Strain identifier

BacDive ID: 158635

Type strain: Yes

Species: Pedobacter agrisoli

Strain Designation: YHM-9

Strain history: Q. Hong; Nanjing Agric. Univ., China; YHM-9.

NCBI tax ID(s): 2081981 (species)

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General

@ref: 65360

BacDive-ID: 158635

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

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

NCBI tax id

  • NCBI tax id: 2081981
  • Matching level: species

strain history

  • @ref: 67770
  • history: Q. Hong; Nanjing Agric. Univ., China; YHM-9.

doi: 10.13145/bacdive158635.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter agrisoli
  • full scientific name: Pedobacter agrisoli Cui et al. 2018

@ref: 65360

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter agrisoli

strain designation: YHM-9

type strain: yes

Morphology

cell morphology

  • @ref: 65360
  • gram stain: negative
  • cell length: 0.9-1.3 µm
  • cell width: 0.3-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65360
  • colony size: 0.5-1 mm
  • colony color: light pink
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowth
65360Reasoner's 2A agar (R2A)yes
65360LB (Luria-Bertani) MEDIUMyes
65360Nutrient agar (NA)yes
65360tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
65360positivegrowth15-30
65360nogrowth10psychrophilic
65360nogrowth37mesophilic
65360positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65360positivegrowth5.5-8.5alkaliphile
65360positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 65360
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65360
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65360NaClpositivegrowth0-3 %(w/v)
65360NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65360645522-hydroxybutyrate-respiration
65360167632-oxobutanoate-respiration
65360309162-oxoglutarate-respiration
65360286442-oxopentanoate-respiration
65360620642,3-butanediol-respiration
65360370543-hydroxybutyrate-respiration
65360182404-hydroxy-L-proline-respiration
65360167244-hydroxybutyrate-respiration
65360181014-hydroxyphenylacetic acid+respiration
6536030089acetate+respiration
6536017128adipate-carbon source
6536017128adipate-energy source
6536015963ribitol-respiration
6536040585alpha-cyclodextrin-respiration
6536017925alpha-D-glucose-respiration
6536036219alpha-lactose+respiration
6536073706bromosuccinate-respiration
6536027689decanoate-carbon source
6536027689decanoate-energy source
65360casein-hydrolysis
6536016383cis-aconitate-respiration
6536016947citrate-carbon source
6536016947citrate-energy source
6536016947citrate-respiration
6536015570D-alanine-respiration
6536018333D-arabitol-respiration
6536017057cellobiose+respiration
6536015824D-fructose+respiration
6536015895D-galactonic acid lactone+respiration
6536012936D-galactose-respiration
6536018024D-galacturonic acid+respiration
6536030612D-glucarate-respiration
653608391D-gluconate-respiration
6536017784D-glucosaminic acid-respiration
6536017634D-glucose+carbon source
6536017634D-glucose+energy source
6536014314D-glucose 6-phosphate+respiration
6536015748D-glucuronate+respiration
6536016899D-mannitol-carbon source
6536016899D-mannitol-energy source
6536016899D-mannitol-respiration
6536016024D-mannose-respiration
6536016024D-mannose+carbon source
6536016024D-mannose+energy source
6536027605D-psicose-respiration
6536016523D-serine-respiration
6536017924D-sorbitol-respiration
6536023652dextrin+respiration
6536017126DL-carnitine-respiration
6536024996lactate+respiration
6536017113erythritol-respiration
653604853esculin+hydrolysis
6536016000ethanolamine-respiration
6536015740formate-respiration
6536016865gamma-aminobutyric acid-respiration
653605291gelatin-hydrolysis
6536028066gentiobiose+respiration
6536024265gluconate-carbon source
6536024265gluconate-energy source
6536029042glucose 1-phosphate-respiration
6536032323glucuronamide-respiration
6536017754glycerol+respiration
6536014336glycerol 1-phosphate-respiration
6536028087glycogen-respiration
6536073804glycyl L-aspartic acid-respiration
6536017368hypoxanthine-hydrolysis
6536017596inosine-respiration
6536017240itaconate-respiration
6536021217L-alaninamide-respiration
6536016977L-alanine-respiration
6536073786L-alanylglycine-respiration
6536030849L-arabinose-carbon source
6536030849L-arabinose-energy source
6536030849L-arabinose-respiration
6536016467L-arginine+carbon source
6536016467L-arginine+energy source
6536017196L-asparagine-respiration
6536029991L-aspartate-respiration
6536018287L-fucose+respiration
6536029985L-glutamate+respiration
6536015971L-histidine-respiration
6536015603L-leucine-respiration
6536015729L-ornithine-respiration
6536017295L-phenylalanine-respiration
6536017203L-proline-respiration
6536018183L-pyroglutamic acid-respiration
6536062345L-rhamnose+respiration
6536017115L-serine-respiration
6536016857L-threonine-respiration
653606359lactulose-respiration
6536025115malate-carbon source
6536025115malate-energy source
6536015792malonate-respiration
6536017306maltose-respiration
6536017306maltose+carbon source
6536017306maltose+energy source
6536028053melibiose+respiration
65360320055methyl beta-D-glucopyranoside-respiration
6536051850methyl pyruvate-respiration
6536075146monomethyl succinate-respiration
6536017268myo-inositol-respiration
6536028037N-acetylgalactosamine+respiration
65360506227N-acetylglucosamine+carbon source
65360506227N-acetylglucosamine+energy source
65360506227N-acetylglucosamine+respiration
6536073784glycyl-l-glutamate-respiration
6536017632nitrate-reduction
6536018401phenylacetate-carbon source
6536018401phenylacetate-energy source
6536050048phenylethylamine-respiration
6536017272propionate-respiration
6536017148putrescine-respiration
6536026490quinate-respiration
6536016634raffinose-respiration
6536041865sebacic acid-respiration
6536028017starch+hydrolysis
65360143136succinamate-respiration
6536030031succinate-respiration
6536017992sucrose-respiration
6536017748thymidine-respiration
6536027082trehalose+respiration
6536032528turanose+respiration
6536053423tween 40+respiration
6536053426tween 80-respiration
6536053426tween 80+hydrolysis
6536016704uridine-respiration
6536027248urocanic acid-respiration
6536015318xanthine-hydrolysis
6536017151xylitol-respiration

metabolite production

  • @ref: 65360
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65360farm soilvicinity of Yangquan, Shanxi provinceChinaCHNAsia38.3833113.983R2A agar3-5 days30dilution plating technique
67770Farmland soil in YangquanShanxi ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Engineered#Food production#Aquaculture

Sequence information

16S sequences

  • @ref: 65360
  • description: 16S rRNA gene sequence
  • accession: MF564194
  • database: nuccore

GC content

  • @ref: 65360
  • GC-content: 38.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65360

culture collection no.: JCM 32093, CCTCC AB 2017125

literature

  • topic: Phylogeny
  • Pubmed-ID: 29458546
  • title: Pedobacter agrisoli sp. nov., isolated from farmland soil.
  • authors: Cui MD, Wang X, Jiang WK, Hu G, Yang ZG, Sun GJ, Zhu SJ, Zhou YD, Hong Q
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002604
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65360Meng-Di Cui, Xiang Wang, Wan-Kui Jiang, Gang Hu, Zhan-Gong Yang, Gao-Jie Sun, Shi-Jun Zhu, Yi-Dong Zhou, Qing HongPedobacter agrisoli sp. nov., isolated from farmland soil10.1099/ijsem.0.002604IJSEM 68: 886-891 201829458546
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/