Strain identifier

BacDive ID: 13727

Type strain: Yes

Species: Paracoccus aestuarii

Strain Designation: B7

Strain history: <- SW Roh, KRIBB

NCBI tax ID(s): 453842 (species)

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General

@ref: 8046

BacDive-ID: 13727

DSM-Number: 19484

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

description: Paracoccus aestuarii B7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 453842
  • Matching level: species

strain history

@refhistory
8046<- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; B7
67770S. W. Roh B7.
67771<- SW Roh, KRIBB

doi: 10.13145/bacdive13727.20230509.8.1

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 aestuarii
  • full scientific name: Paracoccus aestuarii Roh et al. 2009

@ref: 8046

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus aestuarii

full scientific name: Paracoccus aestuarii Roh et al. 2009

strain designation: B7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32603negative1.75 µm0.9 µmrod-shapedno
67771negative
69480negative99.992

pigmentation

  • @ref: 32603
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8046
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8046positivegrowth30mesophilic
32603positivegrowth15-37
32603positiveoptimum26mesophilic
67770positivegrowth30mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32603positivegrowth7.5-9.5alkaliphile
32603positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32603aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.994

halophily

  • @ref: 32603
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <5 %

observation

@refobservation
32603aggregates in clumps
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32603168082-dehydro-D-gluconate+carbon source
32603581435-dehydro-D-gluconate+carbon source
3260315963ribitol+carbon source
3260318403L-arabitol+carbon source
3260317234glucose+carbon source
3260325115malate+carbon source
3260317306maltose+carbon source
3260329864mannitol+carbon source
3260337684mannose+carbon source
32603506227N-acetylglucosamine+carbon source
3260333942ribose+carbon source
3260353258sodium citrate+carbon source
3260318222xylose+carbon source
326034853esculin+hydrolysis

enzymes

@refvalueactivityec
32603acid phosphatase+3.1.3.2
32603alkaline phosphatase+3.1.3.1
32603alpha-galactosidase+3.2.1.22
32603catalase+1.11.1.6
32603cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
8046tidal flat sedimentYeosu (34° 47' 26'' N 127° 34' 01'' E)Republic of KoreaKORAsia34.7906127.567
67770Tidal flat sediment in Yeosu (34° 47' 26" N 127° 34' 01" E)Republic of KoreaKORAsia34.7906127.567
67771From flat tidalRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

  • @ref: 8046
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8046
  • description: Paracoccus aestuarii strain B7 16S ribosomal RNA gene, partial sequence
  • accession: EF660757
  • length: 1300
  • database: ena
  • NCBI tax ID: 453842

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus aestuarii strain DSM 19484453842.8wgspatric453842
66792Paracoccus aestuarii strain DSM 19484453842.7plasmidpatric453842
66792Paracoccus aestuarii strain DSM 19484453842.3plasmidpatric453842
66792Paracoccus aestuarii strain DSM 19484453842.4plasmidpatric453842
66792Paracoccus aestuarii strain DSM 19484453842.6plasmidpatric453842
66792Paracoccus aestuarii strain DSM 19484453842.5plasmidpatric453842
66792Paracoccus aestuarii DSM 194842901860463draftimg453842
67770Paracoccus aestuarii DSM 19484GCA_003594815contigncbi453842
66792Paracoccus aestuarii DSM 19484GCA_028553885completencbi453842

GC content

@refGC-contentmethod
804662.0high performance liquid chromatography (HPLC)
3260362
6777062high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno64.582yes
flagellatedno88.084yes
gram-positiveno97.612no
anaerobicno96.673yes
aerobicyes90.222yes
halophileno57.847no
spore-formingno95.341no
glucose-fermentno88.634no
thermophileno95.089yes
glucose-utilyes92.311no

External links

@ref: 8046

culture collection no.: DSM 19484, JCM 15119, KCTC 22049, BCRC 80158

straininfo link

  • @ref: 82910
  • straininfo: 406104

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329608Paracoccus aestuarii sp. nov., isolated from tidal flat sediment.Roh SW, Nam YD, Chang HW, Kim KH, Kim MS, Shin KS, Yoon JH, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65759-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny22286908Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban).Kampfer P, Lai WA, Arun AB, Young CC, Rekha PD, Martin K, Busse HJ, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.039057-02012Asteraceae/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, TaiwanGenetics
Phylogeny29484518Paracoccus pueri sp. nov., isolated from Pu'er tea.Wang YS, Yan ZF, Lin P, Gao W, Yi THAntonie Van Leeuwenhoek10.1007/s10482-018-1041-92018Base Composition, Carbohydrate Metabolism, China, Fatty Acids/chemistry, Flagella, Nucleic Acid Hybridization, Paracoccus/chemistry/*classification/genetics, Phenotype, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Tea/*microbiology, Ubiquinone/chemistryPhenotype
Phylogeny33528347Paracoccus amoyensis sp. nov., isolated from the surface seawater along the coast of Xiamen Island, China.Lyu L, Lai Q, Li J, Yu Z, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0046852021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8046Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19484)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19484
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32603Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2881628776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82910Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406104.1StrainInfo: A central database for resolving microbial strain identifiers