Strain identifier

BacDive ID: 8017

Type strain: Yes

Species: Micromonospora rhizosphaerae

Strain Designation: 211018

Strain history: CGMCC 4.5599 <-- K. Hong 211018.

NCBI tax ID(s): 568872 (species)

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General

@ref: 16554

BacDive-ID: 8017

DSM-Number: 45431

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

description: Micromonospora rhizosphaerae 211018 is an aerobe, spore-forming, mesophilic bacterium that was isolated from mangrove Excocaria agallocha rhizhosphere soil.

NCBI tax id

  • NCBI tax id: 568872
  • Matching level: species

strain history

@refhistory
16554<- K. Hong, Inst. of Tropical Bioscience & Biotech., Haikou City; 211018 <- X. Xu
67770CGMCC 4.5599 <-- K. Hong 211018.

doi: 10.13145/bacdive8017.20230509.8.1

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 rhizosphaerae
  • full scientific name: Micromonospora rhizosphaerae Wang et al. 2011

@ref: 16554

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora rhizosphaerae

full scientific name: Micromonospora rhizosphaerae Wang et al. 2011

strain designation: 211018

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
29770positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21397Honey yellow (1005)10-14 daysISP 2
21397Beige (1001)10-14 daysISP 3
21397Sand yellow (1002)10-14 daysISP 4
21397Ivory (1014)10-14 daysISP 5
21397Orange brown (8023)10-14 daysISP 7
21397Ochre brown (8001)10-14 daysSuter with tyrosine
21397Beige (1001)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21397noISP 2
21397noISP 3
21397noISP 4
21397noISP 5
21397noISP 7
21397noSuter with tyrosine
21397noSuter without tyrosine

pigmentation

  • @ref: 29770
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16554GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
16554N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
16554GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
21397ISP 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
21397ISP 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:
21397ISP 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
21397ISP 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
21397ISP 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
21397Suter 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
21397Suter 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
16554positivegrowth28mesophilic
29770positivegrowth10-40
29770positiveoptimum34mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29770positivegrowth05-09alkaliphile
29770positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29770
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29770yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
21397NaClpositivemaximum2.5 %
29770NaClpositivegrowth0-2 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2139717234glucose+
2139722599arabinose-
2139717992sucrose+
2139718222xylose+
2139717268myo-inositol-
2139737684mannose+
2139728757fructose+
2139726546rhamnose-
2139716634raffinose-
2139762968cellulose-
2977016449alanine+carbon source
2977028757fructose+carbon source
2977028260galactose+carbon source
2977017234glucose+carbon source
2977027570histidine+carbon source
29770182404-hydroxy-L-proline+carbon source
2977017822serine+carbon source
2977018222xylose+carbon source
2977017632nitrate+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+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
21397---+-++++++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21397+++-++-+-++++-+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16554mangrove Excocaria agallocha rhizhosphere soilExcoecaria agallochaHainan Province, WenchangChinaCHNAsia
67770Mangrove Excocaria agallocha rhizosphere soilExcocaria agallochaHainan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 16554
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16554
  • description: Micromonospora rhizosphaerae strain 211018 16S ribosomal RNA gene, partial sequence
  • accession: FJ261956
  • length: 1481
  • database: ena
  • NCBI tax ID: 568872

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora rhizosphaerae strain DSM 45431568872.4wgspatric568872
66792Micromonospora rhizosphaerae DSM 454312622736626draftimg568872
67770Micromonospora rhizosphaerae DSM 45431GCA_900091465contigncbi568872

GC content

@refGC-contentmethod
1655470.8high performance liquid chromatography (HPLC)
2977070.8
6777071.61genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.454yes
anaerobicno99.028no
halophileno96.599no
spore-formingyes92.723yes
glucose-utilyes89.447yes
thermophileno97.566yes
flagellatedno98.181no
motileno93.596no
aerobicyes90.872no
glucose-fermentno93.734yes

External links

@ref: 16554

culture collection no.: DSM 45431, CGMCC 4.5599, NBRC 110451, JCM 17737

straininfo link

  • @ref: 77447
  • straininfo: 402449

literature

  • topic: Phylogeny
  • Pubmed-ID: 20305066
  • title: Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil.
  • authors: Wang C, Xu XX, Qu Z, Wang HL, Lin HP, Xie QY, Ruan JS, Hong K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.020461-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, DNA, Bacterial/genetics, Euphorbiaceae/*microbiology, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16554Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45431)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45431
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
21397Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45431.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29770Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2615028776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
77447Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402449.1StrainInfo: A central database for resolving microbial strain identifiers