Strain identifier

BacDive ID: 140090

Type strain: Yes

Species: Methylobrevis pamukkalensis

Strain Designation: PK2

Strain history: N. V. Doronina; G. K. Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia; PK2.

NCBI tax ID(s): 1439726 (species)

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General

@ref: 42697

BacDive-ID: 140090

DSM-Number: 29599

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Methylobrevis pamukkalensis PK2 is an aerobe, mesophilic bacterium that was isolated from water of a saline hotspring.

NCBI tax id

  • NCBI tax id: 1439726
  • Matching level: species

strain history

@refhistory
42697<- N. V. Doronina, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; PK2
67770N. V. Doronina; G. K. Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia; PK2.

doi: 10.13145/bacdive140090.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Pleomorphomonadaceae
  • genus: Methylobrevis
  • species: Methylobrevis pamukkalensis
  • full scientific name: Methylobrevis pamukkalensis Poroshina et al. 2015

@ref: 42697

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Pleomorphomonadaceae

genus: Methylobrevis

species: Methylobrevis pamukkalensis

full scientific name: Methylobrevis pamukkalensis Poroshina et al. 2015

strain designation: PK2

type strain: yes

Morphology

colony morphology

  • @ref: 63223
  • incubation period: 5 days

Culture and growth conditions

culture medium

  • @ref: 42697
  • name: MEDIUM K (DSMZ Medium 1122)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1122
  • composition: Name: MEDIUM K (DSMZ Medium 1122) Composition: Agar 20.0 g/l KH2PO4 2.0 g/l (NH4)2SO4 2.0 g/l NaCl 0.5 g/l MgSO4 x 7 H2O 0.125 g/l FeSO4 x 7 H2O 0.002 g/l Methanol Distilled water

culture temp

@refgrowthtypetemperature
63223positivegrowth30
42697positivegrowth28
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
63223aerobe
125439obligate aerobe98.1

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
42697water of a saline hotspringDenizli, Hierapolis, PamukkaleTurkeyTURAsia
63223Saline waterPamukkaleTurkeyTURAsia2011-10-15
67770Saline hot spring of the PamukkaleHierapolis, DenizliTurkeyTURAsia

isolation source categories

Cat1Cat2Cat3
#Condition#Saline
#Condition#Thermophilic (>45°C)
#Environmental#Aquatic#Thermal spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_61851.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_15595;97_34065;98_43870;99_61851&stattab=map
  • Last taxonomy: Methylobrevis pamukkalensis subclade
  • 16S sequence: KF683074
  • Sequence Identity:
  • Total samples: 1118
  • soil counts: 403
  • aquatic counts: 337
  • animal counts: 299
  • plant counts: 79

Safety information

risk assessment

  • @ref: 42697
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42697
  • description: Methylobrevis pamukkalensis strain PK2 16S ribosomal RNA gene, partial sequence
  • accession: KF683074
  • length: 1367
  • database: nuccore
  • NCBI tax ID: 1439726

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobrevis pamukkalensis PK2GCA_001720135contigncbi1439726
66792Methylobrevis pamukkalensis PK22786546839draftimg1439726

GC content

  • @ref: 42697
  • GC-content: 67.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesno87.8
125439BacteriaNetmotilityAbility to perform movementyes64.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative76.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.1

External links

@ref: 42697

culture collection no.: DSM 29599, JCM 30229, VKM B-2849, CCUG 65431

straininfo link

@refstraininfo
96502397290
96503410101

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25667389Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water.Poroshina MN, Trotsenko YA, Doronina NVInt J Syst Evol Microbiol10.1099/ijs.0.0001052015Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, Hydroxybutyrates/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Turkey, Ubiquinone/chemistryGenetics
Phylogeny34152426Methylobrevis albus sp. nov., isolated from freshwater lake sediment.Zou QH, Feng X, Wang TJ, Du ZJArch Microbiol10.1007/s00203-021-02442-z2021*Alphaproteobacteria/classification/genetics, China, Fatty Acids/analysis, *Geologic Sediments/microbiology, *Lakes, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity

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
42697Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29599Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29599)
63223Curators of the CCUGhttps://www.ccug.se/strain?id=65431Culture Collection University of Gothenburg (CCUG) (CCUG 65431)
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/
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/
96502Reimer, 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-ID397290.1
96503Reimer, 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-ID410101.1
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG