Amycolatopsis rhizosphaerae (TBRC 6029, NBRC 112509, DH51B-4-3)

Name: Amycolatopsis rhizosphaerae (TBRC 6029, NBRC 112509, DH51B-4-3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158797

Type strain

Strain Designation DH51B-4-3

Culture col. no. TBRC 6029 NBRC 112509 DH51B-4-3 JCM 32589

NCBI tax ID(s) 2053003

Special Collections JCM Literature strains

Links

Amycolatopsis rhizosphaerae DH51B-4-3 is an aerobe, spore-forming, Gram-positive prokaryote that builds a substrate mycelium and was isolated from rice rhizosphere soil from paddy field.

spore-forming Gram-positive aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 26765

TBRC 6029,NBRC 112509

@ref 20215

Last LPSN update 2025-12-16 10:08:06

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis rhizosphaerae

Full scientific name Amycolatopsis rhizosphaerae Thawai 2018

Morphology

Cell morphology

@ref	Gram stain
65557	positive
125438	positive
125439	positive

Multicellular morphology

@ref	Forms multicellular complex	Complex name	Complex color
65557		substrate mycelium	pale yellowish
65557		aerial mycelium	grey

Culture and growth conditions

Culture medium

@ref	Name	Growth
65557	ISP 2
65557	ISP 3
65557	ISP 4
65557	ISP 5
65557	ISP 6
65557	ISP 7
65557	Nutrient agar (NA)
65557	glucose-asparagine agar
65557	Czapek's sucrose agar

Culture temp

@ref	Growth	Type	Temperature (°C)
65557	positive	growth	15-45
65557	positive	optimum	30
65557	negative	growth	12
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
65557	positive	growth	5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
65557	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore description	Spore formation
65557	spherical

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65557	NaCl	positive	growth	0-5 %(w/v)

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₆), MK-9(H₈), MK-10(H₆), MK-10(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65557	16708 ChEBI	adenine	-	hydrolysis
65557	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
65557	17057 ChEBI	cellobiose	+	builds acid from
65557	15824 ChEBI	D-fructose	+	builds acid from
65557	12936 ChEBI	D-galactose	-	builds acid from
65557	17634 ChEBI	D-glucose	+	builds acid from
65557	16899 ChEBI	D-mannitol	+	builds acid from
65557	16024 ChEBI	D-mannose	+	builds acid from
65557	16988 ChEBI	D-ribose	+	builds acid from
65557	65327 ChEBI	D-xylose	+	builds acid from
65557		DL-2-gamma-aminobutyrate	+	nitrogen source
65557	5291 ChEBI	gelatin	+	hydrolysis
65557	17754 ChEBI	glycerol	+	builds acid from
65557	17368 ChEBI	hypoxanthine	+	hydrolysis
65557	30849 ChEBI	L-arabinose	-	builds acid from
65557	16467 ChEBI	L-arginine	+	nitrogen source
65557	17196 ChEBI	L-asparagine	+	nitrogen source
65557	17561 ChEBI	L-cysteine	+	nitrogen source
65557	16643 ChEBI	L-methionine	-	nitrogen source
65557	17295 ChEBI	L-phenylalanine	+	nitrogen source
65557	17203 ChEBI	L-proline	+	nitrogen source
65557	62345 ChEBI	L-rhamnose	+	builds acid from
65557	17115 ChEBI	L-serine	+	nitrogen source
65557	16857 ChEBI	L-threonine	+	nitrogen source
65557	16414 ChEBI	L-valine	+	nitrogen source
65557	17716 ChEBI	lactose	-	builds acid from
65557		milk	+	hydrolysis
65557	17632 ChEBI	nitrate	+	reduction
65557	16634 ChEBI	raffinose	-	builds acid from
65557	17814 ChEBI	salicin	-	builds acid from
65557	28017 ChEBI	starch	+	hydrolysis
65557	17992 ChEBI	sucrose	+	builds acid from
65557	18186 ChEBI	tyrosine	+	hydrolysis
65557	15318 ChEBI	xanthine	-	hydrolysis

Enzymes

@ref	Value	Activity	Ec
65557	catalase	+	1.11.1.6
65557	cytochrome oxidase	+	1.9.3.1
65557	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	valine metabolism	100	9 of 9
66794	hydrogen production	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	4-hydroxymandelate degradation	100	9 of 9
66794	octane oxidation	100	3 of 3
66794	propanol degradation	100	7 of 7
66794	resorcinol degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	3-chlorocatechol degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	aspartate and asparagine metabolism	100	9 of 9
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cyanate degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	flavin biosynthesis	93.33	14 of 15
66794	heme metabolism	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	glycolysis	88.24	15 of 17
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
66794	purine metabolism	86.17	81 of 94
66794	aclacinomycin biosynthesis	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenol degradation	85	17 of 20
66794	pyrimidine metabolism	84.44	38 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	metabolism of disaccharids	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	factor 420 biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	degradation of hexoses	77.78	14 of 18
66794	methionine metabolism	76.92	20 of 26
66794	urea cycle	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	arginine metabolism	75	18 of 24
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	cyclohexanol degradation	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	lysine metabolism	73.81	31 of 42
66794	oxidative phosphorylation	73.63	67 of 91
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	degradation of sugar acids	72	18 of 25
66794	tyrosine metabolism	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	bile acid biosynthesis, neutral pathway	70.59	12 of 17
66794	coenzyme M biosynthesis	70	7 of 10
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	degradation of sugar alcohols	68.75	11 of 16
66794	degradation of pentoses	67.86	19 of 28
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	d-mannose degradation	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	carotenoid biosynthesis	63.64	14 of 22
66794	cholesterol biosynthesis	63.64	7 of 11
66794	histidine metabolism	62.07	18 of 29
66794	sulfate reduction	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	allantoin degradation	55.56	5 of 9
66794	ascorbate metabolism	50	11 of 22
66794	glycine metabolism	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	polyamine pathway	34.78	8 of 23
66794	methanogenesis from CO2	33.33	4 of 12
66794	chlorophyll metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ginsenoside metabolism	25	4 of 16
66794	catecholamine biosynthesis	25	1 of 4

Fatty acid profile

Metadata FA analysis

@ref

65557

Fatty acid	Percentage
C16:0 iso	30.3
C17:0 cyclo	22.9
C16:0	8.7
C17:0 anteiso	8.2
C15:0 iso	6.4
C17:0 iso	5.2
C18:0	2.7
C16:1 G	2.7
C15:0 anteiso	2.2
C16:1ω6c	2.2
C18:1ω7c	1.5
C16:1ω7c	1.2
C14:0	1.1
C14:0 iso	0.7
C16:0 anteiso	0.6
C16:0 3OH	0.6
C12:0	0.5
C18:1ω9c	0.4
C17:1 anteiso ω9c	0.4
C17:0 2OH	0.4
C17:0	0.4
C17:0 iso 3OH	0.4
C18:0 iso	0.3

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
65557	rice rhizosphere soil from paddy field	Suphanburi Province	Thailand	THA	Asia	humic acid-vitamin agar	supplemented with 20 mg/l nalidixic acid and 50 mg/l nystatin	30 days	30	The soil sample was air-dried at room temperature for 5 days. The dried soil sample was then ground and heated at 100 °C for 1 h. The treated soil was diluted 1000-fold with 0.01 % sterile sodium lauryl sulfate in distilled water.
67770	Rice rhizosphere soil from a paddy field in Suphanburi Province		Thailand	THA	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
66792	ASM771371v1 assembly for Amycolatopsis rhizosphaerae TBRC 6029	contig	GCA_007713715	2053003.4	2899406411	2053003

Genome browser: GCA_007713715

16S sequences

@ref	Description	Accession	Database
65557	Amycolatopsis rhizosphaerae gene for 16S ribosomal RNA, partial sequence	LC333387
124043	Amycolatopsis rhizosphaerae strain TBRC 6029 16S ribosomal RNA gene, partial sequence.	MN399890

GC content

@ref	GC-content (mol%)	Method
65557	68.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amycolatopsis rhizosphaerae TBRC 6029
NCBI: GCA_007713715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	61.50	no
125439	motility	BacteriaNetⓘ	no	85.60	no
125439	gram_stain	BacteriaNetⓘ	positive	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis rhizosphaerae strain TBRC 6029
PATRIC: 2053003.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.08	yes
125438	anaerobic	anaerobicⓘ	no	95.52	yes
125438	spore-forming	spore-formingⓘ	yes	76.08	yes
125438	aerobic	aerobicⓘ	yes	88.30	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Title	Authors	Journal	DOI	Year
The Rare Actinobacterium Crossiella sp. Is a Potential Source of New Bioactive Compounds with Activity against Bacteria and Fungi.	Gonzalez-Pimentel JL, Dominguez-Monino I, Jurado V, Laiz L, Caldeira AT, Saiz-Jimenez C.	Microorganisms	10.3390/microorganisms10081575	2022
New insights into the relationship between the average nucleotide identity and the digital DNA-DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis.	Deng A, Fu L, Mo P, Zheng Y, Tang T, Gao J.	Front Microbiol	10.3389/fmicb.2024.1359021	2024
Amycolatopsis acidicola sp. nov., isolated from peat swamp forest soil.	Teo WFA, Srisuk N, Duangmal K	Int J Syst Evol Microbiol	10.1099/ijsem.0.003933	2020
Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil.	Thawai C	Int J Syst Evol Microbiol	10.1099/ijsem.0.002704	2018

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 )
#65557	Chitti Thawai: Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil. IJSEM 68: 1546 - 1551 2018 ( DOI 10.1099/ijsem.0.002704 , PubMed 29537361 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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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Amycolatopsis rhizosphaerae (TBRC 6029, NBRC 112509, DH51B-4-3)

Name and taxonomic classification