurkov: strain T4

doi: 10.13145/bacdive5381.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Erythrobacter
  • species: Erythrobacter litoralis
  • full scientific name: Erythrobacter litoralis Yurkov et al. 1994

@ref: 3290

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Erythrobacter

species: Erythrobacter litoralis

full scientific name: Erythrobacter litoralis Yurkov et al. 1994

strain designation: T4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23246negative1.0-1.3 µm0.2-0.3 µmrod-shapedyesmonotrichous, polar
69480negative99.975
120629negativerod-shapedyes

colony morphology

  • @ref: 23246
  • colony color: red to orange

pigmentation

@refproductionname
23246yesBacteriochlorophyll a
23246yescarotenoids
23246yesBacteriorubixanthinal
23246yesErythroxanthin sulfate

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3290ERYTHROMICROBIUM AND ROSEOCOCCUS MEDIUM (DSMZ Medium 767)yeshttps://mediadive.dsmz.de/medium/767Name: ERYTHROMICROBIUM AND ROSEOCOCCUS MEDIUM (DSMZ Medium 767) Composition: Yeast extract 1.0 g/l Na-acetate 1.0 g/l Bacto peptone 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.3 g/l NH4Cl 0.3 g/l KCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Vitamin B12 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
37251Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120629CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
3290positivegrowth28mesophilic
23246positiveoptimum25-30mesophilic
37251positivegrowth25mesophilic
120629positivegrowth25-41
120629nogrowth5psychrophilic
120629nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23246aerobe
120629obligate aerobe

nutrition type

  • @ref: 23246
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.973

halophily

  • @ref: 23246
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5-9.6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2324617790methanol-growth
232465291gelatin-hydrolysis
2324628017starch-hydrolysis
2324617632nitrate-reduction
2324630089acetate+growth
2324617968butyrate+growth
2324628757fructose+growth
2324617234glucose+growth
2324629987glutamate+growth
2324624996lactate+growth
2324653426tween 80+hydrolysis
2324630031succinate+/-growth
1206294853esculin-hydrolysis
120629606565hippurate+hydrolysis
12062917632nitrate-reduction
12062916301nitrite-reduction
12062915792malonate-assimilation
12062917632nitrate-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
232468309polymyxin byesyes100 Unit (disc)
2324617334penicillinyesyes20 Unit (disc)
2324617076streptomycinyesyes50 µg (disc)
2324671321fusidateyesyes0.5 µg (disc)
2324617698chloramphenicolyesyes100 µg (disc)
2324627902tetracyclineyesyes

metabolite production

  • @ref: 120629
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23246catalase+1.11.1.6
23246cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120629oxidase+
120629beta-galactosidase-3.2.1.23
120629alcohol dehydrogenase-1.1.1.1
120629gelatinase+/-
120629amylase-
120629caseinase-3.4.21.50
120629catalase+1.11.1.6
120629gamma-glutamyltransferase+2.3.2.2
120629lecithinase-
120629lipase-
120629lysine decarboxylase-4.1.1.18
120629ornithine decarboxylase-4.1.1.17
120629phenylalanine ammonia-lyase-4.3.1.24
120629protease-
120629tryptophan deaminase-
120629urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120629-+++-+++++++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3290cyanobacterial matTexelNetherlandsNLDEurope
23246marine cyanobacterial mat in a supralitoral zone
120629Cyanobacterial matNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Microbial community#Microbial mat
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_4108.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_274;98_2709;99_4108&stattab=map
  • Last taxonomy: Erythrobacter litoralis
  • 16S sequence: AF465836
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 2
  • aquatic counts: 38
  • animal counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32901Risk group (German classification)
1206291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erythrobacter litoralis gene for 16S rRNAAB0133541408ena39960
20218Erythrobacter litoralis strain DSM 8509 16S ribosomal RNA gene, partial sequenceAF4658361413ena39960

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erythrobacter litoralis DSM 8509GCA_001719165completencbi39960
66792Erythrobacter litoralis DSM 8509GCA_000714795contigncbi39960
66792Erythrobacter litoralis strain DSM 850939960.10completepatric39960
66792Erythrobacter litoralis strain DSM 850939960.13completepatric39960
66792Erythrobacter litoralis strain DSM 850939960.3wgspatric39960
66792Erythrobacter litoralis DSM 85092811995009completeimg39960
66792Erythrobacter litoralis DSM 85092585427957draftimg39960

