Name: Marinobacterium rhizophilum CL-YJ9
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 462

Type strain:

Species: Marinobacterium rhizophilum

Strain Designation: CL-YJ9

Culture col. no.: DSM 18822, KCCM 42386

Strain history: <- B. C. Cho, Seoul Nat. Univ., Republic of Korea; CL-YJ9

NCBI tax ID(s): 1122202 (strain), 420402 (species)

SI-ID 403386

DSM 18822

Section

Marinobacterium rhizophilum CL-YJ9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment associated with the roots of the coastal plant Suaeda japonica inhabiting a tidal flat.

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	*Alteromonadales*
	Family	*Alteromonadaceae*
	Genus	*Marinobacterium*
	Species	**Marinobacterium rhizophilum**
	Full Scientific Name (LPSN)	Marinobacterium rhizophilum Kim et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32238]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #32238]	Cell length	0.7 µm

[Ref.: #32238]	Cell width	0.35 µm

[Ref.: #32238]	Cell shape	rod-shaped

[Ref.: #32238]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.493

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7714]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7714]

Culture medium growth

[Ref.: #7714]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7714]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7714]	growth	28 °C
[Ref.: #32238]	growth	05-30 °C
[Ref.: #32238]	optimum	25 °C

[Ref.: #7714]	Temperature range	mesophilic
[Ref.: #32238]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32238]			optimum	7
[Ref.: #32238]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32238]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.974

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32238]		NaCl		growth	01-05	%
[Ref.: #32238]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32238]	arabinose ChEBI	+	carbon source
[Ref.: #32238]	arginine ChEBI	+	carbon source
[Ref.: #32238]	asparagine ChEBI	+	carbon source
[Ref.: #32238]	fructose ChEBI	+	carbon source
[Ref.: #32238]	galactose ChEBI	+	carbon source
[Ref.: #32238]	glucose ChEBI	+	carbon source
[Ref.: #32238]	glutamate ChEBI	+	carbon source
[Ref.: #32238]	glycerol ChEBI	+	carbon source
[Ref.: #32238]	glycine ChEBI	+	carbon source
[Ref.: #32238]	leucine ChEBI	+	carbon source
[Ref.: #32238]	mannitol ChEBI	+	carbon source
[Ref.: #32238]	mannose ChEBI	+	carbon source
[Ref.: #32238]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32238]	sucrose ChEBI	+	carbon source
[Ref.: #32238]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32238]	acid phosphatase	+	3.1.3.2
[Ref.: #32238]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32238]	catalase	+	1.11.1.6
[Ref.: #32238]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #7714]	Sample type/isolated from	sediment associated with the roots of the coastal plant Suaeda japonica inhabiting a tidal flat
[Ref.: #7714]	Host species	Suaeda japonica
[Ref.: #7714]	Geographic location (country and/or sea, region)	Youngjong Island, Eulwangri
[Ref.: #7714]	Country	Republic of Korea
[Ref.: #7714]	Country ISO 3 Code	KOR
[Ref.: #7714]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF192391 (>99% sequence identity) for Marinobacterium rhizophilum subclade from Microbeatlas

Aquatic Samples	403
Soil Samples	110
Animal Samples	40
Plant Samples	16
Total Samples	569

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

[Ref.: #7714]

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.: #7714]	Marinobacterium rhizophilum strain CL-YJ9 16S ribosomal RNA gene, partial sequence	EF192391	1371	ENA	420402 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marinobacterium rhizophilum DSM 18822	GCA_000378045	scaffold	GenBank	1122202 tax ID	*
[Ref.: #66792]	Marinobacterium rhizophilum DSM 18822	1122202.3	wgs	PATRIC	1122202 tax ID	*
[Ref.: #66792]	Marinobacterium rhizophilum DSM 18822	2518645605	draft	JGI IMG/M	1122202 tax ID	*

[Ref.: #7714]	GC-content	61.0 mol%
[Ref.: #32238]	GC-content	61 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Marinobacterium rhizophilum DSM 18822 DSM 18822 NCBI: GCA_000378045.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Marinobacterium rhizophilum DSM 18822 DSM 18822 NCBI: GCA_000378045.1
[Ref.: #69480]	motile	yes	90.244	yes
[Ref.: #69480]	flagellated	yes	79.721	no
[Ref.: #69480]	gram-positive	no	99.127	yes
[Ref.: #69480]	anaerobic	no	97.753	yes
[Ref.: #69480]	aerobic	yes	84.192	yes
[Ref.: #69480]	halophile	yes	70.784	no
[Ref.: #69480]	spore-forming	no	95.109	no
[Ref.: #69480]	glucose-util	yes	92.69	yes
[Ref.: #69480]	thermophile	no	99.544	yes
[Ref.: #69480]	glucose-ferment	no	83.631	no

Availability in culture collections External links

[Ref.: #7714]

Culture collection no.

DSM 18822, KCCM 42386

[Ref.: #70141]

SI-ID 403386

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marinobacterium aestuarii sp. nov., a benzene-degrading marine bacterium isolated from estuary sediment.	Bae SS, Jung J, Chung D, Baek K	Int J Syst Evol Microbiol	10.1099/ijsem.0.002561	2018	*
Genetics	Draft genome sequence of Marinobacterium rhizophilum CL-YJ9(T) (DSM 18822(T)), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.	Choi DH, Jang GI, Lapidus A, Copeland A, Reddy TBK, Mukherjee S, Huntemann M, Varghese N, Ivanova N, Pillay M, Tindall BJ, Goker M, Woyke T, Klenk HP, Kyrpides NC, Cho BC	Stand Genomic Sci	10.1186/s40793-017-0275-x	2017	*
Phylogeny	Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment.	Yeon Hwang C, Jung Yoon S, Lee I, Baek K, Mi Lee Y, Yoo KC, Il Yoon H, Kum Lee H	Int J Syst Evol Microbiol	10.1099/ijsem.0.000918	2016	*
Phylogeny	Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.	Kim YG, Jin YA, Hwang CY, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.65176-0	2008	*

References

#7714

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18822

#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 )

#32238

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 #28479 (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) .

#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 )

#70141

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-ID403386.1 )

#28479

IJSEM 164 2008 ( DOI 10.1099/ijs.0.65176-0 , PubMed 18175703 )

* These data were automatically processed and therefore are not curated

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Marinobacterium rhizophilum DSM 18822 DSM 18822

Marinobacterium rhizophilum DSM 18822 DSM 18822

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