Strain identifier
BacDive ID: 7060
Type strain: 
Species: Methanococcoides burtonii
Strain Designation: ACE-M
Strain history: <- P. D. Franzmann, ACE-M
NCBI tax ID(s): 259564 (strain), 29291 (species)
version 8.1 (current version)
General
@ref: 2553
BacDive-ID: 7060
DSM-Number: 6242
keywords: genome sequence, 16S sequence, Archaea, anaerobe, psychrophilic, Gram-negative
description: Methanococcoides burtonii ACE-M is an anaerobe, psychrophilic, Gram-negative archaeon that was isolated from Ace Lake water at 24 m depth.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 259564 | strain |
| 29291 | species |
strain history
- @ref: 2553
- history: <- P. D. Franzmann, ACE-M
doi: 10.13145/bacdive7060.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanosarcinales
- family: Methanosarcinaceae
- genus: Methanococcoides
- species: Methanococcoides burtonii
- full scientific name: Methanococcoides burtonii Franzmann et al. 1993
@ref: 2553
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanosarcinales
family: Methanosarcinaceae
genus: Methanococcoides
species: Methanococcoides burtonii
full scientific name: Methanococcoides burtonii Franzmann et al. 1993
strain designation: ACE-M
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.973
Culture and growth conditions
culture medium
- @ref: 2553
- name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141c
- composition: Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c) Composition: NaHCO3 4.89237 g/l Trimethylammonium chloride 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l CaCl2 x 2 H2O 0.000978474 g/l FeSO4 x 7 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l Nicotinic acid 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Biotin 1.95695e-05 g/l Folic acid 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water
culture temp
- @ref: 2553
- growth: positive
- type: growth
- temperature: 21
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 2553 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 98.943 |
Isolation, sampling and environmental information
isolation
- @ref: 2553
- sample type: Ace Lake water at 24 m depth
- continent: Australia and Oceania
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Lake (large)
taxonmaps
- @ref: 69479
- File name: preview.99_187177.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17802;96_68841;97_89486;98_121766;99_187177&stattab=map
- Last taxonomy: Methanococcoides burtonii subclade
- 16S sequence: X65537
- Sequence Identity:
- Total samples: 102
- aquatic counts: 101
- plant counts: 1
Safety information
risk assessment
- @ref: 2553
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: M.burtonii gene for 16S rRNA
- accession: X65537
- length: 1476
- database: ena
- NCBI tax ID: 29291
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanococcoides burtonii DSM 6242 | GCA_000013725 | complete | ncbi | 259564 |
| 66792 | Methanococcoides burtonii DSM 6242 | 637000161 | complete | img | 259564 |
| 66792 | Methanococcoides burtonii DSM 6242 | 259564.15 | complete | patric | 259564 |
GC content
- @ref: 2553
- GC-content: 39.6
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.32 | no |
| flagellated | no | 96.483 | no |
| gram-positive | no | 96.72 | no |
| anaerobic | yes | 98.063 | yes |
| halophile | no | 80.102 | no |
| spore-forming | no | 94.59 | no |
| thermophile | no | 93.863 | yes |
| glucose-util | yes | 74.871 | no |
| aerobic | no | 93.934 | yes |
| glucose-ferment | no | 65.937 | no |
External links
@ref: 2553
culture collection no.: DSM 6242, NBRC 107633
straininfo link
- @ref: 76517
- straininfo: 48128
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Stress | 17660421 | Analysis of the AAA+ chaperone clpB gene and stress-response expression in the halophilic methanogenic archaeon Methanohalophilus portucalensis. | Shih CJ, Lai MC | Microbiology (Reading) | 10.1099/mic.0.2007/007633-0 | 2007 | Adaptation, Physiological/*genetics, Adenosine Triphosphatases/genetics, Amino Acid Motifs, Archaeal Proteins/biosynthesis/*genetics, Base Composition, Base Sequence, Blotting, Northern, Blotting, Southern, Chaperonin 10/genetics, Chaperonin 60/genetics, Chaperonins/biosynthesis/*genetics, DNA, Archaeal/chemistry/genetics, Gene Expression Profiling, *Gene Expression Regulation, Archaeal, Heat-Shock Proteins/biosynthesis/*genetics, Hot Temperature, Methanosarcinaceae/*genetics/metabolism, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, RNA, Messenger/biosynthesis, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Sodium Chloride/metabolism | Metabolism |
| Metabolism | 19923734 | Recombinant production, crystallization and preliminary X-ray analysis of PCNA from the psychrophilic archaeon Methanococcoides burtonii DSM 6242. | Byrne-Steele ML, Hughes RC, Ng JD | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/S1744309109037075 | 2009 | Archaeal Proteins/*chemistry/genetics/metabolism, Crystallization, Crystallography, X-Ray, Methanosarcinaceae/*chemistry, Molecular Sequence Data, Proliferating Cell Nuclear Antigen/*chemistry/genetics/metabolism, Recombinant Proteins/*chemistry/genetics/metabolism, X-Ray Diffraction | Genetics |
| Phylogeny | 24614846 | Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides. | L'Haridon S, Chalopin M, Colombo D, Toffin L | Int J Syst Evol Microbiol | 10.1099/ijs.0.058289-0 | 2014 | Base Composition, Betaine/metabolism, Choline/metabolism, DNA, Bacterial/genetics, Deanol/metabolism, Hydrothermal Vents/*microbiology, Mediterranean Sea, Methanosarcinaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| Phylogeny | 35583432 | Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea. | Liang L, Sun Y, Dong Y, Ahmad T, Chen Y, Wang J, Wang F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005384 | 2022 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Methanosarcinaceae, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2553 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6242) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6242 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 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 | |||
| 76517 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48128.1 | StrainInfo: A central database for resolving microbial strain identifiers |