Marinobacterium rhizophilum (DSM 18822, KCCM 42386, CL-YJ9)

Name: Marinobacterium rhizophilum (DSM 18822, KCCM 42386, CL-YJ9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 462

Type strain

Strain Designation CL-YJ9

Culture col. no. DSM 18822 KCCM 42386 CL-YJ9

NCBI tax ID(s) 1122202 420402

Special Collections DSMZ Literature strains

History DSMZ <- B. C. Cho, Seoul Nat. Univ., Republic of Korea; CL-YJ9

Links

Marinobacterium rhizophilum CL-YJ9 is an aerobe, Gram-negative, motile 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 genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403386

DSM 18822

@ref 20215

Last LPSN update 2026-05-29 08:25:02

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Alteromonadaceae

Genus Marinobacterium

Species Marinobacterium rhizophilum

Full scientific name Marinobacterium rhizophilum Kim et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32238	negative	0.7 µm	0.35 µm	rod-shaped
125439					90.502
125439	negative				99.711
125438	negative				98.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7714	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7714	positive	growth	28
32238	positive	growth	05-30
32238	positive	optimum	25

Culture pH

@ref	Ability	Type	PH	PH range
32238	positive	optimum	7
32238	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

32238

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.95

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32238	NaCl	positive	growth	01-05 %
32238	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32238	22599 ChEBI	arabinose	+	carbon source
32238	29016 ChEBI	arginine	+	carbon source
32238	22653 ChEBI	asparagine	+	carbon source
32238	28757 ChEBI	fructose	+	carbon source
32238	28260 ChEBI	galactose	+	carbon source
32238	17234 ChEBI	glucose	+	carbon source
32238	29987 ChEBI	glutamate	+	carbon source
32238	17754 ChEBI	glycerol	+	carbon source
32238	15428 ChEBI	glycine	+	carbon source
32238	25017 ChEBI	leucine	+	carbon source
32238	29864 ChEBI	mannitol	+	carbon source
32238	37684 ChEBI	mannose	+	carbon source
32238	506227 ChEBI	N-acetylglucosamine	+	carbon source
32238	17992 ChEBI	sucrose	+	carbon source
32238	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32238	acid phosphatase	+	3.1.3.2
32238	alkaline phosphatase	+	3.1.3.1
32238	catalase	+	1.11.1.6
32238	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
7714	sediment associated with the roots of the coastal plant Suaeda japonica inhabiting a tidal flat	Suaeda japonica	Youngjong Island, Eulwangri	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7714	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM37804v1 assembly for Marinobacterium rhizophilum DSM 18822	scaffold	GCA_000378045	1122202.3	2518645605	1122202	65.27

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7714	Marinobacterium rhizophilum strain CL-YJ9 16S ribosomal RNA gene, partial sequence	EF192391	1371		420402

GC content

@ref	GC-content (mol%)
7714	61.0
32238	61

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM37804v1 assembly for Marinobacterium rhizophilum DSM 18822
BV-BRC: 1122202.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.87	no
125439	gram_stain	BacteriaNetⓘ	negative	99.71	no
125439	motility	BacteriaNetⓘ	yes	90.50	no
125439	spore_formation	BacteriaNetⓘ	no	99.95	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marinobacterium rhizophilum DSM 18822 DSM 18822
NCBI: GCA_000378045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	91.60	yes
125438	aerobic	aerobicⓘ	yes	76.29	yes
125438	spore-forming	spore-formingⓘ	no	89.22	no
125438	thermophilic	thermophileⓘ	no	98.13	yes
125438	flagellated	motile2+ⓘ	yes	61.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome Sequences and Metagenome-Assembled Genome Sequences of Microbial Communities Enriched on Phytoplankton Exometabolites.	Fu H, Smith CB, Sharma S, Moran MA.	Microbiol Resour Announc	10.1128/mra.00724-20	2020
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 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
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 )
#28479	IJSEM 164 2008 ( DOI 10.1099/ijs.0.65176-0 , PubMed 18175703 )
#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
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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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Marinobacterium rhizophilum (DSM 18822, KCCM 42386, CL-YJ9)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000378045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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