Strain identifier

BacDive ID: 158487

Type strain: Yes

Species: Nitrosopumilus piranensis

Strain Designation: D3C

Strain history: G. J. Herndl; Univ. of Vienna, Austria; D3C.

NCBI tax ID(s): 1582439 (species)

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General

@ref: 65163

BacDive-ID: 158487

DSM-Number: 106147

keywords: genome sequence, 16S sequence, Archaea, aerobe, rod-shaped

description: Nitrosopumilus piranensis D3C is an aerobe, rod-shaped archaeon that was isolated from coastal surface water.

NCBI tax id

  • NCBI tax id: 1582439
  • Matching level: species

strain history

@refhistory
65163<- B. Bayer, Univ. Vienna, Austria; D3C
67770G. J. Herndl; Univ. of Vienna, Austria; D3C.

doi: 10.13145/bacdive158487.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/nitrososphaerota
  • domain: Archaea
  • phylum: Nitrososphaerota
  • class: Nitrososphaeria
  • order: Nitrosopumilales
  • family: Nitrosopumilaceae
  • genus: Nitrosopumilus
  • species: Nitrosopumilus piranensis
  • full scientific name: Nitrosopumilus piranensis Bayer et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Nitrosopumilus piranensis

@ref: 65163

domain: Archaea

phylum: Thaumarchaeota

class: Nitrososphaeria

order: Nitrosopumilales

family: Nitrosopumilaceae

genus: Nitrosopumilus

species: Nitrosopumilus piranensis

full scientific name: Nitrosopumilus piranensis Bayer et al. 2019

strain designation: D3C

type strain: yes

Morphology

cell morphology

  • @ref: 67883
  • cell length: 0.49-2 µm
  • cell width: 0.2-0.25 µm
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture temp

@refgrowthtypetemperature
67770positivegrowth30
67883positivegrowth15-37
67883positiveoptimum32

culture pH

@refabilitytypepH
67883positivegrowth6.8-8
67883positiveoptimum7.1-7.3

Physiology and metabolism

tolerance

@refcompoundconcentration
67883Ammonia30.0 mM
67883Nitrite15.0 mM

oxygen tolerance

  • @ref: 67883
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 99

halophily

@refsaltgrowthtested relationconcentration
67883NaClpositivegrowth15-65 %
67883NaClpositiveoptimum37 %

observation

@refobservation
67770quinones: MK-6
67883The minimum generation time is approximately 27 h.

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
678836104kanamycinyesyes100 µg/mL
6788317076streptomycinyesyes100 µg/mL
678839215spectinomycinyesyes100 µg/mL
678833393carbenicillinyesyes100 µg/mL
6788348923erythromycinyesyes50 µg/mL
678837731ofloxacinyesyes50 µg/mL
6788317698chloramphenicolyesyes25 µg/mL
6788327902tetracyclineyesyes25 µg/mL

enzymes

  • @ref: 67883
  • value: urease
  • activity: +
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
65163coastal surface waterNorthern Adriatic SeaSloveniaSVNEurope45.51813.5679
67770Northern Adriatic coastal surface water sampled off PiranSloveniaSVNEurope
67883coastal surface water (0.5m depth)Northern Adriatic Sea, coast of PiranSloveniaSVNEurope45.51813.5682011-12

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_187103.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17653;96_68790;97_89432;98_121702;99_187103&stattab=map
  • Last taxonomy: Nitrosopumilus
  • 16S sequence: MK139956
  • Sequence Identity:
  • Total samples: 3133
  • soil counts: 75
  • aquatic counts: 3053
  • animal counts: 2
  • plant counts: 3

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Nitrosopumilus piranensis strain D3C, complete genomeCP0108681713078nuccore1582439
67883Nitrosopumilus piranensis strain D3C 16S ribosomal RNA gene, partial sequenceMK1399561471nuccore1582439

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitrosopumilus piranensis D3C2627853696completeimg1582439
67883Nitrosopumilus piranensis D3CGCA_000875775completencbi1582439

GC content

@refGC-contentmethod
6516333.8sequence analysis
6788333.8genome sequence analysis

Genome-based predictions

predictions

  • @ref: 69481
  • trait: spore-forming
  • model: spore-forming
  • description: Ability to form endo- or exospores
  • prediction: no
  • confidence: 99
  • training_data: no

External links

@ref: 65163

culture collection no.: DSM 106147, JCM 32271, NCIMB 15115

straininfo link

  • @ref: 111282
  • straininfo: 398956

literature

  • topic: Phylogeny
  • Pubmed-ID: 30938665
  • title: Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria.
  • authors: Bayer B, Vojvoda J, Reinthaler T, Reyes C, Pinto M, Herndl GJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003360
  • year: 2019
  • mesh: Ammonia/*metabolism, Archaea/*classification/isolation & purification, Base Composition, DNA, Archaeal/genetics, Glyceryl Ethers/chemistry, Hydrogen Peroxide, Oceans and Seas, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
65163Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106147Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106147)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67883Barbara Bayer, Jana Vojvoda, Thomas Reinthaler, Carolina Reyes, Maria Pinto, Gerhard J. HerndlNitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria10.1099/ijsem.0.003360IJSEM 69: 1892-1902 2019
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/
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
111282Reimer, 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-ID398956.1