Name: Croceivirga radicis HSG9
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140752

Type strain:

Species: Croceivirga radicis

Strain Designation: HSG9

Culture col. no.: MCCC 1A06690, KCTC 52589

Strain history: <- Liping Wang, Dong Hu, Third Institute of Oceanography, State Oceanic Administration

NCBI tax ID(s): 1929488 (species)

Section

Croceivirga radicis HSG9 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Rotten tropical mangrove root.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Croceivirga*
	Species	**Croceivirga radicis**
	Full Scientific Name (LPSN)	Croceivirga radicis Hu et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43530]	Gram stain	negative

[Ref.: #43530]	Cell length	1.2-2.2 µm

[Ref.: #43530]	Cell width	0.5-0.8 µm

[Ref.: #43530]	Cell shape	rod-shaped

[Ref.: #43530]	Motility	yes

[Ref.: #43530]	Flagellum arrangement	gliding

[Ref.: #43530]	Colony color	Yellow
[Ref.: #43530]	Colony shape	circular
[Ref.: #43530]	Incubation period	2 days
[Ref.: #43530]	Cultivation medium used	MA medium

[Ref.: #43530]	Pigment production	yes
[Ref.: #43530]	Pigment name	Carotenoid pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43530]

Culture medium

MA medium

[Ref.: #43530]

Culture medium growth

		Temperature
[Ref.: #43530]	growth	10-42 °C
[Ref.: #43530]	optimum	25-35 °C
[Ref.: #67771]	growth	35 °C

[Ref.: #43530]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43530]			optimum	7-8
[Ref.: #43530]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43530]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Salt		Salt conc.
[Ref.: #43530]	Marine salts	growth	0.5-9	%(w/v)
[Ref.: #43530]	Marine salts	optimum	3	%(w/v)
[Ref.: #43530]	NaCl	growth	0.4-6.9	%(w/v)
[Ref.: #43530]	NaCl	optimum	2.3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43530]	adipate ChEBI	-	assimilation
[Ref.: #43530]	amygdalin ChEBI	-	fermentation
[Ref.: #43530]	amygdalin ChEBI	-	oxidation
[Ref.: #43530]	arabinose ChEBI	-	fermentation
[Ref.: #43530]	arabinose ChEBI	-	oxidation
[Ref.: #43530]	casein	-	hydrolysis
[Ref.: #43530]	cellulose ChEBI	-	hydrolysis
[Ref.: #43530]	citrate ChEBI	-	assimilation
[Ref.: #43530]	D-glucose ChEBI	-	assimilation
[Ref.: #43530]	D-glucose ChEBI	-	fermentation
[Ref.: #43530]	D-glucose ChEBI	-	oxidation
[Ref.: #43530]	D-mannitol ChEBI	-	assimilation
[Ref.: #43530]	D-mannose ChEBI	-	assimilation
[Ref.: #43530]	decanoate ChEBI	-	assimilation
[Ref.: #43530]	gelatin ChEBI	+	hydrolysis
[Ref.: #43530]	glucose ChEBI	-	fermentation
[Ref.: #43530]	glucose ChEBI	-	oxidation
[Ref.: #43530]	L-arabinose ChEBI	-	assimilation
[Ref.: #43530]	malate ChEBI	-	assimilation
[Ref.: #43530]	maltose ChEBI	-	assimilation
[Ref.: #43530]	mannitol ChEBI	-	fermentation
[Ref.: #43530]	mannitol ChEBI	-	oxidation
[Ref.: #43530]	melibiose ChEBI	-	fermentation
[Ref.: #43530]	melibiose ChEBI	-	oxidation
[Ref.: #43530]	myo-inositol ChEBI	-	fermentation
[Ref.: #43530]	myo-inositol ChEBI	-	oxidation
[Ref.: #43530]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43530]	nitrate ChEBI	+	reduction
[Ref.: #43530]	phenylacetate ChEBI	-	assimilation
[Ref.: #43530]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43530]	rhamnose ChEBI	-	fermentation
[Ref.: #43530]	rhamnose ChEBI	-	oxidation
[Ref.: #43530]	sodium citrate ChEBI	-	assimilation
[Ref.: #43530]	sorbitol ChEBI	-	fermentation
[Ref.: #43530]	sorbitol ChEBI	-	oxidation
[Ref.: #43530]	starch ChEBI	-	hydrolysis
[Ref.: #43530]	sucrose ChEBI	-	fermentation
[Ref.: #43530]	sucrose ChEBI	-	oxidation
[Ref.: #43530]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43530]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43530]	tween 60 ChEBI	+	hydrolysis
[Ref.: #43530]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43530]	acetoin ChEBI	yes
[Ref.: #43530]	hydrogen sulfide ChEBI	no
[Ref.: #43530]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43530]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #43530]	acid phosphatase	+	3.1.3.2
[Ref.: #43530]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43530]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43530]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43530]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43530]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43530]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43530]	arginine dihydrolase	+	3.5.3.6
[Ref.: #43530]	beta-galactosidase	-	3.2.1.23
[Ref.: #43530]	beta-galactosidase	+	3.2.1.23
[Ref.: #43530]	beta-glucosidase	+/-	3.2.1.21
[Ref.: #43530]	beta-glucosidase	+	3.2.1.21
[Ref.: #43530]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43530]	catalase	+	1.11.1.6
[Ref.: #43530]	cystine aminopeptidase	+/-	3.4.11.3
[Ref.: #43530]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43530]	esterase (C 4)	+
[Ref.: #43530]	esterase Lipase (C 8)	+
[Ref.: #43530]	gelatinase	+
[Ref.: #43530]	leucine aminopeptidase	+	3.4.1.1
[Ref.: #43530]	lipase (C 14)	-
[Ref.: #43530]	lysine decarboxylase	+	4.1.1.18
[Ref.: #43530]	N-acetyl-beta-glucosaminidase	+/-	3.2.1.52
[Ref.: #43530]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #43530]	ornithine decarboxylase	+	4.1.1.17
[Ref.: #43530]	trypsin	-	3.4.21.4
[Ref.: #43530]	tryptophan decarboxylase	+	4.1.1.27
[Ref.: #43530]	urease	+	3.5.1.5
[Ref.: #43530]	valine aminopeptidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43530]

Fatty acid	Percentage
C16:0 iso	22.1
C15:0 iso	19.1
iso-C17:1ω9c / iso-C16:0-10-methyl	18.8
C17:0 iso	9.9
C11:0 iso 3OH	4.5
C11:0 iso	4.1
C15:0 anteiso	3.7
C17:1ω6c	3.1
C16:0	2.7
C16:1ω7c / C16:1ω6c	2.5
C13:0 iso 3OH	2.3
C17:0 anteiso	1.2
C18:0 iso	1.1
C14:0 iso	1.1
C12:0 iso 3OH	1.1
C14:0	0.5
C19:0 iso	0.3
C18:0	0.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	metabolism of amino sugars and derivatives	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #43530]	Sample type/isolated from	Rotten tropical mangrove root
[Ref.: #43530]	Geographic location (country and/or sea, region)	Hainan
[Ref.: #43530]	Country	China
[Ref.: #43530]	Country ISO 3 Code	CHN
[Ref.: #43530]	Continent	Asia
[Ref.: #43530]	Geographic location	19.9660°/110.5660°
[Ref.: #43530]	Isolation date	2010-05

[Ref.: #67771]	Sample type/isolated from	From the rot root of mangrove
[Ref.: #67771]	Geographic location (country and/or sea, region)	Hainan Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Host	#Plants	#Decomposing plant
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY020995 (>99% sequence identity) for Croceivirga radicis subclade from Microbeatlas

Aquatic Samples	1126
Soil Samples	36
Animal Samples	187
Plant Samples	16
Total Samples	1365

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.: #43530]	16S rRNA gene sequence	KY020995		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Croceivirga radicis HSG9	GCA_002072105	contig	GenBank	1929488 tax ID	*
[Ref.: #66792]	Croceivirga radicis HSG9	2788500170	draft	JGI IMG/M	1929488 tax ID	*

[Ref.: #43530]

GC-content

37.1 mol%

genome sequence analysis

Availability in culture collections External links

[Ref.: #43530]

Culture collection no.

MCCC 1A06690, KCTC 52589

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Croceivirga litoralis sp. nov., isolated from coastal surface water, and reclassification of Muricauda lutea as Croceivirga lutea comb. nov.	Zhang J, Xu Y, Chen X, Liu D, Song H, Liu J, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004541	2020	*
Phylogeny	Croceivirga radicis gen. nov., sp. nov., isolated from a rotten tropical mangrove root.	Hu D, Wang L, Chen Y, Li X, Du Y, Sun F, Wang L, Fan C, Zhao R, Tang C, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002179	2017	*

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 )

#43530

Dong Hu, Liping Wang, Yanwu Chen, Xiaoyi Li, Yaping Du, Fengqin Sun, Lei Wang, Chun Fan, Ran Zhao, Chen Tang, Zongze Shao: Croceivirga radicis gen. nov., sp. nov., isolated from a rotten tropical mangrove root. IJSEM 67: 3733 - 3738 2017 ( DOI 10.1099/ijsem.0.002179 , PubMed 28895511 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Croceivirga radicis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF