Name: Agromyces rhizosphaerae 14
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7268

Type strain:

Species: Agromyces rhizosphaerae

Strain Designation: 14

Culture col. no.: DSM 14597, IFO 16236, NBRC 16236, VKM Ac-2086, JCM 11432, CIP 108986, IAM 15153, KCTC 13908

Strain history: CIP <- 2005, JCM <- K. Hatano, IFO

NCBI tax ID(s): 88374 (species)

SI-ID 49558

DSM 14597, IFO 16236, VKM Ac-2086, KCTC 13908, JCM 11432, NBRC 16236, ATCC BAA-402, CIP 108986, IAM 15153

Special Collections

Section

Agromyces rhizosphaerae 14 is a microaerophile, motile, rod-shaped bacterium that was isolated from root of Sonneralia alba.

motile
rod-shaped
microaerophile
16S sequence
Bacteria

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 rhizosphaerae**
	Full Scientific Name (LPSN)	Agromyces rhizosphaerae corrig. Takeuchi and Hatano 2001

Synonym

Agromyces rhizospherae

Information on morphological and physiological properties Morphology

[Ref.: #122214]	Cell shape	rod-shaped

[Ref.: #122214]	Motility	yes

[Ref.: #18387]	Colony color	Saffron yellow (1017)
[Ref.: #18387]	Incubation period	10-14 days
[Ref.: #18387]	Cultivation medium used	ISP 2

[Ref.: #18387]	Colony color	Saffron yellow (1017)
[Ref.: #18387]	Incubation period	10-14 days
[Ref.: #18387]	Cultivation medium used	ISP 3

[Ref.: #18387]	Colony color	Beige (1001)
[Ref.: #18387]	Incubation period	10-14 days
[Ref.: #18387]	Cultivation medium used	ISP 4

[Ref.: #18387]	Colony color	Beige (1001)
[Ref.: #18387]	Incubation period	10-14 days
[Ref.: #18387]	Cultivation medium used	ISP 5

[Ref.: #18387]	Colony color	Beige (1001)
[Ref.: #18387]	Incubation period	10-14 days
[Ref.: #18387]	Cultivation medium used	ISP 6

[Ref.: #18387]	Colony color	Beige (1001)
[Ref.: #18387]	Incubation period	10-14 days
[Ref.: #18387]	Cultivation medium used	ISP 7

[Ref.: #18387]	Multicellular complex forming ability	no
[Ref.: #18387]	Medium Name (multicellularity)	ISP 2

[Ref.: #18387]	Multicellular complex forming ability	no
[Ref.: #18387]	Medium Name (multicellularity)	ISP 3

[Ref.: #18387]	Multicellular complex forming ability	no
[Ref.: #18387]	Medium Name (multicellularity)	ISP 4

[Ref.: #18387]	Multicellular complex forming ability	no
[Ref.: #18387]	Medium Name (multicellularity)	ISP 5

[Ref.: #18387]	Multicellular complex forming ability	no
[Ref.: #18387]	Medium Name (multicellularity)	ISP 6

[Ref.: #18387]	Multicellular complex forming ability	no
[Ref.: #18387]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5400]

Culture medium

PP-MEDIUM (DSMZ Medium 513)

[Ref.: #5400]

Culture medium growth

[Ref.: #5400]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5400]

Culture medium composition

expand / minimize

[Ref.: #18387]

Culture medium

ISP 2

[Ref.: #18387]

Culture medium growth

[Ref.: #18387]

Culture medium composition

expand / minimize

[Ref.: #18387]

Culture medium

ISP 3

[Ref.: #18387]

Culture medium growth

[Ref.: #18387]

Culture medium composition

expand / minimize

[Ref.: #18387]

Culture medium

ISP 4

[Ref.: #18387]

Culture medium growth

[Ref.: #18387]

Culture medium composition

expand / minimize

[Ref.: #18387]

Culture medium

ISP 7

[Ref.: #18387]

