Strain identifier

BacDive ID: 7984

Type strain: Yes

Species: Micromonospora endolithica

Strain Designation: AA-459

Strain history: CIP <- 2004, DSMZ <- P. Hirsch, Kiel Univ., Kiel, Germany: strain AA-459

NCBI tax ID(s): 230091 (species)

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General

@ref: 11722

BacDive-ID: 7984

DSM-Number: 44398

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic

description: Micromonospora endolithica AA-459 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from sandstone of Linnaeus Terrace .

NCBI tax id

  • NCBI tax id: 230091
  • Matching level: species

strain history

@refhistory
11722<- P. Hirsch, Univ. Kiel; AA-459
67770DSM 44398 <-- P. Hirsch AA-459.
119027CIP <- 2004, DSMZ <- P. Hirsch, Kiel Univ., Kiel, Germany: strain AA-459

doi: 10.13145/bacdive7984.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora endolithica
  • full scientific name: Micromonospora endolithica Hirsch et al. 2004

@ref: 11722

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora endolithica

full scientific name: Micromonospora endolithica Hirsch et al. 2004

strain designation: AA-459

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.176
69480100positive
119027nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19662Red orange10-14 daysISP 2
19662Red orange10-14 daysISP 3
19662Pastel yellow10-14 daysISP 4
19662Pastel yellow10-14 daysISP 5
19662Pastel yellow10-14 daysISP 6
19662Pastel yellow10-14 daysISP 7
119027

multicellular morphology

@refforms multicellular complexmedium name
19662noISP 2
19662noISP 3
19662noISP 4
19662noISP 5
19662noISP 6
19662noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11722GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19662ISP 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
19662ISP 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:
19662ISP 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
19662ISP 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
19662ISP 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
19662ISP 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
36434MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
11722TRYPTICASE 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
119027CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119027CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19662positiveoptimum28mesophilic
11722positivegrowth28mesophilic
36434positivegrowth30mesophilic
67770positivegrowth28mesophilic
119027positivegrowth25-37mesophilic
119027nogrowth10psychrophilic
119027nogrowth41thermophilic
119027nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119027
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
119027NaClpositivegrowth0-2 %
119027NaClnogrowth4 %
119027NaClnogrowth6 %
119027NaClnogrowth8 %
119027NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966217234glucose+
1966222599arabinose+
1966217992sucrose+
1966218222xylose+
1966217268myo-inositol+
1966229864mannitol-
1966228757fructose-
1966226546rhamnose+
1966216634raffinose+
1966262968cellulose+
11902716947citrate-carbon source
1190274853esculin-hydrolysis
11902717632nitrate+reduction
11902716301nitrite-reduction
11902717632nitrate-respiration

metabolite production

  • @ref: 119027
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11902715688acetoin-
11902717234glucose-

enzymes

@refvalueactivityec
119027oxidase+
119027beta-galactosidase-3.2.1.23
119027alcohol dehydrogenase-1.1.1.1
119027gelatinase+
119027amylase+
119027DNase-
119027caseinase+3.4.21.50
119027catalase+1.11.1.6
119027tween esterase-
119027lecithinase-
119027lipase-
119027lysine decarboxylase-4.1.1.18
119027ornithine decarboxylase-4.1.1.17
119027phenylalanine ammonia-lyase-4.3.1.24
119027tryptophan deaminase-
119027urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19662+++-+----+-++-+-+--
119027-++-+--+---++-+-+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinent
11722sandstone of Linnaeus Terrace (1600 m)Transantarctic MountainsAustralia and Oceania
67770Antarctic sandstone rock
119027Environment, Sandstone Linnaeus Terrace

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117221Risk group (German classification)
196621Risk group (German classification)
1190271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Micromonospora endolithica 16S rRNA gene, type strain DSM 44398T
  • accession: AJ560635
  • length: 1477
  • database: ena
  • NCBI tax ID: 230091

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora endolithica DSM 44398GCA_007994185contigncbi230091
66792Micromonospora endolithica strain DSM 44398230091.5wgspatric230091
66792Micromonospora endolithica strain JCM 12677230091.4wgspatric230091
66792Micromonospora endolithica AA-4592585427558draftimg230091
67770Micromonospora endolithica JCM 12677GCA_003626595scaffoldncbi230091

GC content

@refGC-contentmethod
1172270.1thermal denaturation, midpoint method (Tm)
6777070.06thermal denaturation, midpoint method (Tm)
6777072.45genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.702no
gram-positiveyes90.773no
anaerobicno99.246no
aerobicyes94.946no
halophileno92.723no
spore-formingyes93.119no
glucose-utilyes86.792yes
flagellatedno97.476no
thermophileno98.681yes
glucose-fermentno90.349no

External links

@ref: 11722

culture collection no.: DSM 44398, CIP 108382, IFAM AA-459, JCM 12677, NBRC 101889, NRRL B-24248

straininfo link

  • @ref: 77417
  • straininfo: 97523

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15046305Cryptoendolithic actinomycetes from antarctic sandstone rock samples: Micromonospora endolithica sp. nov. and two isolates related to Micromonospora coerulea Jensen 1932.Hirsch P, Mevs U, Kroppenstedt RM, Schumann P, Stackebrandt ESyst Appl Microbiol10.1078/0723202043228817812004Antarctic Regions, Base Composition, Base Sequence, Carbohydrates/analysis, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/*isolation & purification/ultrastructure, Microscopy, Electron, Scanning, Microscopy, Phase-Contrast, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, *Soil MicrobiologyGenetics
Phylogeny28230521Micromonospora terminaliae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of the medicinal plant Terminalia mucronata.Kaewkla O, Thamchaipinet A, Franco CMMInt J Syst Evol Microbiol10.1099/ijsem.0.0016002017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Stems/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Terminalia/*microbiology, Thailand, Vitamin K 2/chemistryTranscriptome
Phylogeny28629505Micromonospora fulva sp. nov., isolated from forest soil.Lee HJ, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0018582017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11722Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44398)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44398
19662Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44398.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
36434Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5998
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
77417Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97523.1StrainInfo: A central database for resolving microbial strain identifiers
119027Curators of the CIPCollection of Institut Pasteur (CIP 108382)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108382