Deferrisoma palaeochoriense (DSM 29363, JCM 30394, MAG-PB1)

Name: Deferrisoma palaeochoriense (DSM 29363, JCM 30394, MAG-PB1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132415

Type strain

Strain Designation MAG-PB1

Culture col. no. DSM 29363 JCM 30394 MAG-PB1

NCBI tax ID(s) 1573172

Special Collections DSMZ JCM Literature strains

History DSMZ <- I. Pérez-Rodríguez, Carnegie Inst. of Washington, Geophysical Lab., USA; MAG-PB1 <- I. Pérez-Rodríguez {2013} JCM <-- I. Pérez-Rodríguez; Carnegie Inst. of Washington, USA; MAG-PB1.

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

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

Name and taxonomic classification

SI-ID 398852

JCM 30394,DSM 29363

@ref 20215

Last LPSN update 2026-05-29 08:37:51

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Deferrisomatia

Order Deferrisomatales

Family Deferrisomataceae

Genus Deferrisoma

Species Deferrisoma palaeochoriense

Full scientific name Deferrisoma palaeochoriense Pérez-Rodríguez et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
44025	negative	0.8-1.0 µm	0.5 µm	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24204	THERMOSULFURIMONAS MEDIUM (DSMZ Medium 1210a)		Medium recipe at MediaDive	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

@ref	Growth	Type	Temperature (°C)
24204	positive	growth	60
44025	positive	growth	30-70
44025	positive	optimum	60
44025
67770	positive	growth	60

Culture pH

@ref	Ability	Type	PH
44025	positive	optimum	6
44025	positive	growth	5.5-8.0

Physiology and metabolism

Oxygen tolerance

44025

Oxygen toleranceobligate anaerobe

Nutrition type

44025

Typemixotroph

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44025	NaCl	positive	growth	0-55 g/L
44025	NaCl	positive	optimum	15-20 g/L

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44025	30089 ChEBI	acetate	+/-	growth
44025	17925 ChEBI	alpha-D-glucose	+	electron donor
44025	29125 ChEBI	arsenate	+	electron acceptor
44025	16526 ChEBI	carbon dioxide	+	carbon source
44025		casamino acids	+	electron donor
44025	17108 ChEBI	D-arabinose	+	electron donor
44025	15824 ChEBI	D-fructose	+	electron donor
44025	18276 ChEBI	dihydrogen	+	energy source
44025	33403 ChEBI	elemental sulfur	-	electron acceptor
44025	29034 ChEBI	ferric iron	+	electron acceptor
44025	15740 ChEBI	formate	-	growth
44025	24996 ChEBI	lactate	-	growth
44025	18291 ChEBI	manganese	+	electron acceptor
44025		peptone	+	electron donor
44025	15075 ChEBI	selenate	+	electron acceptor
44025	17992 ChEBI	sucrose	+	electron donor
44025		tryptone	+	electron donor
44025		yeast extract	+	electron donor

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
44025	28971	ampicillin	100 µg/mL
44025	27902	tetracycline	100 µg/mL
44025	28001	vancomycin		100000 µg/mL

Enzymes

@ref	Value	Activity	Ec
44025	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Terrestrial	#Coast
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Isolation procedure
24204	shallow-water hydrothermal vent		Mediterranean Sea, Palaeochori Bay off the coast of the island of Milos	Greece	GRC	Europe
44025	sediments of an active shallow-water vent	2012-05	Palaeochori Bay, Milos	Greece	GRC	Europe	modified basal medium described by Slobodkina et al. 2009	KH2PO4 (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
67770	Shallow-water hydrothermal vent system in Palaeochrobi Bay off the coast of the island of Milos			Greece	GRC	Europe

Taxonmaps

69479

Global distribution of 16S sequence KM386664 (>99% sequence identity) for Deferrisoma palaeochoriense subclade from Microbeatlas

Aquatic Samples	101
Soil Samples	5
Animal Samples	1
Plant Samples	1
Total Samples	108

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24204	1	Risk group (German classification)

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24204	Deferrisoma palaeochoriense strain MAG-PB1 16S ribosomal RNA gene, partial sequence	KM386664	1322		1573172

GC content

@ref	GC-content (mol%)	Method
24204	66.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea.	Perez-Rodriguez I, Rawls M, Coykendall DK, Foustoukos DI	Int J Syst Evol Microbiol	10.1099/ijsem.0.000798	2015

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#24204	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29363
#44025	Ileana Pérez-Rodríguez, Matthew Rawls, D. Katharine Coykendall and Dionysis I. Foustoukos: Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea. IJSEM 66: 830 - 836 2016 ( DOI 10.1099/ijsem.0.000798 , PubMed 26610851 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Deferrisoma palaeochoriense (DSM 29363, JCM 30394, MAG-PB1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Halophily

Metabolite utilization

Antibiotic resistance

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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