Strain identifier

BacDive ID: 140255

Type strain: Yes

Species: Pedobacter zeae

Strain Designation: 22

Strain history: <- J. Gao, Beijing Academy of Agriculture and Forestry Science; 22

NCBI tax ID(s): 1737356 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7 (current version):
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 7 (current version)

General

@ref: 42862

BacDive-ID: 140255

DSM-Number: 100774

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

description: Pedobacter zeae 22 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize.

NCBI tax id

  • NCBI tax id: 1737356
  • Matching level: species

strain history: <- J. Gao, Beijing Academy of Agriculture and Forestry Science; 22

doi: 10.13145/bacdive140255.20220920.7

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 zeae
  • full scientific name: Pedobacter zeae Gao et al. 2017

@ref: 42862

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter zeae

full scientific name: Pedobacter zeae Gao et al. 2017

strain designation: 22

type strain: yes

Morphology

cell morphology

  • @ref: 25201
  • gram stain: negative
  • cell length: 0.6-1.8 µm
  • cell width: 0.2-0.3 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25201
  • colony size: 0.5-1.0 mm
  • colony color: pinkish-yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: LB agar plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25201LB (Luria-Bertani) MEDIUMyes
25201LB agar platesyes
25201nutrient agar (NA)yes
25201Reasoner's 2A agar (R2A)yes
25201tryptic soy agar (TSA)yes
25201Ashby nitrogen-free mediumyes
42862NUTRIENT AGAR (DSMZ Medium 1)yeshttps://bacmedia.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25201positivegrowth15.0-30.0
25201positiveoptimum30mesophilic
42862positivegrowth28mesophilic

culture pH

@refabilitytypepH
25201positivegrowth6.0-7.0
25201positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25201
  • oxygen tolerance: aerobe

halophily

@refsalttested relationconcentrationgrowth
25201NaCloptimum1 %
25201NaClgrowth0.0-1.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25201168082-dehydro-D-gluconate-builds acid from
25201581435-dehydro-D-gluconate-builds acid from
2520117128adipate-assimilation
2520115963ribitol-builds acid from
2520118333D-arabitol-builds acid from
2520128847D-fucose-builds acid from
2520116899D-mannitol-assimilation
2520116899D-mannitol-builds acid from
252016731melezitose-builds acid from
2520117924D-sorbitol-builds acid from
2520127689decanoate-assimilation
2520117113erythritol-builds acid from
2520116813galactitol-builds acid from
2520128066gentiobiose-builds acid from
2520124265gluconate-builds acid from
2520117754glycerol-builds acid from
2520117268myo-inositol-builds acid from
2520115443inulin-builds acid from
2520118403L-arabitol-builds acid from
2520162345L-rhamnose-builds acid from
2520162345L-rhamnose-oxidation
2520117266L-sorbose-builds acid from
2520165328L-xylose-builds acid from
2520125115malate-assimilation
2520174863methyl beta-D-xylopyranoside-builds acid from
2520117632nitrate-reduction
2520117309pectin-oxidation
2520118401phenylacetate-assimilation
2520132032potassium gluconate-assimilation
2520128017starch-builds acid from
2520127897tryptophan-energy source
2520117151xylitol-builds acid from
2520115589L-malate+oxidation
2520127613amygdalin+builds acid from
2520118305arbutin+builds acid from
2520173706bromosuccinate+oxidation
2520117108D-arabinose+builds acid from
2520117057cellobiose+builds acid from
2520115824D-fructose+builds acid from
2520178697D-fructose 6-phosphate+oxidation
2520112936D-galactose+builds acid from
2520112936D-galactose+oxidation
252018391D-gluconate+oxidation
2520117634D-glucose+assimilation
2520117634D-glucose+builds acid from
2520114314D-glucose 6-phosphate+oxidation
2520117716lactose+builds acid from
2520162318D-lyxose+builds acid from
2520117306maltose+builds acid from
2520116024D-mannose+assimilation
2520116024D-mannose+builds acid from
2520128053melibiose+builds acid from
2520116634raffinose+builds acid from
2520116988D-ribose+builds acid from
2520117992sucrose+builds acid from
2520116443D-tagatose+builds acid from
2520116551D-trehalose+builds acid from
2520132528turanose+builds acid from
2520165327D-xylose+builds acid from
252014853esculin+hydrolysis
252014853esculin+builds acid from
252015291gelatin+hydrolysis
2520117234glucose+fermentation
2520128087glycogen+builds acid from
2520130849L-arabinose+assimilation
2520130849L-arabinose+builds acid from
2520118287L-fucose+builds acid from
2520118287L-fucose+oxidation
2520115971L-histidine+oxidation
2520117115L-serine+oxidation
2520117306maltose+assimilation
25201320061methyl alpha-D-glucopyranoside+builds acid from
25201320061methyl alpha-D-glucopyranoside+oxidation
2520143943methyl alpha-D-mannoside+builds acid from
2520128037N-acetylgalactosamine+oxidation
25201506227N-acetylglucosamine+assimilation
25201506227N-acetylglucosamine+builds acid from
2520116634raffinose+oxidation
2520128077rifampicin+oxidation
2520117814salicin+builds acid from
2520153258sodium citrate+assimilation
2520175228sodium lactate+oxidation
2520117164stachyose+oxidation
2520127082trehalose+oxidation
2520132528turanose+oxidation

