Strain identifier

BacDive ID: 11307

Type strain: Yes

Species: Herminiimonas glaciei

Strain Designation: UMB49

Strain history: <- J. Loveland-Curtze, Pennsylvania University <- V. I. Miteva, Pennsylvania University

NCBI tax ID(s): 523788 (species)

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

@ref: 15563

BacDive-ID: 11307

DSM-Number: 21140

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

description: Herminiimonas glaciei UMB49 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from ice core of Greenland Glacier at 3042 m depth.

NCBI tax id

  • NCBI tax id: 523788
  • Matching level: species

strain history

  • @ref: 15563
  • history: <- J. Loveland-Curtze, Pennsylvania University <- V. I. Miteva, Pennsylvania University

doi: 10.13145/bacdive11307.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herminiimonas
  • species: Herminiimonas glaciei
  • full scientific name: Herminiimonas glaciei Loveland-Curtze et al. 2009

@ref: 15563

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herminiimonas

species: Herminiimonas glaciei

full scientific name: Herminiimonas glaciei Loveland-Curtze et al. 2009

strain designation: UMB49

type strain: yes

Morphology

cell morphology

  • @ref: 28924
  • gram stain: negative
  • cell length: 0.7 µm
  • cell width: 0.35 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 28924
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15563
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15563positivegrowth28mesophilic
28924positivegrowth01-35
28924positiveoptimum30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 28924
  • oxygen tolerance: aerobe

spore formation

  • @ref: 28924
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2892416449alanine+carbon source
2892422599arabinose+carbon source
2892416947citrate+carbon source
2892433984fucose+carbon source
2892428260galactose+carbon source
2892424996lactate+carbon source
2892425115malate+carbon source
2892433942ribose+carbon source
2892430031succinate+carbon source
2892418222xylose+carbon source

enzymes

@refvalueactivityec
28924catalase+1.11.1.6
28924cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
15563ice core of Greenland Glacier at 3042 m depthGreenlandGRLNorth America
62136Ice core of Greenland glacier at 3042 m depthGreenlandGRLNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Aquatic#Ice
#Environmental#Terrestrial#Core sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_5056.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_2343;97_2853;98_3549;99_5056&stattab=map
  • Last taxonomy: Herminiimonas
  • 16S sequence: EU489741
  • Sequence Identity:
  • Total samples: 2485
  • soil counts: 780
  • aquatic counts: 491
  • animal counts: 395
  • plant counts: 819

Safety information

risk assessment

  • @ref: 15563
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15563
  • description: Herminiimonas glaciei strain UMB49 16S ribosomal RNA gene, partial sequence
  • accession: EU489741
  • length: 1434
  • database: ena
  • NCBI tax ID: 523788

GC content

@refGC-contentmethod
1556359.0thermal denaturation, midpoint method (Tm)
2892459

External links

@ref: 15563

culture collection no.: DSM 21140, ATCC BAA 1623, CCUG 59859

straininfo link

  • @ref: 80540
  • straininfo: 408231

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502300Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice.Loveland-Curtze J, Miteva VI, Brenchley JEInt J Syst Evol Microbiol10.1099/ijs.0.001685-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genotype, Greenland, *Ice, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny20370834Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov.Sahin N, Gonzalez JM, Iizuka T, Hill JEFEMS Microbiol Lett10.1111/j.1574-6968.2010.01954.x2010Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Chaperones/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny22447701Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals.Kampfer P, P Glaeser S, Lodders N, Busse HJ, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.039073-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, *Drug Contamination, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny29101383Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans.Koh HW, Hur M, Kang MS, Ku YB, Ghai R, Park SJSci Rep10.1038/s41598-017-15164-42017Bacterial Typing Techniques, DNA, Bacterial/*genetics, Oxalobacteraceae/genetics/*physiology, *Phylogeny, *RNA, Ribosomal, 16S

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15563Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21140
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
28924Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2536328776041
62136Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59859)https://www.ccug.se/strain?id=59859
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
80540Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408231.1StrainInfo: A central database for resolving microbial strain identifiers