Strain identifier
BacDive ID: 7490
Type strain:
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)
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
@ref | history |
---|---|
4889 | <- M.K. Männistö; K300 |
40666 | 2001, M. Männistö, Tampere Univ. Technol., Finland: strain K300 |
67770 | DSM 13056 <-- M. K. Männistö K300. |
116844 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 93.945 | ||
69480 | 100 | positive | ||
116844 | no | positive | rod-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18504 | Golden yellow (1004) | 10-14 days | ISP 2 |
18504 | Golden yellow (1004) | 10-14 days | ISP 3 |
18504 | Golden yellow (1004) | 10-14 days | ISP 4 |
18504 | Golden yellow (1004) | 10-14 days | ISP 5 |
18504 | Golden yellow (1004) | 10-14 days | ISP 6 |
18504 | Golden yellow (1004) | 10-14 days | ISP 7 |
116844 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18504 | no | ISP 2 |
18504 | no | ISP 3 |
18504 | no | ISP 4 |
18504 | no | ISP 5 |
18504 | no | ISP 6 |
18504 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4889 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
18504 | 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 | |
18504 | 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: | |
18504 | 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 | |
18504 | 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 | |
18504 | 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 | |
18504 | 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 | |
40666 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
116844 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18504 | positive | optimum | 22 | psychrophilic |
4889 | positive | growth | 24 | psychrophilic |
40666 | positive | growth | 20 | psychrophilic |
55684 | positive | growth | 20 | psychrophilic |
67770 | positive | growth | 17 | psychrophilic |
116844 | positive | growth | 5-18 | psychrophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
55684 | aerobe |
116844 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 94 |
69480 | no | 99.96 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116844 | NaCl | positive | growth | 0-2 % |
116844 | NaCl | no | growth | 4 % |
116844 | NaCl | no | growth | 6 % |
116844 | NaCl | no | growth | 8 % |
116844 | NaCl | no | growth | 10 % |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18504 | 62968 | cellulose | + | |
18504 | 16634 | raffinose | + | |
18504 | 26546 | rhamnose | + | |
18504 | 28757 | fructose | + | |
18504 | 29864 | mannitol | + | |
18504 | 17268 | myo-inositol | + | |
18504 | 18222 | xylose | + | |
18504 | 17992 | sucrose | + | |
18504 | 22599 | arabinose | + | |
18504 | 17234 | glucose | + | |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
116844 | 16947 | citrate | - | carbon source |
116844 | 4853 | esculin | - | hydrolysis |
116844 | 606565 | hippurate | + | hydrolysis |
116844 | 17632 | nitrate | - | reduction |
116844 | 16301 | nitrite | - | reduction |
116844 | 17632 | nitrate | - | respiration |
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 |
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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
116844 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test | methylred-test |
---|---|---|---|---|---|
68368 | 15688 | acetoin | - | ||
68368 | 35581 | indole | - | ||
116844 | 15688 | acetoin | - | ||
116844 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
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 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
116844 | oxidase | - | |
116844 | beta-galactosidase | + | 3.2.1.23 |
116844 | alcohol dehydrogenase | - | 1.1.1.1 |
116844 | gelatinase | - | |
116844 | amylase | - | |
116844 | catalase | + | 1.11.1.6 |
116844 | gamma-glutamyltransferase | - | 2.3.2.2 |
116844 | lecithinase | - | |
116844 | lipase | - | |
116844 | lysine decarboxylase | - | 4.1.1.18 |
116844 | ornithine decarboxylase | - | 4.1.1.17 |
116844 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116844 | tryptophan deaminase | - | |
116844 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18504 | - | + | - | - | + | - | + | - | + | - | - | - | - | - | - | - | - | - | - |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18504 | + | - | - | - | + | + | - | - | - | + | - | - | - | - | + | + | - | - | - | |
116844 | - | + | + | - | + | - | - | - | - | + | + | - | - | - | + | + | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18504 | + | - | - | - | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location | isolation date |
---|---|---|---|---|---|---|
4889 | groundwater | Finland | FIN | Europe | ||
55684 | Groundwater of a shallow aquifer (18m depth) | Finland | FIN | Europe | South,glacial gravel ridge | |
67770 | Groundwater of a shallow aquifer under a glacial gravel ridge | Finland | FIN | Europe | Southern Finland | |
116844 | Environment, Groundwater | Finland | FIN | Europe | Kärkölä | 1996 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Groundwater
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4889 | 1 | Risk group (German classification) |
18504 | 1 | German classification |
116844 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Subtercola boreus partial 16S rRNA gene, type strain DSM 13056 | AM410674 | 1467 | ena | 120213 |
67770 | Subtercola boreus 16S ribosomal RNA gene, partial sequence | AF224722 | 1467 | ena | 120213 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Subtercola boreus strain DSM 13056 | 120213.9 | wgs | patric | 120213 |
66792 | Subtercola boreus strain K300 | 120213.8 | wgs | patric | 120213 |
66792 | Subtercola boreus DSM 13056 | 2814123445 | draft | img | 120213 |
66792 | Subtercola boreus K300 | 2832552210 | draft | img | 120213 |
67770 | Subtercola boreus K300 | GCA_003399685 | contig | ncbi | 120213 |
67770 | Subtercola boreus DSM 13056 | GCA_006716115 | contig | ncbi | 120213 |
GC content
@ref | GC-content | method |
---|---|---|
4889 | 68 | high performance liquid chromatography (HPLC) |
67770 | 67.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 94 | no |
motile | no | 91.716 | no |
gram-positive | yes | 93.582 | no |
anaerobic | no | 99.574 | yes |
aerobic | yes | 91.707 | yes |
halophile | no | 93.284 | no |
spore-forming | no | 94.925 | no |
thermophile | no | 99.774 | no |
glucose-util | yes | 86.381 | yes |
flagellated | no | 98.542 | no |
glucose-ferment | no | 91.748 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11034481 | Subtercola 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 MS | Int J Syst Evol Microbiol | 10.1099/00207713-50-5-1731 | 2000 | Actinobacteria/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, Temperature | Genetics |
Phylogeny | 29214367 | Subtercola 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 JF | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0994-4 | 2017 | Actinomycetales/*genetics/physiology, Altitude, Chile, Lakes, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA/methods | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4889 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13056) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13056 | |||
18504 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM13056.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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
40666 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/19134 | ||||
55684 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 43135) | https://www.ccug.se/strain?id=43135 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68368 | Automatically annotated from API 20E | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
76936 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44310.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116844 | Curators of the CIP | Collection of Institut Pasteur (CIP 106947) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106947 |