Name: Sphingomonas rhizophila THG-T61
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158693

Type strain:

Species: Sphingomonas rhizophila

Strain Designation: THG-T61

Culture col. no.: KACC 19189, CCTCC AB 2016245

NCBI tax ID(s): 2071607 (species)

Section

Sphingomonas rhizophila THG-T61 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from rhizosphere of Hibiscus syriacus collected from Kyung Hee University.

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas rhizophila**
	Full Scientific Name (LPSN)	Sphingomonas rhizophila Yan et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65433]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.845

[Ref.: #65433]	Cell length	0.8-1.2 µm

[Ref.: #65433]	Cell width	0.4-0.6 µm

[Ref.: #65433]	Cell shape	rod-shaped

[Ref.: #65433]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.3

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #65433]			growth	10-37 °C
[Ref.: #65433]			optimum	25-30 °C

[Ref.: #65433]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65433]			optimum	7
[Ref.: #65433]			growth	5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65433]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.98
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65433]		NaCl		growth	0-2	%
[Ref.: #65433]		NaCl		optimum	0	%

[Ref.: #65433]	Observation	the polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified lipid, one unidentified phospholipid, one unidentified glycolipid and one unidentified phosphoglycol
[Ref.: #65433]	Observation	the isoprenoid quinone is Q-10
[Ref.: #65433]	Observation	the polyamine is homospermidine

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65433]	2-dehydro-D-gluconate ChEBI	+	assimilation
[Ref.: #65433]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #65433]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65433]	5-dehydro-D-gluconate ChEBI	+	assimilation
[Ref.: #65433]	adipate ChEBI	+	assimilation
[Ref.: #65433]	casein	+	hydrolysis
[Ref.: #65433]	cellulose ChEBI	+	hydrolysis
[Ref.: #65433]	chitin ChEBI	-	hydrolysis
[Ref.: #65433]	D-glucose ChEBI	+	assimilation
[Ref.: #65433]	D-mannitol ChEBI	+	assimilation
[Ref.: #65433]	D-mannose ChEBI	+	assimilation
[Ref.: #65433]	D-ribose ChEBI	-	assimilation
[Ref.: #65433]	D-sorbitol ChEBI	+	assimilation
[Ref.: #65433]	decanoate ChEBI	-	assimilation
[Ref.: #65433]	dna ChEBI	+	hydrolysis
[Ref.: #65433]	gluconate ChEBI	-	assimilation
[Ref.: #65433]	glucose ChEBI	-	builds acid from
[Ref.: #65433]	glycogen ChEBI	+	assimilation
[Ref.: #65433]	isocitrate ChEBI	+	assimilation
[Ref.: #65433]	itaconate ChEBI	-	assimilation
[Ref.: #65433]	L-alanine 4-nitroanilide	+	assimilation
[Ref.: #65433]	L-arabinose ChEBI	+	assimilation
[Ref.: #65433]	L-fucose ChEBI	-	assimilation
[Ref.: #65433]	L-histidine ChEBI	-	assimilation
[Ref.: #65433]	L-proline ChEBI	+	assimilation
[Ref.: #65433]	L-rhamnose ChEBI	-	assimilation
[Ref.: #65433]	L-serine ChEBI	-	assimilation
[Ref.: #65433]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #65433]	lactate ChEBI	-	assimilation
[Ref.: #65433]	malate ChEBI	+	assimilation
[Ref.: #65433]	maltose ChEBI	+	assimilation
[Ref.: #65433]	melibiose ChEBI	+	assimilation
[Ref.: #65433]	myo-inositol ChEBI	+	assimilation
[Ref.: #65433]	N-acetyl-L-glutamate ChEBI	+	assimilation
[Ref.: #65433]	nitrate ChEBI	-	reduction
[Ref.: #65433]	phenylacetate ChEBI	+	assimilation
[Ref.: #65433]	propionate ChEBI	+	assimilation
[Ref.: #65433]	salicin ChEBI	+	assimilation
[Ref.: #65433]	salicylate ChEBI	-	assimilation
[Ref.: #65433]	sodium acetate ChEBI	-	assimilation
[Ref.: #65433]	sodium citrate ChEBI	-	assimilation
[Ref.: #65433]	sodium malonate ChEBI	-	assimilation
[Ref.: #65433]	starch ChEBI	-	hydrolysis
[Ref.: #65433]	suberic acid ChEBI	+	assimilation
[Ref.: #65433]	sucrose ChEBI	+	assimilation
[Ref.: #65433]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65433]	valerate ChEBI	+	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65433]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65433]	acid phosphatase	+	3.1.3.2
[Ref.: #65433]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65433]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65433]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65433]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65433]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65433]	arginine dihydrolase	+	3.5.3.6
[Ref.: #65433]	beta-galactosidase	+	3.2.1.23
[Ref.: #65433]	beta-glucosidase	+	3.2.1.21
[Ref.: #65433]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65433]	catalase	+	1.11.1.6
[Ref.: #65433]	cystine arylamidase	+	3.4.11.3
[Ref.: #65433]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65433]	esterase	-
[Ref.: #65433]	esterase Lipase (C 8)	+
[Ref.: #65433]	leucine arylamidase	+	3.4.11.1
[Ref.: #65433]	lipase (C 14)	-
[Ref.: #65433]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65433]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65433]	phosphatase	+
[Ref.: #65433]	protease	+
[Ref.: #65433]	trypsin	+	3.4.21.4
[Ref.: #65433]	urease	+	3.5.1.5
[Ref.: #65433]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65433]

