Strain identifier

BacDive ID: 134285

Type strain: Yes

Species: Paracoccus halophilus

Strain Designation: HN-182

Strain history: S. Liu HN-182.

NCBI tax ID(s): 376733 (species)

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

@ref: 32272

BacDive-ID: 134285

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

description: Paracoccus halophilus HN-182 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 376733
  • Matching level: species

strain history

  • @ref: 67770
  • history: S. Liu HN-182.

doi: 10.13145/bacdive134285.20230509.8.1

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 halophilus
  • full scientific name: Paracoccus halophilus Liu et al. 2008

@ref: 32272

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus halophilus

strain designation: HN-182

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32272negative0.9 µm0.45 µmrod-shapedno
69480negative99.994

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32272positivegrowth07-42
32272positiveoptimum25mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32272positivegrowth05-09alkaliphile
32272positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32272
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32272no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32272NaClpositivegrowth0.5-8.5 %
32272NaClpositiveoptimum4.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3227222599arabinose+carbon source
3227217057cellobiose+carbon source
3227228757fructose+carbon source
3227228260galactose+carbon source
3227217234glucose+carbon source
3227217754glycerol+carbon source
3227217306maltose+carbon source
3227229864mannitol+carbon source
3227237684mannose+carbon source
3227226546rhamnose+carbon source
3227233942ribose+carbon source
3227230911sorbitol+carbon source
3227218222xylose+carbon source

enzymes

@refvalueactivityec
32272catalase+1.11.1.6
32272cytochrome oxidase+1.9.3.1
32272urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
32272marine sediment
67770Marine sediment from the South China SeaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3779.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_2334;98_2880;99_3779&stattab=map
  • Last taxonomy: Paracoccus halophilus subclade
  • 16S sequence: DQ423482
  • Sequence Identity:
  • Total samples: 951
  • soil counts: 94
  • aquatic counts: 306
  • animal counts: 541
  • plant counts: 10

Sequence information

16S sequences

  • @ref: 32272
  • description: Paracoccus halophilus strain HN-182 16S ribosomal RNA gene, partial sequence
  • accession: DQ423482
  • length: 1428
  • database: nuccore
  • NCBI tax ID: 376733

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus halophilus JCM 14014376733.3wgspatric376733
66792Paracoccus halophilus strain CGMCC 1.6117376733.15wgspatric376733
66792Paracoccus halophilus JCM 140142713897088draftimg376733
66792Paracoccus halophilus CGMCC 1.61172617270913draftimg376733
67770Paracoccus halophilus CGMCC 1.6117GCA_900111785scaffoldncbi376733
67770Paracoccus halophilus JCM 14014GCA_000763905contigncbi376733

GC content

@refGC-contentmethod
3227267.2
6777067.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.677yes
anaerobicno98.199yes
halophileno50no
spore-formingno97.169yes
glucose-utilyes91.546yes
aerobicyes86.072yes
motileno77.555yes
flagellatedno89.203yes
thermophileno96.347yes
glucose-fermentno85.058no

External links

@ref: 32272

culture collection no.: CGMCC 1.6117, JCM 14014

straininfo link

  • @ref: 91871
  • straininfo: 323987

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175718Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969.Liu ZP, Wang BJ, Liu XY, Dai X, Liu YH, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.65237-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Paracoccus/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
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
Phylogeny31647401Paracoccus luteus sp. nov., isolated from the intestine of grass carp.Ming H, Cheng LJ, Ding CL, Niu MM, Zhao ZL, Ji WL, Zhang LY, Zhang YM, Meng XL, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0037902020Animals, Bacterial Typing Techniques, Base Composition, Carps/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestines/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

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
32272Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172851228776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
91871Reimer, 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-ID323987.1