Pedobacter agrisoli (JCM 32093, CCTCC AB 2017125, YHM-9)

Name: Pedobacter agrisoli (JCM 32093, CCTCC AB 2017125, YHM-9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158635

Type strain

Strain Designation YHM-9

Culture col. no. JCM 32093 CCTCC AB 2017125 YHM-9

NCBI tax ID(s) 2081981

Special Collections JCM Literature strains

History JCM <-- Q. Hong; Nanjing Agric. Univ., China; YHM-9.

Links

Pedobacter agrisoli YHM-9 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from farm soil.

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

Name and taxonomic classification

SI-ID 133677

JCM 32093

@ref 20215

Last LPSN update 2026-05-29 08:44:00

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter agrisoli

Full scientific name Pedobacter agrisoli Cui et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
65360	negative	0.9-1.3 µm	0.3-0.5 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65360	0.5-1 mm	light pink	circular	3 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth
65360	Reasoner's 2A agar (R2A)
65360	LB (Luria-Bertani) MEDIUM
65360	Nutrient agar (NA)
65360	tryptic soy agar

Culture temp

@ref	Growth	Type	Temperature (°C)
65360	positive	growth	15-30
65360	negative	growth	10
65360	negative	growth	37
65360	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
65360	positive	optimum	7
65360	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

65360

Oxygen toleranceaerobe

Spore formation

65360

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65360	NaCl	positive	growth	0-3 %(w/v)
65360	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65360	62064 ChEBI	2,3-butanediol	-	respiration
65360	64552 ChEBI	2-hydroxybutyrate	-	respiration
65360	16763 ChEBI	2-oxobutanoate	-	respiration
65360	30916 ChEBI	2-oxoglutarate	-	respiration
65360	28644 ChEBI	2-oxopentanoate	-	respiration
65360	37054 ChEBI	3-hydroxybutyrate	-	respiration
65360	18240 ChEBI	4-hydroxy-L-proline	-	respiration
65360	16724 ChEBI	4-hydroxybutyrate	-	respiration
65360	18101 ChEBI	4-hydroxyphenylacetic acid	+	respiration
65360	30089 ChEBI	acetate	+	respiration
65360	17128 ChEBI	adipate	-	carbon source
65360	17128 ChEBI	adipate	-	energy source
65360	40585 ChEBI	alpha-cyclodextrin	-	respiration
65360	17925 ChEBI	alpha-D-glucose	-	respiration
65360	36219 ChEBI	alpha-lactose	+	respiration
65360	73706 ChEBI	bromosuccinate	-	respiration
65360		casein	-	hydrolysis
65360	17057 ChEBI	cellobiose	+	respiration
65360	16383 ChEBI	cis-aconitate	-	respiration
65360	16947 ChEBI	citrate	-	carbon source
65360	16947 ChEBI	citrate	-	energy source
65360	16947 ChEBI	citrate	-	respiration
65360	15570 ChEBI	D-alanine	-	respiration
65360	18333 ChEBI	D-arabitol	-	respiration
65360	15824 ChEBI	D-fructose	+	respiration
65360	15895 ChEBI	D-galactonic acid lactone	+	respiration
65360	12936 ChEBI	D-galactose	-	respiration
65360	18024 ChEBI	D-galacturonic acid	+	respiration
65360	30612 ChEBI	D-glucarate	-	respiration
65360	8391 ChEBI	D-gluconate	-	respiration
65360	17784 ChEBI	D-glucosaminic acid	-	respiration
65360	17634 ChEBI	D-glucose	+	carbon source
65360	17634 ChEBI	D-glucose	+	energy source
65360	14314 ChEBI	D-glucose 6-phosphate	+	respiration
65360	15748 ChEBI	D-glucuronate	+	respiration
65360	16899 ChEBI	D-mannitol	-	carbon source
65360	16899 ChEBI	D-mannitol	-	energy source
65360	16899 ChEBI	D-mannitol	-	respiration
65360	16024 ChEBI	D-mannose	-	respiration
65360	16024 ChEBI	D-mannose	+	carbon source
65360	16024 ChEBI	D-mannose	+	energy source
65360	27605 ChEBI	D-psicose	-	respiration
65360	16523 ChEBI	D-serine	-	respiration
65360	17924 ChEBI	D-sorbitol	-	respiration
65360	27689 ChEBI	decanoate	-	carbon source
65360	27689 ChEBI	decanoate	-	energy source
65360	23652 ChEBI	dextrin	+	respiration
65360	17126 ChEBI	DL-carnitine	-	respiration
65360	17113 ChEBI	erythritol	-	respiration
65360	4853 ChEBI	esculin	+	hydrolysis
65360	16000 ChEBI	ethanolamine	-	respiration
65360	15740 ChEBI	formate	-	respiration
65360	16865 ChEBI	gamma-aminobutyric acid	-	respiration
65360	5291 ChEBI	gelatin	-	hydrolysis
65360	28066 ChEBI	gentiobiose	+	respiration
65360	24265 ChEBI	gluconate	-	carbon source
65360	24265 ChEBI	gluconate	-	energy source
65360	29042 ChEBI	glucose 1-phosphate	-	respiration
65360	32323 ChEBI	glucuronamide	-	respiration
65360	17754 ChEBI	glycerol	+	respiration
65360	14336 ChEBI	glycerol 1-phosphate	-	respiration
65360	28087 ChEBI	glycogen	-	respiration
65360	73804 ChEBI	glycyl L-aspartic acid	-	respiration
65360	73784 ChEBI	glycyl-l-glutamate	-	respiration
65360	17368 ChEBI	hypoxanthine	-	hydrolysis
65360	17596 ChEBI	inosine	-	respiration
65360	17240 ChEBI	itaconate	-	respiration
65360	21217 ChEBI	L-alaninamide	-	respiration
65360	16977 ChEBI	L-alanine	-	respiration
65360	73786 ChEBI	L-alanylglycine	-	respiration
65360	30849 ChEBI	L-arabinose	-	carbon source
65360	30849 ChEBI	L-arabinose	-	energy source
65360	30849 ChEBI	L-arabinose	-	respiration
65360	16467 ChEBI	L-arginine	+	carbon source
65360	16467 ChEBI	L-arginine	+	energy source
65360	17196 ChEBI	L-asparagine	-	respiration
65360	29991 ChEBI	L-aspartate	-	respiration
65360	18287 ChEBI	L-fucose	+	respiration
65360	29985 ChEBI	L-glutamate	+	respiration
65360	15971 ChEBI	L-histidine	-	respiration
65360	15603 ChEBI	L-leucine	-	respiration
65360	15729 ChEBI	L-ornithine	-	respiration
65360	17295 ChEBI	L-phenylalanine	-	respiration
65360	17203 ChEBI	L-proline	-	respiration
65360	18183 ChEBI	L-pyroglutamic acid	-	respiration
65360	62345 ChEBI	L-rhamnose	+	respiration
65360	17115 ChEBI	L-serine	-	respiration
65360	16857 ChEBI	L-threonine	-	respiration
65360	24996 ChEBI	lactate	+	respiration
65360	6359 ChEBI	lactulose	-	respiration
65360	25115 ChEBI	malate	-	carbon source
65360	25115 ChEBI	malate	-	energy source
65360	15792 ChEBI	malonate	-	respiration
65360	17306 ChEBI	maltose	-	respiration
65360	17306 ChEBI	maltose	+	carbon source
65360	17306 ChEBI	maltose	+	energy source
65360	28053 ChEBI	melibiose	+	respiration
65360	320055 ChEBI	methyl beta-D-glucopyranoside	-	respiration
65360	51850 ChEBI	methyl pyruvate	-	respiration
65360	75146 ChEBI	monomethyl succinate	-	respiration
65360	17268 ChEBI	myo-inositol	-	respiration
65360	28037 ChEBI	N-acetylgalactosamine	+	respiration
65360	506227 ChEBI	N-acetylglucosamine	+	carbon source
65360	506227 ChEBI	N-acetylglucosamine	+	energy source
65360	506227 ChEBI	N-acetylglucosamine	+	respiration
65360	17632 ChEBI	nitrate	-	reduction
65360	18401 ChEBI	phenylacetate	-	carbon source
65360	18401 ChEBI	phenylacetate	-	energy source
65360	50048 ChEBI	phenylethylamine	-	respiration
65360	17272 ChEBI	propionate	-	respiration
65360	17148 ChEBI	putrescine	-	respiration
65360	26490 ChEBI	quinate	-	respiration
65360	16634 ChEBI	raffinose	-	respiration
65360	15963 ChEBI	ribitol	-	respiration
65360	41865 ChEBI	sebacic acid	-	respiration
65360	28017 ChEBI	starch	+	hydrolysis
65360	143136 ChEBI	succinamate	-	respiration
65360	30031 ChEBI	succinate	-	respiration
65360	17992 ChEBI	sucrose	-	respiration
65360	17748 ChEBI	thymidine	-	respiration
65360	27082 ChEBI	trehalose	+	respiration
65360	32528 ChEBI	turanose	+	respiration
65360	53423 ChEBI	tween 40	+	respiration
65360	53426 ChEBI	tween 80	-	respiration
65360	53426 ChEBI	tween 80	+	hydrolysis
65360	16704 ChEBI	uridine	-	respiration
65360	27248 ChEBI	urocanic acid	-	respiration
65360	15318 ChEBI	xanthine	-	hydrolysis
65360	17151 ChEBI	xylitol	-	respiration

