Name: Parvularcula dongshanensis SH25
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132152

Type strain:

Species: Parvularcula dongshanensis

Strain Designation: SH25

Culture col. no.: DSM 102850, CCTCC AB 2010355, LMG 26158, MCCC 1A06534

Strain history: <- CCTCC <- Z. Yu, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China; SH25

NCBI tax ID(s): 1173995 (species)

SI-ID 371838

LMG 26158

Section

Parvularcula dongshanensis SH25 is a mesophilic, Gram-negative, motile bacterium that was isolated from soft coral growing 4 m below sea surface.

Gram-negative
motile
rod-shaped
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	"Parvularculales"
	Family	"Parvularculaceae"
	Genus	*Parvularcula*
	Species	**Parvularcula dongshanensis**
	Full Scientific Name (LPSN)	Parvularcula dongshanensis Yu et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30786]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #30786]	Cell length	1.45 µm

[Ref.: #30786]	Cell width	0.85 µm

[Ref.: #30786]	Cell shape	rod-shaped

[Ref.: #30786]	Motility	yes

[Ref.: #30786]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23941]

Culture medium

HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)

[Ref.: #23941]

Culture medium growth

[Ref.: #23941]

Culture medium link

Medium recipe at MediaDive

[Ref.: #23941]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #23941]	growth	28 °C
[Ref.: #30786]	growth	10-41 °C
[Ref.: #30786]	optimum	28 °C

[Ref.: #23941]	Temperature range	mesophilic
[Ref.: #30786]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[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.: #30786]		NaCl		growth	0-12	%
[Ref.: #30786]		NaCl		optimum	2	%

	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.: #30786]	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.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[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	yes	* from API 20NE

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

	Enzyme	Enzyme activity	EC number
[Ref.: #30786]	acid phosphatase	+	3.1.3.2
[Ref.: #30786]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30786]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68369]	arginine dihydrolase	+	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #30786]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #30786]	gelatinase	+
[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.: #23941]	24433	-	+	-	+	-	+	-	+	+	-	+	-	-	+	-	-	-	+	-	-	+

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

[Ref.: #23941]	Sample type/isolated from	soft coral growing 4 m below sea surface
[Ref.: #23941]	Geographic location (country and/or sea, region)	Short Sea near Dongshan Island, Fujian Province
[Ref.: #23941]	Country	China
[Ref.: #23941]	Country ISO 3 Code	CHN
[Ref.: #23941]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Host	#Invertebrates (Other)	#Cnidaria (Corals)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ778314 (>99% sequence identity) for Parvularcula dongshanensis subclade from Microbeatlas

Aquatic Samples	116
Soil Samples	3
Animal Samples	2
Plant Samples	1
Total Samples	122

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

[Ref.: #23941]

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.: #23941]	Parvularcula dongshanensis strain SH25 16S ribosomal RNA gene, partial sequence	JQ778314	1428	ENA	1173995 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parvularcula dongshanensis DSM 102850	GCA_014199615	contig	GenBank	1173995 tax ID	*
[Ref.: #66792]	Parvularcula dongshanensis strain DSM 102850	1173995.4	wgs	PATRIC	1173995 tax ID	*
[Ref.: #66792]	Parvularcula dongshanensis DSM 102850	2828645483	draft	JGI IMG/M	1173995 tax ID	*

[Ref.: #30786]

GC-content

61.8 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: Parvularcula dongshanensis strain DSM 102850 PATRIC: 1173995.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parvularcula dongshanensis strain DSM 102850 PATRIC: 1173995.4
[Ref.: #69480]	motile	yes	85.358	yes
[Ref.: #69480]	gram-positive	no	98.624	yes
[Ref.: #69480]	anaerobic	no	99.226	no
[Ref.: #69480]	halophile	no	76.22	no
[Ref.: #69480]	spore-forming	no	96.685	no
[Ref.: #69480]	flagellated	no	91.473	no
[Ref.: #69480]	thermophile	no	91.982	no
[Ref.: #69480]	glucose-util	yes	86.71	no
[Ref.: #69480]	aerobic	yes	92.299	no
[Ref.: #69480]	glucose-ferment	no	90.411	no

Availability in culture collections External links

[Ref.: #23941]

Culture collection no.

DSM 102850, CCTCC AB 2010355, LMG 26158, MCCC 1A06534

[Ref.: #90508]

SI-ID 371838

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parvularcula dongshanensis sp. nov., isolated from soft coral.	Yu Z, Lai Q, Li G, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.044313-0	2012	*

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 )

#23941

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102850

#30786

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 #27117 (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) .

#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 )

#90508

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-ID371838.1 )

#27117

IJSEM 2114 2013 ( DOI 10.1099/ijs.0.044313-0 , PubMed 23087169 )

* These data were automatically processed and therefore are not curated

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Parvularcula dongshanensis strain DSM 102850

Parvularcula dongshanensis strain DSM 102850

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