Strain identifier
BacDive ID: 2396
Type strain: 
Species: Chlorobaculum limnaeum
Strain Designation: 4930
Strain history: <- H. Biebl, 4930
NCBI tax ID(s): 274537 (species)
version 8.1 (current version)
General
@ref: 854
BacDive-ID: 2396
DSM-Number: 1677
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, phototroph, mesophilic, rod-shaped
description: Chlorobaculum limnaeum 4930 is an anaerobe, phototroph, mesophilic bacterium of the family Chlorobiaceae.
NCBI tax id
- NCBI tax id: 274537
- Matching level: species
strain history
- @ref: 854
- history: <- H. Biebl, 4930
doi: 10.13145/bacdive2396.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/chlorobiota
- domain: Bacteria
- phylum: Chlorobiota
- class: Chlorobiia
- order: Chlorobiales
- family: Chlorobiaceae
- genus: Chlorobaculum
- species: Chlorobaculum limnaeum
- full scientific name: Chlorobaculum limnaeum Imhoff 2003
@ref: 854
domain: Bacteria
phylum: Chlorobi
class: Chlorobia
order: Chlorobiales
family: Chlorobiaceae
genus: Chlorobaculum
species: Chlorobaculum limnaeum
full scientific name: Chlorobaculum limnaeum Imhoff 2003
strain designation: 4930
type strain: yes
Morphology
cell morphology
| @ref | cell width | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|---|
| 23074 | 0.6-0.8 µm | rod-shaped | no | ||
| 69480 | negative | 99.999 |
Culture and growth conditions
culture medium
- @ref: 854
- name: PFENNIG'S MEDIUM II (modified 1988, for green sulfur bacteria) (DSMZ Medium 29)
- growth: yes
- link: https://mediadive.dsmz.de/medium/29
- composition: Name: PFENNIG'S MEDIUM II (DSMZ Medium 29) Composition: NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.52 g/l Ammonium chloride 0.364 g/l KCl 0.364 g/l KH2PO4 0.364 g/l Dextrose 0.26 g/l Pyruvic acid sodium salt 0.26 g/l Ammonium acetate 0.26 g/l Yeast extract 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Resazurin 0.00225 g/l HCl 0.002002 g/l FeSO4 x 7 H2O 0.00156 g/l Vitamin B12 0.001 g/l H3BO3 0.000312 g/l CoCl2 x 6 H2O 0.0001976 g/l MnCl2 x 4 H2O 0.000104 g/l ZnCl2 7.28e-05 g/l Na2MoO4 x 2 H2O 3.744e-05 g/l NiCl2 x 6 H2O 2.496e-05 g/l CuCl2 x 2 H2O 2.08e-06 g/l Distilled water
culture temp
- @ref: 854
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 854 | anaerobe | |
| 23074 | obligate anaerobe | |
| 69480 | anaerobe | 99.575 |
nutrition type
- @ref: 23074
- type: phototroph
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.986 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23074 | 30411 | cobalamin | + | growth |
| 23074 | 26710 | sodium chloride | + | growth |
Isolation, sampling and environmental information
isolation
- @ref: 854
- geographic location: Lake Kinnevet
- country: Israel
- origin.country: ISR
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_3099.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_222;96_1618;97_1935;98_2379;99_3099&stattab=map
- Last taxonomy: Chlorobaculum limnaeum
- 16S sequence: HE582773
- Sequence Identity:
- Total samples: 113
- soil counts: 20
- aquatic counts: 92
- animal counts: 1
Safety information
risk assessment
- @ref: 854
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Chlorobaculum limnaeum partial 16S rRNA gene, type strain DSM 1677T | HE582773 | 1492 | ena | 274537 |
| 23074 | Chlorobaculum limnaeum partial 16S rRNA gene, type strain DSM 1677T | AJ290831 | 1241 | nuccore | 274537 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Chlorobaculum limnaeum DSM 1677 | GCA_001747405 | complete | ncbi | 274537 |
| 66792 | Chlorobaculum limnaeum strain DSM 1677 | 274537.5 | complete | patric | 274537 |
| 66792 | Chlorobaculum limnaeum DSM 1677 | 2501846309 | draft | img | 274537 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| flagellated | no | 97.176 | yes |
| gram-positive | no | 98.803 | no |
| anaerobic | yes | 97.899 | yes |
| aerobic | no | 96.92 | no |
| halophile | no | 86.303 | no |
| spore-forming | no | 94.05 | no |
| glucose-util | yes | 55.023 | no |
| thermophile | no | 83.446 | yes |
| motile | no | 88.818 | no |
| glucose-ferment | no | 82.99 | no |
External links
@ref: 854
culture collection no.: DSM 1677
literature
- topic: Genetics
- Pubmed-ID: 28619803
- title: Complete Genome Sequence of the Photoautotrophic and Bacteriochlorophyll e-Synthesizing Green Sulfur Bacterium Chlorobaculum limnaeum DSM 1677(T).
- authors: Tank M, Liu Z, Frigaard NU, Tomsho LP, Schuster SC, Bryant DA
- journal: Genome Announc
- DOI: 10.1128/genomeA.00529-17
- year: 2017
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 854 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1677) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1677 | |||
| 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 | |
| 23074 | Johannes F. Imhoff | 10.1099/ijs.0.02403-0 | Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna-Matthews-Olson protein) gene sequences | IJSEM 53: 941-951 2003 | 12892110 | |
| 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) | |||
| 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 |