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Strain identifier

BacDive ID: 6285

Type strain: Yes

Species: Terrabacter tumescens

Strain history: IAM 12345 <-- CCM 1655 <-- MRI.

NCBI tax ID(s): 60443 (species)

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

@ref: 8710

BacDive-ID: 6285

DSM-Number: 20308

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Terrabacter tumescens DSM 20308 is a mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 60443
  • Matching level: species

strain history

doi: 10.13145/bacdive6285.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Terrabacter
  • species: Terrabacter tumescens
  • full scientific name: Terrabacter tumescens (Jensen 1934) Collins et al. 1989
  • synonyms

    @refsynonym
    20215Corynebacterium tumescens
    20215Arthrobacter tumescens
    20215Pimelobacter tumescens

@ref: 8710

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Terrabacter

species: Terrabacter tumescens

full scientific name: Terrabacter tumescens (Jensen 1934) Collins et al. 1989

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 91.744

colony morphology

@refcolony colorincubation periodmedium used
18741Cream10-14 daysISP 2
1874110-14 daysISP 3
1874110-14 daysISP 4
1874110-14 daysISP 5
1874110-14 daysISP 6
1874110-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18741noISP 2
18741noISP 3
18741noISP 4
18741noISP 5
18741noISP 6
18741noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8710TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
18741ISP 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
18741ISP 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:
18741ISP 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
18741ISP 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
18741ISP 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
18741ISP 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
38977MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8710TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
8710positivegrowth28mesophilic
38977positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 91.685

compound production

  • @ref: 8710
  • compound: 6 aminopenicillanic acid

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
18741NaClpositivemaximum5 %
69480non-halophilic97.705

murein

  • @ref: 8710
  • murein short key: A41.02
  • type: A3gamma LL-Dpm-Gly3; alpha-carboxyl group of D-Glu substituted by Gly

observation

@refobservation
20216Deacylation of benzyl- and phenoxymethyl penicillin tetrazoles
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1874162968cellulose-
1874116634raffinose+
1874126546rhamnose+
1874128757fructose+
1874129864mannitol+
1874117268myo-inositol+
1874118222xylose+
1874117992sucrose+
1874122599arabinose+
1874117234glucose+
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin+hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

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
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18741---+-++-+-+------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18741+-+-++++-++++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18741---------++

Isolation, sampling and environmental information

isolation

@refsample type
8710soil
47861Garden soil
67770Garden soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5002.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2431;97_2983;98_3738;99_5002&stattab=map
  • Last taxonomy: Terrabacter
  • 16S sequence: X83812
  • Sequence Identity:
  • Total samples: 4549
  • soil counts: 2840
  • aquatic counts: 491
  • animal counts: 1084
  • plant counts: 134

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187411Risk group (German classification)
87101Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218T.tumescens 16S rRNA geneX838121461ena60443
20218Terrabacter tumescens 16S ribosomal RNA gene, partial sequenceAF0050231477ena60443
20218Terrabacter tumescens strain KCTC 9133 16S-23S internal transcribed spacer, complete sequenceAF017510386ena60443
20218Terrebacter tumescens partial 16S rRNAX532151399ena60443

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Terrabacter tumescens JCM 1365GCA_014646815scaffoldncbi60443
66792Terrabacter tumescens strain JCM 136560443.3wgspatric60443

GC content

@refGC-contentmethod
871069.8
6777075.2thermal denaturation, midpoint method (Tm)
6777074.7
6777069.8thermal denaturation, midpoint method (Tm)
6777072.4
6777071.3thermal denaturation, midpoint method (Tm)

External links

@ref: 8710

culture collection no.: DSM 20308, ATCC 6947, CCM 1655, IMET 10431, NCIB 8914, NCTC 4216, CCUG 23850, LMG 3818, CCTM La2715, CIP 102515, JCM 1365, BCRC 17052, CCUG 23928, CGMCC 1.2032, IAM 12345, IAM 14295, IFO 12960, IMSNU 21313, KCTC 9133, NBRC 12960, NCDO 1574, NCIMB 8914, NRIC 0156, NRRL B-4012, VKM Ac-1120, VKM B-669

straininfo link

@refpassport
20218http://www.straininfo.net/strains/22161
20218http://www.straininfo.net/strains/22155
20218http://www.straininfo.net/strains/22158
20218http://www.straininfo.net/strains/22165
20218http://www.straininfo.net/strains/22169
20218http://www.straininfo.net/strains/22170

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766880Terrabacter aerolatus sp. nov., isolated from an air sample.Weon HY, Schumann P, Kroppenstedt RM, Kim BY, Song J, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.65040-02007Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis/physiology, *Air Microbiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Locomotion/physiology, Molecular Sequence Data, Mycolic Acids/analysis, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Vitamin K 2/analysisGenetics
Phylogeny18319451Sanguibacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Pulla RK, Kim SY, Yi TH, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65399-02008Actinomycetales/classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny18450693Terrabacter lapilli sp. nov., an actinomycete isolated from stone.Lee JE, Seo JP, Lee DW, Ko YH, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65541-02008Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny25006219Terrabacter koreensis sp. nov., isolated from soil of a flowerbed.Won K, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.063313-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny29721830Terrabacter ginsengisoli sp. nov., isolated from ginseng cultivating soil.Jin MF, Quan XT, Siddiqi MZ, Liu QZ, Yu HS, Im WTJ Microbiol10.1007/s12275-018-8098-z2018Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cardiolipins/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Genotype, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Panax/*microbiology, Phenotype, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8710Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20308)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20308
18741Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20308.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
38977Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14210
47861Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23850)https://www.ccug.se/strain?id=23850
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
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
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)