Strain identifier

BacDive ID: 132415

Type strain: Yes

Species: Deferrisoma palaeochoriense

Strain Designation: MAG-PB1

Strain history: I. Pérez-Rodríguez; Carnegie Inst. of Washington, USA; MAG-PB1.

NCBI tax ID(s): 1573172 (species)

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General

@ref: 24204

BacDive-ID: 132415

DSM-Number: 29363

keywords: 16S sequence, Bacteria, obligate anaerobe, mixotroph, Gram-negative, motile, rod-shaped

description: Deferrisoma palaeochoriense MAG-PB1 is an obligate anaerobe, mixotroph, Gram-negative bacterium that was isolated from shallow-water hydrothermal vent.

NCBI tax id

  • NCBI tax id: 1573172
  • Matching level: species

strain history

@refhistory
24204<- I. Pérez-Rodríguez, Carnegie Inst. of Washington, Geophysical Lab., USA; MAG-PB1 <- I. Pérez-Rodríguez {2013}
67770I. Pérez-Rodríguez; Carnegie Inst. of Washington, USA; MAG-PB1.

doi: 10.13145/bacdive132415.20230509.8.1

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 palaeochoriense
  • full scientific name: Deferrisoma palaeochoriense Pérez-Rodríguez et al. 2016

@ref: 24204

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Deltaproteobacteria, not assigned to order

family: Deferrisomataceae

genus: Deferrisoma

species: Deferrisoma palaeochoriense

full scientific name: Deferrisoma palaeochoriense Pérez-Rodríguez et al. 2016

strain designation: MAG-PB1

type strain: yes

Morphology

cell morphology

  • @ref: 44025
  • gram stain: negative
  • cell length: 0.8-1.0 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 24204
  • name: THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1210a
  • composition: Name: THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a; with strain-specific modifications) 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 (NH4)2SO4 0.498504 g/l CaCl2 x 2 H2O 0.329013 g/l KH2PO4 0.329013 g/l KCl 0.329013 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 Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 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
44025positivegrowth30-70
44025positiveoptimum60thermophilic
44025thermophilic
24204positivegrowth60thermophilic
67770positivegrowth60thermophilic

culture pH

@refabilitytypepH
44025positivegrowth5.5-8.0
44025positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 44025
  • oxygen tolerance: obligate anaerobe

nutrition type

  • @ref: 44025
  • type: mixotroph

halophily

@refsaltgrowthtested relationconcentration
44025NaClpositivegrowth0-55 g/L
44025NaClpositiveoptimum15-20 g/L

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4402533403elemental sulfur-electron acceptor
4402515740formate-growth
4402524996lactate-growth
4402516526carbon dioxide+carbon source
4402529125arsenate+electron acceptor
4402529034ferric iron+electron acceptor
4402518291manganese+electron acceptor
4402515075selenate+electron acceptor
4402517108D-arabinose+electron donor
4402517925alpha-D-glucose+electron donor
44025casamino acids+electron donor
4402515824D-fructose+electron donor
44025peptone+electron donor
4402517992sucrose+electron donor
44025tryptone+electron donor
44025yeast extract+electron donor
4402518276dihydrogen+energy source
4402530089acetate+/-growth

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4402528001vancomycinyesyes100000 µg/mL
4402528971ampicillinyesyes100 µg/mL
4402527902tetracyclineyesyes100 µg/mL

enzymes

  • @ref: 44025
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture compositionisolation procedure
24204shallow-water hydrothermal ventMediterranean Sea, Palaeochori Bay off the coast of the island of MilosGreeceGRCEurope
44025sediments of an active shallow-water ventPalaeochori Bay, MilosGreeceGRCEurope2012-05modified basal medium described by Slobodkina et al. 2009KH2PO4 (0.33 g), (NH4)2SO4 (0.5 g), KCl (0.33 g), MgCl2 . 6H2O (4.0 g), CaCl2 . 2H2O (0.33 g), NaHCO3 (0.8 g), NaCl (18.0 g), 1 ml trace-element solution SL-10 (Sleat et al., 1984), 1 ml selenite-tungstate solution (Tschech & Schink, 1985) and 1 ml vitamin solution (Wolin et al., 1963). The pH of the medium was not adjusted and no reducing agent was added. Fe(III) was provided in the form of amorphous Fe(III) oxide (88 mmol/l), synthesized by titrating a solution of FeCl3 x 6H2O with NaOH (10 %,Upon arrival at the eld laboratory, samples were processed and stored at 4°C under a N2 (100%, v/v; 200 kPa) atmosphere. 10 consecutive series of dilutions at 50°C
67770Shallow-water hydrothermal vent system in Palaeochrobi Bay off the coast of the island of MilosGreeceGRCEurope

isolation source categories

Cat1Cat2Cat3
#Condition#Thermophilic (>45°C)
#Environmental#Terrestrial#Coast
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_55755.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16425;96_986;97_1147;98_39822;99_55755&stattab=map
  • Last taxonomy: Deferrisoma palaeochoriense subclade
  • 16S sequence: KM386664
  • Sequence Identity:
  • Total samples: 108
  • soil counts: 5
  • aquatic counts: 101
  • animal counts: 1
  • plant counts: 1

Safety information

risk assessment

  • @ref: 24204
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24204
  • description: Deferrisoma paleochoriense strain MAG-PB1 16S ribosomal RNA gene, partial sequence
  • accession: KM386664
  • length: 1322
  • database: ena
  • NCBI tax ID: 1573172

GC content

  • @ref: 24204
  • GC-content: 66.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24204

culture collection no.: DSM 29363, JCM 30394

straininfo link

  • @ref: 90755
  • straininfo: 398852

literature

  • topic: Phylogeny
  • Pubmed-ID: 26610851
  • title: Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea.
  • authors: Perez-Rodriguez I, Rawls M, Coykendall DK, Foustoukos DI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000798
  • year: 2015
  • mesh: Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Greece, Hydrothermal Vents/*microbiology, Iron/metabolism, Mediterranean Sea, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24204Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29363Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29363)
44025Ileana Pérez-Rodríguez, Matthew Rawls, D. Katharine Coykendall and Dionysis I. FoustoukosDeferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea10.1099/ijsem.0.000798IJSEM 66: 830-836 201626610851
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90755Reimer, 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 identifiers10.60712/SI-ID398852.1