Strain identifier
BacDive ID: 17853
Type strain: 
Species: Methanolinea tarda
Strain Designation: NOBi-1
Strain history: H. Imachi NOBI-1.
NCBI tax ID(s): 882090 (strain), 263906 (species)
version 8.1 (current version)
General
@ref: 6376
BacDive-ID: 17853
DSM-Number: 16494
keywords: genome sequence, 16S sequence, Archaea, anaerobe, thermophilic, Gram-negative, rod-shaped
description: Methanolinea tarda NOBi-1 is an anaerobe, thermophilic, Gram-negative archaeon that was isolated from anaerobic digested sludge.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 263906 | species |
| 882090 | strain |
strain history
| @ref | history |
|---|---|
| 6376 | <- H. Imachi; NOBI-1 |
| 67770 | H. Imachi NOBI-1. |
doi: 10.13145/bacdive17853.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanoregulaceae
- genus: Methanolinea
- species: Methanolinea tarda
- full scientific name: Methanolinea tarda Imachi et al. 2008
@ref: 6376
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanoregulaceae
genus: Methanolinea
species: Methanolinea tarda
full scientific name: Methanolinea tarda Imachi et al. 2008
strain designation: NOBi-1
type strain: yes
Morphology
cell morphology
- @ref: 32372
- gram stain: negative
- cell length: 2 µm
- cell width: 0.85 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 6376
- incubation period: >14 days
Culture and growth conditions
culture medium
- @ref: 6376
- name: PELOTOMACULUM MEDIUM (DSMZ Medium 960)
- growth: yes
- link: https://mediadive.dsmz.de/medium/960
- composition: Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na-formate 2.71457 g/l Na2CO3 1.49701 g/l NH4Cl 0.538922 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Yeast extract 0.0998004 g/l Na acetate 0.0998004 g/l 2-Mercaptoethanesulfonic acid 0.0798403 g/l Nitrilotriacetic acid 0.0127745 g/l FeCl2 x 4 H2O 0.000998004 g/l NaCl 0.000998004 g/l Sodium resazurin 0.000499002 g/l ZnCl2 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6376 | positive | growth | 50 | thermophilic |
| 32372 | positive | growth | 35-55 | |
| 32372 | positive | optimum | 50 | thermophilic |
| 67770 | positive | growth | 50 | thermophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32372 | positive | growth | 6.7-8 |
| 32372 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 6376 | anaerobe |
| 32372 | anaerobe |
halophily
- @ref: 32372
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1.5 %
metabolite utilization
- @ref: 32372
- Chebi-ID: 30089
- metabolite: acetate
- utilization activity: +
- kind of utilization tested: carbon source
metabolite production
- @ref: 32372
- Chebi-ID: 16183
- metabolite: methane
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6376 | anaerobic digested sludge | Nagaoka | Japan | JPN | Asia |
| 67770 | Mesophilic methanogenic sludge digesting municipal sewage sludge |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_187231.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17869;96_68881;97_89529;98_121810;99_187231&stattab=map
- Last taxonomy: Methanolinea tarda subclade
- 16S sequence: AB162774
- Sequence Identity:
- Total samples: 403
- soil counts: 50
- aquatic counts: 308
- animal counts: 13
- plant counts: 32
Safety information
risk assessment
- @ref: 6376
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6376
- description: Methanolinea tarda gene for 16S ribosomal RNA, partial sequence
- accession: AB162774
- length: 1433
- database: ena
- NCBI tax ID: 882090
Genome sequences
- @ref: 66792
- description: Methanolinea tarda NOBI-1
- accession: 882090.7
- assembly level: wgs
- database: patric
- NCBI tax ID: 882090
GC content
| @ref | GC-content | method |
|---|---|---|
| 32372 | 56.3 | |
| 67770 | 56.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 91.388 | yes |
| flagellated | no | 97.168 | yes |
| gram-positive | no | 97.948 | yes |
| anaerobic | yes | 99.063 | no |
| halophile | no | 89.493 | yes |
| spore-forming | no | 96.708 | no |
| thermophile | yes | 73.417 | yes |
| glucose-util | yes | 68.354 | no |
| aerobic | no | 96.82 | yes |
| glucose-ferment | no | 62.703 | no |
External links
@ref: 6376
culture collection no.: DSM 16494, JCM 12467, NBRC 102358., NBRC 102358
straininfo link
- @ref: 86844
- straininfo: 323978
literature
- topic: Phylogeny
- Pubmed-ID: 18175725
- title: Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge.
- authors: Imachi H, Sakai S, Sekiguchi Y, Hanada S, Kamagata Y, Ohashi A, Harada H
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65394-0
- year: 2008
- mesh: Base Composition, DNA, Archaeal/analysis, Methane/*biosynthesis, Methanomicrobiales/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Oxidoreductases/genetics, Phenotype, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6376 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16494) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16494 | |||
| 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 | |||
| 32372 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28600 | 28776041 | |
| 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/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 86844 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID323978.1 | StrainInfo: A central database for resolving microbial strain identifiers |