Name: Parasphingorhabdus marina FR1087
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14283

Type strain:

Species: Parasphingorhabdus marina

Strain Designation: FR1087

Culture col. no.: DSM 22363, IMSNU 14132, JCM 14161, KCTC 12763

Strain history: <- J Chun, Seoul Nat. Univ.

NCBI tax ID(s): 394732 (species)

SI-ID 359534

JCM 14161, KCTC 12763, DSM 22363

Special Collections

Section

When using BacDive for research please cite our paper

Parasphingorhabdus marina FR1087 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface seawater.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Parasphingorhabdus*
	Species	**Parasphingorhabdus marina**
	Full Scientific Name (LPSN)	Parasphingorhabdus marina (Kim et al. 2008) Feng et al. 2020

	Synonym	Sphingorhabdus marina
	Synonym	Sphingopyxis marina

Information on morphological and physiological properties Morphology

[Ref.: #32518]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.969
[Ref.: #125439]	Gram stain	negative Confidence in %98.5

[Ref.: #32518]	Cell shape	rod-shaped

[Ref.: #32518]	Motility	yes

[Ref.: #32518]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16185]

Culture medium

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

[Ref.: #16185]

Culture medium growth

[Ref.: #16185]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16185]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16185]	growth	30 °C
[Ref.: #32518]	growth	15-34.4 °C
[Ref.: #32518]	optimum	23.7-31.8 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32518]			optimum	7
[Ref.: #32518]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32518]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	aerobe Confidence in %96.7

[Ref.: #32518]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %94.9

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32518]		NaCl		growth	03-07	%
[Ref.: #32518]		NaCl		optimum	03-05	%

[Ref.: #32518]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32518]	adipate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32518]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32518]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32518]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32518]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #32518]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #32518]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #32518]	urease	+	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #16185]	25941	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+

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

[Ref.: #16185]	Sample type/isolated from	surface seawater
[Ref.: #16185]	Geographic location (country and/or sea, region)	Jeju Island
[Ref.: #16185]	Country	Republic of Korea
[Ref.: #16185]	Country ISO 3 Code	KOR
[Ref.: #16185]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ781320 (>99% sequence identity) for Parasphingorhabdus marina from Microbeatlas

Aquatic Samples	481
Soil Samples	54
Animal Samples	62
Plant Samples	7
Total Samples	604

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

[Ref.: #16185]

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.: #16185]	Sphingopyxis marina strain FR1087 16S ribosomal RNA gene, partial sequence	DQ781320	1409	GenBank ENA	1123272 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parasphingorhabdus marina DSM 22363	GCA_900128895	contig	GenBank ENA	1123272 tax ID	*
[Ref.: #66792]	Sphingorhabdus marina DSM 22363	1123272.4	wgs	PATRIC	1123272 tax ID	*
[Ref.: #66792]	Parasphingorhabdus marina DSM 22363	2582580503	draft	JGI IMG/M	1123272 tax ID	*

[Ref.: #16185]

GC-content

56.5 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingorhabdus marina DSM 22363 PATRIC: 1123272.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.969	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.158	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.59	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.031	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.711	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	57.205	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parasphingorhabdus marina DSM 22363 NCBI: GCA_900128895
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	55.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	96.7

Availability in culture collections External links

[Ref.: #16185]

Culture collection no.

DSM 22363, IMSNU 14132, JCM 14161, KCTC 12763

[Ref.: #83438]

SI-ID 359534

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.	Kim SJ, Kim M, Lee KE, Cha IT, Park SJ	Arch Microbiol	10.1007/s00203-021-02366-8	2021	*

References

#16185

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22363

#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 )

#32518

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 #28738 (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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#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 .

#83438

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-ID359534.1 )

#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 .

#28738

IJSEM 2415 2008 ( DOI 10.1099/ijs.0.65614-0 , PubMed 18842866 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Sphingorhabdus marina in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Sphingorhabdus marina DSM 22363

Parasphingorhabdus marina DSM 22363

Change proposal

Change proposal