Name: Nitrosopumilus piranensis D3C
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158487

Type strain:

Species: Nitrosopumilus piranensis

Strain Designation: D3C

Culture col. no.: DSM 106147, JCM 32271, NCIMB 15115

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

NCBI tax ID(s): 1582439 (species)

SI-ID 398956

DSM 106147

Special Collections

Section

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

rod-shaped
aerobe
16S sequence
Archaea
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Nitrososphaerota*
	Class	*Nitrososphaeria*
	Order	*Nitrosopumilales*
	Family	*Nitrosopumilaceae*
	Genus	*Nitrosopumilus*
	Species	**Nitrosopumilus piranensis**
	Full Scientific Name (LPSN)	Nitrosopumilus piranensis Bayer et al. 2019

Synonym

"Candidatus Nitrosopumilus piranensis"

Information on morphological and physiological properties Morphology

[Ref.: #67883]	Cell length	0.49-2 µm

[Ref.: #67883]	Cell width	0.2-0.25 µm

[Ref.: #67883]	Cell shape	rod-shaped

[Ref.: #67883]	Motility	no

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	30 °C
[Ref.: #67883]	growth	15-37 °C
[Ref.: #67883]	optimum	32 °C

	pH	Kind of pH		pH
[Ref.: #67883]			optimum	7.1-7.3
[Ref.: #67883]			growth	6.8-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67883]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #67883]		NaCl		growth	15-65	%
[Ref.: #67883]		NaCl		optimum	37	%

[Ref.: #67770]	Observation	quinones: MK-6
[Ref.: #67883]	Observation	The minimum generation time is approximately 27 h.

[Ref.: #67883]	Name of tolerated compound	Ammonia
[Ref.: #67883]	Tolerated concentration	30
[Ref.: #67883]	Name of tolerated compound	Nitrite
[Ref.: #67883]	Tolerated concentration	15

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #67883]	carbenicillin ChEBI				yes	100	µg/mL
[Ref.: #67883]	chloramphenicol ChEBI	yes	25	µg/mL
[Ref.: #67883]	erythromycin ChEBI				yes	50	µg/mL
[Ref.: #67883]	kanamycin ChEBI				yes	100	µg/mL
[Ref.: #67883]	ofloxacin ChEBI				yes	50	µg/mL
[Ref.: #67883]	spectinomycin ChEBI				yes	100	µg/mL
[Ref.: #67883]	streptomycin ChEBI				yes	100	µg/mL
[Ref.: #67883]	tetracycline ChEBI	yes	25	µg/mL

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #67883]		urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #65163]	Sample type/isolated from	coastal surface water
[Ref.: #65163]	Geographic location (country and/or sea, region)	Northern Adriatic Sea
[Ref.: #65163]	Country	Slovenia
[Ref.: #65163]	Country ISO 3 Code	SVN
[Ref.: #65163]	Continent	Europe
[Ref.: #65163]	Geographic location	45.5180°/13.5679°

[Ref.: #67770]	Sample type/isolated from	Northern Adriatic coastal surface water sampled off Piran
[Ref.: #67770]	Country	Slovenia
[Ref.: #67770]	Country ISO 3 Code	SVN
[Ref.: #67770]	Continent	Europe

[Ref.: #67883]	Sample type/isolated from	coastal surface water (0.5m depth)
[Ref.: #67883]	Sampling date	2011-12
[Ref.: #67883]	Geographic location (country and/or sea, region)	Northern Adriatic Sea, coast of Piran
[Ref.: #67883]	Country	Slovenia
[Ref.: #67883]	Country ISO 3 Code	SVN
[Ref.: #67883]	Continent	Europe
[Ref.: #67883]	Geographic location	45.5180°/13.5680°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67883]	Nitrosopumilus piranensis strain D3C 16S ribosomal RNA gene, partial sequence	MK139956	1471	GenBank ENA	1582439 tax ID
[Ref.: #67770]	Nitrosopumilus piranensis strain D3C, complete genome	CP010868	1713078	GenBank ENA	1582439 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67883]	Nitrosopumilus piranensis D3C	GCA_000875775	complete	GenBank ENA	1582439 tax ID
[Ref.: #66792]	Nitrosopumilus piranensis D3C	2627853696	complete	JGI IMG/M	1582439 tax ID	*

[Ref.: #65163]	GC-content	33.8 mol%	sequence analysis
[Ref.: #67883]	GC-content	33.8 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nitrosopumilus piranensis D3C NCBI: GCA_000875775.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

Availability in culture collections External links

[Ref.: #65163]

Culture collection no.

DSM 106147, JCM 32271, NCIMB 15115

[Ref.: #111282]

SI-ID 398956

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#111282

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID398956.1 )

* These data were automatically processed and therefore are not curated

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