Strain identifier

BacDive ID: 18151

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_24185_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_24185_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_24185_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_24185_4.jpgelectron 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

@refgrowthtypetemperaturerange
17535positivegrowth50thermophilic
30543positivegrowth36-62
30543positiveoptimum50thermophilic

culture pH

@refabilitytypepH
30543positivegrowth5.5-7.5
30543positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17535anaerobe
30543anaerobe

halophily

@refsaltgrowthtested relationconcentration
30543NaClpositivegrowth01-05 %
30543NaClpositiveoptimum2.25 %

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deferrisoma camini S3R1GCA_000526155contigncbi1125863
66792Deferrisoma camini S3R11125863.3wgspatric1125863
66792Deferrisoma camini S3R12517093047draftimg1125863

GC content

  • @ref: 17535
  • GC-content: 64.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.691yes
flagellatedno76.878no
gram-positiveno99.612no
anaerobicyes98.509no
aerobicno97.592no
halophileno64.066no
spore-formingno86.31no
thermophileyes82.86no
glucose-utilyes52.21no
glucose-fermentno82.334no

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17535Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24185)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24185
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30543Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2687428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
69479João 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
87135Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399396.1StrainInfo: A central database for resolving microbial strain identifiers