Strain identifier

BacDive ID: 7490

Type strain: Yes

Species: Subtercola boreus

Strain Designation: K300

Strain history: CIP <- 2001, M. Männistö, Tampere Univ. Technol., Tampere, Finland: strain K300

NCBI tax ID(s): 120213 (species)

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

@ref: 4889

BacDive-ID: 7490

DSM-Number: 13056

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic

description: Subtercola boreus K300 is an aerobe, psychrophilic bacterium that was isolated from groundwater.

NCBI tax id

  • NCBI tax id: 120213
  • Matching level: species

strain history

@refhistory
4889<- M.K. Männistö; K300
406662001, M. Männistö, Tampere Univ. Technol., Finland: strain K300
67770DSM 13056 <-- M. K. Männistö K300.
116844CIP <- 2001, M. Männistö, Tampere Univ. Technol., Tampere, Finland: strain K300

doi: 10.13145/bacdive7490.20230509.8.1

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 boreus
  • full scientific name: Subtercola boreus Männistö et al. 2000

@ref: 4889

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Subtercola

species: Subtercola boreus

full scientific name: Subtercola boreus Männistö et al. 2000

strain designation: K300

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.945
69480100positive
116844nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18504Golden yellow (1004)10-14 daysISP 2
18504Golden yellow (1004)10-14 daysISP 3
18504Golden yellow (1004)10-14 daysISP 4
18504Golden yellow (1004)10-14 daysISP 5
18504Golden yellow (1004)10-14 daysISP 6
18504Golden yellow (1004)10-14 daysISP 7
116844

multicellular morphology

@refforms multicellular complexmedium name
18504noISP 2
18504noISP 3
18504noISP 4
18504noISP 5
18504noISP 6
18504noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4889R2A 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
18504ISP 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
18504ISP 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:
18504ISP 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
18504ISP 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
18504ISP 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
18504ISP 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
40666MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116844CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18504positiveoptimum22psychrophilic
4889positivegrowth24psychrophilic
40666positivegrowth20psychrophilic
55684positivegrowth20psychrophilic
67770positivegrowth17psychrophilic
116844positivegrowth5-18psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55684aerobe
116844obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.96

halophily

@refsaltgrowthtested relationconcentration
116844NaClpositivegrowth0-2 %
116844NaClnogrowth4 %
116844NaClnogrowth6 %
116844NaClnogrowth8 %
116844NaClnogrowth10 %

murein

  • @ref: 4889
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-9, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1850462968cellulose+
1850416634raffinose+
1850426546rhamnose+
1850428757fructose+
1850429864mannitol+
1850417268myo-inositol+
1850418222xylose+
1850417992sucrose+
1850422599arabinose+
1850417234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11684416947citrate-carbon source
1168444853esculin-hydrolysis
116844606565hippurate+hydrolysis
11684417632nitrate-reduction
11684416301nitrite-reduction
11684417632nitrate-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

antibiotic resistance

  • @ref: 116844
  • 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
11684435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11684415688acetoin-
11684417234glucose-

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
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
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
116844oxidase-
116844beta-galactosidase+3.2.1.23
116844alcohol dehydrogenase-1.1.1.1
116844gelatinase-
116844amylase-
116844catalase+1.11.1.6
116844gamma-glutamyltransferase-2.3.2.2
116844lecithinase-
116844lipase-
116844lysine decarboxylase-4.1.1.18
116844ornithine decarboxylase-4.1.1.17
116844phenylalanine ammonia-lyase-4.3.1.24
116844tryptophan deaminase-
116844urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18504-+--+-+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18504+---++---+----++---
116844-++-+----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18504+---+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
4889groundwaterFinlandFINEurope
55684Groundwater of a shallow aquifer (18m depth)FinlandFINEuropeSouth,glacial gravel ridge
67770Groundwater of a shallow aquifer under a glacial gravel ridgeFinlandFINEuropeSouthern Finland
116844Environment, GroundwaterFinlandFINEuropeKärkölä1996

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48891Risk group (German classification)
185041German classification
1168441Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Subtercola boreus partial 16S rRNA gene, type strain DSM 13056AM4106741467ena120213
67770Subtercola boreus 16S ribosomal RNA gene, partial sequenceAF2247221467ena120213

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Subtercola boreus strain DSM 13056120213.9wgspatric120213
66792Subtercola boreus strain K300120213.8wgspatric120213
66792Subtercola boreus DSM 130562814123445draftimg120213
66792Subtercola boreus K3002832552210draftimg120213
67770Subtercola boreus K300GCA_003399685contigncbi120213
67770Subtercola boreus DSM 13056GCA_006716115contigncbi120213

GC content

@refGC-contentmethod
488968high performance liquid chromatography (HPLC)
6777067.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno91.716no
gram-positiveyes93.582no
anaerobicno99.574yes
aerobicyes91.707yes
halophileno93.284no
spore-formingno94.925no
thermophileno99.774no
glucose-utilyes86.381yes
flagellatedno98.542no
glucose-fermentno91.748no

External links

@ref: 4889

culture collection no.: DSM 13056, ATCC BAA 168, CCUG 43135, JCM 11267, CIP 106947, IAM 15123, NBRC 103085, NCIMB 13774, VKM Ac-2508

straininfo link

  • @ref: 76936
  • straininfo: 44310

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
4889Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13056)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13056
18504Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13056.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
40666Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19134
55684Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43135)https://www.ccug.se/strain?id=43135
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
68379Automatically annotated from API Coryne
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
76936Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44310.1StrainInfo: A central database for resolving microbial strain identifiers
116844Curators of the CIPCollection of Institut Pasteur (CIP 106947)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106947