Strain identifier
BacDive ID: 7042
Type strain: 
Species: Methanoplanus limicola
Strain Designation: M3
Strain history: <- K.O. Stetter, M3
NCBI tax ID(s): 937775 (strain), 2315 (species)
version 8.1 (current version)
General
@ref: 1014
BacDive-ID: 7042
DSM-Number: 2279
keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative
description: Methanoplanus limicola M3 is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from mud of drilling swamp .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 2315 | species |
| 937775 | strain |
strain history
- @ref: 1014
- history: <- K.O. Stetter, M3
doi: 10.13145/bacdive7042.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Methanomicrobia
- order: Methanomicrobiales
- family: Methanomicrobiaceae
- genus: Methanoplanus
- species: Methanoplanus limicola
- full scientific name: Methanoplanus limicola Wildgruber et al. 1984
@ref: 1014
domain: Archaea
phylum: Euryarchaeota
class: Methanomicrobia
order: Methanomicrobiales
family: Methanomicrobiaceae
genus: Methanoplanus
species: Methanoplanus limicola
full scientific name: Methanoplanus limicola Wildgruber et al. 1984 emend. Göker et al. 2014
strain designation: M3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.976
multimedia
- @ref: 66793
- multimedia content: EM_DSM_2279_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1014
- name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141)
- growth: yes
- link: https://mediadive.dsmz.de/medium/141
- composition: Name: METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141) Composition: NaHCO3 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 FeSO4 x 7 H2O 0.000978474 g/l CaCl2 x 2 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 Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l Nicotinic acid 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Folic acid 1.95695e-05 g/l Biotin 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: 1014
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1014 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.96 |
Isolation, sampling and environmental information
isolation
- @ref: 1014
- sample type: mud of drilling swamp (Mofette II)
- geographic location: Baia
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | ||
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Terrestrial | #Wetland (Swamp) |
Safety information
risk assessment
- @ref: 1014
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1014
- description: Methanoplanus limicola DSM 2279 16S ribosomal RNA gene, partial sequence
- accession: M59143
- length: 1469
- database: ena
- NCBI tax ID: 937775
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Methanoplanus limicola DSM 2279 | GCA_000243255 | chromosome | ncbi | 937775 |
| 66792 | Methanoplanus limicola M3, DSM 2279 | 2506381025 | draft | img | 937775 |
| 66792 | Methanoplanus limicola DSM 2279 | 937775.13 | complete | patric | 937775 |
GC content
- @ref: 1014
- GC-content: 42
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.736 | no |
| flagellated | no | 96.665 | no |
| gram-positive | no | 97.127 | no |
| anaerobic | yes | 99.014 | no |
| halophile | no | 79.065 | no |
| spore-forming | no | 94.315 | no |
| glucose-util | yes | 75.283 | no |
| aerobic | no | 95.193 | no |
| thermophile | no | 97.893 | no |
| glucose-ferment | no | 66.791 | no |
External links
@ref: 1014
culture collection no.: DSM 2279, ATCC 35062, OCM 101
straininfo link
- @ref: 76501
- straininfo: 40848
literature
- topic: Genetics
- Pubmed-ID: 25197484
- title: Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia.
- authors: Goker M, Lu M, Fiebig A, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Mayilraj S, Rohde M, Detter JC, Bunk B, Spring S, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP
- journal: Stand Genomic Sci
- DOI: 10.4056/sigs.5138968
- year: 2014
- topic2: Phylogeny
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1014 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2279) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2279 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |
| 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 | |||
| 76501 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40848.1 | StrainInfo: A central database for resolving microbial strain identifiers |