Name: Pseudoflavitalea rhizosphaerae T16R-265
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133145

Type strain:

Species: Pseudoflavitalea rhizosphaerae

Strain Designation: T16R-265

Culture col. no.: KACC 18655, NBRC 111880

NCBI tax ID(s): 1884793 (species)

Special Collections

Literature strains

Section

Pseudoflavitalea rhizosphaerae T16R-265 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from rhizosphere of tomato.

colony-forming
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	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Pseudoflavitalea*
	Species	**Pseudoflavitalea rhizosphaerae**
	Full Scientific Name (LPSN)	Pseudoflavitalea rhizosphaerae Kim et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24914]	Gram stain	negative
[Ref.: #24914]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %90.363

[Ref.: #24914]	Cell length	1.2-1.5 µm
[Ref.: #24914]	Cell length	1.0-2.5 µm
[Ref.: #24914]	Cell length	7 µm

[Ref.: #24914]	Cell width	0.5-0.7 µm
[Ref.: #24914]	Cell width	0.5-0.6 µm
[Ref.: #24914]	Cell width	0.3-0.5 µm

[Ref.: #24914]	Cell shape	rod-shaped
[Ref.: #24914]	Cell shape	rod-shaped
[Ref.: #24914]	Cell shape	rod-shaped

[Ref.: #24914]	Motility	no
[Ref.: #24914]	Motility	no

[Ref.: #24914]	Colony color	light yellow
[Ref.: #24914]	Colony shape	irregular
[Ref.: #24914]	Cultivation medium used	R2A agar medium

[Ref.: #24914]	Colony color	yellow
[Ref.: #24914]	Colony shape	irregular
[Ref.: #24914]	Cultivation medium used	R2A agar medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24914]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #24914]

Culture medium growth

		Temperature
[Ref.: #24914]	growth	10-40 °C
[Ref.: #24914]	growth	10-37 °C
[Ref.: #24914]	optimum	28-30 °C

		pH
[Ref.: #24914]	optimum	7
[Ref.: #24914]	growth	6.0-9.0
[Ref.: #24914]	growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24914]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24914]		NaCl		maximum	3	%(w/v)
[Ref.: #24914]		NaCl		maximum	1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24914]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #24914]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #24914]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #24914]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #24914]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #24914]	adipate ChEBI	-	assimilation
[Ref.: #24914]	casein	+	hydrolysis
[Ref.: #24914]	cellulose ChEBI	-	hydrolysis
[Ref.: #24914]	cellulose ChEBI	+	hydrolysis
[Ref.: #24914]	chitin ChEBI	-	hydrolysis
[Ref.: #24914]	D-glucose ChEBI	+	assimilation
[Ref.: #24914]	D-mannitol ChEBI	-	assimilation
[Ref.: #24914]	D-mannose ChEBI	+	assimilation
[Ref.: #24914]	D-ribose ChEBI	+	assimilation
[Ref.: #24914]	D-sorbitol ChEBI	-	assimilation
[Ref.: #24914]	decanoate ChEBI	-	assimilation
[Ref.: #24914]	disodium malate ChEBI	-	assimilation
[Ref.: #24914]	dna ChEBI	+	hydrolysis
[Ref.: #24914]	esculin ChEBI	+	hydrolysis
[Ref.: #24914]	gelatin ChEBI	+	hydrolysis
[Ref.: #24914]	glucose ChEBI	-	fermentation
[Ref.: #24914]	glycogen ChEBI	+	assimilation
[Ref.: #24914]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #24914]	itaconate ChEBI	-	assimilation
[Ref.: #24914]	L-alanine ChEBI	-	assimilation
[Ref.: #24914]	L-arabinose ChEBI	-	assimilation
[Ref.: #24914]	L-arabinose ChEBI	+	assimilation
[Ref.: #24914]	L-fucose ChEBI	-	assimilation
[Ref.: #24914]	L-histidine ChEBI	+	assimilation
[Ref.: #24914]	L-proline ChEBI	+	assimilation
[Ref.: #24914]	L-rhamnose ChEBI	-	assimilation
[Ref.: #24914]	L-rhamnose ChEBI	+	assimilation
[Ref.: #24914]	L-serine ChEBI	-	assimilation
[Ref.: #24914]	lactate ChEBI	-	assimilation
[Ref.: #24914]	malate ChEBI	+	assimilation
[Ref.: #24914]	malonate ChEBI	-	assimilation
[Ref.: #24914]	maltose ChEBI	+	assimilation
[Ref.: #24914]	melibiose ChEBI	+	assimilation
[Ref.: #24914]	myo-inositol ChEBI	-	assimilation
[Ref.: #24914]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #24914]	nitrate ChEBI	-	reduction
[Ref.: #24914]	phenylacetate ChEBI	-	assimilation
[Ref.: #24914]	potassium gluconate ChEBI	-	assimilation
[Ref.: #24914]	propionate ChEBI	-	assimilation
[Ref.: #24914]	salicin ChEBI	+	assimilation
[Ref.: #24914]	sodium acetate ChEBI	-	assimilation
[Ref.: #24914]	sodium citrate ChEBI	-	assimilation
[Ref.: #24914]	starch ChEBI	-	hydrolysis
[Ref.: #24914]	suberic acid ChEBI	-	assimilation
[Ref.: #24914]	sucrose ChEBI	-	assimilation
[Ref.: #24914]	sucrose ChEBI	+	assimilation
[Ref.: #24914]	tryptophan ChEBI	-	energy source
[Ref.: #24914]	tween 80 ChEBI	-	hydrolysis
[Ref.: #24914]	tween 80 ChEBI	+	hydrolysis
[Ref.: #24914]	tyrosine ChEBI	-	hydrolysis
[Ref.: #24914]	tyrosine ChEBI	+	hydrolysis
[Ref.: #24914]	urea ChEBI	-	hydrolysis
[Ref.: #24914]	valerate ChEBI	-	assimilation
[Ref.: #24914]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24914]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #24914]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #24914]	acid phosphatase	+	3.1.3.2
[Ref.: #24914]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24914]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #24914]	alpha-fucosidase	+	3.2.1.51
[Ref.: #24914]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24914]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24914]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24914]	alpha-mannosidase	+	3.2.1.24
[Ref.: #24914]	arginine dihydrolase	-	3.5.3.6
[Ref.: #24914]	beta-galactosidase	+	3.2.1.23
[Ref.: #24914]	beta-glucosidase	+	3.2.1.21
[Ref.: #24914]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24914]	cystine arylamidase	-	3.4.11.3
[Ref.: #24914]	cystine arylamidase	+	3.4.11.3
[Ref.: #24914]	esterase	+
[Ref.: #24914]	esterase (C 4)	+
[Ref.: #24914]	esterase lipase (C 8)	+
[Ref.: #24914]	esterase lipase (C 8)	-
[Ref.: #24914]	leucine arylamidase	+	3.4.11.1
[Ref.: #24914]	lipase (C 14)	-
[Ref.: #24914]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24914]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24914]	trypsin	+	3.4.21.4
[Ref.: #24914]	trypsin	-	3.4.21.4
[Ref.: #24914]	tryptophan deaminase	-	4.1.99.1
[Ref.: #24914]	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.: #24914]	Sample type/isolated from	rhizosphere of tomato
[Ref.: #24914]	Geographic location (country and/or sea, region)	Buyeo-gun, Chungcheongnam-do
[Ref.: #24914]	Country	Republic of Korea
[Ref.: #24914]	Country ISO 3 Code	KOR
[Ref.: #24914]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

