Name: Methylomarinum vadi IT-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24177

Type strain:

Species: Methylomarinum vadi

Strain Designation: IT-4

Culture col. no.: DSM 18976, JCM 13665

Strain history: H. Hirayama IT-4.

NCBI tax ID(s): 438855 (species)

SI-ID 398898

DSM 18976

Section

Methylomarinum vadi IT-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from microbial mat at a shallow submarine hot spring.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Gammaproteobacteria*
	Order	*Methylococcales*
	Family	*Methylococcaceae*
	Genus	*Methylomarinum*
	Species	**Methylomarinum vadi**
	Full Scientific Name (LPSN)	Methylomarinum vadi Hirayama et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30626]	Gram stain	negative

[Ref.: #30626]	Cell length	1.95 µm

[Ref.: #30626]	Cell width	1 µm

[Ref.: #30626]	Cell shape	rod-shaped

[Ref.: #30626]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21161]

Culture medium

METHYLOTHERMUS MEDIUM (DSMZ Medium 1412)

[Ref.: #21161]

Culture medium growth

[Ref.: #21161]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21161]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21161]	growth	37 °C
[Ref.: #30626]	growth	20-44 °C
[Ref.: #30626]	optimum	40 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #21161]	Temperature range	mesophilic
[Ref.: #30626]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30626]			optimum	6.4
[Ref.: #30626]			growth	4.5-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30626]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30626]		NaCl		growth	01-08	%
[Ref.: #30626]		NaCl		optimum	2.5	%

[Ref.: #67770]

Observation

quinones: MQ-8

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

[Ref.: #21161]	Sample type/isolated from	microbial mat at a shallow submarine hot spring
[Ref.: #21161]	Geographic location (country and/or sea, region)	Okinawa, off Taketomi Island
[Ref.: #21161]	Country	Japan
[Ref.: #21161]	Country ISO 3 Code	JPN
[Ref.: #21161]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Shallow submarine hydrothermal system off Taketomi Island
[Ref.: #67770]	Geographic location (country and/or sea, region)	Okinawa
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Thermal spring
#Environmental	#Microbial community	#Microbial mat
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB301717 (>99% sequence identity) for Methylomarinum vadi subclade from Microbeatlas

Aquatic Samples	1882
Soil Samples	365
Animal Samples	48
Plant Samples	55
Total Samples	2350

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21161]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #21161]	Methylomarinum vadi gene for 16S ribosomal RNA, partial sequence, strain: IT-4	AB301717	1464	ENA	438855 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Methylomarinum vadi IT-4	GCA_000733935	contig	GenBank	438855 tax ID
[Ref.: #66792]	Methylomarinum vadi IT-4	2574179779	draft	JGI IMG/M	438855 tax ID	*

[Ref.: #21161]	GC-content	51.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30626]	GC-content	51 mol%
[Ref.: #67770]	GC-content	50.9-51.0 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #21161]

Culture collection no.

DSM 18976, JCM 13665

[Ref.: #88131]

SI-ID 398898

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.	Flynn JD, Hirayama H, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJ, Jetten MS, Khmelenina VN, Trotsenko YA, Murrell JC, Semrau JD, Svenning MM, Stein LY, Kyrpides N, Shapiro N, Woyke T, Bringel F, Vuilleumier S, DiSpirito AA, Kalyuzhnaya MG	Genome Announc	10.1128/genomeA.01629-15	2016	*
Phylogeny	Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments.	Hirayama H, Fuse H, Abe M, Miyazaki M, Nakamura T, Nunoura T, Furushima Y, Yamamoto H, Takai K	Int J Syst Evol Microbiol	10.1099/ijs.0.040568-0	2012	*

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 )

#21161

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18976

#30626

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26957 (see below)

#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 .

#88131

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID398898.1 )

#26957

IJSEM 1073 2013 ( DOI 10.1099/ijs.0.040568-0 , PubMed 22707534 )

* These data were automatically processed and therefore are not curated

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