Name: Pedobacter lycopersici T16R-88
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133256

Type strain:

Species: Pedobacter lycopersici

Strain Designation: T16R-88

Culture col. no.: KACC 18652, NBRC 111984

NCBI tax ID(s): 1911527 (species)

Section

Pedobacter lycopersici T16R-88 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from rhizosphere soil of a tomato plant.

colony-forming
Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter lycopersici**
	Full Scientific Name (PNU)	Pedobacter lycopersici Cho et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25059]	Gram stain	negative
[Ref.: #25059]	Cell length	1.2-2.5 µm
[Ref.: #25059]	Cell width	0.6-0.9 µm
[Ref.: #25059]	Cell shape	rod-shaped

[Ref.: #25059]	Colony color	white
[Ref.: #25059]	Colony shape	irregular

[Ref.: #25059]	Pigment production	no
[Ref.: #25059]	Pigment name	no Flexirubin-type pigments

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #25059]			growth	4-35 °C
[Ref.: #25059]			optimum	28-30 °C

[Ref.: #25059]

Temperature range

mesophilic

	pH	Kind of pH		pH	pH range
[Ref.: #25059]			optimum	7
[Ref.: #25059]			growth	6.0-9.0	alkaliphile

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25059]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25059]		NaCl		optimum	0	%
[Ref.: #25059]		NaCl		growth	0-4.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25059]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #25059]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #25059]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #25059]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #25059]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #25059]	adipate ChEBI	-	assimilation
[Ref.: #25059]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #25059]	casein	-	hydrolysis
[Ref.: #25059]	chitin ChEBI	-	hydrolysis
[Ref.: #25059]	D-glucose ChEBI	+	assimilation
[Ref.: #25059]	D-mannitol ChEBI	-	assimilation
[Ref.: #25059]	D-mannose ChEBI	+	assimilation
[Ref.: #25059]	D-ribose ChEBI	-	assimilation
[Ref.: #25059]	D-sorbitol ChEBI	-	assimilation
[Ref.: #25059]	decanoate ChEBI	-	assimilation
[Ref.: #25059]	dna ChEBI	-	hydrolysis
[Ref.: #25059]	esculin ChEBI	+	hydrolysis
[Ref.: #25059]	gelatin ChEBI	+	hydrolysis
[Ref.: #25059]	glucose ChEBI	-	fermentation
[Ref.: #25059]	glycogen ChEBI	-	assimilation
[Ref.: #25059]	hypoxanthine ChEBI	+	hydrolysis
[Ref.: #25059]	itaconate ChEBI	-	assimilation
[Ref.: #25059]	L-alanine ChEBI	-	assimilation
[Ref.: #25059]	L-arabinose ChEBI	-	assimilation
[Ref.: #25059]	L-fucose ChEBI	-	assimilation
[Ref.: #25059]	L-histidine ChEBI	-	assimilation
[Ref.: #25059]	L-proline ChEBI	-	assimilation
[Ref.: #25059]	L-rhamnose ChEBI	-	assimilation
[Ref.: #25059]	L-serine ChEBI	-	assimilation
[Ref.: #25059]	lactate ChEBI	-	assimilation
[Ref.: #25059]	malate ChEBI	-	assimilation
[Ref.: #25059]	maltose ChEBI	+	assimilation
[Ref.: #25059]	melibiose ChEBI	+	assimilation
[Ref.: #25059]	myo-inositol ChEBI	-	assimilation
[Ref.: #25059]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #25059]	nitrate ChEBI	+	reduction
[Ref.: #25059]	phenylacetate ChEBI	-	assimilation
[Ref.: #25059]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25059]	propionate ChEBI	-	assimilation
[Ref.: #25059]	salicin ChEBI	+	assimilation
[Ref.: #25059]	sodium acetate ChEBI	-	assimilation
[Ref.: #25059]	sodium citrate ChEBI	-	assimilation
[Ref.: #25059]	sodium malonate ChEBI	-	assimilation
[Ref.: #25059]	starch ChEBI	-	hydrolysis
[Ref.: #25059]	suberic acid ChEBI	-	assimilation
[Ref.: #25059]	sucrose ChEBI	+	assimilation
[Ref.: #25059]	tryptophan ChEBI	-	energy source
[Ref.: #25059]	tween 80 ChEBI	-	hydrolysis
[Ref.: #25059]	tyrosine ChEBI	-	hydrolysis
[Ref.: #25059]	urea ChEBI	-	hydrolysis
[Ref.: #25059]	valerate ChEBI	-	assimilation
[Ref.: #25059]	xanthine ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #25059]		indole ChEBI

	Physiological tests	Metabolite	Methylred-test	Indole test
[Ref.: #25059]		glucose ChEBI	-
[Ref.: #25059]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #25059]	acid phosphatase	+	3.1.3.2
[Ref.: #25059]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25059]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25059]	alpha-fucosidase	+	3.2.1.51
[Ref.: #25059]	alpha-galactosidase	+	3.2.1.22
[Ref.: #25059]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25059]	alpha-mannosidase	+	3.2.1.24
[Ref.: #25059]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25059]	beta-galactosidase	+	3.2.1.23
[Ref.: #25059]	beta-glucosidase	+	3.2.1.21
[Ref.: #25059]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25059]	catalase	+	1.11.1.6
[Ref.: #25059]	cystine arylamidase	+	3.4.11.3
[Ref.: #25059]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25059]	esterase (C 4)	+
[Ref.: #25059]	esterase lipase (C 8)	+
[Ref.: #25059]	leucine arylamidase	+	3.4.11.1
[Ref.: #25059]	lipase (C 14)	-
[Ref.: #25059]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25059]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25059]	trypsin	-	3.4.21.4
[Ref.: #25059]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25059]	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.: #25059]	Sample type/isolated from	rhizosphere soil of a tomato plant
[Ref.: #25059]	Geographic location (country and/or sea, region)	Buyeo-gun, Chungcheongnam-do
[Ref.: #25059]	Country	Republic of Korea
[Ref.: #25059]	Country ISO 3 Code	KOR
[Ref.: #25059]	Continent	Asia
[Ref.: #25059]	Geographic location	36.2750°/126.9120°
[Ref.: #25059]	Isolation date	2015-04
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#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.: #25059]	Pedobacter sp. strain T16R-88 16S ribosomal RNA gene, partial sequence	KU379664	1460	GenBank	1911527 tax ID

[Ref.: #25059]

GC-content

35.6 mol%

Thermal denaturation, fluorometry

Availability in culture collections External links

[Ref.: #25059]

Culture collection no.

KACC 18652, NBRC 111984

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacterlycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).	Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001532	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 )

#25059

H. A. Cho, J. H.,Weon, H. Y.,Joa, J. H.,Kwon, S. W.,Kim, S. J.: Pedobacter lycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.). IJSEM 66: 5406 - 5411 2016 ( DOI 10.1099/ijsem.0.001532 , PubMed 27902181 )

* 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 Pedobacter lycopersici in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF