Strain identifier

BacDive ID: 6298

Type strain: Yes

Species: Phycicoccus elongatus

Strain Designation: Lp2

Strain history: CIP <- 2002, JCM <- 2001, S. Hanada: strain Lp2

NCBI tax ID(s): 101689 (species)

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General

@ref: 5243

BacDive-ID: 6298

DSM-Number: 14184

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Phycicoccus elongatus Lp2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 101689
  • Matching level: species

strain history

@refhistory
5243<- S. Hanada; Lp2
67770S. Hanada Lp2.
119016CIP <- 2002, JCM <- 2001, S. Hanada: strain Lp2

doi: 10.13145/bacdive6298.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Phycicoccus
  • species: Phycicoccus elongatus
  • full scientific name: Phycicoccus elongatus (Hanada et al. 2002) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Tetrasphaera elongata

@ref: 5243

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Phycicoccus

species: Phycicoccus elongatus

full scientific name: Phycicoccus elongatus (Hanada et al. 2002) Nouioui et al. 2018

strain designation: Lp2

type strain: yes

Morphology

cell morphology

  • @ref: 119016
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18510Ivory (1014)10-14 daysISP 2
18510Ivory (1014)10-14 daysISP 3
18510Beige (1001)10-14 daysISP 4
18510Colorless10-14 daysISP 5
18510Ivory (1014)10-14 daysISP 6
18510Beige (1001)10-14 daysISP 7
119016

multicellular morphology

@refforms multicellular complexmedium name
18510noISP 2
18510noISP 3
18510noISP 4
18510noISP 5
18510noISP 6
18510noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5243RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
18510ISP 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
18510ISP 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:
18510ISP 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
18510ISP 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
18510ISP 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
18510ISP 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
40713MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
5243TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
119016CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18510positiveoptimum28mesophilic
5243positivegrowth28mesophilic
40713positivegrowth30mesophilic
57266positivegrowth37mesophilic
67770positivegrowth30mesophilic
119016positivegrowth15-37
119016nogrowth10psychrophilic
119016nogrowth41thermophilic
119016nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57266aerobe
119016obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119016NaClpositivegrowth0-4 %
119016NaClnogrowth6 %
119016NaClnogrowth8 %
119016NaClnogrowth10 %

murein

  • @ref: 5243
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1851062968cellulose+
1851016634raffinose-
1851026546rhamnose-
1851028757fructose+
1851029864mannitol+
1851017268myo-inositol-
1851018222xylose-
1851017992sucrose+
1851022599arabinose-
1851017234glucose+
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1190164853esculin+hydrolysis
119016606565hippurate+hydrolysis
11901617632nitrate+reduction
11901616301nitrite-reduction
11901617632nitrate-respiration
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11901615688acetoin-
11901617234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
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
119016oxidase-
119016beta-galactosidase-3.2.1.23
119016alcohol dehydrogenase-1.1.1.1
119016amylase+
119016caseinase-3.4.21.50
119016catalase+1.11.1.6
119016tween esterase-
119016gamma-glutamyltransferase-2.3.2.2
119016lecithinase-
119016lipase-
119016lysine decarboxylase-4.1.1.18
119016ornithine decarboxylase-4.1.1.17
119016phenylalanine ammonia-lyase-4.3.1.24
119016protease-
119016tryptophan deaminase-
119016urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18510------+-++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18510+++-++++----+-++---
119016+++-++---++---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119016----------+/-+/-------------+/-+/-+/-+/---+/---------+/---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119016++-++--+-++----++-+---+--------+---+---+---------+----+-----+--------------+---++---+---++++-+-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5243activated sludgeJapanJPNAsia
57266Anaerobic-aerobic sequential batch reactorJapanJPNAsia
67770Activated sludge reactorJapanJPNAsia
119016Environment, Activated sludge reactorJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_5926.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1391;97_3482;98_4404;99_5926&stattab=map
  • Last taxonomy: Phycicoccus elongatus subclade
  • 16S sequence: AB030911
  • Sequence Identity:
  • Total samples: 3115
  • soil counts: 707
  • aquatic counts: 1843
  • animal counts: 208
  • plant counts: 357

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185101
52431Risk group (German classification)
1190161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5243
  • description: Actinomycete Lp2 gene for 16S rRNA, partial sequence
  • accession: AB030911
  • length: 1443
  • database: ena
  • NCBI tax ID: 1193181

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phycicoccus elongatus Lp22600254961draftimg1193181
67770Phycicoccus elongatus Lp2GCA_000367525contigncbi1193181

GC content

@refGC-contentmethod
524369.6high performance liquid chromatography (HPLC)
6777068.99genome sequence analysis

External links

@ref: 5243

culture collection no.: DSM 14184, JCM 11141, CCUG 46560, CIP 107623, IAM 14965, NBRC 103079, KCTC 39572, NCIMB 14348

straininfo link

  • @ref: 75773
  • straininfo: 100994

literature

  • topic: Phylogeny
  • Pubmed-ID: 12054253
  • title: Tetrasphaera elongata sp. nov., a polyphosphate-accumulating bacterium isolated from activated sludge.
  • authors: Hanada S, Liu WT, Shintani T, Kamagata Y, Nakamura K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-3-883
  • year: 2002
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Diaminopimelic Acid/analysis, Molecular Sequence Data, Phenotype, Phylogeny, Polyphosphates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5243Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14184)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14184
18510Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14184.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
40713Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5079
57266Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46560)https://www.ccug.se/strain?id=46560
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
75773Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100994.1StrainInfo: A central database for resolving microbial strain identifiers
119016Curators of the CIPCollection of Institut Pasteur (CIP 107623)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107623