Strain identifier

BacDive ID: 8022

Type strain: Yes

Species: Micromonospora zamorensis

Strain Designation: CR 38

Strain history: CECT 7892 <-- M. E. Trujillo, Univ. Salamanca, Spain; CR38.

NCBI tax ID(s): 709883 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 17741

BacDive-ID: 8022

DSM-Number: 45600

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

description: Micromonospora zamorensis CR 38 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere of Pisum sativum.

NCBI tax id

  • NCBI tax id: 709883
  • Matching level: species

strain history

@refhistory
17741<- M. E. Trujillo, Universidad de Salamanca, Spain; CR 38 <- L. Carro
67770CECT 7892 <-- M. E. Trujillo, Univ. Salamanca, Spain; CR38.

doi: 10.13145/bacdive8022.20250331.9.3

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 zamorensis
  • full scientific name: Micromonospora zamorensis Carro et al. 2012

@ref: 17741

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora zamorensis

full scientific name: Micromonospora zamorensis Carro et al. 2012

strain designation: CR 38

type strain: yes

Morphology

cell morphology

@refgram staincell widthmotilityconfidence
30559positive0.4 µmno
125438positive92.865
125439positive99.7

pigmentation

  • @ref: 30559
  • production: yes

multimedia

  • @ref: 17741
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45600.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17741N-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
17741GYM 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
17741TRYPTICASE 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
17741GPHF-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

culture temp

@refgrowthtypetemperature
17741positivegrowth28
30559positivegrowth10-37
67770positivegrowth28

culture pH

  • @ref: 30559
  • ability: positive
  • type: growth
  • pH: 6.5-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30559aerobe
125439obligate aerobe99.5

spore formation

@refspore formationconfidence
30559yes
125438yes92.512

halophily

  • @ref: 30559
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 3 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6), MK-9(H4), MK-10(H2), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3055922599arabinose+carbon source
3055929016arginine+carbon source
3055928757fructose+carbon source
3055917234glucose+carbon source
3055917306maltose+carbon source
3055937684mannose+carbon source
3055926271proline+carbon source
3055916634raffinose+carbon source
3055917814salicin+carbon source
3055917822serine+carbon source
3055917992sucrose+carbon source

enzymes

@refvalueactivityec
30559acid phosphatase+3.1.3.2
30559alkaline phosphatase+3.1.3.1
30559catalase+1.11.1.6
30559gelatinase+
30559cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
17741rhizosphere of Pisum sativumPisum sativumZamora province, Canizal (41° 49' 00'' N 6° 13' 00'' W)SpainESPEurope41.8167-6.2167
67770Rhizosphere of a Pisum sativum plantPisum sativumZamoraSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_10152.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_10152&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: FN658656
  • Sequence Identity:
  • Total samples: 53
  • soil counts: 33
  • aquatic counts: 11
  • animal counts: 7
  • plant counts: 2

Safety information

risk assessment

  • @ref: 17741
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17741
  • description: Micromonospora zamorensis partial 16S rRNA gene, type strain CR38T
  • accession: FN658656
  • length: 1451
  • database: nuccore
  • NCBI tax ID: 709883

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora zamorensis DSM 45600GCA_900090275chromosomencbi709883
66792Micromonospora zamorensis strain DSM 45600709883.12completepatric709883
66792Micromonospora zamorensis DSM 456002617270899draftimg709883

GC content

@refGC-contentmethod
1774171.8thermal denaturation, midpoint method (Tm)
3055971.8
6777071.21genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.865yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.892yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes92.512yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.536yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno88.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes80.1
125439BacteriaNetmotilityAbility to perform movementno86.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5

External links

@ref: 17741

culture collection no.: DSM 45600, CECT 7892, JCM 31702

straininfo link

  • @ref: 77452
  • straininfo: 382399

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22286910Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum.Carro L, Pukall R, Sproer C, Kroppenstedt RM, Trujillo MEInt J Syst Evol Microbiol10.1099/ijs.0.038695-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peas/*microbiology, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analysisGenetics
Phylogeny32915290Actinoplanes solisilvae sp. nov., Isolated from Birch Forest Soil.Ma Q, Zhang Q, Jiang X, Kong D, Han X, Xue H, Zhou Y, Zhang Y, Zhang W, Ruan ZCurr Microbiol10.1007/s00284-020-02192-z2020*Actinoplanes, Bacterial Typing Techniques, Betula, China, DNA, Bacterial/genetics, Forests, Micromonospora, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17741Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45600)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45600
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
30559Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2689028776041
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/
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
77452Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID382399.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1