Culture medium growth

[Ref.: #18387]

Culture medium composition

expand / minimize

[Ref.: #18387]

Culture medium

ISP 6

[Ref.: #18387]

Culture medium growth

[Ref.: #18387]

Culture medium composition

expand / minimize

[Ref.: #18387]

Culture medium

ISP 5

[Ref.: #18387]

Culture medium growth

[Ref.: #18387]

Culture medium composition

expand / minimize

[Ref.: #40501]

Culture medium

MEDIUM 563 - for Novosphingobium roseae

[Ref.: #40501]

Culture medium growth

[Ref.: #40501]

Culture medium composition

expand / minimize

[Ref.: #122214]

Culture medium

CIP Medium 563

[Ref.: #122214]

Culture medium growth

[Ref.: #122214]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #5400]	growth	28 °C
[Ref.: #18387]	optimum	28 °C
[Ref.: #40501]	growth	25 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122214]

Oxygen tolerance

microaerophile

[Ref.: #5400]	Murein short key	B07
[Ref.: #5400]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #67770]

Observation

quinones: MK-12, MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-glucose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #122214]	nitrate ChEBI	-	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122214]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne
[Ref.: #122214]	catalase	-	1.11.1.6
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122214]	oxidase	+
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #122214]	urease	-	3.5.1.5
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #122214]	11435	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #18387]	73	-	-	-	+	-	-	-	-	-	-	-	not determinedn.d.	+	-	-	-	+	-	+	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #18387]	97	not determinedn.d.	+	+	+	-	-	-	-	-	-	+	+	-	+	-	+	-	-	-	-
[Ref.: #122214]	11591	-	-	+	+	+	+	+	+	+	-	+	+	-	+	+	-	+	-	-	-

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

[Ref.: #5400]	Sample type/isolated from	root of Sonneralia alba
[Ref.: #5400]	Host species	Sonneratia alba
[Ref.: #5400]	Geographic location (country and/or sea, region)	Japan, Okinawa, Iriomote Island
[Ref.: #5400]	Country	Japan
[Ref.: #5400]	Country ISO 3 Code	JPN
[Ref.: #5400]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of the rhizosphere of Sonneratia alba, mangrove in the estuary of the Shiira River
[Ref.: #67770]	Host species	Sonneratia alba
[Ref.: #67770]	Geographic location (country and/or sea, region)	Iriomote Island
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #122214]	Sample type/isolated from	Environment, Soil, rhizosphere of Sonneralia alba
[Ref.: #122214]	Geographic location (country and/or sea, region)	Shiira river, Iriomote Island
[Ref.: #122214]	Country	Japan
[Ref.: #122214]	Country ISO 3 Code	JPN
[Ref.: #122214]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

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

[Ref.: #18387]	Biosafety level	1	German classification
[Ref.: #5400]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122214]	Biosafety level	1	Risk group (French classification)

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.: #5400]	Agromyces sp. IFO16237 gene for 16S rRNA	AB023357	1510	GenBank ENA	88374 tax ID

[Ref.: #5400]	GC-content	71.2 mol%
[Ref.: #67770]	GC-content	71.2 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #5400]

Culture collection no.

DSM 14597, IFO 16236, NBRC 16236, VKM Ac-2086, JCM 11432, CIP 108986, IAM 15153, KCTC 13908

[Ref.: #76719]

SI-ID 49558

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove.	Hamada M, Saitou S, Tamura T	Arch Microbiol	10.1007/s00203-018-1504-4	2018	*
Phylogeny	Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere.	Takeuchi M, Hatano K	Int J Syst Evol Microbiol	10.1099/00207713-51-4-1529	2001	*

References

#5400

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14597

#18387

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#40501 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#76719

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-ID49558.1 )

#122214 Collection of Institut Pasteur ; Curators of the CIP; CIP 108986
* These data were automatically processed and therefore are not curated

Change proposal

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