metabolite production

  • @ref: 25201
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25201
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25201acid phosphatase+3.1.3.2
25201alkaline phosphatase+3.1.3.1
25201alpha-chymotrypsin-3.4.21.1
25201alpha-fucosidase+3.2.1.51
25201alpha-galactosidase+3.2.1.22
25201alpha-glucosidase+3.2.1.20
25201alpha-mannosidase+3.2.1.24
25201arginine dihydrolase-3.5.3.6
25201beta-galactosidase+3.2.1.23
25201beta-glucosidase+3.2.1.21
25201beta-glucuronidase+3.2.1.31
25201catalase+1.11.1.6
25201cystine arylamidase+3.4.11.3
25201cytochrome oxidase+1.9.3.1
25201esterase (C 4)+
25201esterase Lipase (C 8)+
25201leucine arylamidase+3.4.11.1
25201lipase (C 14)-
25201N-acetyl-beta-glucosaminidase+3.2.1.52
25201naphthol-AS-BI-phosphohydrolase+
25201trypsin+3.4.21.4
25201tryptophan deaminase-4.1.99.1
25201urease-3.5.1.5
25201valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25201C15:0 anteiso0.5
    25201C13:1 at 12-130.4
    25201C14:02.6
    25201C14:0 2OH0.3
    25201C14:1ω5c0.3
    25201C15:1ω6c0.6
    25201C16:00.8
    25201C16:0 3OH0.8
    25201C16:1ω5c1.4
    25201C16:1ω7c / C16:1ω6c31.4
    25201C18:1ω5c0.4
    25201C19:1ω11c / C19:1ω9c4.1
    25201C11:0 iso0.4
    25201C13:0 iso0.3
    25201C15:0 iso37
    25201C15:0 iso 3OH3
    25201C15:1 iso F0.2
    25201C15:1 iso h / C13:0 3OH1
    25201C16:0 iso 3OH0.9
    25201C17:0 iso0.2
    25201C17:0 iso 3OH7.9
    25201C17:1 iso I /C17:1 anteiso B0.9
    25201C17:1 iso ω9c / C16:0 10-methyl4.5
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA medium
  • incubation temperature: 28
  • incubation time: 3
  • library/peak naming table: TSBA 6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
25201surface-sterilized root tissue of maizeFangshan District of BeijingRepublic of ChinaCHNAsiaAshby nitrogen-free medium3 days28
42862surface-sterilized root tissue of maizeFangshan District of BeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 42862
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25201Pedobacter sp. 22 16S ribosomal RNA gene, partial sequenceKR610524.21480nuccore1737356
42862Pedobacter zeae strain 22 16S ribosomal RNA gene, partial sequenceKR6105241480ena1737356

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter zeae CGMCC 1.15287GCA_014641575scaffoldncbi1737356
66792Pedobacter zeae DSM 100774GCA_014196715scaffoldncbi1737356
66792Pedobacter zeae strain CGMCC 1.152871737356.4wgspatric1737356
66792Pedobacter zeae strain DSM 1007741737356.3wgspatric1737356
66792Pedobacter zeae DSM 1007742829961646draftimg1737356

GC content

@refGC-contentmethod
2520140.7-41.7thermal denaturation, midpoint method (Tm)
4286241.2thermal denaturation, midpoint method (Tm)

External links

@ref: 42862

culture collection no.: DSM 100774, CGMCC 1.15287

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902277
  • title: Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.
  • authors: Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001603
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
  • topic2: Enzymology

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
25201J. L. S. Gao, P.,Mao, X. J.,Du, Y. L.,Liu, B. Y.,Sun, J. G.Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root10.1099/ijsem.0.001603IJSEM 67: 231-236 201727902277
42862Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100774Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100774)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes