Strain identifier

BacDive ID: 8031

Type strain: Yes

Species: Micromonospora sediminimaris

Strain Designation: MS 426

Strain history: J. Wang MS426.

NCBI tax ID(s): 547162 (species)

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General

@ref: 17644

BacDive-ID: 8031

DSM-Number: 45558

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Micromonospora sediminimaris MS 426 is an aerobe, spore-forming, mesophilic bacterium that was isolated from deep marine sediment.

NCBI tax id

  • NCBI tax id: 547162
  • Matching level: species

strain history

@refhistory
17644<- JCM <- J. Wang; MS 426
67770J. Wang MS426.

doi: 10.13145/bacdive8031.20230509.8.1

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 sediminimaris
  • full scientific name: Micromonospora sediminimaris Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Verrucosispora sediminis

@ref: 17644

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora sediminimaris

full scientific name: Micromonospora sediminimaris Nouioui et al. 2018

strain designation: MS 426

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
29617positive0.2 µmrod-shapedno
69480no92.95
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21434Deep orange (2011)10-14 daysISP 2
21434Deep orange (2011)10-14 daysISP 3
21434Melon yellow (1028)10-14 daysISP 4
21434Deep orange (2011)10-14 daysISP 5
21434Deep orange (2011)10-14 daysISP 7
21434Deep orange (2011)10-14 daysSuter with tyrosine
21434Deep orange (2011)10-14 daysSuter without tyrosine

pigmentation

  • @ref: 29617
  • production: no

multimedia

  • @ref: 17644
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45558.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17644GYM 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
17644TRYPTICASE 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
17644GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
21434ISP 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
21434ISP 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:
21434ISP 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
21434ISP 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
21434ISP 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
21434Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21434Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
17644positivegrowth28mesophilic
29617positivegrowth20-45
29617positiveoptimum28-37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29617positivegrowth3.5-10alkaliphile
29617positiveoptimum5-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29617
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29617yes
69481yes100
69480yes99.611

halophily

@refsaltgrowthtested relationconcentration
21434NaClpositivemaximum5 %
29617NaClpositivegrowth0-6 %
29617NaClpositiveoptimum3.5 %

observation

@refobservation
29617aggregates in chains
67770quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2143417234glucose+
2143422599arabinose+
2143417992sucrose+
2143418222xylose+
2143417268myo-inositol-
2143437684mannose-
2143428757fructose+
2143426546rhamnose-
2143416634raffinose-
2143462968cellulose-
2961722599arabinose+carbon source
2961718403L-arabitol+carbon source
2961717234glucose+carbon source
2961717754glycerol+carbon source
2961717716lactose+carbon source
2961728053melibiose+carbon source
2961733942ribose+carbon source
2961717814salicin+carbon source
2961727082trehalose+carbon source
2961717632nitrate+reduction
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

enzymes

@refvalueactivityec
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21434---+--+++-+------++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21434+++-+++/-++/-++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinent
17644deep marine sedimentSouth China SeaAsia
67770Deep marine sedimentSouth China Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4596.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_2781;98_3452;99_4596&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: EU870859
  • Sequence Identity:
  • Total samples: 449
  • soil counts: 308
  • aquatic counts: 47
  • animal counts: 71
  • plant counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
176441Risk group (German classification)
21434L1German classification

Sequence information

16S sequences

  • @ref: 17644
  • description: Verrucosispora sediminis strain MS426 16S ribosomal RNA gene, partial sequence
  • accession: EU870859
  • length: 1458
  • database: ena
  • NCBI tax ID: 547162

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora sediminimaris NBRC 107745GCA_016863575contigncbi547162
66792Micromonospora sediminimaris strain NBRC 107745547162.4wgspatric547162
66792Verrucosispora sediminis strain CGMCC 4.3550547162.3wgspatric547162
66792Verrucosispora sediminis CGMCC 4.35502663762750draftimg547162
67770Micromonospora sediminimaris CGMCC 4.3550GCA_900112325scaffoldncbi547162

GC content

@refGC-contentmethod
1764466.8thermal denaturation, midpoint method (Tm)
2961766.8
6777071genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.76yes
anaerobicno99.484yes
halophileno88.185no
spore-formingyes93.565yes
glucose-utilyes87.704yes
thermophileno97.726yes
aerobicyes93.413yes
motileno92.495yes
flagellatedno97.637no
glucose-fermentno89.946yes

External links

@ref: 17644

culture collection no.: DSM 45558, CGMCC 4.3550, JCM 15670, NBRC 107745

straininfo link

  • @ref: 77461
  • straininfo: 400987

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19767367Verrucosispora sediminis sp. nov., a cyclodipeptide-producing actinomycete from deep-sea sediment.Dai HQ, Wang J, Xin YH, Pei G, Tang SK, Ren B, Ward A, Ruan JS, Li WJ, Zhang LXInt J Syst Evol Microbiol10.1099/ijs.0.017053-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Dipeptides/*metabolism, Geologic Sediments/*microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny21873512Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus Verrucosispora.Xi L, Zhang L, Ruan J, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.033787-02011Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, WetlandsGenetics
Phylogeny21989685Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins.Goodfellow M, Stach JE, Brown R, Bonda AN, Jones AL, Mexson J, Fiedler HP, Zucchi TD, Bull ATAntonie Van Leeuwenhoek10.1007/s10482-011-9651-52011Amino Acids/analysis, Anti-Bacterial Agents/*metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/*microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Metabolism29974366Actinoplanes deserti sp. nov., isolated from a desert soil sample.Habib N, Khan IU, Chu X, Xiao M, Li S, Fang BZ, Zhi XY, Li WJAntonie Van Leeuwenhoek10.1007/s10482-018-1121-x2018Base Composition, Cell Wall/*chemistry/metabolism, China, Desert Climate, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Galactose/metabolism, Glucose/metabolism, Glycolipids/metabolism, Mannose/metabolism, Micromonosporaceae/classification/*genetics/isolation & purification, Peptidoglycan/*chemistry/metabolism, Phospholipids/metabolism, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Ribose/metabolism, Soil Microbiology, Spores, Bacterial/chemistry/growth & development, Vitamin K 2/metabolism, Xylose/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17644Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45558)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45558
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
21434Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45558.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
29617Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2600728776041
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/
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)
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
77461Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400987.1StrainInfo: A central database for resolving microbial strain identifiers