Name: Pelagivirga sediminicola BH-SD19
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159840

Type strain:

Species: Pelagivirga sediminicola

Strain Designation: BH-SD19

Culture col. no.: CCTCC AB 2017074, KCTC 62202

Strain history: <- Ji Xiaofei, Binzhou Medicial Univ.

NCBI tax ID(s): 2170575 (species)

Section

Pelagivirga sediminicola BH-SD19 is an aerobe, slightly halophilic, psychrophilic bacterium that forms circular colonies and was isolated from sediment from the bohai sea.

colony-forming
Gram-negative
rod-shaped
aerobe
psychrophilic
slightly halophilic
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	*Pelagivirga*
	Species	**Pelagivirga sediminicola**
	Full Scientific Name (LPSN)	Pelagivirga sediminicola Ji et al. 2018

Synonym

"Roseovarius sediminicola"

Information on morphological and physiological properties Morphology

[Ref.: #66729]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #66729]	Cell length	1.0-2.0 µm

[Ref.: #66729]	Cell width	0.5-1.0 µm

[Ref.: #66729]	Cell shape	rod-shaped

[Ref.: #66729]	Motility	no

[Ref.: #66729]	Colony size	0.4 mm
[Ref.: #66729]	Colony color	grayish-white
[Ref.: #66729]	Colony shape	circular
[Ref.: #66729]	Incubation period	3 days
[Ref.: #66729]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66729]

Culture medium

Marine agar (MA)

[Ref.: #66729]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #66729]	no	growth	10 °C
[Ref.: #66729]		optimum	35 °C
[Ref.: #66729]	no	growth	45 °C
[Ref.: #66729]		growth	15-40 °C
[Ref.: #67771]		growth	30 °C

[Ref.: #66729]	Temperature range	psychrophilic
[Ref.: #66729]	Temperature range	mesophilic
[Ref.: #66729]	Temperature range	thermophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66729]			optimum	7.0-7.5
[Ref.: #66729]			growth	6.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66729]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #66729]

Halophily / tolerance level

slightly halophilic

	Salt	Tested relation		Salt conc.
[Ref.: #66729]	NaCl		growth	1-10	%(w/v)
[Ref.: #66729]	NaCl		optimum	2	%(w/v)
[Ref.: #66729]	NaCl	no	growth	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66729]	adipate ChEBI	+	carbon source
[Ref.: #66729]	amygdalin ChEBI	-	builds acid from
[Ref.: #66729]	casein	-	hydrolysis
[Ref.: #66729]	D-glucose ChEBI	+	carbon source
[Ref.: #66729]	D-mannitol ChEBI	+	carbon source
[Ref.: #66729]	D-mannose ChEBI	+	carbon source
[Ref.: #66729]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #66729]	decanoate ChEBI	-	carbon source
[Ref.: #66729]	gelatin ChEBI	-	degradation
[Ref.: #66729]	L-arabinose ChEBI	+	carbon source
[Ref.: #66729]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #66729]	malate ChEBI	+	carbon source
[Ref.: #66729]	maltose ChEBI	+	carbon source
[Ref.: #66729]	melibiose ChEBI	-	builds acid from
[Ref.: #66729]	myo-inositol ChEBI	-	builds acid from
[Ref.: #66729]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #66729]	nitrate ChEBI	-	reduction
[Ref.: #66729]	nitrite ChEBI	-	reduction
[Ref.: #66729]	phenylacetate ChEBI	+	carbon source
[Ref.: #66729]	potassium gluconate ChEBI	+	carbon source
[Ref.: #66729]	sodium citrate ChEBI	+	carbon source
[Ref.: #66729]	starch ChEBI	-	hydrolysis
[Ref.: #66729]	sucrose ChEBI	-	builds acid from
[Ref.: #66729]	tween 20 ChEBI	-	hydrolysis
[Ref.: #66729]	tween 40 ChEBI	-	hydrolysis
[Ref.: #66729]	tween 60 ChEBI	-	hydrolysis
[Ref.: #66729]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66729]		hydrogen sulfide ChEBI	no
[Ref.: #66729]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66729]	acid phosphatase	+	3.1.3.2
[Ref.: #66729]	alkaline phosphatase	-	3.1.3.1
[Ref.: #66729]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #66729]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66729]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66729]	alpha-glucosidase	-	3.2.1.20
[Ref.: #66729]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66729]	beta-galactosidase	-	3.2.1.23
[Ref.: #66729]	beta-glucosidase	-	3.2.1.21
[Ref.: #66729]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66729]	catalase	+	1.11.1.6
[Ref.: #66729]	cystine arylamidase	-	3.4.11.3
[Ref.: #66729]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66729]	esterase (C 4)	+
[Ref.: #66729]	esterase Lipase (C 8)	+
[Ref.: #66729]	leucine aminopeptidase	+	3.4.1.1
[Ref.: #66729]	leucine arylamidase	+	3.4.11.1
[Ref.: #66729]	lipase (C 14)	+
[Ref.: #66729]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66729]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #66729]	trypsin	-	3.4.21.4
[Ref.: #66729]	urease	-	3.5.1.5
[Ref.: #66729]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #66729]	Sample type/isolated from	sediment from the bohai sea
[Ref.: #66729]	Geographic location (country and/or sea, region)	Bohai sea
[Ref.: #66729]	Country	China
[Ref.: #66729]	Country ISO 3 Code	CHN
[Ref.: #66729]	Continent	Asia
[Ref.: #66729]	Geographic location	38.9997°/120.9940°
[Ref.: #66729]	Enrichment culture	marine agar 2216
[Ref.: #66729]	Enrichment culture temperature	25 ̊C
[Ref.: #66729]	Isolation/enrichment procedure	Marine sediment samples were collected from the Bohai Sea for the purpose of isolating bacterial strains. It was isolated by a standard dilution-plating method on marine agar 2216 after incubation at 25°C.