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65360	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65360	acid phosphatase	+	3.1.3.2
65360	alkaline phosphatase	+	3.1.3.1
65360	alpha-chymotrypsin	-	3.4.21.1
65360	alpha-fucosidase	-	3.2.1.51
65360	alpha-galactosidase	-	3.2.1.22
65360	alpha-glucosidase	+	3.2.1.20
65360	alpha-mannosidase	-	3.2.1.24
65360	beta-galactosidase	+	3.2.1.23
65360	beta-glucosidase	+	3.2.1.21
65360	beta-glucuronidase	-	3.2.1.31
65360	catalase	+	1.11.1.6
65360	cystine arylamidase	+	3.4.11.3
65360	cytochrome oxidase	+	1.9.3.1
65360	esterase (C 4)	+
65360	esterase Lipase (C 8)	+
65360	leucine arylamidase	+	3.4.11.1
65360	lipase (C 14)	-
65360	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65360	naphthol-AS-BI-phosphohydrolase	+
65360	trypsin	-	3.4.21.4
65360	urease	-	3.5.1.5
65360	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Engineered	#Food production	#Aquaculture

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
65360	farm soil	vicinity of Yangquan, Shanxi province	China	CHN	Asia	38.3833	113.983 38.3833/113.983	R2A agar	3-5 days	30	dilution plating technique
67770	Farmland soil in Yangquan	Shanxi Province	China	CHN	Asia

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Database
65360	Pedobacter agrisoli strain YHM-9 16S ribosomal RNA gene, partial sequence	MF564194

GC content

@ref	GC-content (mol%)	Method
65360	38.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter agrisoli sp. nov., isolated from farmland soil.	Cui MD, Wang X, Jiang WK, Hu G, Yang ZG, Sun GJ, Zhu SJ, Zhou YD, Hong Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.002604	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 )
#65360	Meng-Di Cui, Xiang Wang, Wan-Kui Jiang, Gang Hu, Zhan-Gong Yang, Gao-Jie Sun, Shi-Jun Zhu, Yi-Dong Zhou, Qing Hong: Pedobacter agrisoli sp. nov., isolated from farmland soil. IJSEM 68: 886 - 891 2018 ( DOI 10.1099/ijsem.0.002604 , PubMed 29458546 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pedobacter agrisoli (JCM 32093, CCTCC AB 2017125, YHM-9)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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