Strain identifier

BacDive ID: 132607

Type strain: Yes

Species: Micromonospora noduli

Strain history: <- A. Trujillo, Depart. Microbiol. y Gen., Univ. Salamanca, Spain; GUI43

NCBI tax ID(s): 709876 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
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 8.1 (current version)

General

@ref: 24396

BacDive-ID: 132607

DSM-Number: 101694

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

description: Micromonospora noduli DSM 101694 is an aerobe, chemoorganotroph, spore-forming bacterium that builds a substrate mycelium and was isolated from nitrogen fixing nodule from Pisum sativum.

NCBI tax id

  • NCBI tax id: 709876
  • Matching level: species

strain history

  • @ref: 24396
  • history: <- A. Trujillo, Depart. Microbiol. y Gen., Univ. Salamanca, Spain; GUI43

doi: 10.13145/bacdive132607.20230509.8.1

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 noduli
  • full scientific name: Micromonospora noduli Carro et al. 2016

@ref: 24396

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora noduli

full scientific name: Micromonospora noduli Carro et al. 2016

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43106positiveno
69480no93.642
69480positive100

multicellular morphology

  • @ref: 43106
  • forms multicellular complex: yes
  • complex name: Substrate mycelium
  • complex color: beige to dark brown
  • medium name: SA1
  • further description: extensively branched and non-fragmented hyphae

multimedia

  • @ref: 24396
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_101694.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24396N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
43106YMAyes
43106SA1yes
43106IPS 2yes
43106ISP 3yes
24396GYM 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
43106positiveoptimum28mesophilic
43106positivegrowth12-37
24396positivegrowth28mesophilic

culture pH

  • @ref: 43106
  • ability: positive
  • type: growth
  • pH: 7-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43106
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43106
  • type: chemoorganotroph

spore formation

@refspore descriptionspore formationconfidence
43106Single, non-motile, smooth-surfaced spores, at the end of the hyphal tipsyes
69481yes100
69480yes100

halophily

  • @ref: 43106
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4310618305arbutin+degradation
43106casein+degradation
431064853esculin+degradation
431065291gelatin+degradation
4310653426tween 80+degradation
4310628017starch+degradation
4310637166xylan+degradation
4310653424tween 20-degradation
4310618186tyrosine-degradation
4310616199urea-degradation
4310630849L-arabinose+carbon source
4310617057cellobiose+carbon source
4310648095(-)-D-fructose+carbon source
4310612936D-galactose+carbon source
4310624265gluconate+carbon source
4310617634D-glucose+carbon source
4310615971L-histidine+carbon source
4310617306maltose+carbon source
4310616024D-mannose+carbon source
4310628053melibiose+carbon source
4310616634raffinose+carbon source
4310628017starch+carbon source
4310617992sucrose+carbon source
4310627082trehalose+carbon source
4310665327D-xylose+carbon source
4310616449alanine-carbon source
4310616467L-arginine-carbon source
4310618024D-galacturonic acid-carbon source
4310617859glutaric acid-carbon source
4310618019L-lysine-carbon source
431066731melezitose-carbon source
4310617113erythritol-carbon source
4310617203L-proline-carbon source
4310617272propionate-carbon source
4310617521(-)-quinic acid-carbon source
4310662345L-rhamnose-carbon source
4310617814salicin-carbon source
4310617115L-serine-carbon source
4310630911sorbitol-carbon source
4310617266L-sorbose-carbon source
4310618186tyrosine-carbon source
4310616414L-valine-carbon source
4310617151xylitol-carbon source

enzymes

@refvalueactivityec
43106cytochrome oxidase+1.9.3.1
43106catalase+1.11.1.6
43106alkaline phosphatase+3.1.3.1
43106naphthol-AS-BI-phosphohydrolase+
43106alpha-galactosidase+3.2.1.22
43106alpha-glucosidase+3.2.1.20
43106esterase (C 4)+
43106leucine arylamidase+3.4.11.1
43106valine arylamidase+
43106cystine arylamidase+3.4.11.3
43106trypsin+3.4.21.4
43106alpha-chymotrypsin+3.4.21.1
43106beta-galactosidase+3.2.1.23
43106beta-glucuronidase-3.2.1.31
43106lipase (C 14)-
43106acid phosphatase-3.1.3.2
43106beta-glucosidase-3.2.1.21
43106alpha-mannosidase-3.2.1.24
43106alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
24396nitrogen fixing nodule from Pisum sativumPisum sativumZamora, CanizalSpainESPEurope40.7939-5.6656
43106root nodules of Pisum sativumCañizal, ZamoraSpainESPEuropeyeast mannitol agar (YMA)

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3471.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_3471&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: FN658649
  • Sequence Identity:
  • Total samples: 1419
  • soil counts: 1017
  • aquatic counts: 161
  • animal counts: 219
  • plant counts: 22

Safety information

risk assessment

  • @ref: 24396
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24396
  • description: Micromonospora sp. GUI43 partial 16S rRNA gene, isolate GUI43
  • accession: FN658649
  • length: 1440
  • database: ena
  • NCBI tax ID: 709876

Genome sequences

  • @ref: 66792
  • description: Micromonospora noduli strain GUI43
  • accession: 709876.6
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 709876

GC content

@refGC-contentmethod
4310671.3Thermal denaturation, fluorometry
2439671.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes91.008yes
anaerobicno99.35no
halophileno94.51no
spore-formingyes95.069no
glucose-utilyes88.889no
thermophileno98.784yes
flagellatedno97.476yes
aerobicyes96.214no
glucose-fermentno90.911no
motileno92.661no

External links

@ref: 24396

culture collection no.: DSM 101694, CECT 9020, GUI 43

straininfo link

  • @ref: 90922
  • straininfo: 401228

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27282917Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules.Carro L, Riesco R, Sproer C, Trujillo MEInt J Syst Evol Microbiol10.1099/ijsem.0.0012312016Bacterial Typing Techniques, DNA, Bacterial/genetics, Micromonospora/*classification, Peas/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, SpainTranscriptome
Phylogeny27902235Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching.Zhao S, Liu C, Zheng W, Ma Z, Cao T, Zhao J, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0016142017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptophyta/*microbiologyTranscriptome
Genetics29988535Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics.Riesco R, Carro L, Roman-Ponce B, Prieto C, Blom J, Klenk HP, Normand P, Trujillo MEFront Microbiol10.3389/fmicb.2018.013602018

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24396Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101694Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101694)
43106Lorena Carro, Raúl Riesco, Cathrin Spröer, Martha E. TrujilloMicromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules10.1099/ijsem.0.001231IJSEM 66: 3509-3514 201627282917
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90922Reimer, 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-ID401228.1