Strain identifier

BacDive ID: 5382

Type strain: Yes

Species: Qipengyuania citrea

Strain Designation: RE35F/1

Strain history: CIP <- 2001, E.B.M. Denner, Inst. Mikrobiol. Genetik, Vienna, Austria: strain RE35F/1 <- D. Vybiral

NCBI tax ID(s): 225971 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5351

BacDive-ID: 5382

DSM-Number: 14432

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

description: Qipengyuania citrea RE35F/1 is a psychrophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 225971
  • Matching level: species

strain history

@refhistory
5351<- E. B. M. Denner; RE35F/1 <- D. Vybiral
67770IAM 15372 <-- KCTC 12214 <-- CIP 107092 <-- E. B. M. Denner RE35F/1 <-- D. Vybiral.
118302CIP <- 2001, E.B.M. Denner, Inst. Mikrobiol. Genetik, Vienna, Austria: strain RE35F/1 <- D. Vybiral

doi: 10.13145/bacdive5382.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Qipengyuania
  • species: Qipengyuania citrea
  • full scientific name: Qipengyuania citrea (Denner et al. 2002) Xu et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Erythrobacter citreus

@ref: 5351

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Erythrobacter

species: Erythrobacter citreus

full scientific name: Erythrobacter citreus Denner et al. 2002

strain designation: RE35F/1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.992
118302negativeoval-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5351BACTO 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
38663Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118302CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5351positivegrowth20psychrophilic
38663positivegrowth25mesophilic
67770positivegrowth25mesophilic
118302positivegrowth25-37mesophilic
118302nogrowth5psychrophilic
118302nogrowth15psychrophilic
118302nogrowth41thermophilic
118302nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.984

halophily

@refsaltgrowthtested relationconcentration
118302NaClnogrowth0 %
118302NaClnogrowth2 %
118302NaClnogrowth4 %
118302NaClnogrowth6 %
118302NaClnogrowth8 %
118302NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11830216947citrate-carbon source
1183024853esculin-hydrolysis
118302606565hippurate+hydrolysis
11830217632nitrate-builds gas from
11830217632nitrate-reduction
11830216301nitrite-builds gas from
11830216301nitrite-reduction
11830215792malonate-assimilation
11830217234glucose-degradation
11830217632nitrate-respiration

metabolite production

  • @ref: 118302
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11830215688acetoin-
11830217234glucose-

enzymes

@refvalueactivityec
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
118302oxidase+
118302beta-galactosidase-3.2.1.23
118302alcohol dehydrogenase-1.1.1.1
118302gelatinase-
118302amylase-
118302caseinase-3.4.21.50
118302catalase+1.11.1.6
118302tween esterase+
118302gamma-glutamyltransferase+2.3.2.2
118302lecithinase-
118302lipase-
118302lysine decarboxylase-4.1.1.18
118302ornithine decarboxylase-4.1.1.17
118302phenylalanine ammonia-lyase-4.3.1.24
118302protease-
118302tryptophan deaminase-
118302urease-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
118302-+++-+++--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5351seawaterCorsica, Bay of CalviFranceFRAEurope
67770Western Mediterranean Sea
118302Environment, SeawaterCorsicaFranceFRAEurope1994

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_361.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_274;98_305;99_361&stattab=map
  • Last taxonomy: Qipengyuania
  • 16S sequence: AF118020
  • Sequence Identity:
  • Total samples: 563
  • soil counts: 28
  • aquatic counts: 489
  • animal counts: 32
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53511Risk group (German classification)
1183021Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5351Erythrobacter citreus strain RE35F/1 16S ribosomal RNA gene, partial sequenceAF1180201444ena225971
67770Erythrobacter citreus 16S ribosomal RNA gene, partial sequenceAF2272591359ena225971

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erythrobacter citreus strain CGMCC 1.8703225971.7wgspatric225971
66792Erythrobacter citreus DSM 144322928592673draftimg225971
67770Qipengyuania citrea CGMCC 1.8703GCA_009828015contigncbi225971

GC content

@refGC-contentmethod
535162.0-62.4high performance liquid chromatography (HPLC)
6777064.2genome sequence analysis
6777062high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno87.261no
gram-positiveno96.467no
anaerobicno99.198no
aerobicyes95.583no
halophileno82.897no
spore-formingno92.858no
glucose-utilyes83.585no
flagellatedno96.969no
thermophileno97.567no
glucose-fermentno92.654no

External links

@ref: 5351

culture collection no.: DSM 14432, CIP 107092, JCM 21816, CGMCC 1.8703, CGMCC 1.8709, IAM 15372, KCTC 12214

straininfo link

  • @ref: 74872
  • straininfo: 100645

literature

  • topic: Phylogeny
  • Pubmed-ID: 34047831
  • title: Qipengyuania soli sp. nov., Isolated from Mangrove Soil.
  • authors: Liu Y, Pei T, Deng MR, Zhu H
  • journal: Curr Microbiol
  • DOI: 10.1007/s00284-021-02538-1
  • year: 2021
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, *Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitle
5351Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14432)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14432
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
38663Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19294
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/
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
74872Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100645.1StrainInfo: A central database for resolving microbial strain identifiers
118302Curators of the CIPCollection of Institut Pasteur (CIP 107092)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107092