Strain identifier

BacDive ID: 132611

Type strain: Yes

Species: Agromyces aureus

Strain Designation: AR33

Strain history: LMG 29235 <-- G. Brader; AIT Austrian Inst. of Technol., Austria; AR33.

NCBI tax ID(s): 453304 (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: 24400

BacDive-ID: 132611

DSM-Number: 101731

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, motile, rod-shaped

description: Agromyces aureus AR33 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from rhizosphere of willow tree growing in a heavy-metal-contaminated soil of a former zinc/lead mining site.

NCBI tax id

  • NCBI tax id: 453304
  • Matching level: species

strain history

@refhistory
24400<- G. Brader, AIT Austrian Inst. of Technology GmbH, Tulln, Austria; AR33
67770LMG 29235 <-- G. Brader; AIT Austrian Inst. of Technol., Austria; AR33.

doi: 10.13145/bacdive132611.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces aureus
  • full scientific name: Agromyces aureus Corretto et al. 2016

@ref: 24400

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces aureus

full scientific name: Agromyces aureus Corretto et al. 2016

strain designation: AR33

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43114positive1.0-6.0 µm0.3-0.5 µmrod-shapedyesmonotrichous
125439positive97.7
125438no92.5
125438positive91.073

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43114Landy mediumyes
24400RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
43114positiveoptimum28
43114positivegrowth10-30
24400positivegrowth28
67770positivegrowth28

culture pH

  • @ref: 43114
  • ability: positive
  • type: optimum
  • pH: 6.5-7.5

Physiology and metabolism

tolerance

@refcompoundconcentration
43114zinc6.0 mM
43114cadmium1.0 mM

oxygen tolerance

@refoxygen toleranceconfidence
43114microaerophile
43114aerobe
125438aerobe91.243
125439obligate aerobe97.5

halophily

  • @ref: 43114
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-10, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4311416708adenine-hydrolysis
43114606565hippurate+hydrolysis
4311417368hypoxanthine+hydrolysis
4311453424tween 20+hydrolysis
4311453426tween 80+hydrolysis
4311418186tyrosine+hydrolysis
4311415318xanthine+hydrolysis
43114casein-hydrolysis
431145291gelatin-hydrolysis
4311416199urea-hydrolysis
4311417632nitrate-reduction
4311428017starch+builds acid from
4311418305arbutin+builds acid from
4311417108D-arabinose+builds acid from
4311417306maltose+builds acid from
431144853esculin+builds acid from
4311417754glycerol+builds acid from
4311428087glycogen+builds acid from
4311418287L-fucose+builds acid from
4311415963ribitol-builds acid from
4311418333D-arabitol-builds acid from
4311428847D-fucose-builds acid from
4311462318D-lyxose-builds acid from
431146731melezitose-builds acid from
4311417924D-sorbitol-builds acid from
4311416443D-tagatose-builds acid from
4311416813galactitol-builds acid from
4311417113erythritol-builds acid from
4311417268myo-inositol-builds acid from
4311418403L-arabitol-builds acid from
4311417266L-sorbose-builds acid from
4311465328L-xylose-builds acid from
43114320061methyl alpha-D-glucopyranoside-builds acid from
4311474863methyl beta-D-xylopyranoside-builds acid from
43114potassium 2-dehydro-D-gluconate-builds acid from
4311432032potassium gluconate-builds acid from
4311417151xylitol-builds acid from
4311427613amygdalin+assimilation
4311417634D-glucose+assimilation
4311417992sucrose+assimilation
4311430849L-arabinose+assimilation
4311462345L-rhamnose+assimilation
4311416899D-mannitol-assimilation
4311428053melibiose-assimilation
4311417924D-sorbitol-assimilation
4311417268myo-inositol-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4311448923erythromycinyesyes10 µg (disc)
4311417833gentamicinyesyes30 µg (disc)
431146104kanamycinyesyes30 µg (disc)
43114100147nalidixic acidyesyes30 µg (disc)
431147507neomycinyesyes30 µg (disc)
4311428077rifampicinyesyes5 µg (disc)
4311417076streptomycinyesyes10 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4311416136hydrogen sulfideno
4311435581indoleno
4311415688acetoinno

metabolite tests

  • @ref: 43114
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
43114acid phosphatase+3.1.3.2
43114leucine arylamidase+3.4.11.1
43114naphthol-AS-BI-phosphohydrolase+
43114alpha-glucosidase+3.2.1.20
43114beta-glucosidase+3.2.1.21
43114esterase (C 4)+
43114esterase Lipase (C 8)+
43114beta-galactosidase+3.2.1.23
43114trypsin-3.4.21.4
43114alpha-galactosidase-3.2.1.22
43114alpha-fucosidase-3.2.1.51
43114tryptophan deaminase+4.1.99.1
43114arginine decarboxylase-4.1.1.19
43114lysine decarboxylase-4.1.1.18
43114ornithine decarboxylase-4.1.1.17

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperatureisolation procedure
24400rhizosphere of willow tree (Salix caprea L.) growing in a heavy-metal-contaminated soil of a former zinc/lead mining siteSalix capreaArnoldsteinAustriaAUTEurope
43114Salix caprea L. rhizosphere samplesformer zinc/lead mining and processing site, ArnoldsteinAustriaAUTEuropeR2A (Difco)containing 1 mM Cd(NO3)2, 1 mM Pb(NO3)2 and 1 mM Zn(NO3)221serial dilution plating method
67770Rhizosphere of willow trees (Salix caprea L.) grown in a former mining site in ArnoldsteinSalix caprea L.AustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Heavy metal
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_2105.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_1358;98_1647;99_2105&stattab=map
  • Last taxonomy: Agromyces
  • 16S sequence: KU141339
  • Sequence Identity:
  • Total samples: 605
  • soil counts: 342
  • aquatic counts: 89
  • animal counts: 154
  • plant counts: 20

Safety information

risk assessment

  • @ref: 24400
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
43114Agromyces aureus strain AR33 16S ribosomal RNA variant 1 gene, complete sequenceKU1413391518nuccore453304
24400Agromyces aureus strain AR33 16S ribosomal RNA variant 2 gene, complete sequenceKU1413381520nuccore453304

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces aureus AR33GCA_001660485completencbi453304
66792Agromyces aureus strain JCM 32431453304.8wgspatric453304
66792Agromyces sp. AR33453304.3completepatric453304
67770Agromyces aureus JCM 32431GCA_009749365contigncbi453304

GC content

@refGC-contentmethod
2440070.1sequence analysis
6777070.1genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.073yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.222yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.243no
125438spore-formingspore-formingAbility to form endo- or exosporesno70.718no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99yes
125438motile2+flagellatedAbility to perform flagellated movementno92.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno72.5
125439BacteriaNetmotilityAbility to perform movementno61.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive97.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.5

External links

@ref: 24400

culture collection no.: DSM 101731, LMG 29235, JCM 32431

straininfo link

  • @ref: 90925
  • straininfo: 396805

literature

  • topic: Phylogeny
  • Pubmed-ID: 27373912
  • title: Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil.
  • authors: Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M, Kuffner M, Brader G
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001260
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Austria, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Metals, Heavy, Mining, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salix/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Vitamin K 2/chemistry
  • topic2: Transcriptome

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
24400Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101731Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101731)
43114Erika Corretto, Livio Antonielli, Angela Sessitsch, Stephane Compant, Markus Gorfer, Melanie Kuffner, Günter BraderAgromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil10.1099/ijsem.0.001260IJSEM 66: 3749-3754 201627373912
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90925Reimer, 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-ID396805.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG