Name: Agromyces aureus AR33
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132611

Type strain:

Species: Agromyces aureus

Strain Designation: AR33

Culture col. no.: DSM 101731, LMG 29235, JCM 32431

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

NCBI tax ID(s): 453304 (species)

SI-ID 396805

DSM 101731

Section

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.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Agromyces*
	Species	**Agromyces aureus**
	Full Scientific Name (LPSN)	Agromyces aureus Corretto et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43114]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43114]	Cell length	1.0-6.0 µm

[Ref.: #43114]	Cell width	0.3-0.5 µm

[Ref.: #43114]	Cell shape	rod-shaped

[Ref.: #43114]	Motility	yes

[Ref.: #43114]	Flagellum arrangement	monotrichous

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43114]

Culture medium

Landy medium

[Ref.: #43114]

Culture medium growth

[Ref.: #24400]

Culture medium

RICH MEDIUM (DSMZ Medium 736)

[Ref.: #24400]

Culture medium growth

[Ref.: #24400]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24400]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24400]	growth	28 °C
[Ref.: #43114]	optimum	28 °C
[Ref.: #43114]	growth	10-30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #24400]	Temperature range	mesophilic
[Ref.: #43114]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43114]			optimum	6.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43114]	Oxygen tolerance	microaerophile
[Ref.: #43114]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.977

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43114]		NaCl		growth	0-3	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-11, MK-10, MK-12

[Ref.: #43114]	Name of tolerated compound	zinc
[Ref.: #43114]	Tolerated concentration	6
[Ref.: #43114]	Name of tolerated compound	cadmium
[Ref.: #43114]	Tolerated concentration	1

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43114]	adenine ChEBI	-	hydrolysis
[Ref.: #43114]	amygdalin ChEBI	+	assimilation
[Ref.: #43114]	arbutin ChEBI	+	builds acid from
[Ref.: #43114]	casein	-	hydrolysis
[Ref.: #43114]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43114]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43114]	D-fucose ChEBI	-	builds acid from
[Ref.: #43114]	D-glucose ChEBI	+	assimilation
[Ref.: #43114]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43114]	D-mannitol ChEBI	-	assimilation
[Ref.: #43114]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43114]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43114]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43114]	erythritol ChEBI	-	builds acid from
[Ref.: #43114]	esculin ChEBI	+	builds acid from
[Ref.: #43114]	galactitol ChEBI	-	builds acid from
[Ref.: #43114]	gelatin ChEBI	-	hydrolysis
[Ref.: #43114]	glycerol ChEBI	+	builds acid from
[Ref.: #43114]	glycogen ChEBI	+	builds acid from
[Ref.: #43114]	hippurate ChEBI	+	hydrolysis
[Ref.: #43114]	hypoxanthine ChEBI	+	hydrolysis
[Ref.: #43114]	L-arabinose ChEBI	+	assimilation
[Ref.: #43114]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43114]	L-fucose ChEBI	+	builds acid from
[Ref.: #43114]	L-rhamnose ChEBI	+	assimilation
[Ref.: #43114]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43114]	L-xylose ChEBI	-	builds acid from
[Ref.: #43114]	maltose ChEBI	+	builds acid from
[Ref.: #43114]	melezitose ChEBI	-	builds acid from
[Ref.: #43114]	melibiose ChEBI	-	assimilation
[Ref.: #43114]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43114]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43114]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43114]	myo-inositol ChEBI	-	assimilation
[Ref.: #43114]	nitrate ChEBI	-	reduction
[Ref.: #43114]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #43114]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #43114]	ribitol ChEBI	-	builds acid from
[Ref.: #43114]	starch ChEBI	+	builds acid from
[Ref.: #43114]	sucrose ChEBI	+	assimilation
[Ref.: #43114]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43114]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43114]	tyrosine ChEBI	+	hydrolysis
[Ref.: #43114]	urea ChEBI	-	hydrolysis
[Ref.: #43114]	xanthine ChEBI	+	hydrolysis
[Ref.: #43114]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43114]	erythromycin ChEBI	yes	10	µg (disc)
[Ref.: #43114]	gentamicin ChEBI	yes	30	µg (disc)
[Ref.: #43114]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #43114]	nalidixic acid ChEBI				yes	30	µg (disc)
[Ref.: #43114]	neomycin ChEBI	yes	30	µg (disc)
[Ref.: #43114]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #43114]	streptomycin ChEBI	yes	10	µg (disc)

