Strain identifier

BacDive ID: 132947

Type strain: Yes

Species: Massilia eurypsychrophila

Strain Designation: B528-3

Strain history: Y. Liu B528-3.

NCBI tax ID(s): 1485217 (species)

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General

@ref: 24735

BacDive-ID: 132947

DSM-Number: 104958

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile

description: Massilia eurypsychrophila B528-3 is a psychrophilic, motile bacterium that was isolated from ice core from glacier.

NCBI tax id

  • NCBI tax id: 1485217
  • Matching level: species

strain history

@refhistory
24735<- JCM; JCM 30074 <- Y. Liu, Chinese Acad. Sci. (CAS), Beijing; B528-3
67770Y. Liu B528-3.

doi: 10.13145/bacdive132947.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Massilia
  • species: Massilia eurypsychrophila
  • full scientific name: Massilia eurypsychrophila Shen et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Mokoshia eurypsychrophila

@ref: 24735

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia eurypsychrophila

full scientific name: Massilia eurypsychrophila Shen et al. 2015

strain designation: B528-3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes95.742
6948099.995negative

Culture and growth conditions

culture medium

  • @ref: 24735
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
24735positivegrowth15psychrophilic
67770positivegrowth10psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.994

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24735-----+-------+---++/--+
24735-----+-------+------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24735ice core (163 m) from glacierMuztagh Glacier, XinjiangChinaCHNAsia36.066787.05
67770Ice core drilled from Muztagh GlacierXinjiangChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 24735
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24735
  • description: Massilia eurypsychrophila strain B528-3 16S ribosomal RNA gene, partial sequence
  • accession: KJ361504
  • length: 1434
  • database: ena
  • NCBI tax ID: 1485217

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Massilia eurypsychrophila strain JCM 300741485217.3wgspatric1485217
66792Massilia eurypsychrophila JCM 300742791355051draftimg1485217
67770Massilia eurypsychrophila JCM 30074GCA_002760655contigncbi1485217

GC content

  • @ref: 24735
  • GC-content: 62.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.832no
gram-positiveno98.728no
anaerobicno98.619no
aerobicyes91.819no
halophileno95.598no
spore-formingno92.63no
glucose-utilno54.712yes
flagellatedyes76.92no
thermophileno99.623no
glucose-fermentno92.924yes

External links

@ref: 24735

culture collection no.: DSM 104958, CGMCC 1.12828, JCM 30074, CCM 8735

straininfo link

  • @ref: 91224
  • straininfo: 398497

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25851590Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core.Shen L, Liu Y, Gu Z, Xu B, Wang N, Jiao N, Liu H, Zhou YInt J Syst Evol Microbiol10.1099/ijs.0.0002292015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ice, Ice Cover/*microbiology, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27432318Massilia psychrophila sp. nov., isolated from an ice core.Guo B, Liu Y, Gu Z, Shen L, Liu K, Wang N, Xing T, Liu H, Zhou Y, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0013152016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28901899Massilia glaciei sp. nov., isolated from the Muztagh Glacier.Gu Z, Liu Y, Xu B, Wang N, Jiao N, Shen L, Liu H, Zhou Y, Liu X, Li J, Sun JInt J Syst Evol Microbiol10.1099/ijsem.0.0022522017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny29851375Massilia violaceinigra sp. nov., a novel purple-pigmented bacterium isolated from glacier permafrost.Wang H, Zhang X, Wang S, Zhao B, Lou K, Xing XHInt J Syst Evol Microbiol10.1099/ijsem.0.0028262018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Permafrost/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny31140962Massilia atriviolacea sp. nov., a dark purple-pigmented bacterium isolated from soil.Yang E, Zhao M, Li S, Wang Y, Sun L, Liu J, Wang WInt J Syst Evol Microbiol10.1099/ijsem.0.0034492019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny33864512Massilia aromaticivorans sp. nov., a BTEX Degrading Bacterium Isolated from Arctic Soil.Son J, Lee H, Kim M, Kim DU, Ka JOCurr Microbiol10.1007/s00284-021-02379-y2021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, Nucleic Acid Hybridization, Oxalobacteraceae, *Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SoilTranscriptome
Phylogeny35119982Massilia soli sp. nov., isolated from soil.Baek JH, Baek W, Ruan W, Jung HS, Lee SC, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0052272022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24735Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104958Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104958)
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/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
91224Reimer, 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-ID398497.1