Strain identifier

BacDive ID: 13728

Type strain: Yes

Species: Paracoccus saliphilus

Strain history: <- S.-K. Tang and Y. Wang, YIM; YIM 90738 <- S.-K. Tang, Y. Wang et al.

NCBI tax ID(s): 405559 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7476

BacDive-ID: 13728

DSM-Number: 18447

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

description: Paracoccus saliphilus DSM 18447 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from saline-alkali soil.

NCBI tax id

  • NCBI tax id: 405559
  • Matching level: species

strain history

  • @ref: 7476
  • history: <- S.-K. Tang and Y. Wang, YIM; YIM 90738 <- S.-K. Tang, Y. Wang et al.

doi: 10.13145/bacdive13728.20230509.8.1

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 saliphilus
  • full scientific name: Paracoccus saliphilus Wang et al. 2009

@ref: 7476

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus saliphilus

full scientific name: Paracoccus saliphilus Wang et al. 2009

type strain: yes

Morphology

cell morphology

  • @ref: 29088
  • gram stain: negative
  • cell length: 4 µm
  • cell width: 1.8 µm
  • cell shape: coccus-shaped
  • motility: no

pigmentation

  • @ref: 29088
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7476
  • name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/636
  • composition: Name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636) Composition: NaCl 50.0 g/l Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7476positivegrowth37mesophilic
29088positivegrowth10-55
29088positiveoptimum37mesophilic

culture pH

@refabilitytypepH
29088positivegrowth6.0-8.0
29088positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29088
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29088
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29088NaClpositivegrowth1.0-15 %
29088NaClpositiveoptimum8 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2908830089acetate+carbon source
2908815963ribitol+carbon source
2908821217L-alaninamide+carbon source
2908816449alanine+carbon source
2908840585alpha-cyclodextrin+carbon source
2908822599arabinose+carbon source
2908818403L-arabitol+carbon source
2908822653asparagine+carbon source
2908835391aspartate+carbon source
2908817126DL-carnitine+carbon source
2908816947citrate+carbon source
2908815740formate+carbon source
2908828757fructose+carbon source
2908833984fucose+carbon source
2908828260galactose+carbon source
2908824175galacturonate+carbon source
2908824265gluconate+carbon source
2908817234glucose+carbon source
2908829987glutamate+carbon source
2908817754glycerol+carbon source
2908828087glycogen+carbon source
2908827570histidine+carbon source
29088182404-hydroxy-L-proline+carbon source
2908817596inosine+carbon source
2908824996lactate+carbon source
2908817716lactose+carbon source
2908825017leucine+carbon source
2908837684mannose+carbon source
2908828053melibiose+carbon source
2908851850methyl pyruvate+carbon source
2908818257ornithine+carbon source
2908850048phenylethylamine+carbon source
2908826271proline+carbon source
2908817148putrescine+carbon source
2908826490quinate+carbon source
2908817822serine+carbon source
2908830911sorbitol+carbon source
2908830031succinate+carbon source
2908817992sucrose+carbon source
2908826986threonine+carbon source
2908817748thymidine+carbon source
2908816704uridine+carbon source
2908827248urocanic acid+carbon source
2908817151xylitol+carbon source
290884853esculin+hydrolysis

enzymes

@refvalueactivityec
29088acid phosphatase+3.1.3.2
29088alkaline phosphatase+3.1.3.1
29088catalase+1.11.1.6
29088gelatinase+
29088cytochrome oxidase+1.9.3.1
29088urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 7476
  • sample type: saline-alkali soil
  • geographic location: Xinjiang province, edge of Ebinur Lake wetland natural reserve
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_3628.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1884;97_2262;98_2776;99_3628&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: DQ923133
  • Sequence Identity:
  • Total samples: 176
  • soil counts: 31
  • aquatic counts: 124
  • animal counts: 19
  • plant counts: 2

Safety information

risk assessment

  • @ref: 7476
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7476
  • description: Paracoccus saliphilus strain YIM 90738 16S ribosomal RNA gene, partial sequence
  • accession: DQ923133
  • length: 1389
  • database: ena
  • NCBI tax ID: 405559

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus saliphilus strain DSM 18447405559.3wgspatric405559
66792Paracoccus saliphilus DSM 184472681813562draftimg405559
66792Paracoccus saliphilus DSM 18447GCA_028553805completencbi405559

GC content

@refGC-contentmethod
747660.3high performance liquid chromatography (HPLC)
2908860.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno66.295yes
flagellatedno90.65yes
gram-positiveno97.949yes
anaerobicno98.304no
aerobicyes92.399no
halophileyes51.982yes
spore-formingno94.45yes
glucose-fermentno81.621no
thermophileno95.405no
glucose-utilyes89.53yes

External links

@ref: 7476

culture collection no.: DSM 18447, CCTCC AB 206074, KCTC 22163, YIM 90738

straininfo link

  • @ref: 82911
  • straininfo: 402335

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567556Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil.Wang Y, Tang SK, Lou K, Mao PH, Jin X, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.005918-02009Bacterial Typing Techniques, Base Composition, Benzoquinones/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny32039746Paracoccus alkanivorans sp. nov., isolated from a deep well with oil reservoir water.Zhang YX, Li X, Li FL, Ma SC, Zheng GD, Chen WF, Li WJ, Wang LInt J Syst Evol Microbiol10.1099/ijsem.0.0040362020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome
Phylogeny34388083Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave.Gutierrez-Patricio S, Gonzalez-Pimentel JL, Miller AZ, Hermosin B, Saiz-Jimenez C, Jurado VInt J Syst Evol Microbiol10.1099/ijsem.0.0049422021Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Paracoccus/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7476Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18447)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18447
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
29088Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2551728776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82911Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402335.1StrainInfo: A central database for resolving microbial strain identifiers