Strain identifier

BacDive ID: 133615

Type strain: Yes

Species: Paracoccus sphaerophysae

Strain Designation: Zy-3

NCBI tax ID(s): 690417 (species)

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General

@ref: 29792

BacDive-ID: 133615

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

description: Paracoccus sphaerophysae Zy-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from plant associated.

NCBI tax id

  • NCBI tax id: 690417
  • Matching level: species

doi: 10.13145/bacdive133615.20230509.8.1

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 sphaerophysae
  • full scientific name: Paracoccus sphaerophysae Deng et al. 2011

@ref: 29792

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus sphaerophysae

strain designation: Zy-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29792negative1.9 µm0.6 µmrod-shapedno
69480no94.001
69480negative99.991

pigmentation

  • @ref: 29792
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29792positivegrowth04-60
29792positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29792positivegrowth05-11alkaliphile
29792positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29792
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29792no
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
29792NaClpositivegrowth01-06 %
29792NaClpositiveoptimum3 %

observation

  • @ref: 29792
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2979216449alanine+carbon source
2979222599arabinose+carbon source
2979229016arginine+carbon source
2979222653asparagine+carbon source
2979235391aspartate+carbon source
2979228757fructose+carbon source
2979228260galactose+carbon source
2979229987glutamate+carbon source
2979217754glycerol+carbon source
2979227570histidine+carbon source
2979217716lactose+carbon source
2979225017leucine+carbon source
2979215792malonate+carbon source
2979217306maltose+carbon source
2979237684mannose+carbon source
2979228053melibiose+carbon source
2979215361pyruvate+carbon source
2979216634raffinose+carbon source
2979226546rhamnose+carbon source
2979233942ribose+carbon source
2979217822serine+carbon source
2979230911sorbitol+carbon source
2979230031succinate+carbon source
2979226986threonine+carbon source
2979216296D-tryptophan+carbon source
2979218222xylose+carbon source

enzymes

@refvalueactivityec
29792catalase+1.11.1.6
29792cytochrome oxidase+1.9.3.1
29792urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 29792
  • sample type: plant associated

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_4955.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_2004;98_2464;99_4955&stattab=map
  • Last taxonomy: Paracoccus sphaerophysae
  • 16S sequence: GU129567
  • Sequence Identity:
  • Total samples: 1597
  • soil counts: 74
  • aquatic counts: 518
  • animal counts: 931
  • plant counts: 74

Sequence information

16S sequences

  • @ref: 29792
  • description: Paracoccus sphaerophysae strain Zy-3 16S ribosomal RNA gene, partial sequence
  • accession: GU129567
  • length: 1368
  • database: nuccore
  • NCBI tax ID: 690417

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus sphaerophysae HAMBI 3106GCA_000763805contigncbi690417
66792Paracoccus sphaerophysae HAMBI 3106690417.3wgspatric690417
66792Paracoccus sphaerophysae HAMBI 31062713897090draftimg690417

GC content

  • @ref: 29792
  • GC-content: 67.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
gram-positiveno97.216no
anaerobicno98.233no
halophileno82.909no
spore-formingno95.627yes
glucose-utilyes82.234no
flagellatedno89.628no
thermophileno84.974yes
aerobicyes93.211yes
glucose-fermentno90.543no
motileno64.995yes

External links

@ref: 29792

culture collection no.: ACCC 05413, HAMBI 3106

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20400662Paracoccus sphaerophysae sp. nov., a siderophore-producing, endophytic bacterium isolated from root nodules of Sphaerophysa salsula.Deng ZS, Zhao LF, Xu L, Kong ZY, Zhao P, Qin W, Chang JL, Wei GHInt J Syst Evol Microbiol10.1099/ijs.0.021071-02010Antibiosis, Antifungal Agents/metabolism, Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fabaceae/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siderophores/*metabolismMetabolism
Phylogeny25701850Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng.Nguyen NL, Kim YJ, Hoang VA, Tran BT, Pham HS, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.0001252015Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry, VietnamGenetics
Phylogeny25792366Paracoccus sanguinis sp. nov., isolated from clinical specimens of New York State patients.McGinnis JM, Cole JA, Dickinson MC, Mingle LA, Lapierre P, Musser KA, Wolfgang WJInt J Syst Evol Microbiol10.1099/ijs.0.0001932015Aged, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Humans, Male, Middle Aged, Molecular Sequence Data, New York, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationPathogenicity

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
29792Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172617028776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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