[Ref.: #67771]	Sample type/isolated from	From marine sediment of Bohai Sea
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pelagivirga sediminicola BH-SD19	GCA_003072125	scaffold	GenBank	2170575 tax ID	*
[Ref.: #66792]	Pelagivirga sediminicola BH-SD19	2831602983	draft	JGI IMG/M	2170575 tax ID	*

[Ref.: #66729]

GC-content

64 mol%

genome sequence analysis

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: Pelagivirga sediminicola BH-SD19 NCBI: GCA_003072125.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pelagivirga sediminicola BH-SD19 NCBI: GCA_003072125.1
[Ref.: #69480]	flagellated	no	92.967	yes
[Ref.: #69480]	gram-positive	no	97.962	yes
[Ref.: #69480]	anaerobic	no	97.294	yes
[Ref.: #69480]	halophile	yes	56.488	no
[Ref.: #69480]	spore-forming	no	95.84	no
[Ref.: #69480]	glucose-util	yes	51.198	yes
[Ref.: #69480]	aerobic	yes	86.21	yes
[Ref.: #69480]	thermophile	no	98.618	no
[Ref.: #69480]	motile	no	64.832	yes
[Ref.: #69480]	glucose-ferment	no	93.856	no

Availability in culture collections External links

[Ref.: #66729]

Culture collection no.

CCTCC AB 2017074, KCTC 62202

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pukyongiella litopenaei gen. nov., sp. nov., a novel bacterium isolated from the gut content of a whiteleg shrimp Litopenaeus vannamei.	Kim YS, Kim SE, Kim SJ, Jung HK, Kim KH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004269	2020	*
Phylogeny	Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge.	Zhuang L, Luo L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003750	2020	*
Phylogeny	Pelagivirga sediminicola gen. nov., sp. nov. isolated from the Bohai Sea.	Ji X, Zhang C, Zhang X, Xu Z, Ding Y, Zhang Y, Song Q, Li B, Zhao H	Int J Syst Evol Microbiol	10.1099/ijsem.0.003015	2018	*
Phylogeny	Pelagivirga dicentrarchi sp. nov., a member of the family Rhodobacteraceae isolated from the gut microflora of sea bass (Dicentrarchus labrax L.).	Li CM, Wang XP, Zhou LY, Chen GJ, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-019-01337-w	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 )

#66729

Xiaofei Ji, Cong Zhang, Xiying Zhang, Zheng Xu, Yunfei Ding, Yimei Zhang, Qing Song, Boqing Li, Huilin Zhao: Pelagivirga sediminicola gen. nov., sp. nov. Isolated from the Bohai Sea. IJSEM 68: 3494 - 3499 2018 ( DOI 10.1099/ijsem.0.003015 , PubMed 30222096 )

#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;

#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 )

* These data were automatically processed and therefore are not curated

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