Strain identifier

BacDive ID: 140949

Type strain: Yes

Species: Paracoccus hibiscisoli

Strain Designation: THG-T2.31

NCBI tax ID(s): 2023261 (species)

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General

@ref: 43842

BacDive-ID: 140949

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

description: Paracoccus hibiscisoli THG-T2.31 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Rizosphere of Mugunghwa in Kyung Hee University, Yongin, South Korea.

NCBI tax id

  • NCBI tax id: 2023261
  • Matching level: species

doi: 10.13145/bacdive140949.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus hibiscisoli
  • full scientific name: Paracoccus hibiscisoli Lin et al. 2017

@ref: 43842

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus hibiscisoli

strain designation: THG-T2.31

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43842negative1.2-1.4 µm0.8-1.0 µmrod-shapedno
69480negative99.985

colony morphology

  • @ref: 43842
  • colony size: 1-2 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Tryptic soy agar

Culture and growth conditions

culture medium

@refnamegrowth
43842Luria agaryes
43842MacConkey agarno
43842Marine agar (MA)no
43842Nutrient agar (NA)yes
43842Reasoner's 2A agar (R2A)yes
43842Tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
43842positivegrowth10-35
43842positiveoptimum28mesophilic

culture pH

@refabilitytypepH
43842positivegrowth5.0-8.0
43842positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43842
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
43842NaClpositivegrowth0-4 %(w/v)
43842NaClpositiveoptimum1 %(w/v)

observation

  • @ref: 43842
  • observation: quinone Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43842161933-hydroxybenzoate-carbon source
43842178794-hydroxybenzoate-carbon source
43842581435-dehydro-D-gluconate-carbon source
4384227689decanoate-carbon source
4384228087glycogen-carbon source
4384217240itaconate-carbon source
4384218287L-fucose-carbon source
4384262345L-rhamnose-carbon source
43842506227N-acetylglucosamine-carbon source
4384217790methanol-growth
4384216830methylamine-growth
43842casein-hydrolysis
4384217029chitin-hydrolysis
4384217895L-tyrosine-hydrolysis
4384253426tween 80-hydrolysis
4384217632nitrate-reduction
4384217234glucose+builds acid from
43842168082-dehydro-D-gluconate+carbon source
43842370543-hydroxybutyrate+carbon source
4384217128adipate+carbon source
4384216947citrate+carbon source
4384217634D-glucose+carbon source
4384216899D-mannitol+carbon source
4384216024D-mannose+carbon source
4384216988D-ribose+carbon source
4384217924D-sorbitol+carbon source
4384224996lactate+carbon source
4384224265gluconate+carbon source
4384217268myo-inositol+carbon source
43842L-alanine 4-nitroanilide+carbon source
4384230849L-arabinose+carbon source
4384215971L-histidine+carbon source
4384217203L-proline+carbon source
4384217115L-serine+carbon source
4384225115malate+carbon source
4384217306maltose+carbon source
4384228053melibiose+carbon source
4384218401phenylacetate+carbon source
4384217272propionate+carbon source
4384217814salicin+carbon source
4384232954sodium acetate+carbon source
4384253258sodium citrate+carbon source
4384262983sodium malonate+carbon source
438429300suberic acid+carbon source
43842sucrose+carbon source
4384231011valerate+carbon source
4384262968cellulose+hydrolysis
4384216991dna+hydrolysis
4384228017starch+hydrolysis
4384253424tween 20+hydrolysis

metabolite production

  • @ref: 43842
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43842cytochrome oxidase+1.9.3.1
43842catalase+1.11.1.6
43842arginine dihydrolase+3.5.3.6
43842urease+3.5.1.5
43842protease+
43842alkaline phosphatase+3.1.3.1
43842esterase (C 4)+
43842esterase Lipase (C 8)+
43842valine arylamidase+
43842cystine arylamidase+3.4.11.3
43842trypsin+3.4.21.4
43842acid phosphatase+3.1.3.2
43842alpha-galactosidase+3.2.1.22
43842beta-galactosidase+3.2.1.23
43842alpha-glucosidase+3.2.1.20
43842beta-glucosidase+3.2.1.21
43842alpha-mannosidase+3.2.1.24
43842leucine arylamidase+/-3.4.11.1
43842naphthol-AS-BI-phosphohydrolase+/-
43842beta-glucuronidase+/-3.2.1.31
43842lipase (C 14)-
43842alpha-chymotrypsin-3.4.21.1
43842N-acetyl-beta-glucosaminidase-3.2.1.52
43842alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43842C10:0 3OH5.2
    43842C14:0 3OH / C16:1 iso I1.5
    43842C16:03.2
    43842C18:04.3
    43842C18:1ω7c83.4
    43842C18:3ω6c1.1
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43842
  • sample type: Rizosphere of Mugunghwa (Hibiscus syriacus) in Kyung Hee University, Yongin, South Korea
  • sampling date: 2015-10-05
  • geographic location: Yogin
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 37.2758
  • longitude: 127.178
  • enrichment culture: Tryptone soy agar
  • enrichment culture duration: 1 week
  • enrichment culture temperature: 30

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_889.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_610;98_701;99_889&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: KX456191
  • Sequence Identity:
  • Total samples: 10998
  • soil counts: 923
  • aquatic counts: 3236
  • animal counts: 6383
  • plant counts: 456

Sequence information

16S sequences

  • @ref: 43842
  • description: 16S rRNA gene sequence
  • accession: KX456191
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus hibiscisoli CCTCC AB2016182GCA_005048265contigncbi2023261
66792Paracoccus hibiscisoli strain CCTCC AB20161822023261.3wgspatric2023261
66792Paracoccus hibiscisoli CCTCC AB20161822899275550draftimg2023261

GC content

  • @ref: 43842
  • GC-content: 69.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno66.227yes
gram-positiveno97.36yes
anaerobicno97.606yes
aerobicyes91.266yes
halophileno71.909yes
spore-formingno95.379no
glucose-utilyes91.534yes
flagellatedno91.41yes
thermophileno98.346yes
glucose-fermentno85.319no

External links

@ref: 43842

culture collection no.: KACC 18933, CCTCC AB 2016182

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28741997Paracoccus hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus).Lin P, Yan ZF, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0019902017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny31674893Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii).Li J, Lu S, Jin D, Yang J, Lai XH, Huang Y, Tian Z, Dong K, Zhang S, Lei W, Pu J, Zhang G, Wu X, Huang Y, Ren Z, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0038072020Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Ubiquinone/analogs & derivatives/chemistryTranscriptome

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
43842Pei Lin, Zheng-Fei Yan, Kyung-Hwa Won, Jung-Eun Yang, Chang-Tian Li, MooChang Kook, Qi-Jun Wang, Tae-Hoo YiParacoccus hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus)10.1099/ijsem.0.001990IJSEM 67: 2452-2458 201728741997
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
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