Strain identifier

BacDive ID: 7273

Type strain: Yes

Species: Agromyces salentinus

Strain Designation: 108989, 20-5

Culture col. no.: DSM 16198, HKI 0320

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 5.0 (current version):
version 4.1:
version 4.0:
version 3.0:
version 2.1:
version 2.0:
version 1.0:
version 5.0 (current version)

General

@ref: 6320

BacDive-ID: 7273

DSM-Number: 16198

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

description: Agromyces salentinus 108989 is an aerobe, mesophilic, gram-positive bacterium that was isolated from soil sample.

strain history: <- I. Groth, HKI; 20-5 <- Ch. Weigel

doi: 10.13145/bacdive7273.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinobacteria
  • domain: Bacteria
  • phylum: Actinobacteria
  • class: Actinobacteria
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces salentinus
  • full scientific name: Agromyces salentinus Jurado et al. 2005

@ref: 6320

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces salentinus

full scientific name: Agromyces salentinus Jurado et al. 2005

strain designation: 108989, 20-5

type strain: yes

Morphology

cell morphology

  • @ref: 31281
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18303Rapeseed yellow (1021)10-14 daysISP 2
18303Rapeseed yellow (1021)10-14 daysISP 3
18303Rapeseed yellow (1021)10-14 daysISP 4
18303Rapeseed yellow (1021)10-14 daysISP 5
18303Rapeseed yellow (1021)10-14 daysISP 6
18303Rapeseed yellow (1021)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18303noISP 2
18303noISP 3
18303noISP 4
18303noISP 5
18303noISP 6
18303noISP 7

pigmentation

  • @ref: 31281
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6320R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
6320TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
18303ISP 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
18303ISP 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:
18303ISP 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
18303ISP 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
18303ISP 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
18303ISP 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
36774MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
18303positiveoptimum28mesophilic
6320positivegrowth28mesophilic
31281positivegrowth10-37
31281positiveoptimum24psychrophilic
36774positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31281
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
31281NaClpositivegrowth0-4 %
31281NaClpositiveoptimum2 %

observation

  • @ref: 31281
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3128130089acetate+carbon source
3128122599arabinose+carbon source
3128117057cellobiose+carbon source
3128128757fructose+carbon source
3128133984fucose+carbon source
3128128260galactose+carbon source
3128117234glucose+carbon source
3128117754glycerol+carbon source
3128128087glycogen+carbon source
3128117306maltose+carbon source
3128116634raffinose+carbon source
3128126546rhamnose+carbon source
3128133942ribose+carbon source
3128117814salicin+carbon source
3128117992sucrose+carbon source
3128127082trehalose+carbon source
3128118222xylose+carbon source
312814853esculin+hydrolysis

metabolite production

  • @ref: 31281
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31281catalase+1.11.1.6
31281cytochrome oxidase+1.9.3.1
31281urease+3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18303+++/--++-++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18303-++-++++-++++++++++

Isolation, sampling and environmental information

isolation

  • @ref: 6320
  • sample type: soil sample
  • geographic location: Porto Badisco
  • country: Italy
  • origin.country: ITA
  • continent: Europe

isolation source categories

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

Safety information

risk assessment

  • @ref: 6320
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6320
  • description: Agromyces salentinus strain 20-5 16S ribosomal RNA gene, partial sequence
  • accession: AY507129
  • length: 1381
  • database: ena
  • NCBI tax ID: 269421

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces salentinus JCM 14323GCA_009749395contigncbi269421
66792Agromyces salentinus strain JCM 14323269421.3wgspatric269421

GC content

  • @ref: 6320
  • GC-content: 72.3

External links

@ref: 6320

culture collection no.: DSM 16198, HKI 0320

straininfo link

@refpassport
20218http://www.straininfo.net/strains/382639
20218http://www.straininfo.net/strains/382640

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6320Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16198)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16198
18303Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16198.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
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
2760110.1099/ijs.0.63199-0
31281Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information27601
36774Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6679
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)