Strain identifier

BacDive ID: 160625

Type strain: Yes

Species: Salaquimonas pukyongi

Strain Designation: RR3-28

Strain history: <- K.-H. Kim, univ. Puykong National; RR3-28 <- K.-H. Kim, univ. Puykong National; RR3-28

NCBI tax ID(s): 2712698 (species)

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General

@ref: 67533

BacDive-ID: 160625

DSM-Number: 107947

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

description: Salaquimonas pukyongi RR3-28 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Biofilter of a seawater recirculating aquaculture system.

NCBI tax id

  • NCBI tax id: 2712698
  • Matching level: species

strain history

  • @ref: 67533
  • history: <- K.-H. Kim, univ. Puykong National; RR3-28 <- K.-H. Kim, univ. Puykong National; RR3-28

doi: 10.13145/bacdive160625.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Salaquimonas
  • species: Salaquimonas pukyongi
  • full scientific name: Salaquimonas pukyongi Kim et al. 2019

@ref: 67533

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Phyllobacteriaceae

genus: Salaquimonas

species: Salaquimonas pukyongi

full scientific name: Salaquimonas pukyongi Kim et al. 2019

strain designation: RR3-28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68218negative1-2 µm0.4-0.5 µmrod-shapedno
69480negative99

colony morphology

  • @ref: 68218
  • colony size: 1 mm
  • colony color: ivory
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Marine agar (MA)

Culture and growth conditions

culture medium

  • @ref: 67533
  • name: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514f
  • composition: Name: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) Composition: NaCl 19.4 g/l Agar 15.0 g/l MgCl2 8.8 g/l 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
67533positivegrowth28
68218positivegrowth20-35
68218positiveoptimum25-30

culture pH

@refabilitytypepHPH range
68218positivegrowth5-9.5alkaliphile
68218positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 68218
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no90.764

halophily

@refsaltgrowthtested relationconcentration
68218NaClpositivegrowth0-7 %(w/v)
68218NaClpositiveoptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6821817632nitrate+reduction
682184853esculin-hydrolysis
682185291gelatin-hydrolysis
68218581435-dehydro-D-gluconate+builds acid from
6821817754glycerol-builds acid from
6821817113erythritol-builds acid from
6821822599arabinose-builds acid from
6821816988D-ribose-builds acid from
6821865328L-xylose-builds acid from
6821815963ribitol-builds acid from
6821874863methyl beta-D-xylopyranoside-builds acid from
6821812936D-galactose-builds acid from
6821817634D-glucose-builds acid from
6821815824D-fructose-builds acid from
6821816024D-mannose-builds acid from
6821817266L-sorbose-builds acid from
6821862345L-rhamnose-builds acid from
6821816813galactitol-builds acid from
6821817268myo-inositol-builds acid from
6821816899D-mannitol-builds acid from
6821817924D-sorbitol-builds acid from
6821843943methyl alpha-D-mannoside-builds acid from
68218320061methyl alpha-D-glucopyranoside-builds acid from
6821859640N-acetylglucosamine-builds acid from
6821827613amygdalin-builds acid from
6821818305arbutin-builds acid from
682184853esculin-builds acid from
6821817814salicin-builds acid from
6821817057cellobiose-builds acid from
6821817306maltose-builds acid from
6821817716lactose-builds acid from
6821828053melibiose-builds acid from
6821817992sucrose-builds acid from
6821827082trehalose-builds acid from
6821815443inulin-builds acid from
682186731melezitose-builds acid from
6821816634raffinose-builds acid from
6821828017starch-builds acid from
6821828087glycogen-builds acid from
6821817151xylitol-builds acid from
6821828066gentiobiose-builds acid from
6821832528turanose-builds acid from
6821862318D-lyxose-builds acid from
6821816443D-tagatose-builds acid from
6821833984fucose-builds acid from
6821818333D-arabitol-builds acid from
6821818403L-arabitol-builds acid from
68218168082-dehydro-D-gluconate-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6821815688acetoinno
6821835581indoleno

enzymes

@refvalueactivityec
68218urease-3.5.1.5
68218alkaline phosphatase+3.1.3.1
68218esterase (C 4)+
68218esterase Lipase (C 8)+
68218lipase (C 14)+
68218leucine arylamidase+3.4.11.1
68218valine arylamidase+
68218cystine arylamidase+3.4.11.3
68218acid phosphatase+3.1.3.2
68218naphthol-AS-BI-phosphohydrolase+
68218trypsin+/-3.4.21.4
68218alpha-chymotrypsin+/-3.4.21.1
68218alpha-galactosidase-3.2.1.22
68218beta-galactosidase-3.2.1.23
68218beta-glucuronidase-3.2.1.31
68218alpha-glucosidase-3.2.1.20
68218beta-glucosidase-3.2.1.21
68218N-acetyl-beta-glucosaminidase-3.2.1.52
68218alpha-mannosidase-3.2.1.24
68218alpha-fucosidase-3.2.1.51
68218cytochrome oxidase+1.9.3.1
68218catalase-1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68218C16:04.3
    68218C17:01.1
    68218C18:01.4
    68218C19:0 10-methyl5.5
    68218C18:1 w7c 11-methyl14.4
    68218C18:1 w6c/C18:1 w7c71.1
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • incubation temperature: 28
  • incubation time: 4
  • software version: Sherlock 6.3
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
67533Biofilter of a seawater recirculating aquaculture systemBusanRepublic of KoreaKORAsia35.1899129.221
68218biofilm from the surface of a mesh biofilterBusanRepublic of KoreaKORAsia35.1899129.221marine agar5 days25

taxonmaps

  • @ref: 69479
  • File name: preview.99_4662.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2317;97_2815;98_3497;99_4662&stattab=map
  • Last taxonomy: Salaquimonas pukyongi subclade
  • 16S sequence: MG889584
  • Sequence Identity:
  • Total samples: 5144
  • soil counts: 820
  • aquatic counts: 3401
  • animal counts: 646
  • plant counts: 277

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67533Salaquimonas pukyongi strain RR3-28 16S ribosomal RNA gene, partial sequenceMG889584.21598nuccore2023282
68218Salaquimonas pukyongi strain RR3-28 16S ribosomal RNA gene, partial sequenceMG8895841447nuccore2712698

Genome sequences

  • @ref: 68218
  • description: Salaquimonas pukyongi RR3-28
  • accession: GCA_001953055
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2712698

GC content

  • @ref: 68218
  • GC-content: 58.6
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.467yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.732no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.764no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.648no
69480flagellatedmotile2+Ability to perform flagellated movementyes52.615no

External links

@ref: 67533

culture collection no.: DSM 107947, KCTC 52649

straininfo link

  • @ref: 112863
  • straininfo: 398313

literature

  • topic: Phylogeny
  • Pubmed-ID: 31486764
  • title: Salaquimonas pukyongi gen. nov., sp. nov., a novel bacterium within the family Phyllobacteriaceae.
  • authors: Kim YS, Jeon YJ, Kim KH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003659
  • year: 2019
  • mesh: Aquaculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phyllobacteriaceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
67533Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107947Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107947)
68218Young-Sam Kim, Young Jae Jeon and Kyoung-Ho KimSalaquimonas pukyongi gen. nov., sp. nov., a novel bacterium within the family Phyllobacteriaceae10.1099/ijsem.0.003659IJSEM 69: 3751-3756 2019
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
112863Reimer, 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-ID398313.1