Fatty acid	Percentage
C18:1ω7c, C18:1ω9t and/or C18:1ω	42.5
C17:1ω6c	20.6
C15:0 iso 2OH and/or C16:1ω7c	16.2
C16:0	9.1
C15:0	3.6
C17:1ω8c	1.9
C17:0	1.6
C16:1ω5c	1.4
C18:1ω5c	1.2
C14:0 2OH	1

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

[Ref.: #65433]	Sample type/isolated from	rhizosphere of Hibiscus syriacus collected from Kyung Hee University
[Ref.: #65433]	Geographic location (country and/or sea, region)	Yongin
[Ref.: #65433]	Country	Republic of Korea
[Ref.: #65433]	Country ISO 3 Code	KOR
[Ref.: #65433]	Continent	Asia
[Ref.: #65433]	Enrichment culture	nutrient agar (NA, Oxoid)
[Ref.: #65433]	Enrichment culture duration	1 week
[Ref.: #65433]	Enrichment culture temperature	30 ̊C
* marker position based on {}

Isolation sources categories

#Host Body-Site	#Plant	#Rhizosphere
#Host	#Plants	#Shrub (Scrub)
#Environmental	#Terrestrial	#Soil

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.: #65433]	16S rRNA gene sequence	KY287249		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas rhizophila KACC 19189	GCA_014396585	complete	GenBank	2071607 tax ID	*
[Ref.: #66792]	Sphingomonas rhizophila strain KACC 19189	2071607.3	complete	PATRIC	2071607 tax ID	*
[Ref.: #66792]	Sphingomonas rhizophila KACC 19189	2896429255	complete	JGI IMG/M	2071607 tax ID	*

[Ref.: #65433]

GC-content

65.6 mol%

high performance liquid chromatography (HPLC)

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: Sphingomonas rhizophila KACC 19189 NCBI: GCA_014396585.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas rhizophila KACC 19189 NCBI: GCA_014396585.1
[Ref.: #69480]	flagellated	no	95.634	no
[Ref.: #69480]	gram-positive	no	97.542	yes
[Ref.: #69480]	anaerobic	no	99.184	yes
[Ref.: #69480]	aerobic	yes	91.648	yes
[Ref.: #69480]	halophile	no	93.675	yes
[Ref.: #69480]	spore-forming	no	96.134	no
[Ref.: #69480]	thermophile	no	89.709	yes
[Ref.: #69480]	glucose-util	yes	83.286	no
[Ref.: #69480]	motile	no	87.162	yes
[Ref.: #69480]	glucose-ferment	no	88.187	no

Availability in culture collections External links

[Ref.: #65433]

Culture collection no.

KACC 19189, CCTCC AB 2016245

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea.	Kim H, Chhetri G, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.003780	2020	*
Phylogeny	Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus.	Yan ZF, Lin P, Won KH, Li CT, Park G, Chin B, Kook M, Wang QJ, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002566	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 )

#65433

Zheng-Fei Yan, Pei Lin, Kyung-Hwa Won, Chang-Tian Li, GyungSoo Park, ByungSun Chin, MooChang Kook, Qi-Jun Wang and Tae-Hoo Yi: Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus. IJSEM 68: 681 - 686 2018 ( DOI 10.1099/ijsem.0.002566 , PubMed 29388549 )

#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) .

#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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Sphingomonas rhizophila KACC 19189

Sphingomonas rhizophila KACC 19189

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