Strain identifier

BacDive ID: 133013

Type strain: Yes

Species: Croceicoccus pelagius

Strain Designation: Ery9

Strain history: <- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; Ery9 <- L. Wang

NCBI tax ID(s): 1703341 (species)

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General

@ref: 24801

BacDive-ID: 133013

DSM-Number: 101479

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

description: Croceicoccus pelagius Ery9 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface seawater.

NCBI tax id

  • NCBI tax id: 1703341
  • Matching level: species

strain history

  • @ref: 24801
  • history: <- Y.-H. Wu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China; Ery9 <- L. Wang

doi: 10.13145/bacdive133013.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Croceicoccus
  • species: Croceicoccus pelagius
  • full scientific name: Croceicoccus pelagius Wu et al. 2016

@ref: 24801

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Croceicoccus

species: Croceicoccus pelagius

full scientific name: Croceicoccus pelagius Wu et al. 2016

strain designation: Ery9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25039negative1.0-1.4 µm0.3-0.5 µmrod-shapedno
69480negative99.985

colony morphology

  • @ref: 25039
  • colony size: 1.0-2.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25039MA agaryes
24801BACTO 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
25039positivegrowth15-45
25039positiveoptimum30-37mesophilic
24801positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
25039positivegrowth5.5-8.5alkaliphile
25039positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25039
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.967

halophily

@refsaltgrowthtested relationconcentration
25039NaClpositivegrowth0-10.0 %(w/v)
25039NaCloptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2503917128adipate-carbon source
2503917128adipate-energy source
2503936219alpha-lactose-builds acid from
2503915824D-fructose-builds acid from
2503912936D-galactose-builds acid from
2503916024D-mannose-carbon source
2503916024D-mannose-energy source
2503916024D-mannose-builds acid from
250396731melezitose-builds acid from
2503915963ribitol-builds acid from
2503916988D-ribose-builds acid from
2503965327D-xylose-builds acid from
2503916236ethanol-builds acid from
250395291gelatin-hydrolysis
2503917268myo-inositol-builds acid from
2503930849L-arabinose-carbon source
2503930849L-arabinose-energy source
2503962345L-rhamnose-builds acid from
2503925115malate-carbon source
2503925115malate-energy source
2503929864mannitol-builds acid from
2503918401phenylacetate-carbon source
2503918401phenylacetate-energy source
2503932032potassium gluconate-carbon source
2503932032potassium gluconate-energy source
2503916634raffinose-builds acid from
2503953258sodium citrate-carbon source
2503953258sodium citrate-energy source
2503930911sorbitol-builds acid from
2503927922sorbose-builds acid from
2503928017starch-hydrolysis
2503917992sucrose-builds acid from
2503927082trehalose-builds acid from
2503927897tryptophan-energy source
2503953423tween 40-hydrolysis
2503917057cellobiose+builds acid from
2503916947citrate+carbon source
2503917634D-glucose+carbon source
2503917634D-glucose+energy source
2503916899D-mannitol+carbon source
2503916899D-mannitol+energy source
2503927689decanoate+carbon source
2503927689decanoate+energy source
250394853esculin+hydrolysis
2503917234glucose+builds acid from
2503925115malate+energy source
2503925115malate+carbon source
2503917306maltose+carbon source
2503917306maltose+energy source
2503917306maltose+builds acid from
2503917632nitrate+reduction
25039peptone+carbon source
25039peptone+energy source
25039tryptone+carbon source
25039tryptone+energy source
25039yeast extract+carbon source
25039yeast extract+energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
250393534cephalexinyesyes30 µg (disc)
2503917698chloramphenicolyesyes30 µg (disc)
250396104kanamycinyesyes30 µg (disc)
250397507neomycinyesyes30 µg (disc)
2503971415nitrofurantoinyesyes300 µg (disc)
2503928368novobiocinyesyes30 µg (disc)
2503928077rifampicinyesyes5 µg (disc)
2503928001vancomycinyesyes30 µg (disc)
250398309polymyxin byesyes300 Unit (disc)
25039100147nalidixic acidyesyes30 µg (disc)
2503917076streptomycinyesyes10 µg (disc)
2503928971ampicillinyesyes10 µg (disc)
2503948923erythromycinyesyes10 µg (disc)
2503917334penicillinyesyes10 Unit (disc)
2503927902tetracyclineyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2503935581indoleno
2503915688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2503915688acetoin+
2503935581indole-

