Name: Chitinophaga rhizosphaerae T16R-86
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140710

Type strain:

Species: Chitinophaga rhizosphaerae

Strain Designation: T16R-86

Culture col. no.: KACC 18790, JCM 31600

Strain history: S.-W. Kwon; KACC, South Korea; T16R-86.

NCBI tax ID(s): 1864947 (species)

Section

Chitinophaga rhizosphaerae T16R-86 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from rhizosphere of a tomato plant collected from a farm on Buyeo-gun.

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	*Chitinophaga*
	Species	**Chitinophaga rhizosphaerae**
	Full Scientific Name (LPSN)	Chitinophaga rhizosphaerae Kim et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43485]	Gram stain	negative

[Ref.: #43485]	Cell length	1.2-3 µm

[Ref.: #43485]	Cell width	0.5-0.6 µm

[Ref.: #43485]	Cell shape	rod-shaped

[Ref.: #43485]	Colony color	Yellow
[Ref.: #43485]	Colony shape	irregular
[Ref.: #43485]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43485]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43485]

Culture medium growth

		Temperature
[Ref.: #43485]	growth	10-37 °C
[Ref.: #43485]	optimum	28 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #43485]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43485]			optimum	7
[Ref.: #43485]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43485]

Oxygen tolerance

aerobe

[Ref.: #43485]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43485]		NaCl		growth	0-2	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43485]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43485]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #43485]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43485]	adipate ChEBI	-	assimilation
[Ref.: #43485]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #43485]	casein	+	hydrolysis
[Ref.: #43485]	chitin ChEBI	-	hydrolysis
[Ref.: #43485]	D-glucose ChEBI	+	assimilation
[Ref.: #43485]	D-mannitol ChEBI	-	assimilation
[Ref.: #43485]	D-mannose ChEBI	+	assimilation
[Ref.: #43485]	D-ribose ChEBI	+	assimilation
[Ref.: #43485]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43485]	decanoate ChEBI	-	assimilation
[Ref.: #43485]	dna ChEBI	-	hydrolysis
[Ref.: #43485]	esculin ChEBI	+	hydrolysis
[Ref.: #43485]	gelatin ChEBI	+	hydrolysis
[Ref.: #43485]	glucose ChEBI	-	fermentation
[Ref.: #43485]	glycogen ChEBI	-	assimilation
[Ref.: #43485]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #43485]	itaconate ChEBI	-	assimilation
[Ref.: #43485]	L-alanine ChEBI	-	assimilation
[Ref.: #43485]	L-arabinose ChEBI	-	assimilation
[Ref.: #43485]	L-fucose ChEBI	-	assimilation
[Ref.: #43485]	L-histidine ChEBI	+	assimilation
[Ref.: #43485]	L-proline ChEBI	-	assimilation
[Ref.: #43485]	L-rhamnose ChEBI	-	assimilation
[Ref.: #43485]	L-serine ChEBI	+	assimilation
[Ref.: #43485]	lactate ChEBI	-	assimilation
[Ref.: #43485]	malate ChEBI	-	assimilation
[Ref.: #43485]	maltose ChEBI	+	assimilation
[Ref.: #43485]	melibiose ChEBI	+	assimilation
[Ref.: #43485]	myo-inositol ChEBI	-	assimilation
[Ref.: #43485]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43485]	nitrate ChEBI	-	reduction
[Ref.: #43485]	phenylacetate ChEBI	-	assimilation
[Ref.: #43485]	potassium 2-dehydro-D-gluconate	-	assimilation
[Ref.: #43485]	potassium 5-dehydro-D-gluconate	-	assimilation
[Ref.: #43485]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43485]	propionate ChEBI	-	assimilation
[Ref.: #43485]	salicin ChEBI	+	assimilation
[Ref.: #43485]	sodium acetate ChEBI	-	assimilation
[Ref.: #43485]	sodium citrate ChEBI	-	assimilation
[Ref.: #43485]	sodium malonate ChEBI	-	assimilation
[Ref.: #43485]	starch ChEBI	-	hydrolysis
[Ref.: #43485]	suberic acid ChEBI	-	assimilation
[Ref.: #43485]	sucrose ChEBI	+	assimilation
[Ref.: #43485]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43485]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43485]	urea ChEBI	-	hydrolysis
[Ref.: #43485]	valerate ChEBI	-	assimilation
[Ref.: #43485]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43485]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43485]	acid phosphatase	+	3.1.3.2
[Ref.: #43485]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43485]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43485]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43485]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43485]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43485]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43485]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43485]	beta-galactosidase	+	3.2.1.23
[Ref.: #43485]	beta-glucosidase	+	3.2.1.21
[Ref.: #43485]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43485]	catalase	+	1.11.1.6
[Ref.: #43485]	cystine arylamidase	+	3.4.11.3
[Ref.: #43485]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43485]	esterase (C 4)	+
[Ref.: #43485]	esterase Lipase (C 8)	+
[Ref.: #43485]	leucine arylamidase	+	3.4.11.1
[Ref.: #43485]	lipase (C 14)	-
[Ref.: #43485]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43485]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43485]	trypsin	+	3.4.21.4
[Ref.: #43485]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43485]

Fatty acid	Percentage	ECL
C15:0 iso	37.9
C16:1ω5c	20.5
C17:0 iso 3OH	18.9
C15:0 iso 3OH	4.9
C16:0	3.6
C15:0 iso 2OH / C16:1ω7c	2.7
C16:0 iso	1.9
C16:1ω11c	1.8
Unknown ECL 16.582	1.4	16582
C17:0 3OH	1.2
C17:0 2OH	1

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

[Ref.: #43485]	Sample type/isolated from	rhizosphere of a tomato plant collected from a farm on Buyeo-gun
[Ref.: #43485]	Geographic location (country and/or sea, region)	Buyeo-gun, Chungcheongnam-do
[Ref.: #43485]	Country	Republic of Korea
[Ref.: #43485]	Country ISO 3 Code	KOR
[Ref.: #43485]	Continent	Asia
[Ref.: #43485]	Geographic location	36.2930°/126.9310°

[Ref.: #67770]	Sample type/isolated from	Rhizosphere soil of a tomato plant from a farm on Buyeo-gun
[Ref.: #67770]	Geographic location (country and/or sea, region)	Chungcheongnam-do
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX417377 (>99% sequence identity) for Chitinophaga from Microbeatlas

Aquatic Samples	347
Soil Samples	2519
Animal Samples	203
Plant Samples	579
Total Samples	3648

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.: #43485]	16S rRNA gene sequence	KX417377		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chitinophaga rhizosphaerae T16R-86	GCA_003958645	contig	GenBank	1864947 tax ID	*
[Ref.: #66792]	Chitinophaga rhizosphaerae T16R-86	2883068021	draft	JGI IMG/M	1864947 tax ID	*

[Ref.: #43485]	GC-content	53.6 mol%	Thermal denaturation, fluorometry
[Ref.: #67770]	GC-content	53.6 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #43485]

Culture collection no.

KACC 18790, JCM 31600

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga deserti sp. nov., isolated from desert soil.	Kong XK, Chen D, Huang JW, Cheng XK, Jiang JD	Int J Syst Evol Microbiol	10.1099/ijsem.0.003395	2019	*
Phylogeny	Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant.	Kim SJ, Cho H, Ahn JH, Weon HY, Joa JH, Hong SB, Seok SJ, Kim JS, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002134	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 )

#43485

Soo-Jin Kim, Hayoung Cho, Jae-Hyung Ahn, Hang-Yeon Weon, Jae-Ho Joa, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon: Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant. IJSEM 67: 3435 - 3439 2017 ( DOI 10.1099/ijsem.0.002134 , PubMed 28875897 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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

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