Strain identifier

BacDive ID: 140640

Type strain: Yes

Species: Micromonospora sediminis

Strain Designation: CH3-3

Strain history: S. Tanasupawat; Chulalongkorn Univ., Thailand; CH3-3.

NCBI tax ID(s): 1429073 (species)

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General

@ref: 67665

BacDive-ID: 140640

DSM-Number: 111297

keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, pigmented

description: Micromonospora sediminis CH3-3 is an aerobe, spore-forming, mesophilic bacterium that builds a substrate mycelium and has a Dark greenish-yellow pigmentation.

NCBI tax id

  • NCBI tax id: 1429073
  • Matching level: species

strain history

  • @ref: 67770
  • history: S. Tanasupawat; Chulalongkorn Univ., Thailand; CH3-3.

doi: 10.13145/bacdive140640.20230509.8.1

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 sediminis
  • full scientific name: Micromonospora sediminis Phongsopitanun et al. 2016

@ref: 67665

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micromonosporales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora sediminis

full scientific name: Micromonospora sediminis Phongsopitanun et al. 2016

strain designation: CH3-3

type strain: yes

Morphology

cell morphology

  • @ref: 43076
  • gram stain: positive

colony morphology

@refcolony colormedium used
43076dark greyish-yellowISP2
43076ISP4
43076marine agar
43076pale yellowISP3
43076Nutrient agar
43076moderate yellow to greyish-yellowISP5
43076light yellowISP7

multicellular morphology

  • @ref: 43076
  • forms multicellular complex: yes
  • complex name: substrate mycelium
  • further description: branched substrate mycelium

pigmentation

  • @ref: 43076
  • production: yes
  • color: Dark greenish-yellow
  • name: soluble pigments

multimedia

  • @ref: 67665
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_111297.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43076ISP2yes
43076ISP4yes
43076Marine agar (MA)yes
43076ISP3yes
43076Nutrient agar (NA)yes
43076ISP5yes
43076ISP7yes
67665N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
67665TRYPTICASE 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
67665BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
67665GYM 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

culture temp

@refgrowthtypetemperaturerange
43076positivegrowth28-37mesophilic
67770positivegrowth28mesophilic
67665positivegrowth28mesophilic

culture pH

  • @ref: 43076
  • ability: positive
  • type: growth
  • pH: 7-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43076
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43076
  • type of spore: spore
  • spore formation: yes

halophily

  • @ref: 43076
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4307617632nitrate+reduction
4307628017starch+hydrolysis
430765291gelatin-hydrolysis
4307630849L-arabinose+assimilation
4307617057cellobiose+assimilation
4307628260galactose+assimilation
4307616899D-mannitol+assimilation
4307662345L-rhamnose+assimilation
4307617992sucrose+assimilation
4307617814salicin+/-assimilation
4307665327D-xylose+/-assimilation
4307628757fructose-assimilation
4307617268myo-inositol-assimilation
4307616634raffinose-assimilation
4307616988D-ribose-assimilation

enzymes

@refvalueactivityec
43076alpha-chymotrypsin+3.4.21.1
43076esterase (C 4)+
43076alpha-glucosidase+3.2.1.20
43076leucine arylamidase+3.4.11.1
43076acid phosphatase+/-3.1.3.2
43076esterase Lipase (C 8)+/-
43076beta-galactosidase+/-3.2.1.23
43076beta-glucosidase+/-3.2.1.21
43076naphthol-AS-BI-phosphohydrolase+/-
43076trypsin+/-3.4.21.4
43076N-acetyl-beta-glucosaminidase-3.2.1.52
43076alkaline phosphatase-3.1.3.1
43076cystine arylamidase-3.4.11.3
43076alpha-fucosidase-3.2.1.51
43076alpha-galactosidase-3.2.1.22
43076beta-glucuronidase-3.2.1.31
43076lipase (C 14)-
43076alpha-mannosidase-3.2.1.24
43076valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43076C15:0 iso30.2
    43076C16:0 iso27.9
    43076C17:0 iso14.8
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP2 broth
  • agar/liquid: liquid
  • incubation temperature: 30
  • incubation time: 6
  • software version: Sherlock 6.0
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43076mangrove sedimentChonburi Province, ThailandThailandTHAAsia
67665Mangrove sedimentChonburi ProvinceThailandTHAAsia
67770Mangrove sediment from Chonburi ProvinceThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Environmental#Aquatic#Sediment
#Host#Plants#Tree

Safety information

risk assessment

  • @ref: 67665
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4307616S rRNA gene sequencesAB8895411469ena1429073
67665Micromonospora sediminis strain PCU 350 16S ribosomal RNA gene, partial sequenceMT7600351356ena1429073

GC content

  • @ref: 67665
  • GC-content: 73.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 67665

culture collection no.: TISTR 2396, PCU 350, JCM 18523, DSM 111297

straininfo link

  • @ref: 96766
  • straininfo: 407350

literature

  • topic: Phylogeny
  • Pubmed-ID: 27220280
  • title: Micromonospora sediminis sp. nov., isolated from mangrove sediment.
  • authors: Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K, Tanasupawat S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001175
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistry, *Wetlands
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43076Wongsakorn Phongsopitanun, Takuji Kudo, Moriya Ohkuma, Pattama Pittayakhajonwut, Khanit Suwanborirux and Somboon TanasupawatMicromonospora sediminis sp. nov., isolated from mangrove sediment10.1099/ijsem.0.001175IJSEM 66: 3235-3240 201627220280
67665Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-111297Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 111297)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
96766Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID407350.1