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Strain identifier

BacDive ID: 12620

Type strain: Yes

Species: Granulicoccus phenolivorans

Strain Designation: PG-02

Strain history: DSM 17626 <-- A. M. Maszenan <-- H. L. Jiang PG-02.

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

@ref: 6916

BacDive-ID: 12620

DSM-Number: 17626

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Granulicoccus phenolivorans PG-02 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from aerobic granules, bioremidation of phenolic wastewater.

NCBI tax id

NCBI tax idMatching level
266854species
1121933strain

strain history

doi: 10.13145/bacdive12620.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Granulicoccus
  • species: Granulicoccus phenolivorans
  • full scientific name: Granulicoccus phenolivorans Maszenan et al. 2007

@ref: 6916

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Granulicoccus

species: Granulicoccus phenolivorans

full scientific name: Granulicoccus phenolivorans Maszenan et al. 2007

strain designation: PG-02

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31932positive0.3-1.4 µmcoccus-shapedno
69480positive93.859

colony morphology

@refcolony colorincubation periodmedium used
18407Beige (1001)10-14 daysISP 2
18407Beige (1001)10-14 daysISP 3
18407Beige (1001)10-14 daysISP 4
18407Beige (1001)10-14 daysISP 5
18407Beige (1001)10-14 daysISP 6
18407Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18407noISP 2
18407noISP 3
18407noISP 4
18407noISP 5
18407noISP 6
18407noISP 7

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17626_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17626_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17626_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17626_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17626_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6916TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18407ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18407ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18407ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18407ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18407ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18407ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
6916positivegrowth28mesophilic
18407positiveoptimum28mesophilic
31932positivegrowth15-37
31932positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31932positivegrowth5-8.5alkaliphile
31932positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31932
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
31932no
69480no95.076

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 99.291

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3193216449alanine+carbon source
3193222599arabinose+carbon source
3193222653asparagine+carbon source
3193216947citrate+carbon source
3193224148galactonate+carbon source
3193224265gluconate+carbon source
3193217234glucose+carbon source
3193217754glycerol+carbon source
3193217716lactose+carbon source
3193217306maltose+carbon source
3193229864mannitol+carbon source
3193237684mannose+carbon source
3193228053melibiose+carbon source
3193251850methyl pyruvate+carbon source
3193228044phenylalanine+carbon source
3193226271proline+carbon source
3193217272propionate+carbon source
3193215361pyruvate+carbon source
3193226490quinate+carbon source
3193216634raffinose+carbon source
3193226546rhamnose+carbon source
3193233942ribose+carbon source
3193217814salicin+carbon source
3193217822serine+carbon source
3193230911sorbitol+carbon source
3193230031succinate+carbon source
3193217992sucrose+carbon source
3193227082trehalose+carbon source
3193253423tween 40+carbon source
3193253426tween 80+carbon source
3193216704uridine+carbon source
3193217151xylitol+carbon source
3193218222xylose+carbon source
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose+fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose+fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
683794853esculin-hydrolysis
6837917632nitrate+reduction

enzymes

@refvalueactivityec
31932catalase+1.11.1.6
31932urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18407++--+----+-+---+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18407----+--+--+--+-+---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6916aerobic granules, bioremidation of phenolic wastewaterSingaporeSGPAsia
67770Aerobic granules, bioremidation of phenolic wastewaterSingaporeSGPAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_50129.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_72;96_174;97_188;98_36043;99_50129&stattab=map
  • Last taxonomy: Granulicoccus
  • 16S sequence: AY566575
  • Sequence Identity:
  • Total samples: 5
  • aquatic counts: 1
  • animal counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184071German classification
69161Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6916
  • description: Granulicoccus phenolivorans 16S ribosomal RNA gene, partial sequence
  • accession: AY566575
  • length: 1315
  • database: ena
  • NCBI tax ID: 1121933

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570 JCM 15570GCA_001313465contigncbi1121933
66792Granulicoccus phenolivorans DSM 176261121933.4wgspatric1121933
66792Granulicoccus phenolivorans JCM 155701303682.4wgspatric1121933
66792Granulicoccus phenolivorans NBRC 1077891220580.4wgspatric1121933
66792Granulicoccus phenolivorans JCM 155702734481947draftimg1303682
66792Granulicoccus phenolivorans NBRC 1077892731957581draftimg1220580
66792Granulicoccus phenolivorans DSM 176262522572156draftimg1121933
67770Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570 DSM 17626GCA_000423085scaffoldncbi1121933
67770Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570 NBRC 107789GCA_001552335contigncbi1121933
66792Euryarchaeota archaeon SI034_bin33GCA_018645945contigpatric2026739
66792Alphaproteobacteria bacterium CP_BM_RX_R9_30GCA_019247845contigpatric1913988
66792Hyphomicrobiales bacterium AFS065984GCA_900471105scaffoldpatric1909294

GC content

@refGC-contentmethod
691669
6777069high performance liquid chromatography (HPLC)

External links

@ref: 6916

culture collection no.: DSM 17626, ATCC BAA 1292, CIP 109593, JCM 15570, NBRC 107789

straininfo link

@refpassport
20218http://www.straininfo.net/strains/701748
20218http://www.straininfo.net/strains/701747
20218http://www.straininfo.net/strains/842061

literature

  • topic: Phylogeny
  • Pubmed-ID: 17392196
  • title: Granulicoccus phenolivorans gen. nov., sp. nov., a Gram-positive, phenol-degrading coccus isolated from phenol-degrading aerobic granules.
  • authors: Maszenan AM, Jiang HL, Tay JH, Schumann P, Kroppenstedt RM, Tay ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64671-0
  • year: 2007
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/metabolism, Aerobiosis, *Biodegradation, Environmental, Bioreactors, DNA, Bacterial/genetics, Molecular Sequence Data, Phenol/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6916Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17626)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17626
18407Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17626.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2818910.1099/ijs.0.64671-017392196
31932Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128189
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)