Strain identifier

BacDive ID: 140252

Type strain: Yes

Species: Advenella kashmirensis subsp. methylica

Strain Designation: PK1

Strain history: <- N. V. Doronina, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; PK1

NCBI tax ID(s): 1439717 (subspecies)

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

@ref: 42859

BacDive-ID: 140252

DSM-Number: 27514

keywords: 16S sequence, Bacteria, mesophilic

description: Advenella kashmirensis subsp. methylica PK1 is a mesophilic bacterium that was isolated from root of Carex L. sp..

NCBI tax id

  • NCBI tax id: 1439717
  • Matching level: subspecies

strain history

  • @ref: 42859
  • history: <- N. V. Doronina, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; PK1

doi: 10.13145/bacdive140252.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Advenella
  • species: Advenella kashmirensis subsp. methylica
  • full scientific name: Advenella kashmirensis subsp. methylica Shmareva et al. 2017

@ref: 42859

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Advenella

species: Advenella kashmirensis subsp. methylica

full scientific name: Advenella kashmirensis subsp. methylica Shmareva et al. 2017

strain designation: PK1

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 42859
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

  • @ref: 42859
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-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
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
42859----+---+++/----++/-+++-

Isolation, sampling and environmental information

isolation

  • @ref: 42859
  • sample type: root of Carex L. sp.
  • host species: Carex
  • geographic location: Pamukkale
  • country: Turkey
  • origin.country: TUR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1770.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1003;97_1169;98_1397;99_1770&stattab=map
  • Last taxonomy: Advenella
  • 16S sequence: KF683075
  • Sequence Identity:
  • Total samples: 2457
  • soil counts: 822
  • aquatic counts: 378
  • animal counts: 766
  • plant counts: 491

Safety information

risk assessment

  • @ref: 42859
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42859
  • description: Advenella kashmirensis subsp. methylica strain PK1 16S ribosomal RNA gene, partial sequence
  • accession: KF683075
  • length: 1415
  • database: ena
  • NCBI tax ID: 1439717

External links

@ref: 42859

culture collection no.: DSM 27514, VKM B-2850

straininfo link

  • @ref: 96560
  • straininfo: 398117

literature

  • topic: Phylogeny
  • Pubmed-ID: 25916151
  • title: [Advenella kashmirensis subsp. methylica PK1, a facultative methylotroph from carex rhizosphere].
  • authors: Poroshina MN, Doronina NV, Kaparullina EN, Trotsenko IuA
  • journal: Mikrobiologiia
  • year: 2015
  • mesh: Alcaligenaceae/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition, Cyperus/microbiology, DNA, Bacterial/chemistry/*genetics, Fatty Acids/metabolism, Hydrogen-Ion Concentration, Metabolic Networks and Pathways, Methanol/metabolism, Methylobacterium/*classification/genetics/isolation & purification/*metabolism, Phospholipids/metabolism, *Phylogeny, RNA, Ribosomal, 16S/chemistry/*genetics, Rhizosphere, Sequence Analysis, DNA, Temperature, Turkey
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogue
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
42859Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27514Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27514)
68369Automatically annotated from API 20NE
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/
96560Reimer, 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-ID398117.1