Name: Carboxylicivirga sediminis JR1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158815

Type strain:

Species: Carboxylicivirga sediminis

Strain Designation: JR1

Culture col. no.: MCCC 1K03323, KCTC 52869

Strain history: <- Fengqing Wang, Shandong Marine Resources and Environment Research Institute

NCBI tax ID(s): 2006564 (species)

Section

Carboxylicivirga sediminis JR1 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sediment sample from a tidal flat at the mouth of a river.

colony-forming
Gram-negative
rod-shaped
facultative anaerobe
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Marinilabiliaceae*
	Genus	*Carboxylicivirga*
	Species	**Carboxylicivirga sediminis**
	Full Scientific Name (LPSN)	Carboxylicivirga sediminis Wang et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65579]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #65579]	Cell length	2.0-15.5 µm

[Ref.: #65579]	Cell width	0.1-0.4 µm

[Ref.: #65579]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #65579]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #65579]	Colony size	0.5-1.0 mm
[Ref.: #65579]	Colony color	yellow
[Ref.: #65579]	Colony shape	circular
[Ref.: #65579]	Incubation period	2.5 days
[Ref.: #65579]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65579]

Culture medium

Marine agar (MA)

[Ref.: #65579]

Culture medium growth

		Temperature
[Ref.: #65579]	growth	15-42 °C
[Ref.: #65579]	optimum	33 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #65579]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65579]			optimum	7.0-7.5
[Ref.: #65579]			growth	6.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65579]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65579]		NaCl		growth	0-10	%(w/v)
[Ref.: #65579]		NaCl		optimum	2.0-3.0	%(w/v)

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65579]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #65579]	2-hydroxybutyrate ChEBI	+	energy source
[Ref.: #65579]	2-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #65579]	agar ChEBI	+	hydrolysis
[Ref.: #65579]	alginate ChEBI	+	hydrolysis
[Ref.: #65579]	cellobiose ChEBI	+	carbon source
[Ref.: #65579]	cellobiose ChEBI	+	energy source
[Ref.: #65579]	cellobiose ChEBI	+	oxidation
[Ref.: #65579]	D-glucuronate ChEBI	+	carbon source
[Ref.: #65579]	D-glucuronate ChEBI	+	energy source
[Ref.: #65579]	D-glucuronate ChEBI	+	oxidation
[Ref.: #65579]	dextrin ChEBI	+	carbon source
[Ref.: #65579]	dextrin ChEBI	+	energy source
[Ref.: #65579]	dextrin ChEBI	+	oxidation
[Ref.: #65579]	gelatin ChEBI	+	hydrolysis
[Ref.: #65579]	gentiobiose ChEBI	+	carbon source
[Ref.: #65579]	gentiobiose ChEBI	+	energy source
[Ref.: #65579]	gentiobiose ChEBI	+	oxidation
[Ref.: #65579]	glucuronamide ChEBI	+	carbon source
[Ref.: #65579]	glucuronamide ChEBI	+	energy source
[Ref.: #65579]	glucuronamide ChEBI	+	oxidation
[Ref.: #65579]	lactose ChEBI	+	carbon source
[Ref.: #65579]	lactose ChEBI	+	energy source
[Ref.: #65579]	lactose ChEBI	+	oxidation
[Ref.: #65579]	maltose ChEBI	+	carbon source
[Ref.: #65579]	maltose ChEBI	+	energy source
[Ref.: #65579]	maltose ChEBI	+	oxidation
[Ref.: #65579]	melibiose ChEBI	+	carbon source
[Ref.: #65579]	melibiose ChEBI	+	energy source
[Ref.: #65579]	melibiose ChEBI	+	oxidation
[Ref.: #65579]	n-acetylneuraminate ChEBI	+	carbon source
[Ref.: #65579]	n-acetylneuraminate ChEBI	+	energy source
[Ref.: #65579]	n-acetylneuraminate ChEBI	+	oxidation
[Ref.: #65579]	nitrate ChEBI	-	reduction
[Ref.: #65579]	stachyose ChEBI	+	carbon source
[Ref.: #65579]	stachyose ChEBI	+	energy source
[Ref.: #65579]	stachyose ChEBI	+	oxidation
[Ref.: #65579]	starch ChEBI	+	hydrolysis
[Ref.: #65579]	turanose ChEBI	+	carbon source
[Ref.: #65579]	turanose ChEBI	+	energy source
[Ref.: #65579]	turanose ChEBI	+	oxidation
[Ref.: #65579]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65579]		hydrogen sulfide ChEBI	no
[Ref.: #65579]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #65579]	acid phosphatase	+	3.1.3.2
[Ref.: #65579]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65579]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65579]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65579]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65579]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65579]	beta-galactosidase	+	3.2.1.23
[Ref.: #65579]	beta-glucosidase	+	3.2.1.21
[Ref.: #65579]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65579]	catalase	+/-	1.11.1.6
[Ref.: #65579]	cystine arylamidase	-	3.4.11.3
[Ref.: #65579]	DNase	+
[Ref.: #65579]	esterase (C 4)	-
[Ref.: #65579]	esterase Lipase (C 8)	-
[Ref.: #65579]	leucine arylamidase	-	3.4.11.1
[Ref.: #65579]	lipase (C 14)	-
[Ref.: #65579]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65579]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65579]	trypsin	+	3.4.21.4
[Ref.: #65579]	urease	-	3.5.1.5
[Ref.: #65579]	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.: #65579]	Sample type/isolated from	sediment sample from a tidal flat at the mouth of a river
[Ref.: #65579]	Sampling date	2016-12
[Ref.: #65579]	Geographic location (country and/or sea, region)	Yantai, Jia River
[Ref.: #65579]	Country	China
[Ref.: #65579]	Country ISO 3 Code	CHN
[Ref.: #65579]	Continent	Asia
[Ref.: #65579]	Geographic location	37.5607°/121.2850°
[Ref.: #65579]	Enrichment culture	MA
[Ref.: #65579]	Enrichment culture duration	7 days

[Ref.: #67771]	Sample type/isolated from	From sediment, marine solar saltern
[Ref.: #67771]	Geographic location (country and/or sea, region)	the coastal area of Yantai
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	37.6094°/121.2920°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat

What are isolation sources categories?

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.: #65579]	16S rRNA gene sequence	KY800901		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Carboxylicivirga sediminis JR1	GCA_018156225	contig	GenBank	2006564 tax ID	*

[Ref.: #65579]	GC-content	42.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	42.3 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Carboxylicivirga sediminis JR1 NCBI: GCA_018156225.1
[Ref.: #69480]	flagellated	no	91.094	yes
[Ref.: #69480]	gram-positive	no	98.527	yes
[Ref.: #69480]	anaerobic	no	58.664	yes
[Ref.: #69480]	aerobic	no	87.129	no
[Ref.: #69480]	halophile	no	75.058	no
[Ref.: #69480]	spore-forming	no	92.215	no
[Ref.: #69480]	thermophile	no	97.773	yes
[Ref.: #69480]	glucose-util	yes	90.892	no
[Ref.: #69480]	motile	no	75.766	no
[Ref.: #69480]	glucose-ferment	no	63.482	no

Availability in culture collections External links

[Ref.: #65579]

Culture collection no.

MCCC 1K03323, KCTC 52869

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Carboxylicivirga sediminis sp. nov., isolated from coastal sediment.	Wang FQ, Ren LH, Zou RJ, Sun YZ, Liu XJ, Jiang F, Liu LJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002761	2018	*

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 )

#65579

Feng-Qing Wang, Li-Hua Ren, Rong-Jie Zou, Yu-Zeng Sun, Xiao-Jing Liu, Fang Jiang and Li-Juan Liu: Carboxylicivirga sediminis sp. nov., isolated from coastal sediment. IJSEM 68: 1896 - 1901 2018 ( DOI 10.1099/ijsem.0.002761 , PubMed 29658858 )

#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) .

* These data were automatically processed and therefore are not curated

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