Strain identifier
BacDive ID: 12620
Type strain:
Species: Granulicoccus phenolivorans
Strain Designation: PG-02
Strain history: DSM 17626 <-- A. M. Maszenan <-- H. L. Jiang PG-02.
NCBI tax ID(s): 1121933 (strain), 266854 (species)
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 id | Matching level |
---|---|
266854 | species |
1121933 | strain |
strain history
@ref | history |
---|---|
6916 | <- A.M. Maszenan <- He Long Jiang, PG-02 |
67770 | DSM 17626 <-- A. M. Maszenan <-- H. L. Jiang PG-02. |
doi: 10.13145/bacdive12620.20230509.8.1
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
@ref | gram stain | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|
31932 | positive | 0.3-1.4 µm | coccus-shaped | no | |
69480 | no | 93.258 | |||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18407 | Beige (1001) | 10-14 days | ISP 2 |
18407 | Beige (1001) | 10-14 days | ISP 3 |
18407 | Beige (1001) | 10-14 days | ISP 4 |
18407 | Beige (1001) | 10-14 days | ISP 5 |
18407 | Beige (1001) | 10-14 days | ISP 6 |
18407 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18407 | no | ISP 2 |
18407 | no | ISP 3 |
18407 | no | ISP 4 |
18407 | no | ISP 5 |
18407 | no | ISP 6 |
18407 | no | ISP 7 |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_17626_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17626_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17626_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17626_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17626_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6916 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
18407 | ISP 2 | yes | Name: 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 | |
18407 | ISP 3 | yes | Name: 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: | |
18407 | ISP 4 | yes | Name: 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 | |
18407 | ISP 5 | yes | Name: 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 | |
18407 | ISP 6 | yes | Name: 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 | |
18407 | ISP 7 | yes | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
6916 | positive | growth | 28 | mesophilic |
18407 | positive | optimum | 28 | mesophilic |
31932 | positive | growth | 15-37 | |
31932 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31932 | positive | growth | 5-8.5 | alkaliphile |
31932 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31932
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31932 | no | |
69481 | no | 96 |
69480 | no | 99.688 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31932 | 16449 | alanine | + | carbon source |
31932 | 22599 | arabinose | + | carbon source |
31932 | 22653 | asparagine | + | carbon source |
31932 | 16947 | citrate | + | carbon source |
31932 | 24148 | galactonate | + | carbon source |
31932 | 24265 | gluconate | + | carbon source |
31932 | 17234 | glucose | + | carbon source |
31932 | 17754 | glycerol | + | carbon source |
31932 | 17716 | lactose | + | carbon source |
31932 | 17306 | maltose | + | carbon source |
31932 | 29864 | mannitol | + | carbon source |
31932 | 37684 | mannose | + | carbon source |
31932 | 28053 | melibiose | + | carbon source |
31932 | 51850 | methyl pyruvate | + | carbon source |
31932 | 28044 | phenylalanine | + | carbon source |
31932 | 26271 | proline | + | carbon source |
31932 | 17272 | propionate | + | carbon source |
31932 | 15361 | pyruvate | + | carbon source |
31932 | 26490 | quinate | + | carbon source |
31932 | 16634 | raffinose | + | carbon source |
31932 | 26546 | rhamnose | + | carbon source |
31932 | 33942 | ribose | + | carbon source |
31932 | 17814 | salicin | + | carbon source |
31932 | 17822 | serine | + | carbon source |
31932 | 30911 | sorbitol | + | carbon source |
31932 | 30031 | succinate | + | carbon source |
31932 | 17992 | sucrose | + | carbon source |
31932 | 27082 | trehalose | + | carbon source |
31932 | 53423 | tween 40 | + | carbon source |
31932 | 53426 | tween 80 | + | carbon source |
31932 | 16704 | uridine | + | carbon source |
31932 | 17151 | xylitol | + | carbon source |
31932 | 18222 | xylose | + | carbon source |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31932 | catalase | + | 1.11.1.6 |
31932 | urease | + | 3.5.1.5 |
68379 | gelatinase | - | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | + | 3.2.1.31 |
68379 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18407 | + | + | - | - | + | - | - | - | - | + | - | + | - | - | - | + | - | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18407 | - | - | - | - | + | - | - | + | - | - | + | - | - | + | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
6916 | aerobic granules, bioremidation of phenolic wastewater | Singapore | SGP | Asia |
67770 | Aerobic granules, bioremidation of phenolic wastewater | Singapore | SGP | Asia |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
18407 | 1 | German classification |
6916 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570 | GCA_001313465 | contig | ncbi | 1121933 |
66792 | Granulicoccus phenolivorans DSM 17626 | 1121933.4 | wgs | patric | 1121933 |
66792 | Granulicoccus phenolivorans JCM 15570 | 1303682.4 | wgs | patric | 1121933 |
66792 | Granulicoccus phenolivorans NBRC 107789 | 1220580.4 | wgs | patric | 1121933 |
66792 | Granulicoccus phenolivorans JCM 15570 | 2734481947 | draft | img | 1303682 |
66792 | Granulicoccus phenolivorans NBRC 107789 | 2731957581 | draft | img | 1220580 |
66792 | Granulicoccus phenolivorans DSM 17626 | 2522572156 | draft | img | 1121933 |
67770 | Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570 | GCA_000423085 | scaffold | ncbi | 1121933 |
67770 | Granulicoccus phenolivorans DSM 17626 = NBRC 107789 = JCM 15570 | GCA_001552335 | contig | ncbi | 1121933 |
GC content
@ref | GC-content | method |
---|---|---|
6916 | 69 | |
67770 | 69 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 96 | no |
motile | no | 93.407 | yes |
flagellated | no | 98.227 | no |
gram-positive | yes | 88.895 | yes |
anaerobic | no | 98.063 | yes |
halophile | no | 96.092 | no |
spore-forming | no | 86.531 | yes |
thermophile | no | 99.066 | no |
glucose-util | yes | 82.16 | yes |
aerobic | yes | 81.94 | no |
glucose-ferment | no | 87.482 | no |
External links
@ref: 6916
culture collection no.: DSM 17626, ATCC BAA 1292, CIP 109593, JCM 15570, NBRC 107789
straininfo link
- @ref: 81834
- straininfo: 403354
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
6916 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17626) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17626 | ||||
18407 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM17626.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
31932 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28189 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
81834 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403354.1 | StrainInfo: A central database for resolving microbial strain identifiers |