GC content

  • @ref: 23246
  • GC-content: 67
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno89.684no
gram-positiveno96.809yes
anaerobicno99.274yes
aerobicyes94.34yes
halophileno71.993no
spore-formingno93.857no
glucose-utilyes78.172no
thermophileno90.782yes
motileyes67.201yes
glucose-fermentno91.698no

External links

@ref: 3290

culture collection no.: DSM 8509, IAM 14332, CIP 106926

straininfo link

  • @ref: 74871
  • straininfo: 93007

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361270Erythrobacter citreus sp. nov., a yellow-pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea.Denner EBM, Vybiral D, Koblizek M, Kampfer P, Busse HJ, Velimirov BInt J Syst Evol Microbiol10.1099/00207713-52-5-16552002Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Mediterranean Sea, Molecular Sequence Data, Phenotype, Phylogeny, Pigmentation, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyGenetics
Phylogeny19671726Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater.Lee YS, Lee DH, Kahng HY, Kim EM, Jung JSInt J Syst Evol Microbiol10.1099/ijs.0.015743-02009Anti-Bacterial Agents/pharmacology, Base Sequence, DNA Primers, Enzymes/metabolism, Fatty Acids/analysis, Likelihood Functions, Molecular Sequence Data, Phylogeny, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/chemistry/genetics, Republic of Korea, Seawater/*microbiology, Sequence Homology, Nucleic Acid, Sphingomonadaceae/classification/drug effects/*genetics/isolation & purification/metabolismEnzymology
Phylogeny23241657Erythrobacter westpacificensis sp. nov., a marine bacterium isolated from the Western Pacific.Wei J, Mao Y, Zheng Q, Zhang R, Wang YN, Jiao NCurr Microbiol10.1007/s00284-012-0287-02012Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Pacific Ocean, Phospholipids/analysis, Phylogeny, Pigments, Biological, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/chemistry/*classification/genetics/*isolation & purificationGenetics
Genetics25059862Draft Genome Sequences of Two Marine Phototrophic Bacteria, Erythrobacter longus Strain DSM 6997 and Erythrobacter litoralis Strain DSM 8509.Wang Y, Zhang R, Zheng Q, Jiao NGenome Announc10.1128/genomeA.00677-142014
Phylogeny28592325Isolation and characterization of the first phage infecting ecologically important marine bacteria Erythrobacter.Lu L, Cai L, Jiao N, Zhang RVirol J10.1186/s12985-017-0773-x2017Aquatic Organisms/*virology, Bacteriophages/*classification/genetics/*isolation & purification/ultrastructure, China, Microscopy, Electron, Transmission, Molecular Sequence Annotation, Pacific Ocean, Sequence Analysis, DNA, Sphingomonadaceae/*virology, Viral Proteins/genetics, Water Microbiology, Whole Genome SequencingTranscriptome
Metabolism31120626Shining light on the alphaproteobacterial general stress response: Comment on: Fiebig et al., Mol Microbiol, 2019.Dikiy I, Gardner KHMol Microbiol10.1111/mmi.143112019Alphaproteobacteria/genetics/*metabolism/*radiation effects, Bacterial Proteins/genetics/*metabolism, Gene Expression Regulation, Bacterial/radiation effects, Histidine Kinase/genetics/metabolism, Light, Sigma Factor/genetics/*metabolism, Signal Transduction/radiation effects, Stress, PhysiologicalStress
Metabolism31125464Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light.Fiebig A, Varesio LM, Alejandro Navarreto X, Crosson SMol Microbiol10.1111/mmi.143102019Bacterial Proteins/genetics/*metabolism, Gene Expression Regulation, Bacterial/radiation effects, Light, Phototrophic Processes, Protein Kinases/genetics/*metabolism, Sigma Factor/genetics/metabolism, Sphingomonadaceae/*enzymology/genetics/metabolism/*radiation effects, Stress, Physiological/radiation effectsStress
35620087The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus.Li X, Guo R, Zou X, Yao Y, Lu LFront Microbiol10.3389/fmicb.2022.8617932022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3290Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8509)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8509
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
23246VLADIMIR YURKOV, ERKO STACKEBRANDT, ANDREW HOLMES, JOHN A. FUERST, P. HUGENHOLTZ, JOCHEN GOLECKI, NASSER GAD'ON, VLADIMIR M. GORLENKO, ELENA I. KOMPANTSEVA, GERHART DREWS10.1099/00207713-44-3-427Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll a-Containing Bacteria and Description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov.IJSEM 44: 427-434 19947520734
37251Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19110
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74871Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93007.1StrainInfo: A central database for resolving microbial strain identifiers
120629Curators of the CIPCollection of Institut Pasteur (CIP 106926)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106926