enzymes

@refvalueactivityec
25039acid phosphatase+3.1.3.2
25039alkaline phosphatase+3.1.3.1
25039alpha-chymotrypsin-3.4.21.1
25039alpha-galactosidase-3.2.1.22
25039alpha-glucosidase+3.2.1.20
25039alpha-mannosidase-3.2.1.24
25039arginine dihydrolase+3.5.3.6
25039beta-D-fucosidase-3.2.1.38
25039beta-galactosidase-3.2.1.23
25039beta-glucosidase-3.2.1.21
25039beta-glucuronidase-3.2.1.31
25039catalase+1.11.1.6
25039cystine arylamidase+3.4.11.3
25039esterase (C 4)+
25039esterase lipase (C 8)-
25039leucine arylamidase+3.4.11.1
25039lipase (C 14)-
25039lysine decarboxylase-4.1.1.18
25039N-acetyl-beta-glucosaminidase-3.2.1.52
25039naphthol-AS-BI-phosphohydrolase+
25039ornithine decarboxylase-4.1.1.17
25039trypsin-3.4.21.4
25039tryptophan deaminase+4.1.99.1
25039tryptophan deaminase-4.1.99.1
25039urease-3.5.1.5
25039valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudecountry
24801surface seawaterAtlantic Ocean (24° 10' S 5° 29' E)-24.16675.4833
25039surface seawaterAtlantic Ocean (24° 10' S 5° 29' E)Atlantic Ocean

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6200.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_344;97_3631;98_4596;99_6200&stattab=map
  • Last taxonomy: Croceicoccus
  • 16S sequence: KT383844
  • Sequence Identity:
  • Total samples: 1477
  • soil counts: 222
  • aquatic counts: 1073
  • animal counts: 88
  • plant counts: 94

Safety information

risk assessment

  • @ref: 24801
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24801
  • description: Croceicoccus pelagius strain Ery9 16S ribosomal RNA gene, complete sequence
  • accession: KT383844
  • length: 1477
  • database: ena
  • NCBI tax ID: 1703341

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Croceicoccus pelagius Ery9GCA_001661915scaffoldncbi1703341
66792Croceicoccus pelagius CGMCC 1.15358GCA_014642495contigncbi1703341
66792Croceicoccus pelagius strain CGMCC 1.153581703341.5wgspatric1703341
66792Croceicoccus pelagius Ery92832283248draftimg1703341

GC content

@refGC-contentmethod
2503962.8genome sequence analysis
2480162.8sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.876yes
gram-positiveno97.36no
anaerobicno99.282yes
aerobicyes94.761yes
halophileno85.588no
spore-formingno96.412no
thermophileno97.206yes
glucose-utilyes91.265yes
motileno87.554no
glucose-fermentno92.165no

External links

@ref: 24801

culture collection no.: DSM 101479, CGMCC 1.15358

straininfo link

  • @ref: 91287
  • straininfo: 404682

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27503117Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments.Wu YH, Li GY, Jian SL, Cheng H, Huo YY, Wang CS, Shao ZZ, Xu XWInt J Syst Evol Microbiol10.1099/ijsem.0.0013812016Alphaproteobacteria/*classification/genetics/isolation & purification, Atlantic Ocean, Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, DNA, Bacterial/genetics, Geologic Sediments/*microbiology, Indian Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny30990392Croceicoccus ponticola sp. nov., a lipolytic bacterium isolated from seawater.Park S, Won SM, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0033012019Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24801Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101479Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101479)
25039Y. H. L. Wu, G. Y.,Jian, S. L.,Cheng, H.,Huo, Y. Y.,Wang, C. S.,Shao, Z. Z.,Xu, X. W.Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments10.1099/ijsem.0.001381IJSEM 66: 4506-4511 201627503117
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
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
91287Reimer, 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-ID404682.1