Strain identifier

BacDive ID: 23513

Type strain: Yes

Species: Humitalea rosea

Strain Designation: W37

Strain history: CIP <- 2011, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain W37, Acetobacteraceae sp.

NCBI tax ID(s): 990373 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.1 (current version)

General

@ref: 21247

BacDive-ID: 23513

DSM-Number: 24525

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

description: Humitalea rosea W37 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from petroleum-contaminated soil from a former military site.

NCBI tax id

  • NCBI tax id: 990373
  • Matching level: species

strain history

@refhistory
21247<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; W37
122250CIP <- 2011, R. Margesin, Innsbruck Univ., Innsbruck, Austria: strain W37, Acetobacteraceae sp.

doi: 10.13145/bacdive23513.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Humitalea
  • species: Humitalea rosea
  • full scientific name: Humitalea rosea Margesin and Zhang 2013

@ref: 21247

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Humitalea

species: Humitalea rosea

full scientific name: Humitalea rosea Margesin and Zhang 2013

strain designation: W37

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30722negative1.55 µm0.9 µmrod-shapedno
122250negativeoval-shapedno
69480negative98.804

colony morphology

  • @ref: 21247
  • incubation period: 8-14 days

pigmentation

  • @ref: 30722
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21247R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
122250CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperature
21247positivegrowth28
30722positivegrowth01-30

culture pH

  • @ref: 30722
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

  • @ref: 30722
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
30722NaClpositivegrowth0-3 %
30722NaClpositiveoptimum1 %

observation

  • @ref: 30722
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3072222599arabinose+carbon source
3072217234glucose+carbon source
3072224996lactate+carbon source
3072237684mannose+carbon source
3072253423tween 40+carbon source
3072253426tween 80+carbon source
12225017632nitrate-reduction
12225016301nitrite-reduction

metabolite production

  • @ref: 122250
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30722acid phosphatase+3.1.3.2
30722alkaline phosphatase+3.1.3.1
30722alpha-galactosidase+3.2.1.22
30722catalase+1.11.1.6
30722cytochrome oxidase+1.9.3.1
30722urease+3.5.1.5
122250oxidase+
122250catalase+1.11.1.6
122250urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122250--+--------+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
21247petroleum-contaminated soil from a former military siteSouth Tyrol, WelsbergItalyITAEurope
122250Environment, Soil from a former military site contaminated with petroleum hydrocarbons.Welsberg, south TyrolItalyITAEurope2010

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_105296.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_266;96_42383;97_54203;98_71663;99_105296&stattab=map
  • Last taxonomy: Humitalea rosea subclade
  • 16S sequence: HQ882802
  • Sequence Identity:
  • Total samples: 1238
  • soil counts: 641
  • aquatic counts: 329
  • animal counts: 168
  • plant counts: 100

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
212471Risk group (German classification)
1222501Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21247
  • description: Humitalea rosea strain W37 16S ribosomal RNA gene, partial sequence
  • accession: HQ882802
  • length: 1479
  • database: nuccore
  • NCBI tax ID: 990373

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Humitalea rosea DSM 24525GCA_003253705scaffoldncbi990373
66792Humitalea rosea strain DSM 24525990373.3wgspatric990373
66792Humitalea rosea DSM 245252734482251draftimg990373

GC content

@refGC-contentmethod
2124768.2high performance liquid chromatography (HPLC)
3072268.2

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.804no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.554yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.436yes
69480spore-formingspore-formingAbility to form endo- or exosporesno83.695no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.513yes
69480flagellatedmotile2+Ability to perform flagellated movementyes70.007no

External links

@ref: 21247

culture collection no.: DSM 24525, CIP 110261, LMG 26243

straininfo link

  • @ref: 87620
  • straininfo: 375107

literature

  • topic: Phylogeny
  • Pubmed-ID: 22821736
  • title: Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil.
  • authors: Margesin R, Zhang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.043018-0
  • year: 2012
  • mesh: Acetobacteraceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Italy, Molecular Sequence Data, Petroleum Pollution/analysis, *Phylogeny, Polyhydroxyalkanoates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thiosulfates/metabolism
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21247Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24525Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24525)
30722Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172705328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87620Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID375107.1
122250Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110261Collection of Institut Pasteur (CIP 110261)