Strain identifier
BacDive ID: 18151
Type strain:
Species: Deferrisoma camini
Strain Designation: S3R1
Strain history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; S3R1 <- G. Slobodkina and A. Slobodkin {2010}
NCBI tax ID(s): 1035120 (species)
General
@ref: 17535
BacDive-ID: 18151
DSM-Number: 24185
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, ovoid-shaped
description: Deferrisoma camini S3R1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from deep-sea hydrothermal chimney, depth 2104-2163 m.
NCBI tax id
- NCBI tax id: 1035120
- Matching level: species
strain history
- @ref: 17535
- history: <- G. Slobodkina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; S3R1 <- G. Slobodkina and A. Slobodkin {2010}
doi: 10.13145/bacdive18151.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Deferrisomatales
- family: Deferrisomataceae
- genus: Deferrisoma
- species: Deferrisoma camini
- full scientific name: Deferrisoma camini Slobodkina et al. 2012
@ref: 17535
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Deltaproteobacteria, not assigned to order
family: Deferrisomataceae
genus: Deferrisoma
species: Deferrisoma camini
full scientific name: Deferrisoma camini Slobodkina et al. 2012
strain designation: S3R1
type strain: yes
Morphology
cell morphology
- @ref: 30543
- gram stain: negative
- cell length: 1.1 µm
- cell width: 0.55 µm
- cell shape: ovoid-shaped
- motility: yes
colony morphology
- @ref: 17535
- incubation period: 2-3 days
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_24185_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_24185_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_24185_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_24185_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 17535
- name: DEFERRISOMA MEDIUM (DSMZ Medium 1451)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1451
- composition: Name: DEFERRISOMA MEDIUM (DSMZ Medium 1451) Composition: NaCl 17.9462 g/l MgCl2 x 6 H2O 3.98804 g/l Fe(III) citrate 2.49252 g/l Na2CO3 0.997009 g/l NH4Cl 0.329013 g/l KCl 0.329013 g/l KH2PO4 0.329013 g/l CaCl2 x 2 H2O 0.329013 g/l Yeast extract 0.199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17535 | positive | growth | 50 | thermophilic |
30543 | positive | growth | 36-62 | |
30543 | positive | optimum | 50 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
30543 | positive | growth | 5.5-7.5 |
30543 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
17535 | anaerobe |
30543 | anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30543 | NaCl | positive | growth | 01-05 % |
30543 | NaCl | positive | optimum | 2.25 % |
Isolation, sampling and environmental information
isolation
- @ref: 17535
- sample type: deep-sea hydrothermal chimney, depth 2104-2163 m
- geographic location: Pacific Ocean, ABE hydrothermal field on the Eastern Lau Spreading Centre
- country: Tonga
- origin.country: TON
- continent: Australia and Oceania
- latitude: -20.7633
- longitude: -176.192
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Hydrothermal vent |
#Environmental | #Aquatic | #Marine |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_1732.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16425;96_986;97_1147;98_1370;99_1732&stattab=map
- Last taxonomy: Deferrisoma camini subclade
- 16S sequence: JF802205
- Sequence Identity:
- Total samples: 785
- soil counts: 138
- aquatic counts: 616
- animal counts: 15
- plant counts: 16
Safety information
risk assessment
- @ref: 17535
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17535
- description: Deferrisoma camini S3R1 16S ribosomal RNA gene, partial sequence
- accession: JF802205
- length: 1503
- database: ena
- NCBI tax ID: 1125863
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Deferrisoma camini S3R1 | GCA_000526155 | contig | ncbi | 1125863 |
66792 | Deferrisoma camini S3R1 | 1125863.3 | wgs | patric | 1125863 |
66792 | Deferrisoma camini S3R1 | 2517093047 | draft | img | 1125863 |
GC content
- @ref: 17535
- GC-content: 64.4
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 86.691 | yes |
flagellated | no | 76.878 | no |
gram-positive | no | 99.612 | no |
anaerobic | yes | 98.509 | no |
aerobic | no | 97.592 | no |
halophile | no | 64.066 | no |
spore-forming | no | 86.31 | no |
thermophile | yes | 82.86 | no |
glucose-util | yes | 52.21 | no |
glucose-ferment | no | 82.334 | no |
External links
@ref: 17535
culture collection no.: DSM 24185, VKM B-2672
straininfo link
- @ref: 87135
- straininfo: 399396
literature
- topic: Phylogeny
- Pubmed-ID: 22140176
- title: Deferrisoma camini gen. nov., sp. nov., a moderately thermophilic, dissimilatory iron(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in the Deltaproteobacteria.
- authors: Slobodkina GB, Reysenbach AL, Panteleeva AN, Kostrikina NA, Wagner ID, Bonch-Osmolovskaya EA, Slobodkin AI
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038372-0
- year: 2011
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification/metabolism, Ferric Compounds/*metabolism, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17535 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24185) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24185 | ||||
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 | ||||
30543 | 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 | 26874 | 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) | ||||
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 | 28604660 | 35: 676-683 2017 | ||
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 | ||||
87135 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399396.1 | StrainInfo: A central database for resolving microbial strain identifiers |