Name: Ruegeria atlantica 1480
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13780

Type strain:

Species: Ruegeria atlantica

Strain Designation: 1480, Rüger, Rüger, 1480

Culture col. no.: DSM 5823, JCM 21234, ATCC 700000, CIP 105975, IAM 14463, IFO 15792, NBRC 15792

Strain history: CIP <- 1999, IAM <- DSMZ <- H.J. Rüger: strain 1480

NCBI tax ID(s): 81569 (species)

SI-ID 368535

ATCC 700000, DSM 5823, IAM 14463, CIP 105975, IFO 15792, CECT 4292, NBRC 15792, KCTC 12424, LMG 23161, NBRC 101135, JCM 21234

Other strains from Ruegeria atlantica

R. atlantica 1513, DSM 5824, JCM 21235, ATCC ...

Section

Ruegeria atlantica 1480 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from marine upwelling area.

Gram-negative
rod-shaped
psychrophilic
16S sequence
Bacteria

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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Ruegeria*
	Species	**Ruegeria atlantica**
	Full Scientific Name (LPSN)	Ruegeria atlantica (Rüger and Höfle 1992) Uchino et al. 1999

Synonym

Agrobacterium atlanticum

Information on morphological and physiological properties Morphology

[Ref.: #116537]	Gram stain	negative

[Ref.: #116537]	Cell shape	rod-shaped

[Ref.: #116537]	Motility	no

[Ref.: #2328]

Incubation period

2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2328]

Culture medium

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

[Ref.: #2328]

Culture medium growth

[Ref.: #2328]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2328]

Culture medium composition

expand / minimize

[Ref.: #39412]

Culture medium

Marine agar (MA)

[Ref.: #39412]

Culture medium growth

[Ref.: #39412]

Culture medium composition

expand / minimize

[Ref.: #116537]

Culture medium

CIP Medium 13

[Ref.: #116537]

Culture medium growth

[Ref.: #116537]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #2328]		growth	20 °C
[Ref.: #39412]		growth	22 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #116537]		growth	15-30 °C
[Ref.: #116537]	no	growth	5 °C
[Ref.: #116537]	no	growth	37 °C
[Ref.: #116537]	no	growth	41 °C
[Ref.: #116537]	no	growth	45 °C

[Ref.: #2328]	Temperature range	psychrophilic
[Ref.: #39412]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #116537]	Temperature range	psychrophilic
[Ref.: #116537]	Temperature range	mesophilic
[Ref.: #116537]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

	Salt	Tested relation		Salt conc.
[Ref.: #116537]	NaCl	no	growth	0	%
[Ref.: #116537]	NaCl	no	growth	2	%
[Ref.: #116537]	NaCl	no	growth	4	%
[Ref.: #116537]	NaCl	no	growth	6	%
[Ref.: #116537]	NaCl	no	growth	8	%
[Ref.: #116537]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[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.: #116537]	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.: #116537]	glucose ChEBI	-	degradation
[Ref.: #116537]	hippurate ChEBI	+	hydrolysis
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #116537]	malonate ChEBI	-	assimilation
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #116537]	nitrate ChEBI	+	builds gas from
[Ref.: #116537]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #116537]	nitrite ChEBI	+	builds gas from
[Ref.: #116537]	nitrite ChEBI	+	reduction
[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.: #116537]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #116537]	acetoin ChEBI	-
[Ref.: #116537]	glucose ChEBI		-
[Ref.: #68369]	indole ChEBI			-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116537]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116537]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #116537]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE, API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116537]	caseinase	-	3.4.21.50
[Ref.: #2328]	catalase	+	1.11.1.6
[Ref.: #116537]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #2328]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #116537]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #116537]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #116537]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #116537]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116537]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116537]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116537]	oxidase	+
[Ref.: #116537]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #116537]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116537]	tryptophan deaminase	-
[Ref.: #116537]	tween esterase	-
[Ref.: #116537]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #2328]	23576	+	-	-	-	-	-	-	+	-	-	-	-	+/-	-	-	-	-	-	-	-	not determinedn.d.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #116537]	1446	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116537]	9136	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #2328]	Sample type/isolated from	marine upwelling area
[Ref.: #2328]	Geographic location (country and/or sea, region)	Africa NW (21° 24.6' N; 17° 53.6' W)
[Ref.: #2328]	Geographic location	21.4100°/-17.8933°

[Ref.: #67770]	Sample type/isolated from	Marine sediments of the eastern Atlantic Ocean

[Ref.: #116537]	Sample type/isolated from	Marine urwelling area
[Ref.: #116537]	Country	Atlantic Ocean
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D88526 (>99% sequence identity) for Ruegeria from Microbeatlas

Aquatic Samples	4771
Soil Samples	60
Animal Samples	398
Plant Samples	22
Total Samples	5251

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

[Ref.: #2328]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116537]	Biosafety level	1	Risk group (French classification)

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.: #67770]	Ruegeria atlantica gene for 16S ribosomal RNA, partial sequence	AB255399	1385	ENA	81569 tax ID
[Ref.: #2328]	Agrobacterium atlanticum gene for 16S rRNA, partial sequence	D88526	1384	ENA	81569 tax ID

[Ref.: #67770]

GC-content

55 mol%

thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #2328]

Culture collection no.

DSM 5823, JCM 21234, ATCC 700000, CIP 105975, IAM 14463, IFO 15792, NBRC 15792

[Ref.: #82959]

SI-ID 368535

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.	Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.066142-0	2014	*
Phylogeny	Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean.	Lee K, Choo YJ, Giovannoni SJ, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.65032-0	2007	*
Phylogeny	Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev.	Uchino Y, Hirata A, Yokota A, Sugiyama J	J Gen Appl Microbiol	10.2323/jgam.44.201	1998	*
Phylogeny	Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev.	Ruger HJ, Hofle MG	Int J Syst Bacteriol	10.1099/00207713-42-1-133	1992	*

References

#2328

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5823

#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 )

#39412 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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 .

#82959

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-ID368535.1 )

#116537 Collection of Institut Pasteur ; Curators of the CIP; CIP 105975
* These data were automatically processed and therefore are not curated

Change proposal

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