Agromyces tardus (DSM 105049, CGMCC 4.7419, SJ-23)

Name: Agromyces tardus (DSM 105049, CGMCC 4.7419, SJ-23)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159616

Type strain

Strain Designation SJ-23

Culture col. no. DSM 105049 CGMCC 4.7419 SJ-23

NCBI tax ID(s) 2583849

Special Collections DSMZ Wink compendium Literature strains

History DSMZ <- J. Zhao; Northeast Agricultural University, Harbin, P.R. CHINA; SJ-23<-J. Song; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing

Links

Agromyces tardus SJ-23 is an aerobe, heterotroph, Gram-positive bacterium that was isolated from Wheat rhizosphere soil.

Gram-positive rod-shaped aerobe heterotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398872

DSM 105049

@ref 20215

Last LPSN update 2026-05-29 08:44:14

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Agromyces

Species Agromyces tardus

Full scientific name Agromyces tardus Sun et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
68199	positive	1-1.4 µm	0.2-0.4 µm	rod-shaped
125438					93.5
125438	positive				93.711

Colony morphology

@ref	Colony color	Medium used
69281	Golden yellow (1004), yellow orange (2000)	ISP 7
68199	light yellow
69281	Honey yellow (1005)	ISP 2
69281	Ivory (1014)	ISP 6
69281	Pastel yellow (1034)	ISP 4
69281	Pastel yellow (1034)	ISP 5
69281	Red orange (2001)	suter without tyrosine
69281	Signal brown (8002)	suter with tyrosine
69281	Signal yellow (1003)	ISP 3

Multicellular morphology

@ref	Complex name	Complex color	Medium name	Further description
68199		non-transparent, light yellow		forms branched vegetative hyphae which fragment into rod-like, diphtheroid, irregular, non-motile fragments
69281	Aerial mycelium	Signal white (9003)	ISP 2
69281	Aerial mycelium	Signal white (9003)	ISP 3
69281	Aerial mycelium	Cream (9001)	ISP 4
69281	Aerial mycelium	Traffic white (9016)	ISP 5
69281	Aerial mycelium		ISP 6
69281	Aerial mycelium	Traffic white (9016)	ISP 7
69281	Aerial mycelium		suter with tyrosine
69281	Aerial mycelium		suter without tyrosine

Pigmentation

@ref	Production	Color	Name
69281			melanin pigment
69281		Ochre brown (8001)	soluble pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66442	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
66442	positive	growth	28
68199	positive	growth	4-37
68199	positive	optimum	28

Culture pH

@ref	Ability	Type	PH	PH range
68199	positive	optimum	7
68199	positive	growth	6-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
68199	aerobe
125438	aerobe	92.074

Nutrition type

68199

Typeheterotroph

Spore formation

68199

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68199	NaCl	positive	growth	0-5 %(w/v)
69281	NaCl	positive	growth	0 %

Observation

68199

Observationforms branched vegetative hyphae which fragment into rod-like, diphtheroid, irregular, non-motile fragments