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.: #24914]	Pseudoflavitalea rhizosphaerae strain T16R-265 16S ribosomal RNA gene, partial sequence	KU379667	1463	GenBank ENA	1884793 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoflavitalea rhizosphaerae KACC 18655	GCA_003991355	scaffold	GenBank ENA	1884793 tax ID	*
[Ref.: #66792]	Pseudoflavitalea rhizosphaerae strain KACC 18655	1884793.3	wgs	PATRIC	1884793 tax ID	*
[Ref.: #66792]	Pseudoflavitalea rhizosphaerae KACC 18655	2837695235	draft	JGI IMG/M	1884793 tax ID	*

[Ref.: #24914]	GC-content	46.2 mol%	Thermal denaturation, fluorometry
[Ref.: #24914]	GC-content	55.7 mol%	Thermal denaturation, fluorometry

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pseudoflavitalea rhizosphaerae KACC 18655 NCBI: GCA_003991355.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoflavitalea rhizosphaerae KACC 18655 NCBI: GCA_003991355.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	90.363	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.275	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.508	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.312	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.686	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	83.784	yes

Availability in culture collections External links

[Ref.: #24914]

Culture collection no.

KACC 18655, NBRC 111880

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraflavitalea devenefica sp. nov., isolated from urban soil.	Hou X, Liu H, Shang Y, Mao S, Li S, Sang F, Deng H, Wang L, Kong L, Zhang C, Ding Z, Gao Y, Wei S, Chen Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004587	2020	*
Phylogeny	Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov.	Lawson PA, Patel NB, Mohammed A, Moore ERB, Lo AS, Sardi A, Davis JM, Doyle DA, Hui Y, Testerman T	Int J Syst Evol Microbiol	10.1099/ijsem.0.004204	2020	*
Phylogeny	Paraflavitalea soli gen. nov., sp. nov., isolated from greenhouse soil.	Heo J, Weon HY, Cho H, Hong SB, Kim JS, Kim SJ, Kwon SW	J Microbiol	10.1007/s12275-020-9236-y	2019	*
Phylogeny	Gynurincola endophyticus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae.	Zhang X, Song S, Tang L, Wang Y, Zhang X, Li X, Yu X, Zhang J, Kwon SW, Zhang L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003246	2019	*
Phylogeny	Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov.	Kim SJ, Cho H, Ahn JH, Weon HY, Seok SJ, Kim JS, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001330	2016	*

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 )

#24914

S.-J. C. Kim, Hayoung,Ahn, Jae-Hyung,Weon, Hang-Yeon,Seok, Soon-Ja,Kim, Jeong-Seon,Kwon, Soon-Wo: Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov. IJSEM 66: 4167 - 4171 2016 ( DOI 10.1099/ijsem.0.001330 , PubMed 27469002 )

#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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