Name: Iodidimonas muriae C-3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133277

Type strain:

Species: Iodidimonas muriae

Strain Designation: C-3

Culture col. no.: JCM 17843, LMG 28660

Strain history: S. Amachi C-3.

NCBI tax ID(s): 261467 (species)

Special Collections

Section

Iodidimonas muriae C-3 is an aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from iodide-rich brine associated with natural gas.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
chemoorganotroph
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Iodidimonadales*
	Family	*Iodidimonadaceae*
	Genus	*Iodidimonas*
	Species	**Iodidimonas muriae**
	Full Scientific Name (LPSN)	Iodidimonas muriae Iino et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25125]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96

[Ref.: #25125]	Cell length	1.3-3.6 µm

[Ref.: #25125]	Cell width	0.5-1.1 µm

[Ref.: #25125]	Cell shape	rod-shaped

[Ref.: #25125]	Motility	yes

[Ref.: #25125]	Colony size	0.5-1.5 mm
[Ref.: #25125]	Colony color	creamy white
[Ref.: #25125]	Colony shape	circular
[Ref.: #25125]	Incubation period	7 days
[Ref.: #25125]	Cultivation medium used	MA (marine agar)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25125]

Culture medium

MA (marine agar 2216)

[Ref.: #25125]

Culture medium growth

[Ref.: #25125]

Culture medium

Marine agar (MA)

[Ref.: #25125]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #25125]		optimum	30 °C
[Ref.: #25125]		growth	4.0-40.0 °C
[Ref.: #25125]	no	growth	45 °C
[Ref.: #67770]		growth	30 °C

	Kind of pH		pH
[Ref.: #25125]		optimum	7.5
[Ref.: #25125]		growth	4.5-8.5
[Ref.: #25125]	no	growth	4
[Ref.: #25125]	no	growth	9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25125]

Oxygen tolerance

aerobe

[Ref.: #25125]

Nutrition type

chemoorganotroph

[Ref.: #25125]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %92.559
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #25125]

Halophily / tolerance level

moderately halophilic

	Salt	Tested relation		Salt conc.
[Ref.: #25125]	NaCl		optimum	3	%(w/v)
[Ref.: #25125]	NaCl		growth	0.5-9.0	%(w/v)
[Ref.: #25125]	NaCl	no	growth	0	%(w/v)
[Ref.: #25125]	NaCl	no	growth	10	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25125]	acetate ChEBI	+	electron donor
[Ref.: #25125]	ammonium ChEBI	-	electron donor
[Ref.: #25125]	citrate ChEBI	-	electron donor
[Ref.: #25125]	D-glucose ChEBI	+	electron donor
[Ref.: #25125]	D-mannose ChEBI	-	electron donor
[Ref.: #25125]	D-ribose ChEBI	-	electron donor
[Ref.: #25125]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #25125]	esculin ChEBI	+	hydrolysis
[Ref.: #25125]	ferric oxide ChEBI	-	electron acceptor
[Ref.: #25125]	iodide ChEBI	-	electron donor
[Ref.: #25125]	iodide ChEBI	+	oxidation
[Ref.: #25125]	iron trichloride ChEBI	-	electron acceptor
[Ref.: #25125]	lactate ChEBI	-	electron donor
[Ref.: #25125]	lactose ChEBI	-	electron donor
[Ref.: #25125]	malate ChEBI	-	electron donor
[Ref.: #25125]	maltose ChEBI	+	electron donor
[Ref.: #25125]	methane ChEBI	-	electron donor
[Ref.: #25125]	methanol ChEBI	-	electron donor
[Ref.: #25125]	nitrate ChEBI	-	electron acceptor
[Ref.: #25125]	nitrite ChEBI	-	electron acceptor
[Ref.: #25125]	nitrite ChEBI	-	electron donor
[Ref.: #25125]	pyruvate ChEBI	-	electron donor
[Ref.: #25125]	starch ChEBI	+	electron donor
[Ref.: #25125]	succinate ChEBI	-	electron donor
[Ref.: #25125]	sucrose ChEBI	+	electron donor
[Ref.: #25125]	sulfate ChEBI	-	electron acceptor
[Ref.: #25125]	sulfide ChEBI	-	electron donor
[Ref.: #25125]	sulfite ChEBI	-	electron acceptor
[Ref.: #25125]	sulfite ChEBI	-	electron donor
[Ref.: #25125]	thiosulfate ChEBI	-	electron acceptor
[Ref.: #25125]	thiosulfate ChEBI	-	electron donor
[Ref.: #25125]	tryptophan ChEBI	-	energy source
[Ref.: #25125]	yeast extract	+	electron donor
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25125]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25125]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25125]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25125]	beta-galactosidase	-	3.2.1.23
[Ref.: #25125]	catalase	+	1.11.1.6
[Ref.: #25125]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25125]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25125]	urease	-	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #25125]	Sample type/isolated from	iodide-rich brine associated with natural gas
[Ref.: #25125]	Geographic location (country and/or sea, region)	Kujukuri, Chiba
[Ref.: #25125]	Country	Japan
[Ref.: #25125]	Country ISO 3 Code	JPN
[Ref.: #25125]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Natural gas brine of an iodine recovery facility in Kujukuri
[Ref.: #67770]	Geographic location (country and/or sea, region)	Chiba
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC127220 (>99% sequence identity) for Iodidimonas from Microbeatlas

Aquatic Samples	357
Soil Samples	30
Animal Samples	37
Plant Samples	5
Total Samples	429

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #25125]	Iodidimonas muriae gene for 16S ribosomal RNA, partial sequence, strain: C-3	LC127220	1437	GenBank ENA	261467 tax ID
[Ref.: #67770]	Iodide-oxidizing bacterium C-3 gene for 16S rRNA, partial sequence	AB159205	1328	GenBank ENA	261467 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Kordiimonadales bacterium JCM 17843 C-3	GCA_008579105	contig	GenBank ENA	1236965 tax ID	*
[Ref.: #66792]	Iodidimonas muriae JCM 17843	GCA_014647255	scaffold	GenBank ENA	261467 tax ID	*
[Ref.: #66792]	Iodidimonas muriae strain JCM 17843	261467.5	wgs	PATRIC	261467 tax ID	*
[Ref.: #66792]	Kordiimonadales bacterium JCM 17843 strain C-3	1236965.3	wgs	PATRIC	1236965 tax ID	*

[Ref.: #25125]	GC-content	58.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	55.6 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Iodidimonas muriae JCM 17843 NCBI: GCA_014647255.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Iodidimonas muriae JCM 17843 NCBI: GCA_014647255.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.439	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.913	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.559	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.088	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.758	no

Availability in culture collections External links

[Ref.: #25125]

Culture collection no.

JCM 17843, LMG 28660

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov.	Iino T, Ohkuma M, Kamagata Y, Amachi S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001462	2016	*

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 )

#25125

T. O. Iino, M.,Kamagata, Y.,Amachi, S.: Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov. IJSEM 66: 5016 - 5022 2016 ( DOI 10.1099/ijsem.0.001462 , PubMed 27566239 )

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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