	Metabolite	Production
[Ref.: #43114]	acetoin ChEBI	no
[Ref.: #43114]	hydrogen sulfide ChEBI	no
[Ref.: #43114]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43114]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43114]	acid phosphatase	+	3.1.3.2
[Ref.: #43114]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43114]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43114]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43114]	arginine decarboxylase	-	4.1.1.19
[Ref.: #43114]	beta-galactosidase	+	3.2.1.23
[Ref.: #43114]	beta-glucosidase	+	3.2.1.21
[Ref.: #43114]	esterase (C 4)	+
[Ref.: #43114]	esterase Lipase (C 8)	+
[Ref.: #43114]	leucine arylamidase	+	3.4.11.1
[Ref.: #43114]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43114]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43114]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43114]	trypsin	-	3.4.21.4
[Ref.: #43114]	tryptophan deaminase	+	4.1.99.1
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24400]	Sample type/isolated from	rhizosphere of willow tree (Salix caprea L.) growing in a heavy-metal-contaminated soil of a former zinc/lead mining site
[Ref.: #24400]	Host species	Salix caprea
[Ref.: #24400]	Geographic location (country and/or sea, region)	Arnoldstein
[Ref.: #24400]	Country	Austria
[Ref.: #24400]	Country ISO 3 Code	AUT
[Ref.: #24400]	Continent	Europe

[Ref.: #43114]	Sample type/isolated from	Salix caprea L. rhizosphere samples
[Ref.: #43114]	Geographic location (country and/or sea, region)	former zinc/lead mining and processing site, Arnoldstein
[Ref.: #43114]	Country	Austria
[Ref.: #43114]	Country ISO 3 Code	AUT
[Ref.: #43114]	Continent	Europe
[Ref.: #43114]	Enrichment culture	R2A (Difco)
[Ref.: #43114]	Enrichment culture composition	containing 1 mM Cd(NO3)2, 1 mM Pb(NO3)2 and 1 mM Zn(NO3)2
[Ref.: #43114]	Enrichment culture temperature	21 ̊C
[Ref.: #43114]	Isolation/enrichment procedure	serial dilution plating method

[Ref.: #67770]	Sample type/isolated from	Rhizosphere of willow trees (Salix caprea L.) grown in a former mining site in Arnoldstein
[Ref.: #67770]	Host species	Salix caprea L.
[Ref.: #67770]	Country	Austria
[Ref.: #67770]	Country ISO 3 Code	AUT
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU141339 (>99% sequence identity) for Agromyces from Microbeatlas

Aquatic Samples	89
Soil Samples	342
Animal Samples	154
Plant Samples	20
Total Samples	605

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #24400]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #43114]	Agromyces aureus strain AR33 16S ribosomal RNA variant 1 gene, complete sequence	KU141339	1518	GenBank	453304 tax ID
[Ref.: #24400]	Agromyces aureus strain AR33 16S ribosomal RNA variant 2 gene, complete sequence	KU141338	1520	ENA	453304 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agromyces aureus JCM 32431	GCA_009749365	contig	GenBank	453304 tax ID
[Ref.: #66792]	Agromyces aureus AR33	GCA_001660485	complete	GenBank	453304 tax ID	*
[Ref.: #66792]	Agromyces aureus strain JCM 32431	453304.8	wgs	PATRIC	453304 tax ID	*
[Ref.: #66792]	Agromyces sp. AR33	453304.3	complete	PATRIC	453304 tax ID	*

[Ref.: #24400]	GC-content	70.1 mol%	sequence analysis
[Ref.: #67770]	GC-content	70.1 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Agromyces aureus AR33 NCBI: GCA_001660485.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agromyces aureus AR33 NCBI: GCA_001660485.1
[Ref.: #69480]	flagellated	no	97.463	no
[Ref.: #69480]	gram-positive	yes	92.8	yes
[Ref.: #69480]	anaerobic	no	99.755	yes
[Ref.: #69480]	aerobic	yes	96.321	no
[Ref.: #69480]	halophile	no	93.749	no
[Ref.: #69480]	spore-forming	no	88.009	no
[Ref.: #69480]	glucose-util	yes	88.923	yes
[Ref.: #69480]	motile	no	89.037	yes
[Ref.: #69480]	thermophile	no	99.608	no
[Ref.: #69480]	glucose-ferment	no	90.395	no

Availability in culture collections External links

[Ref.: #24400]

Culture collection no.

DSM 101731, LMG 29235, JCM 32431

[Ref.: #90925]

SI-ID 396805

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil.	Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M, Kuffner M, Brader G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001260	2016	*

References

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#24400

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101731

#43114

Erika Corretto, Livio Antonielli, Angela Sessitsch, Stephane Compant, Markus Gorfer, Melanie Kuffner, Günter Brader: Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. IJSEM 66: 3749 - 3754 2016 ( DOI 10.1099/ijsem.0.001260 , PubMed 27373912 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João 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 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#90925

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID396805.1 )

* These data were automatically processed and therefore are not curated

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