Name: Ruegeria halocynthiae MA1-6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24503

Type strain:

Species: Ruegeria halocynthiae

Strain Designation: MA1-6

Culture col. no.: DSM 27839, CCUG 60744, KCTC 23463

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 985054 (species)

SI-ID 402546

DSM 27839, CCUG 60744

Section

Ruegeria halocynthiae MA1-6 is a facultative aerobe, mesophilic, Gram-variable bacterium that was isolated from sea squirt Halocynthia roretzi.

Gram-variable
rod-shaped
facultative 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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Ruegeria*
	Species	**Ruegeria halocynthiae**
	Full Scientific Name (LPSN)	Ruegeria halocynthiae Kim et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30246]	Gram stain	variable
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #30246]	Cell length	01-10 µm

[Ref.: #30246]	Cell width	0.2-0.6 µm

[Ref.: #30246]	Cell shape	rod-shaped

[Ref.: #30246]	Motility	no

[Ref.: #20791]	Incubation period	2-3 days

[Ref.: #62426]	Incubation period	2 days

[Ref.: #30246]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20791]

Culture medium

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

[Ref.: #20791]

Culture medium growth

[Ref.: #20791]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20791]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20791]	growth	30 °C
[Ref.: #30246]	growth	10-37 °C
[Ref.: #30246]	optimum	30 °C
[Ref.: #62426]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #20791]	Temperature range	mesophilic
[Ref.: #30246]	Temperature range	mesophilic
[Ref.: #62426]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30246]			optimum	07-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30246]	Oxygen tolerance	facultative aerobe
[Ref.: #62426]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30246]		NaCl		optimum	2-3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30246]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30246]	cellobiose ChEBI	+	carbon source
[Ref.: #30246]	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.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30246]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30246]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #30246]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30246]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #30246]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #30246]	succinate ChEBI	+	carbon source
[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.: #30246]	acid phosphatase	+	3.1.3.2
[Ref.: #30246]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #20791]	catalase	+	1.11.1.6
[Ref.: #20791]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[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.: #20791]	23977	+	-	-	-	-	-	-	-	+	-	+	+	+	+	-	-	-	-	-	-	not determinedn.d.

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

[Ref.: #20791]	Sample type/isolated from	sea squirt Halocynthia roretzi
[Ref.: #20791]	Host species	Halocynthia roretzi
[Ref.: #20791]	Geographic location (country and/or sea, region)	South Sea
[Ref.: #20791]	Country	Republic of Korea
[Ref.: #20791]	Country ISO 3 Code	KOR
[Ref.: #20791]	Continent	Asia

[Ref.: #62426]	Sample type/isolated from	Sea squirt (Halocynthia roretzi)
[Ref.: #62426]	Sampling date	2009
[Ref.: #62426]	Geographic location (country and/or sea, region)	South Sea
[Ref.: #62426]	Country	Republic of Korea
[Ref.: #62426]	Country ISO 3 Code	KOR
[Ref.: #62426]	Continent	Asia

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

Isolation sources categories

#Host

#Invertebrates (Other)

#Tunicata

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ852038 (>99% sequence identity) for Ruegeria from Microbeatlas

Aquatic Samples	3119
Soil Samples	37
Animal Samples	116
Plant Samples	2
Total Samples	3274

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

[Ref.: #20791]

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.: #30246]	Ruegeria halocynthiae strain MA1-6 16S ribosomal RNA gene, partial sequence	HQ852038	1386	GenBank	985054 tax ID
[Ref.: #20791]		HQ85203		ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ruegeria halocynthiae DSM 27839	GCA_900106805	contig	GenBank	985054 tax ID	*
[Ref.: #66792]	Ruegeria halocynthiae strain DSM 27839	985054.8	wgs	PATRIC	985054 tax ID	*
[Ref.: #66792]	Ruegeria halocynthiae DSM 27839	2693429872	draft	JGI IMG/M	985054 tax ID	*

[Ref.: #20791]	GC-content	58.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30246]	GC-content	58.6 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: Ruegeria halocynthiae strain DSM 27839 PATRIC: 985054.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruegeria halocynthiae strain DSM 27839 PATRIC: 985054.8
[Ref.: #69480]	motile	no	61.167	no
[Ref.: #69480]	flagellated	no	81.223	no
[Ref.: #69480]	gram-positive	no	98.141	no
[Ref.: #69480]	anaerobic	no	98.879	yes
[Ref.: #69480]	halophile	yes	81.584	no
[Ref.: #69480]	spore-forming	no	95.429	no
[Ref.: #69480]	thermophile	no	96.907	yes
[Ref.: #69480]	glucose-util	yes	68.793	yes
[Ref.: #69480]	aerobic	yes	93.135	no
[Ref.: #69480]	glucose-ferment	no	91.635	no

Availability in culture collections External links

[Ref.: #20791]

Culture collection no.

DSM 27839, CCUG 60744, KCTC 23463

[Ref.: #88361]

SI-ID 402546

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi.	Kim YO, Park S, Nam BH, Kang SJ, Hur YB, Lee SJ, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.031609-0	2011	*
Phylogeny	Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea.	Kim J, Kim DY, Yang KH, Kim S, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.003568	2019	*

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 )

#20791

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27839

#30246

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 #26588 (see below)

#62426 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 60744

#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 .

#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 )

#88361

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-ID402546.1 )

#26588

IJSEM 925 2012 ( DOI 10.1099/ijs.0.031609-0 , PubMed 21669923 )

* These data were automatically processed and therefore are not curated

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Ruegeria halocynthiae strain DSM 27839

Ruegeria halocynthiae strain DSM 27839

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