Nitrosopumilus piranensis (DSM 106147, JCM 32271, NCIMB 15115)

Name: Nitrosopumilus piranensis (DSM 106147, JCM 32271, NCIMB 15115)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158487

Type strain

Strain Designation D3C

Culture col. no. DSM 106147 JCM 32271 NCIMB 15115 D3C

NCBI tax ID(s) 1582439

Special Collections DSMZ JCM Literature strains

Links

Nitrosopumilus piranensis D3C is an aerobe, mesophilic, rod-shaped prokaryote that was isolated from coastal surface water.

rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398956

JCM 32271,DSM 106147

@ref 20215

Last LPSN update 2025-12-16 10:08:02

Domain Thermoproteati

Phylum Thermoproteota

Class Nitrososphaeria

Order Nitrosopumilales

Family Nitrosopumilaceae

Genus Nitrosopumilus

Species Nitrosopumilus piranensis

Full scientific name Nitrosopumilus piranensis Bayer et al. 2019

Synonyms (1)

"Candidatus Nitrosopumilus piranensis"

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Motility	Gram stain	Confidence
67883	0.49-2 µm	0.2-0.25 µm	rod-shaped
125439					negative	99.5

Multimedia

@ref:	65163
multimedia content:	DSM_106147.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_106147.jpg
caption:	cells of DSM 106147 on medium 1630a at 28 °C
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65163	NITROSOPUMILUS MEDIUM (DSMZ Medium 1630a)		Medium recipe at MediaDive	Name: NITROSOPUMILUS MEDIUM (DSMZ Medium 1630a) Composition: NaCl 26.0 g/l MgCl2 x 6 H2O 5.0 g/l MgSO4 x 7 H2O 5.0 g/l HEPES 2.384 g/l CaCl2 x 2 H2O 1.5 g/l NaHCO3 0.25 g/l NaOH 0.24 g/l KBr 0.1 g/l Na-pyruvate 0.05 g/l NH4Cl 0.05 g/l Na2-EDTA x 2 H2O 0.0052 g/l KH2PO4 0.002 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l ZnCl2 7e-05 g/l Nicotinic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65163	positive	growth	30
67770	positive	growth	30	mesophilic
67883	positive	growth	15-37
67883	positive	optimum	32	mesophilic

Culture pH

@ref	Ability	Type	PH
67883	positive	optimum	7.1-7.3
67883	positive	growth	6.8-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67883	aerobe
125439	obligate aerobe	93.4

Spore formation

@ref	Spore formation	Confidence
125439		96

Halophily

@ref	Salt	Growth	Tested relation	Concentration
67883	NaCl	positive	growth	1.5-6.5 %
67883	NaCl	positive	optimum	3.7 %

Observation

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

Tolerance

@ref	Compound	Concentration
67883	Ammonia	30.0 mM
67883	Nitrite	15.0 mM

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
67883	3393	carbenicillin	100 µg/mL
67883	17698	chloramphenicol		25 µg/mL
67883	48923	erythromycin	50 µg/mL
67883	6104	kanamycin	100 µg/mL
67883	7731	ofloxacin	50 µg/mL
67883	9215	spectinomycin	100 µg/mL
67883	17076	streptomycin	100 µg/mL
67883	27902	tetracycline		25 µg/mL

Enzymes

@ref	Value	Activity	Ec
67883	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Coast
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
65163	coastal surface water		Northern Adriatic Sea	Slovenia	SVN	Europe	45.518	13.5679 45.518/13.5679
67770	Northern Adriatic coastal surface water sampled off Piran			Slovenia	SVN	Europe
67883	coastal surface water (0.5m depth)	2011-12	Northern Adriatic Sea, coast of Piran	Slovenia	SVN	Europe	45.518	13.568 45.518/13.568

Taxonmaps

69479

Global distribution of 16S sequence MK139956 (>99% sequence identity) for Nitrosopumilus from Microbeatlas

Aquatic Samples	3053
Soil Samples	75
Animal Samples	2
Plant Samples	3
Total Samples	3133

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
65163	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67883	ASM87577v1 assembly for Nitrosopumilus piranensis D3C	complete	GCA_000875775	1582439.9	2627853696	1582439	93.19

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67883	Nitrosopumilus piranensis strain D3C 16S ribosomal RNA gene, partial sequence	MK139956	1471		1582439

GC content

@ref	GC-content (mol%)	Method
65163	33.8	sequence analysis
67883	33.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nitrosopumilus piranensis D3C
NCBI: GCA_000875775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.00	no
125439	motility	BacteriaNetⓘ	no	77.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.	Hernandez-Magana E, Kraft B.	Front Microbiol	10.3389/fmicb.2024.1410251	2024
Phylogeny	Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria.	Bayer B, Vojvoda J, Reinthaler T, Reyes C, Pinto M, Herndl GJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003360	2019

References

#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#65163	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106147
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67883	Barbara Bayer, Jana Vojvoda, Thomas Reinthaler, Carolina Reyes, Maria Pinto, Gerhard J. Herndl: Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. IJSEM 69: 1892 - 1902 2019 ( DOI 10.1099/ijsem.0.003360 )
#69479	João 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 beta .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Nitrosopumilus piranensis (DSM 106147, JCM 32271, NCIMB 15115)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Tolerance

Antibiotic resistance

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000875775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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