Strain identifier

BacDive ID: 3811

Type strain: Yes

Species: Hymenobacter psychrophilus

Strain Designation: BZ33r

Strain history: CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck, Autria: strain BZ33r

NCBI tax ID(s): 651662 (species)

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General

@ref: 16177

BacDive-ID: 3811

DSM-Number: 22290

keywords: 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, rod-shaped

description: Hymenobacter psychrophilus BZ33r is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from soil with high levels of heavy oil and heavy metals from an industrial site.

NCBI tax id

  • NCBI tax id: 651662
  • Matching level: species

strain history

@refhistory
364302010, R. Margesin, Innsbruck Univ., Innsbruck, Autria: strain BZ33r
16177<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; BZ33r
122030CIP <- 2010, R. Margesin, Innsbruck Univ., Innsbruck, Autria: strain BZ33r

doi: 10.13145/bacdive3811.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter psychrophilus
  • full scientific name: Hymenobacter psychrophilus Zhang et al. 2011

@ref: 16177

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter psychrophilus

full scientific name: Hymenobacter psychrophilus Zhang et al. 2011

strain designation: BZ33r

type strain: yes

Morphology

cell morphology

  • @ref: 122030
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16177NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36430MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122030CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
16177positivegrowth20psychrophilic
36430positivegrowth20psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122030
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12203017632nitrate-reduction
12203016301nitrite-reduction

metabolite production

  • @ref: 122030
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
122030oxidase-
122030catalase+1.11.1.6
122030urease-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
122030-++--+---+++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16177soil with high levels of heavy oil and heavy metals from an industrial siteSouth Tyrol, BozenItalyITAEurope
122030Environment, SoilTyrolItalyITAEurope2008

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Heavy metal
#Engineered#Contamination#Oil (Fuel)
#Engineered#Waste#Industrial waste
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_20463.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_10398;97_12570;98_15474;99_20463&stattab=map
  • Last taxonomy: Hymenobacter psychrophilus
  • 16S sequence: GQ131579
  • Sequence Identity:
  • Total samples: 105
  • soil counts: 82
  • aquatic counts: 7
  • animal counts: 15
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
161771Risk group (German classification)
1220301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16177
  • description: Hymenobacter psychrophilus strain BZ33r 16S ribosomal RNA gene, partial sequence
  • accession: GQ131579
  • length: 1511
  • database: ena
  • NCBI tax ID: 651662

GC content

  • @ref: 16177
  • GC-content: 61.6
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 16177

culture collection no.: DSM 22290, CIP 110132, CGMCC 1.8975

straininfo link

  • @ref: 73322
  • straininfo: 368628

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20495040Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil.Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.023465-02010Aerobiosis, Base Composition, Cluster Analysis, Cold Temperature, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny30587382Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica.Sedlacek I, Pantucek R, Kralova S, Maslanova I, Holochova P, Stankova E, Vrbovska V, Svec P, Busse HJSyst Appl Microbiol10.1016/j.syapm.2018.12.0042018Antarctic Regions, Bacteroidetes/chemistry/*classification/genetics/*physiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Bacterial/genetics, Lipids/analysis, Phylogeny, Pigmentation, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitle
16177Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22290)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22290
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
36430Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7956
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
73322Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID368628.1StrainInfo: A central database for resolving microbial strain identifiers
122030Curators of the CIPCollection of Institut Pasteur (CIP 110132)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110132