Strain identifier
BacDive ID: 7131
Type strain: 
Species: Methanosarcina horonobensis
Strain Designation: HB-1
Strain history: S. Shimizu HB-1.
NCBI tax ID(s): 1434110 (strain), 418008 (species)
version 8.1 (current version)
General
@ref: 15813
BacDive-ID: 7131
DSM-Number: 21571
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative
description: Methanosarcina horonobensis HB-1 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from deep subsurface groundwater from a Miocene Wakkanai Formation aquifer consisting of siliceous mudstone.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 418008 | species |
| 1434110 | strain |
strain history
| @ref | history |
|---|---|
| 15813 | <- S. Shimizu, Horonobe RISE; HB-1 |
| 67770 | S. Shimizu HB-1. |
doi: 10.13145/bacdive7131.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanosarcinales
- family: Methanosarcinaceae
- genus: Methanosarcina
- species: Methanosarcina horonobensis
- full scientific name: Methanosarcina horonobensis Shimizu et al. 2011
@ref: 15813
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanosarcina
species: Methanosarcina horonobensis
full scientific name: Methanosarcina horonobensis Shimizu et al. 2011
strain designation: HB-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.992
Culture and growth conditions
culture medium
- @ref: 15813
- name: METHANOSARCINA MEDIUM (DSMZ Medium 120)
- growth: yes
- link: https://mediadive.dsmz.de/medium/120
- composition: Name: METHANOSARCINA MEDIUM (DSMZ Medium 120; with strain-specific modifications) Composition: Methanol 15.4688 g/l NaCl 5.85938 g/l Na-acetate 2.44141 g/l NaHCO3 1.95312 g/l Casitone 1.95312 g/l Yeast extract 1.95312 g/l NH4Cl 0.488281 g/l MgSO4 x 7 H2O 0.488281 g/l K2HPO4 0.341797 g/l Na2S x 9 H2O 0.292969 g/l L-Cysteine HCl x H2O 0.292969 g/l CaCl2 x 2 H2O 0.244141 g/l KH2PO4 0.224609 g/l HCl 0.00244141 g/l FeSO4 x 7 H2O 0.00195312 g/l FeCl2 x 4 H2O 0.00146484 g/l Sodium resazurin 0.000488281 g/l CoCl2 x 6 H2O 0.000185547 g/l Pyridoxine hydrochloride 9.76563e-05 g/l MnCl2 x 4 H2O 9.76563e-05 g/l ZnCl2 6.83594e-05 g/l Riboflavin 4.88281e-05 g/l Calcium D-(+)-pantothenate 4.88281e-05 g/l Nicotinic acid 4.88281e-05 g/l (DL)-alpha-Lipoic acid 4.88281e-05 g/l Thiamine HCl 4.88281e-05 g/l p-Aminobenzoic acid 4.88281e-05 g/l Na2MoO4 x 2 H2O 3.51562e-05 g/l NiCl2 x 6 H2O 2.34375e-05 g/l Folic acid 1.95312e-05 g/l Biotin 1.95312e-05 g/l H3BO3 5.85938e-06 g/l CuCl2 x 2 H2O 1.95313e-06 g/l Vitamin B12 9.76563e-07 g/l H2SO4 Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15813 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 15813 | anaerobe | |
| 69480 | anaerobe | 98.65 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.016 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 15813 | deep subsurface groundwater from a Miocene Wakkanai Formation aquifer consisting of siliceous mudstone | Horonobe, Hokkaido | Japan | JPN | Asia |
| 67770 | Groundwater sampled from a subsurface Miocene formation located in Horonobe | Hokkaido | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Groundwater |
| #Environmental | #Terrestrial | #Geologic |
Safety information
risk assessment
- @ref: 15813
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15813
- description: Methanosarcina horonobensis gene for 16S rRNA, partial sequence
- accession: AB288262
- length: 1432
- database: ena
- NCBI tax ID: 418008
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanosarcina horonobensis HB-1 = JCM 15518 | GCA_000970285 | complete | ncbi | 1434110 |
| 66792 | Methanosarcina horonobensis HB-1 = JCM 15518 | GCA_001316205 | contig | ncbi | 1434110 |
| 66792 | Methanosarcina horonobensis JCM 15518 | 2684622506 | draft | img | 1434110 |
| 66792 | Methanosarcina horonobensis HB-1 | 2627854269 | complete | img | 1434110 |
| 66792 | Methanosarcina horonobensis HB-1 = JCM 15518 | 1434110.4 | complete | patric | 1434110 |
| 66792 | Methanosarcina horonobensis HB-1 = JCM 15518 | 1434110.5 | wgs | patric | 1434110 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 15813 | 41 | high performance liquid chromatography (HPLC) |
| 67770 | 41.4 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | no | 91.019 | no |
| flagellated | no | 97.589 | no |
| gram-positive | no | 96.187 | no |
| anaerobic | yes | 97.818 | yes |
| aerobic | no | 93.561 | yes |
| halophile | no | 88.328 | no |
| spore-forming | no | 95.1 | no |
| thermophile | no | 98.541 | no |
| glucose-util | yes | 67.933 | no |
| glucose-ferment | no | 68.612 | no |
External links
@ref: 15813
culture collection no.: DSM 21571, JCM 15518, NBRC 102577
straininfo link
- @ref: 76586
- straininfo: 401545
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21112985 | Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation. | Shimizu S, Upadhye R, Ishijima Y, Naganuma T | Int J Syst Evol Microbiol | 10.1099/ijs.0.028548-0 | 2010 | Base Composition, Carbon/metabolism, Cluster Analysis, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Groundwater/*microbiology, Hydrogen-Ion Concentration, Japan, Methanosarcina/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature | Genetics |
| Phylogeny | 23378113 | Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil. | Wagner D, Schirmack J, Ganzert L, Morozova D, Mangelsdorf K | Int J Syst Evol Microbiol | 10.1099/ijs.0.046565-0 | 2013 | Base Composition, DNA, Archaeal/genetics, Methanosarcina/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siberia, *Soil Microbiology | Genetics |
| Phylogeny | 25052394 | Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake. | Ganzert L, Schirmack J, Alawi M, Mangelsdorf K, Sand W, Hillebrand-Voiculescu A, Wagner D | Int J Syst Evol Microbiol | 10.1099/ijs.0.064956-0 | 2014 | Base Composition, *Biofilms, Caves/microbiology, DNA, Archaeal/genetics, DNA, Bacterial/genetics, Lakes/microbiology, Lipids/chemistry, Methanosarcina/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Romania, Sequence Analysis, DNA, Sulfur, *Water Microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15813 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21571) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21571 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 76586 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401545.1 | StrainInfo: A central database for resolving microbial strain identifiers |