Strain identifier

BacDive ID: 133094

Type strain: Yes

Species: Paenibacillus aceris

Strain Designation: KUDC4121

Strain history: <- SY Ghim, Kyungpook Natl. Univ.

NCBI tax ID(s): 869555 (species)

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General

@ref: 24882

BacDive-ID: 133094

DSM-Number: 24950

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, rod-shaped, colony-forming

description: Paenibacillus aceris KUDC4121 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from rhizosphere of Acer okamotoanum.

NCBI tax id

  • NCBI tax id: 869555
  • Matching level: species

strain history

@refhistory
24882<- G. Sa-Youl, Kyungpook Natl. Univ., Daegu, South Korea; KUDC4121
67771<- SY Ghim, Kyungpook Natl. Univ.

doi: 10.13145/bacdive133094.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus aceris
  • full scientific name: Paenibacillus aceris Hwang and Ghim 2017

@ref: 24882

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus aceris

full scientific name: Paenibacillus aceris Hwang and Ghim 2017

strain designation: KUDC4121

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25289positive2.0-2.5 µm0.2-0.4 µmrod-shapedno
67771rod-shapedno
67771positive
69480yes97.374
69480positive100

colony morphology

  • @ref: 25289
  • colony size: 2.0-3.0 mm
  • colony color: creamy white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25289Reasoner's 2A agar (R2A)yes
25289tryptic soy agar (TSA)yes
24882CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25289positivegrowth18-37
25289positiveoptimum30mesophilic
24882positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
25289positivegrowth6.0-7.0
25289positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25289facultative anaerobe
67771facultative anaerobe

spore formation

@refspore formationconfidence
25289no
67771no
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
25289NaClpositivegrowth0.0-0.5 %(w/v)
25289NaCloptimum0.5 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25289168082-dehydro-D-gluconate-builds acid from
2528915963ribitol-builds acid from
2528918333D-arabitol-builds acid from
2528928847D-fucose-builds acid from
2528962318D-lyxose-builds acid from
2528916443D-tagatose-builds acid from
2528917113erythritol-builds acid from
2528916813galactitol-builds acid from
2528917368hypoxanthine-hydrolysis
2528915443inulin-builds acid from
2528918403L-arabitol-builds acid from
2528965328L-xylose-builds acid from
2528929864mannitol-builds acid from
2528917632nitrate-reduction
2528928017starch-builds acid from
2528953425tween 60-hydrolysis
2528915318xanthine-hydrolysis
252893-O-methyl alpha-D-glucopyranoside+builds acid from
252893557154-nitrophenyl beta-D-galactopyranoside+hydrolysis
25289581435-dehydro-D-gluconate+builds acid from
2528927613amygdalin+builds acid from
2528918305arbutin+builds acid from
2528917057cellobiose+builds acid from
2528917108D-arabinose+builds acid from
2528932528turanose+builds acid from
2528965327D-xylose+builds acid from
252894853esculin+hydrolysis
252894853esculin+builds acid from
2528928757fructose+builds acid from
2528928260galactose+builds acid from
2528928066gentiobiose+builds acid from
2528924265gluconate+builds acid from
2528917234glucose+hydrolysis
2528917234glucose+builds acid from
2528917754glycerol+builds acid from
2528928087glycogen+builds acid from
2528917268myo-inositol+builds acid from
2528930849L-arabinose+builds acid from
2528918287L-fucose+builds acid from
2528917716lactose+builds acid from
2528917306maltose+hydrolysis
2528917306maltose+builds acid from
2528937684mannose+hydrolysis
2528937684mannose+builds acid from
252896731melezitose+builds acid from
2528928053melibiose+builds acid from
2528943943methyl alpha-D-mannoside+builds acid from
2528974863methyl beta-D-xylopyranoside+builds acid from
25289506227N-acetylglucosamine+hydrolysis
25289506227N-acetylglucosamine+builds acid from
2528932032potassium gluconate+hydrolysis
2528916634raffinose+builds acid from
2528926546rhamnose+builds acid from
2528933942ribose+builds acid from
2528917814salicin+builds acid from
2528930911sorbitol+builds acid from
2528927922sorbose+builds acid from
2528917992sucrose+builds acid from
2528927082trehalose+builds acid from
2528917151xylitol+builds acid from

metabolite production

  • @ref: 25289
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
25289acid phosphatase-3.1.3.2
25289alkaline phosphatase+3.1.3.1
25289alpha-chymotrypsin-3.4.21.1
25289alpha-fucosidase-3.2.1.51
25289alpha-galactosidase+3.2.1.22
25289alpha-glucosidase-3.2.1.20
25289alpha-mannosidase-3.2.1.24
25289beta-galactosidase+3.2.1.23
25289beta-glucosidase-3.2.1.21
25289beta-glucuronidase-3.2.1.31
25289catalase+1.11.1.6
25289cystine arylamidase-3.4.11.3
25289cytochrome oxidase+1.9.3.1
25289esterase Lipase (C 8)+
25289leucine arylamidase-3.4.11.1
25289lipase-
25289N-acetyl-beta-glucosaminidase+3.2.1.52
25289naphthol-AS-BI-phosphohydrolase+
25289trypsin-3.4.21.4
25289valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25289C15:0 anteiso62.5
    25289C17:0 anteiso2.7
    25289C14:02.5
    25289C15:01.5
    25289C16:010.8
    25289C18:01.1
    25289C14:0 iso4.3
    25289iso-C15.02.9
    25289C16:0 iso11.6
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 4.0
  • library/peak naming table: TSBA 40
  • system: MIS MIDI
  • instrument: Hewlett Packard, 6890
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
24882rhizosphere of Acer okamotoanumAcer okamotoanumUlleungdo IslandRepublic of KoreaKORAsia
25289rhizosphere of Acer okamotoanumUlleungdo IslandRepublic of KoreaKORAsia37.488130.858tryptic soy agar (TSA, Difco)7 days25serial dilution
67771From rhizosphere of `Acer okamotoanum`Ulleungdo IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_162914.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2674;97_3282;98_4131;99_162914&stattab=map
  • Last taxonomy: Paenibacillus aceris
  • 16S sequence: KU879057
  • Sequence Identity:
  • Total samples: 3
  • soil counts: 3

Safety information

risk assessment

  • @ref: 24882
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25289Paenibacillus sp. KUDC4121 16S ribosomal RNA gene, partial sequenceKU8790571502nuccore869555
24882Paenibacillus aceris strain KUDC4121 16S ribosomal RNA gene, partial sequenceHM0279261369ena869555

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus aceris DSM 24950GCA_017874035contigncbi869555
66792Paenibacillus aceris strain DSM 24950869555.4wgspatric869555
66792Paenibacillus aceris DSM 249502913432798draftimg869555

GC content

@refGC-contentmethod
2528948.8high performance liquid chromatography (HPLC)
2488248.2high performance liquid chromatography (HPLC)
6777148.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes82.944yes
flagellatedyes84.423no
gram-positiveyes79.751no
anaerobicno98.985no
halophileno95.937yes
spore-formingyes88.882yes
thermophileno99.625no
glucose-utilyes91.624no
aerobicyes82.349yes
glucose-fermentno90.977no

External links

@ref: 24882

culture collection no.: DSM 24950, KCTC 13870

straininfo link

  • @ref: 91359
  • straininfo: 403144

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27995861Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea.Hwang YJ, Ghim SYInt J Syst Evol Microbiol10.1099/ijsem.0.0017482017Acer/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Islands, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny32556479Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil.Huq MACurr Microbiol10.1007/s00284-020-02086-02020Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Metal Nanoparticles, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silver, Soil, Soil MicrobiologyTranscriptome
Phylogeny33388935Paenibacillus silvestris sp. nov., Isolated from Forest Soil.Kim J, Jung HS, Baek JH, Chun BH, Khan SA, Jeon COCurr Microbiol10.1007/s00284-020-02333-42021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Forests, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, Vitamin K 2/analysisTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24882Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24950Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24950)
25289Y.-J. G. Hwang, S.-Y.Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea10.1099/ijsem.0.001748IJSEM 67: 1039-1045 201727995861
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91359Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403144.1