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69281	22599 ChEBI	arabinose	+/-	growth
68199	29016 ChEBI	arginine	+	nitrogen source
68199	62968 ChEBI	cellulose	-	assimilation
69281	62968 ChEBI	cellulose	-	growth
68199	16919 ChEBI	creatine	+	nitrogen source
68199	15824 ChEBI	D-fructose	-	carbon source
68199	12936 ChEBI	D-galactose	-	carbon source
68199	17634 ChEBI	D-glucose	+	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68199	16899 ChEBI	D-mannitol	+	carbon source
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68199	16024 ChEBI	D-mannose	+	carbon source
68199	16988 ChEBI	D-ribose	-	carbon source
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68199	17924 ChEBI	D-sorbitol	-	carbon source
68199	65327 ChEBI	D-xylose	-	carbon source
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68199	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
69281	28757 ChEBI	fructose	+/-	growth
68199	16813 ChEBI	galactitol	-	carbon source
68199	5291 ChEBI	gelatin	-	hydrolysis
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
69281	17234 ChEBI	glucose	+	growth
68199	15428 ChEBI	glycine	+	nitrogen source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68199	16977 ChEBI	L-alanine	+	nitrogen source
68199	30849 ChEBI	L-arabinose	-	carbon source
68199	17196 ChEBI	L-asparagine	+	nitrogen source
68199	29991 ChEBI	L-aspartate	+	nitrogen source
68199	29985 ChEBI	L-glutamate	+	nitrogen source
68199	18050 ChEBI	L-glutamine	+	nitrogen source
68199	17203 ChEBI	L-proline	-	nitrogen source
68199	62345 ChEBI	L-rhamnose	+	carbon source
68199	17115 ChEBI	L-serine	+	nitrogen source
68199	16857 ChEBI	L-threonine	+	nitrogen source
68199	17895 ChEBI	L-tyrosine	+	nitrogen source
68199	17716 ChEBI	lactose	-	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68199	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69281	37684 ChEBI	mannose	+	growth
68199		milk	-	assimilation
68199	17268 ChEBI	myo-inositol	+	carbon source
69281	17268 ChEBI	myo-inositol	-	growth
68199	17632 ChEBI	nitrate	-	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68199	16634 ChEBI	raffinose	-	carbon source
69281	16634 ChEBI	raffinose	+	growth
69281	26546 ChEBI	rhamnose	+/-	growth
68199	28017 ChEBI	starch	-	hydrolysis
68199	17992 ChEBI	sucrose	-	carbon source
69281	17992 ChEBI	sucrose	+/-	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68199	53424 ChEBI	tween 20	-	hydrolysis
68199	53423 ChEBI	tween 40	-	hydrolysis
68199	53426 ChEBI	tween 80	-	hydrolysis
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69281	18222 ChEBI	xylose	+/-	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68199	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68379	beta-glucuronidase	+	3.2.1.31	from API Coryne
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68199	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne

Fatty acid profile

Metadata FA analysis

@ref

68199

Fatty acid	Percentage
C17:0 anteiso	44.9
C15:0 anteiso	31.2
C16:0 iso	22.7
C14:0 iso	0.9
C17:0	0.3

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69281	-	-	-	-	+	+	+	+	+	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
69281	not determinedn.d.	-	+	+	+	+	+/-	+	-	-	+/-	+	+/-	+	+/-	+	+	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture temperature
66442	Wheat rhizosphere soil	Langfang, Hebei province (38° 32' N, 114° 89' E)	China	CHN	Asia
68199	rhizosphere soil of wheat (Triticum aestivum L.)	Langfang, Hebei Province	China	CHN	Asia	39.5333	116.667 39.5333/116.667	humic acid-vitamin agar	supplemented with cycloheximide and nalidixic acid	28

Taxonmaps

69479

Global distribution of 16S sequence MH342641 (>99% sequence identity) for Agromyces from Microbeatlas

Aquatic Samples	399
Soil Samples	2909
Animal Samples	151
Plant Samples	439
Total Samples	3898

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68199	ASM371080v1 assembly for Agromyces tardus SJ-23	contig	GCA_003710805	33879.3	2841884086	2583849	51.12
124043	ASM4265590v1 assembly for Agromyces tardus CGMCC 4.7419	contig	GCA_042655905			2583849	34.81

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66442	Agromyces tardus strain SJ-23 16S ribosomal RNA gene, partial sequence	MH342641	1516		2583849

GC content

@ref	GC-content (mol%)	Method
68199	71.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agromyces tardus SJ-23
NCBI: GCA_003710805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.71	yes
125438	anaerobic	anaerobicⓘ	no	97.45	no
125438	aerobic	aerobicⓘ	yes	92.07	no
125438	spore-forming	spore-formingⓘ	no	77.44	yes
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	93.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces humi sp. nov., actinobacterium isolated from farm soil.	Lee JC, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004376	2020
Phylogeny	Agromyces tardus sp. nov., an actinobacterium isolated from the rhizosphere soil of wheat (Triticum aestivum L.).	Sun T, Cao P, Sun K, Li C, Jiang M, Jia W, Wang X, Zhao J, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.003621	2019

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 )
#66442	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105049
#68199	Tianyu Sun, Peng Cao, Kexin Sun, Chenxu Li, Mengqi Jiang, Weiqi Jia, Xiangjing Wang, Junwei Zhao and Wensheng Xiang: Agromyces tardus sp. nov., an actinobacterium isolated from the rhizosphere soil of wheat (Triticum aestivum L.). IJSEM 69: 3268 - 3275 2019 ( DOI 10.1099/ijsem.0.003621 )
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69281	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Agromyces tardus (DSM 105049, CGMCC 4.7419, SJ-23)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003710805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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