Strain identifier

BacDive ID: 14283

Type strain: Yes

Species: Parasphingorhabdus marina

Strain Designation: FR1087

Strain history: <- J Chun, Seoul Nat. Univ.

NCBI tax ID(s): 394732 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 16185

BacDive-ID: 14283

DSM-Number: 22363

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

description: Parasphingorhabdus marina FR1087 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface seawater.

NCBI tax id

  • NCBI tax id: 394732
  • Matching level: species

strain history

@refhistory
16185<- KCTC <- J. Chun, Seoul Natl. Univ., Republic of Korea
67771<- J Chun, Seoul Nat. Univ.

doi: 10.13145/bacdive14283.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Parasphingorhabdus
  • species: Parasphingorhabdus marina
  • full scientific name: Parasphingorhabdus marina (Kim et al. 2008) Feng et al. 2020

  • synonyms

    @refsynonym
    20215Sphingorhabdus marina
    20215Sphingopyxis marina

@ref: 16185

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingorhabdus

species: Sphingorhabdus marina

full scientific name: Sphingorhabdus marina (Kim et al. 2008) Jogler et al. 2013

strain designation: FR1087

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32518negativerod-shapedyes
67771negative
125438negative96.969
125439negative98.5

pigmentation

  • @ref: 32518
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16185
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperature
16185positivegrowth30
32518positivegrowth15-34.4
32518positiveoptimum23.7-31.8
67771positivegrowth30

culture pH

@refabilitytypepH
32518positivegrowth7
32518positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32518aerobe
67771aerobe
125439aerobe96.7

spore formation

@refspore formationconfidence
32518no
125439no94.9

halophily

@refsaltgrowthtested relationconcentration
32518NaClpositivegrowth03-07 %
32518NaClpositiveoptimum03-05 %

observation

  • @ref: 32518
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3251817128adipate+carbon source
3251822599arabinose+carbon source
3251816947citrate+carbon source
3251817234glucose+carbon source
3251825115malate+carbon source
325184853esculin+hydrolysis
6836917306maltose-assimilation
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32518cytochrome oxidase+1.9.3.1
32518urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16185------++------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16185surface seawaterJeju IslandRepublic of KoreaKORAsia
67771From seawaterJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_3586.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1750;97_2092;98_2569;99_3586&stattab=map
  • Last taxonomy: Parasphingorhabdus marina
  • 16S sequence: DQ781320
  • Sequence Identity:
  • Total samples: 604
  • soil counts: 54
  • aquatic counts: 481
  • animal counts: 62
  • plant counts: 7

Safety information

risk assessment

  • @ref: 16185
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16185
  • description: Sphingopyxis marina strain FR1087 16S ribosomal RNA gene, partial sequence
  • accession: DQ781320
  • length: 1409
  • database: nuccore
  • NCBI tax ID: 1123272

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parasphingorhabdus marina DSM 22363GCA_900128895contigncbi1123272
66792Sphingorhabdus marina DSM 223631123272.4wgspatric1123272
66792Parasphingorhabdus marina DSM 223632582580503draftimg1123272

GC content

  • @ref: 16185
  • GC-content: 56.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.969yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.158yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.59yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.031yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.711yes
125438motile2+flagellatedAbility to perform flagellated movementyes57.205no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.9
125439BacteriaNetmotilityAbility to perform movementno55.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe96.7

External links

@ref: 16185

culture collection no.: DSM 22363, IMSNU 14132, JCM 14161, KCTC 12763

straininfo link

  • @ref: 83438
  • straininfo: 359534

literature

  • topic: Phylogeny
  • Pubmed-ID: 33993373
  • title: Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.
  • authors: Kim SJ, Kim M, Lee KE, Cha IT, Park SJ
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-021-02366-8
  • year: 2021
  • mesh: Adenoma, Islet Cell, Fatty Acids/analysis, *Geologic Sediments/microbiology, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Species Specificity, *Sphingomonadaceae/classification/genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16185Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22363)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22363
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
32518Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2873828776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
83438Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359534.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1