Strain identifier
BacDive ID: 159828
Type strain: 
Species: Nitrosarchaeum koreense
Strain Designation: MY1
Strain history: <- Sung-Keun Rhee, Chungbuk National Univ.
NCBI tax ID(s): 1088740 (species)
version 9.1 (current version)
General
@ref: 66656
BacDive-ID: 159828
keywords: genome sequence, 16S sequence, Archaea, aerobe, non-halophilic, chemolithotroph, Gram-negative, rod-shaped
description: Nitrosarchaeum koreense MY1 is an aerobe, non-halophilic, chemolithotroph archaeon that was isolated from agricultural soil.
NCBI tax id
- NCBI tax id: 1088740
- Matching level: species
strain history
| @ref | history |
|---|---|
| 67770 | S.-K. Rhee; Dept. of Microbiol., Chungbuk Natl. Univ., South Korea; MY1. |
| 67771 | <- Sung-Keun Rhee, Chungbuk National Univ. |
doi: 10.13145/bacdive159828.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/nitrososphaerota
- domain: Archaea
- phylum: Nitrososphaerota
- class: Nitrososphaeria
- order: Nitrosopumilales
- family: Nitrosopumilaceae
- genus: Nitrosarchaeum
- species: Nitrosarchaeum koreense
- full scientific name: Candidatus Nitrosarchaeum koreense corrig. Kim et al. 2011
synonyms
@ref synonym 20215 Nitrosoarchaeum koreensis 20215 Nitrosarchaeum koreense
@ref: 66656
domain: Archaea
phylum: Thaumarchaeota
class: Nitrososphaeria
order: Nitrosopumilales
family: Nitrosopumilaceae
genus: Nitrosarchaeum
species: Nitrosarchaeum koreense
strain designation: MY1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 66656 | negative | 0.6-1.0 µm | 0.3-0.5 µm | rod-shaped | no |
| 67771 | rod-shaped | ||||
| 67771 | negative |
Culture and growth conditions
culture medium
- @ref: 66656
- name: AFM
- growth: yes
- composition: with 0.5mM pyruvate
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 66656 | positive | optimum | 25 |
| 66656 | positive | growth | 15-30 |
| 67770 | positive | growth | 30 |
| 67771 | positive | growth | 25 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 66656 | positive | optimum | 7 |
| 66656 | positive | growth | 6.0-8.0 |
Physiology and metabolism
tolerance
| @ref | compound | concentration |
|---|---|---|
| 66656 | Nitrite | 2.5 mM |
| 66656 | Ammonia | 5.0 mM |
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 66656 | aerobe |
| 67771 | aerobe |
nutrition type
- @ref: 66656
- type: chemolithotroph
halophily
| @ref | halophily level | salt | growth | tested relation | concentration |
|---|---|---|---|---|---|
| 66656 | non-halophilic | NaCl | positive | growth | 0.1-0.6 % |
| 66656 | NaCl | positive | optimum | 0.2-0.4 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 66656 | 16526 | carbon dioxide | + | carbon source |
| 66656 | 16199 | urea | - | energy source |
| 66656 | 16134 | ammonia | + | energy source |
| 66656 | 16199 | urea | - | nitrogen source |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|---|---|
| 66656 | 6104 | kanamycin | yes | yes | 50 µg/mL | ||
| 66656 | 28971 | ampicillin | yes | yes | 50 µg/mL | ||
| 66656 | 18208 | penicillin g | yes | yes | 50 µg/mL | ||
| 66656 | 3732 | clarithromycin | yes | yes | 2 µg/mL | ||
| 66656 | 17076 | streptomycin | yes | yes | 50 µg/mL | ||
| 66656 | 17698 | chloramphenicol | yes | yes | 25 µg/mL |
metabolite production
- @ref: 66656
- Chebi-ID: 17045
- metabolite: dinitrogen oxide
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | isolation procedure |
|---|---|---|---|---|---|---|---|---|---|---|
| 66656 | agricultural soil | Chungbuk National University | Republic of Korea | KOR | Asia | 36.6167 | 127.45 | artificial freshwater medium | 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. | 1 g soil was transferred into 100 ml of artificial freshwater medium. The enrichment cultures were grown aerobically in the dark without shaking. |
| 67770 | Soil of an experimental agricultural station at the Chungbuk Natinonal University | Republic of Korea | KOR | Asia | ||||||
| 67771 | From agricultural soil | Chungbuk National University | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | |
| #Environmental | #Terrestrial | #Soil |
Sequence information
16S sequences
- @ref: 66656
- description: Nitrosarchaeum koreense MY1 16S ribosomal RNA gene, partial sequence
- accession: HQ331116
- length: 1358
- database: nuccore
- NCBI tax ID: 1001994
Genome sequences
- @ref: 67771
- description: Nitrosarchaeum koreense MY1
- accession: GCA_000220175
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1001994
GC content
- @ref: 67771
- GC-content: 32.7
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 72.308 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 60.148 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 52.359 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.854 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 59.37 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.75 | yes |
External links
@ref: 66656
culture collection no.: JCM 31640, KCTC 4249
literature
- topic: Phylogeny
- Pubmed-ID: 30124400
- title: Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil.
- authors: Jung MY, Islam MA, Gwak JH, Kim JG, Rhee SK
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002926
- year: 2018
- mesh: Agriculture, Ammonia/*metabolism, Archaea/*classification/genetics/isolation & purification, Base Composition, Genes, Archaeal, Glyceryl Ethers/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | journal | pubmed |
|---|---|---|---|---|---|
| 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 | 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 | 10.1099/ijsem.0.002926 | IJSEM 68: 3084-3095 2018 | 30124400 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/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) | https://diaspora-project.de/progress.html#genomes |