Strain identifier
BacDive ID: 24289
Type strain: 
Species: Paenibacillus darwinianus
Strain Designation: Br
Strain history: <- M. Dsouza, University of Auckland, New Zealand; strain Br
NCBI tax ID(s): 1380763 (species)
version 9.3 (current version)
General
@ref: 20713
BacDive-ID: 24289
DSM-Number: 27245
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, psychrophilic
description: Paenibacillus darwinianus Br is a spore-forming, psychrophilic bacterium that was isolated from gamma-irradiated soil.
NCBI tax id
- NCBI tax id: 1380763
- Matching level: species
strain history
- @ref: 20713
- history: <- M. Dsouza, University of Auckland, New Zealand; strain Br
doi: 10.13145/bacdive24289.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus darwinianus
- full scientific name: Paenibacillus darwinianus Dsouza et al. 2014
@ref: 20713
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus darwinianus
full scientific name: Paenibacillus darwinianus Dsouza et al. 2014
strain designation: Br
type strain: yes
Morphology
cell morphology
- @ref: 125439
- motility: yes
- confidence: 90.9
colony morphology
- @ref: 20713
- incubation period: >14 days
Culture and growth conditions
culture medium
- @ref: 20713
- name: PYGV AGAR (DSMZ Medium 621)
- growth: yes
- link: https://mediadive.dsmz.de/medium/621
- composition: Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
culture temp
- @ref: 20713
- growth: positive
- type: growth
- temperature: 20
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 96.4
spore formation
- @ref: 125439
- spore formation: yes
- confidence: 93.5
Isolation, sampling and environmental information
isolation
- @ref: 20713
- sample type: gamma-irradiated soil
- geographic location: Britannia drift, Lake Wellman Region in the the south-eastern Darwin Mountains (79° 55' 16.2'' S 156° 55' 30.7'' E)
- continent: Australia and Oceania
- latitude: -54.665
- longitude: -69.664
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2752.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_1464;97_1746;98_2135;99_2752&stattab=map
- Last taxonomy: Paenibacillus darwinianus subclade
- 16S sequence: KF264455
- Sequence Identity:
- Total samples: 635
- soil counts: 168
- aquatic counts: 79
- animal counts: 357
- plant counts: 31
Safety information
risk assessment
- @ref: 20713
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20713 | Paenibacillus darwinianus strain Br 16S ribosomal RNA gene, partial sequence | KF264455 | 1412 | nuccore | 1380763 |
| 124043 | Paenibacillus darwinianus strain MB 16S ribosomal RNA gene, partial sequence. | KF264456 | 1412 | nuccore | 1380763 |
| 124043 | Paenibacillus darwinianus strain MB 16S ribosomal RNA gene, partial sequence. | KF264457 | 1409 | nuccore | 1380763 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenibacillus darwinianus Br | GCA_000598065 | scaffold | ncbi | 1380763 |
| 66792 | Paenibacillus darwinianus Br | 2609460045 | draft | img | 1380763 |
GC content
- @ref: 20713
- GC-content: 55.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 71.566 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 92.247 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 73.295 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 84.425 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 76.02 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 79.743 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 93.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 90.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 81.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 96.4 |
External links
@ref: 20713
culture collection no.: DSM 27245, ICMP 19912
straininfo link
- @ref: 88226
- straininfo: 403781
literature
- topic: Phylogeny
- Pubmed-ID: 24449790
- title: Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil.
- authors: Dsouza M, Taylor MW, Ryan J, MacKenzie A, Lagutin K, Anderson RF, Turner SJ, Aislabie J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.056697-0
- year: 2014
- mesh: Antarctic Regions, Bacterial Typing Techniques, Base Composition, Fatty Acids/chemistry, Molecular Sequence Data, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20713 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27245 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27245) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 88226 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID403781.1 | |||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |