Strain identifier

BacDive ID: 157948

Type strain: Yes

Species: Nitrosopumilus adriaticus

Strain Designation: NF5

Strain history: G. J. Herndl; Univ. of Vienna, Austria; NF5.

NCBI tax ID(s): 1580092 (species)

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General

@ref: 64520

BacDive-ID: 157948

DSM-Number: 106890

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

description: Nitrosopumilus adriaticus NF5 is an aerobe, mesophilic, rod-shaped archaeon that was isolated from coastal surface water.

NCBI tax id

  • NCBI tax id: 1580092
  • Matching level: species

strain history

@refhistory
64520<- B. Bayer, Univ. Vienna, Fac. of Life Scs, Austria; NF5
67770G. J. Herndl; Univ. of Vienna, Austria; NF5.

doi: 10.13145/bacdive157948.20230509.8.1

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 adriaticus
  • full scientific name: Nitrosopumilus adriaticus Bayer et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Nitrosopumilus adriaticus

@ref: 64520

domain: Archaea

phylum: Thaumarchaeota

class: Nitrososphaeria

order: Nitrosopumilales

family: Nitrosopumilaceae

genus: Nitrosopumilus

species: Nitrosopumilus adriaticus

full scientific name: Nitrosopumilus adriaticus Bayer et al. 2019

strain designation: NF5

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapegram stainconfidence
678830.59-1.74 µm0.2-0.25 µmrod-shaped
69480negative99.858

multimedia

  • @ref: 64520
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_106890.jpg
  • caption: Medium 1630a, 30°C, cell suspension concentrated by centrifugation
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth30mesophilic
67883positivegrowth15-34
67883positiveoptimum30-32mesophilic

culture pH

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

Physiology and metabolism

tolerance

@refcompoundconcentration
67883Ammonia25.0 mM
67883Nitrite10.0 mM

oxygen tolerance

  • @ref: 67883
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.994
69481no100

halophily

@refsaltgrowthtested relationconcentration
67883NaClpositivegrowth10-55 %
67883NaClpositiveoptimum34 %

observation

@refobservation
67770quinones: MK-6
67883Cells are occasionally flagellated.
67883The minimum generation time is approximately 34 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: 67884
  • value: urease
  • activity: -
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
64520coastal surface waterNorthern Adriatic SeaSloveniaSVNEurope
67770Northern Adriatic coastal surface water sampled off PiranSloveniaSVNEurope
67883coastal surface water (0.5m depth)Northern Adriatic Sea, coast of PiranSloveniaSVNEurope2011-1145.51813.568

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_187113.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17653;96_68790;97_89432;98_121702;99_187113&stattab=map
  • Last taxonomy: Nitrosopumilus
  • 16S sequence: MK139955
  • Sequence Identity:
  • Total samples: 62
  • soil counts: 2
  • aquatic counts: 60

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Nitrosopumilus adriaticus strain NF5 chromosome, complete genomeCP0110701803090ena1580092
67883Nitrosopumilus adriaticus strain NF5 16S ribosomal RNA gene, partial sequenceMK1399551471ena1580092

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitrosopumilus adriaticus NF52627854092completeimg1580092
67883Nitrosopumilus adriaticus NF5GCA_000956175completencbi1580092

GC content

@refGC-contentmethod
6452033.4sequence analysis
6777033.4genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 64520

culture collection no.: DSM 106890, JCM 32270, NCIMB 15114

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
64520Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106890Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106890)
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
67884Zhendong Zhang, Qiangchuan Hou, Yurong Wang, Weicheng Li, Huijun Zhao, Zhihong Sun, Zhuang GuoLactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili10.1099/ijsem.0.003362IJSEM 69: 2196-2201 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/
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