Name: Nitrosarchaeum koreense MY1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159828

Type strain:

Species: Nitrosarchaeum koreense

Strain Designation: MY1

Culture col. no.: JCM 31640, KCTC 4249

Strain history: <- Sung-Keun Rhee, Chungbuk National Univ.

NCBI tax ID(s): 1088740 (species)

Section

Nitrosarchaeum koreense MY1 is an aerobe, non-halophilic, chemolithotroph archaeon that was isolated from agricultural soil.

Gram-negative
rod-shaped
aerobe
chemolithotroph
mesophilic
non-halophilic
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	"Candidatus Nitrosarchaeum"
	Species	"Candidatus Nitrosarchaeum koreense"
	Full Scientific Name (LPSN)	Candidatus Nitrosarchaeum koreense corrig. Kim et al. 2011

	Synonym	"Candidatus* Nitrosoarchaeum koreensis"*
	Synonym	**Nitrosarchaeum koreense**

Information on morphological and physiological properties Morphology

[Ref.: #66656]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #66656]	Cell length	0.6-1.0 µm

[Ref.: #66656]	Cell width	0.3-0.5 µm

[Ref.: #66656]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #66656]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66656]

Culture medium

AFM

[Ref.: #66656]

Culture medium growth

[Ref.: #66656]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #66656]	optimum	25 °C
[Ref.: #66656]	growth	15-30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #66656]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66656]			optimum	7
[Ref.: #66656]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66656]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #66656]

Nutrition type

chemolithotroph

[Ref.: #66656]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66656]		NaCl		growth	0.1-0.6	%
[Ref.: #66656]		NaCl		optimum	0.2-0.4	%

[Ref.: #66656]	Name of tolerated compound	Nitrite
[Ref.: #66656]	Tolerated concentration	2.5
[Ref.: #66656]	Name of tolerated compound	Ammonia
[Ref.: #66656]	Tolerated concentration	5

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66656]	ammonia ChEBI	+	energy source
[Ref.: #66656]	carbon dioxide ChEBI	+	carbon source
[Ref.: #66656]	urea ChEBI	-	energy source
[Ref.: #66656]	urea ChEBI	-	nitrogen source

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #66656]	ampicillin ChEBI				yes	50	µg/mL
[Ref.: #66656]	chloramphenicol ChEBI	yes	25	µg/mL
[Ref.: #66656]	clarithromycin ChEBI				yes	2	µg/mL
[Ref.: #66656]	kanamycin ChEBI				yes	50	µg/mL
[Ref.: #66656]	penicillin g ChEBI				yes	50	µg/mL
[Ref.: #66656]	streptomycin ChEBI	yes	50	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #66656]		dinitrogen oxide ChEBI	yes

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

[Ref.: #66656]	Sample type/isolated from	agricultural soil
[Ref.: #66656]	Geographic location (country and/or sea, region)	Chungbuk National University
[Ref.: #66656]	Country	Republic of Korea
[Ref.: #66656]	Country ISO 3 Code	KOR
[Ref.: #66656]	Continent	Asia
[Ref.: #66656]	Geographic location	36.6167°/127.4500°
[Ref.: #66656]	Enrichment culture	artificial freshwater medium
[Ref.: #66656]	Enrichment culture composition	containing (l-1) 0.4 g MgCl2 x 6H2O, 0.5 g KCl, 0.2 g KH2PO4, 1.0 g NaCl and 0.1 g CaCl2 x 2H2O, 1 mM NH4Cl as the energy source, 1 ml non-chelated trace element, 1 ml of 7.5 mM sodium iron EDTAsolution, and 2 ml of 1 M NaHCO3 . Allylthiourea (ATU,50 µM) and chlorate (50 µM) were used to selectively inhibit the growth of AOB and nitrite-oxidizing bacteria (NOB), respectively. The pH of the medium was maintained between pH 6.8 to 7.0 during the whole cultivation period.
[Ref.: #66656]	Isolation/enrichment procedure	1 g soil was transferred into 100 ml of artificial freshwater medium. The enrichment cultures were grown aerobically in the dark without shaking.

[Ref.: #67770]	Sample type/isolated from	Soil of an experimental agricultural station at the Chungbuk Natinonal University
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From agricultural soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Chungbuk National University
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	-
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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.: #66656]	Nitrosopumilaceae archaeon MY1 16S ribosomal RNA gene, partial sequence	HQ331116	1358	ENA	1001994 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Nitrosarchaeum koreense MY1	GCA_000220175	contig	GenBank	1001994 tax ID

[Ref.: #67771]

GC-content

32.7 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nitrosarchaeum koreense MY1 MY1 NCBI: GCA_000220175.2
[Ref.: #69480]	motile	no	91.157	yes
[Ref.: #69480]	flagellated	no	96.806	no
[Ref.: #69480]	gram-positive	no	97.32	yes
[Ref.: #69480]	anaerobic	no	63.261	yes
[Ref.: #69480]	aerobic	no	50	yes
[Ref.: #69480]	halophile	no	93.949	yes
[Ref.: #69480]	spore-forming	no	95.53	no
[Ref.: #69480]	thermophile	yes	80.375	yes
[Ref.: #69480]	glucose-util	yes	85.636	no
[Ref.: #69480]	glucose-ferment	no	67.787	no

Availability in culture collections External links

[Ref.: #66656]

Culture collection no.

JCM 31640, KCTC 4249

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil.	Jung MY, Islam MA, Gwak JH, Kim JG, Rhee SK	Int J Syst Evol Microbiol	10.1099/ijsem.0.002926	2018	*

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 )

#66656

Man-Young Jung, Md. Arafat Islam, Joo-Han Gwak, Jong-Geol Kim, Sung-Keun Rhee: Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil. IJSEM 68: 3084 - 3095 2018 ( DOI 10.1099/ijsem.0.002926 , PubMed 30124400 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

* These data were automatically processed and therefore are not curated

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Nitrosarchaeum koreense MY1 MY1

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