Strain identifier

BacDive ID: 7491

Type strain: Yes

Species: Subtercola frigoramans

Strain Designation: K265

Strain history: CIP <- 2001, M. Männistö, Tampere Univ. Technol., Tampere, Finland: strain K265

NCBI tax ID(s): 120298 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4890

BacDive-ID: 7491

DSM-Number: 13057

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive

description: Subtercola frigoramans K265 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from groundwater.

NCBI tax id

  • NCBI tax id: 120298
  • Matching level: species

strain history

@refhistory
4890<- M.K. Männistö; K265
396212001, M. Männistö, Tampere Univ. Technol., Finland: strain K265
67770DSM 13057 <-- M. K. Männistö K265.
119465CIP <- 2001, M. Männistö, Tampere Univ. Technol., Tampere, Finland: strain K265

doi: 10.13145/bacdive7491.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Subtercola
  • species: Subtercola frigoramans
  • full scientific name: Subtercola frigoramans Männistö et al. 2000

@ref: 4890

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Subtercola

species: Subtercola frigoramans

full scientific name: Subtercola frigoramans Männistö et al. 2000

strain designation: K265

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119465positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18505Beige (1001)10-14 daysISP 2
18505Beige (1001)10-14 daysISP 3
18505Beige (1001)10-14 daysISP 4
18505Beige (1001)10-14 daysISP 5
18505Beige (1001)10-14 daysISP 6
18505Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18505noISP 2
18505noISP 3
18505noISP 4
18505noISP 5
18505noISP 6
18505noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4890R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18505ISP 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
18505ISP 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:
18505ISP 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
18505ISP 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
18505ISP 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
18505ISP 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
39621MEDIUM 298 - for Arthrobacter duodecadisyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g);Vitamins solution - M0539 (10.000 ml)
119465CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18505positiveoptimum22psychrophilic
4890positivegrowth24psychrophilic
39621positivegrowth20psychrophilic
55685positivegrowth20psychrophilic
67770positivegrowth17psychrophilic
119465positivegrowth5-18psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 55685
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
119465NaClpositivegrowth0 %
119465NaClnogrowth2 %
119465NaClnogrowth4 %
119465NaClnogrowth6 %
119465NaClnogrowth8 %
119465NaClnogrowth10 %

murein

  • @ref: 4890
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1850562968cellulose+
1850516634raffinose+
1850526546rhamnose+
1850528757fructose+
1850529864mannitol+
1850517268myo-inositol+
1850518222xylose+
1850517992sucrose+
1850522599arabinose+
1850517234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
11946516947citrate-carbon source
1194654853esculin-hydrolysis
119465606565hippurate-hydrolysis
11946517632nitrate-reduction
11946516301nitrite-reduction

antibiotic resistance

  • @ref: 119465
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11946535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11946515688acetoin-
11946517234glucose-

enzymes

@refvalueactivityec
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
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
119465oxidase-
119465beta-galactosidase-3.2.1.23
119465alcohol dehydrogenase-1.1.1.1
119465gelatinase-
119465amylase-
119465catalase+1.11.1.6
119465gamma-glutamyltransferase-2.3.2.2
119465lecithinase-
119465lipase-
119465lysine decarboxylase-4.1.1.18
119465ornithine decarboxylase-4.1.1.17
119465phenylalanine ammonia-lyase-4.3.1.24
119465tryptophan deaminase-
119465urease-3.5.1.5

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18505+-+-+++--+----++---
119465-++-+----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18505+++++-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119465---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
4890groundwaterFinlandFINEurope
55685Groundwater of a shallow aquifer (18m depth)FinlandFINEuropeSouth,glacial gravel ridge
67770Groundwater of a shallow aquifer under a glacial gravel ridgeFinlandFINEuropeSouthern Finland
119465Environment, GroundwaterFinlandFINEuropeKärkölä1996

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Groundwater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48901Risk group (German classification)
185051German classification
1194651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Subtercola frigoramans partial 16S rRNA gene, type strain DSM 13057AM4106731473ena120298
67770Subtercola frigoramans 16S ribosomal RNA gene, partial sequenceAF2247231473ena120298

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Subtercola frigoramans DSM 13057GCA_016907385contigncbi120298
66792Subtercola frigoramans strain DSM 13057120298.3wgspatric120298
66792Subtercola frigoramans DSM 130572893543475draftimg120298

GC content

@refGC-contentmethod
489064high performance liquid chromatography (HPLC)
6777064.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno93.68no
gram-positiveyes94.326no
anaerobicno99.588yes
aerobicyes90.619yes
halophileno93.293no
spore-formingno93.503no
thermophileno99.511no
glucose-utilyes87.765yes
flagellatedno98.261no
glucose-fermentno93.874no

External links

@ref: 4890

culture collection no.: DSM 13057, ATCC BAA 169, CCUG 43136, JCM 11268, CIP 106948, IAM 15152, NBRC 103086, NCIMB 13775, VKM Ac-2509

straininfo link

  • @ref: 76937
  • straininfo: 44311

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11034481Subtercola boreus gen. nov., sp. nov. and Subtercola frigoramans sp. nov., two new psychrophilic actinobacteria isolated from boreal groundwater.Mannisto MK, Schumann P, Rainey FA, Kampfer P, Tsitko I, Tiirola MA, Salkinoja-Salonen MSInt J Syst Evol Microbiol10.1099/00207713-50-5-17312000Actinobacteria/chemistry/*classification/isolation & purification/physiology/ultrastructure, Cold Temperature, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny29214367Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile.Villalobos AS, Wiese J, Aguilar P, Dorador C, Imhoff JFAntonie Van Leeuwenhoek10.1007/s10482-017-0994-42017Actinomycetales/*genetics/physiology, Altitude, Chile, Lakes, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA/methodsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4890Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13057)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13057
18505Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13057.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
39621Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19135
55685Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43136)https://www.ccug.se/strain?id=43136
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/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76937Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44311.1StrainInfo: A central database for resolving microbial strain identifiers
119465Curators of the CIPCollection of Institut Pasteur (CIP 106948)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106948