Strain identifier

BacDive ID: 140981

Type strain: Yes

Species: Salipiger pallidus

Strain Designation: DCSW07

Strain history: <- Xiao-Hua Zhang, Ocean Univ. of China

NCBI tax ID(s): 1775170 (species)

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General

@ref: 64869

BacDive-ID: 140981

DSM-Number: 108666

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

description: Salipiger pallidus DCSW07 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from From surface seawater of the Bohai Sea.

NCBI tax id

  • NCBI tax id: 1775170
  • Matching level: species

strain history

@refhistory
64869<- J.-S. Lee, KCTC; KCTC 52369 <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; DCSW07
67770X.-H. Zhang and Y. Wang; Coll. of Mar. Life Sci., Ocean Univ. of China, China; DCSW07.
67771<- Xiao-Hua Zhang, Ocean Univ. of China

doi: 10.13145/bacdive140981.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Salipiger
  • species: Salipiger pallidus
  • full scientific name: Salipiger pallidus (Cai et al. 2017) Du et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Paraphaeobacter pallidus

@ref: 64869

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paraphaeobacter

species: Paraphaeobacter pallidus

full scientific name: Paraphaeobacter pallidus Cai et al. 2017

strain designation: DCSW07

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43870negative1.8-2.2 µm0.4-0.5 µmrod-shapedyespolar
69480negative99.995

colony morphology

  • @ref: 43870
  • colony color: light orange
  • colony shape: circular
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43870Marine agar (MA)yes
64869BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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

@refgrowthtypetemperaturerange
43870positivegrowth10-45
43870positiveoptimum28mesophilic
64869positivegrowth28mesophilic
67770positivegrowth30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43870positivegrowth5.0-9.0alkaliphile
43870positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43870aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
43870NaClpositivegrowth0-15 %(w/v)
43870NaClpositiveoptimum6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4387016024D-mannose-builds acid from
4387016467L-arginine-builds acid from
4387015603L-leucine-builds acid from
4387017306maltose-builds acid from
4387017992sucrose-builds acid from
4387027082trehalose-builds acid from
4387018222xylose-builds acid from
4387016899D-mannitol-carbon source
4387017924D-sorbitol-carbon source
438703-O-methyl alpha-D-glucopyranoside+builds acid from
4387017057cellobiose+builds acid from
4387017108D-arabinose+builds acid from
4387015824D-fructose+builds acid from
4387012936D-galactose+builds acid from
4387017634D-glucose+builds acid from
4387062318D-lyxose+builds acid from
4387016899D-mannitol+builds acid from
4387016988D-ribose+builds acid from
4387016443D-tagatose+builds acid from
4387032528turanose+builds acid from
43870esculin ferric citrate+builds acid from
4387017754glycerol+builds acid from
4387028087glycogen+builds acid from
4387017268myo-inositol+builds acid from
4387030849L-arabinose+builds acid from
4387018287L-fucose+builds acid from
4387028053melibiose+builds acid from
4387074863methyl beta-D-xylopyranoside+builds acid from
4387017814salicin+builds acid from
4387017992sucrose+builds acid from
43870309162-oxoglutarate+carbon source
4387030089acetate+carbon source
4387017925alpha-D-glucose+carbon source
4387073706bromosuccinate+carbon source
4387016947citrate+carbon source
4387015570D-alanine+carbon source
4387015824D-fructose+carbon source
4387014314D-glucose 6-phosphate+carbon source
4387016024D-mannose+carbon source
4387027605D-psicose+carbon source
4387016523D-serine+carbon source
4387024996lactate+carbon source
43870495056gamma-cyclodextrin+carbon source
4387028066gentiobiose+carbon source
4387017754glycerol+carbon source
4387014336glycerol 1-phosphate+carbon source
4387028087glycogen+carbon source
4387073804glycyl L-aspartic acid+carbon source
4387017596inosine+carbon source
4387021217L-alaninamide+carbon source
4387016977L-alanine+carbon source
4387029991L-aspartate+carbon source
4387015971L-histidine+carbon source
4387017203L-proline+carbon source
4387017115L-serine+carbon source
4387016857L-threonine+carbon source
43870maltose hydrate+carbon source
43870320055methyl beta-D-glucopyranoside+carbon source
4387051850methyl pyruvate+carbon source
4387075146monomethyl succinate+carbon source
4387044337N-acetyl-L-glutamate+carbon source
43870506227N-acetylglucosamine+carbon source
4387017272propionate+carbon source
43870143136succinamate+carbon source
4387030031succinate+carbon source
4387017992sucrose+carbon source
4387017748thymidine+carbon source
4387027082trehalose+carbon source
4387053423tween 40+carbon source
4387053426tween 80+carbon source
4387016704uridine+carbon source
4387015688acetoin+/-carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-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

@refChebi-IDmetaboliteproduction
4387015688acetoinyes
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
43870catalase+1.11.1.6
43870urease+3.5.1.5
43870alkaline phosphatase+3.1.3.1
43870esterase (C 4)+
43870leucine arylamidase+3.4.11.1
43870trypsin+3.4.21.4
43870alpha-chymotrypsin+3.4.21.1
43870alpha-galactosidase+3.2.1.22
43870beta-glucuronidase+3.2.1.31
43870alpha-glucosidase+3.2.1.20
43870N-acetyl-beta-glucosaminidase+3.2.1.52
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43870C10:0 3OH6.62
    43870C12:1 3OH1.62
    43870C16:07.28
    43870C16:1ω7c / C15:0 iso 2OH5.52
    43870C17:0 cyclo1.37
    43870C18:1ω7c68.27
    4387011-methyl C18:1ω7c1.37
    43870C19:0ω8c cyclo5.89
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6 6.10
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64869-----+---------+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64869----+---------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
67771From surface seawater of the Bohai SeaChinaCHNAsia
43870surface water of Bohai Sea, ChinaChinaCHNAsiaBohai Sea39.05119.92Marine agar 22164 days28
64869surface seawaterChinaCHNAsiaBohai Sea, station B60 (39° 3' 00'' N, 119° 55' 12'' E)39.05119.92
67770Surface water of the Bohai SeaChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 64869
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64869
  • description: Paraphaeobacter pallidus strain DCSW07 16S ribosomal RNA gene, partial sequence
  • accession: KU315483
  • length: 1425
  • database: ena
  • NCBI tax ID: 1775170

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salipiger pallidus CGMCC 1.15762GCA_014643635contigncbi1775170
66792Paraphaeobacter pallidus strain CGMCC 1.157621775170.3wgspatric1775170

GC content

  • @ref: 43870
  • GC-content: 64.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes70.623yes
gram-positiveno98.634yes
anaerobicno97.757yes
aerobicyes90.666no
halophileyes87.416yes
spore-formingno97.579no
thermophileno98.54yes
glucose-utilyes91.734no
flagellatedno70.602yes
glucose-fermentno88.54yes

External links

@ref: 64869

culture collection no.: KCTC 52369, MCCC 1K03197, JCM 31458, CGMCC 1.15762, DSM 108666

straininfo link

  • @ref: 96822
  • straininfo: 406006

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43870Xiulei Cai, Yanan Wang, Xiaoting Yang, Ji Liu, Yanhong Wu, Xiao-Hua ZhangParaphaeobacter pallidus gen. nov., sp. nov., isolated from seawater10.1099/ijsem.0.001935IJSEM 67: 2520-2526 201728809139
64869Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108666Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108666)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
96822Reimer, 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-ID406006.1