Arthrobacter cupressi (DSM 24664, CGMCC 1.10783, CIP 110640)

Name: Arthrobacter cupressi (DSM 24664, CGMCC 1.10783, CIP 110640)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7630

Type strain

Strain Designation D48

Culture col. no. DSM 24664 CGMCC 1.10783 CIP 110640 D48 JCM 19662

NCBI tax ID(s) 1045773

Special Collections DSMZ JCM CIP Literature strains

Links

Arthrobacter cupressi D48 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from rhizosphere soil, cypress tree .

Gram-positive ovoid-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398746

DSM 24664,CIP 110640

@ref 20215

Last LPSN update 2025-12-16 09:48:38

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter cupressi

Full scientific name Arthrobacter cupressi Zhang et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
30474	positive	ovoid-shaped
118819	positive	rod-shaped
125438			91
125438	positive		92.202

Pigmentation

30474

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
41616	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
17726	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
118819	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17726	positive	growth	28	mesophilic
30474	positive	growth	12-37
30474	positive	optimum	28	mesophilic
41616	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30474	positive	optimum	7
30474	positive	growth	5.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30474	aerobe
125439	obligate aerobe	94.3

Spore formation

30474

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30474	NaCl	positive	growth	0-2 %
30474	NaCl	positive	optimum	0.5 %

Observation

67770

Observationquinones: MK-9(H₂), MK-7(H₂), MK-10(H₂), MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30474	30089 ChEBI	acetate	+	carbon source
30474	16449 ChEBI	alanine	+	carbon source
30474	22653 ChEBI	asparagine	+	carbon source
30474	23652 ChEBI	dextrin	+	carbon source
30474	4853 ChEBI	esculin	+	hydrolysis
30474	28757 ChEBI	fructose	+	carbon source
30474	28260 ChEBI	galactose	+	carbon source
30474	24265 ChEBI	gluconate	+	carbon source
30474	17234 ChEBI	glucose	+	carbon source
30474	29987 ChEBI	glutamate	+	carbon source
30474	17754 ChEBI	glycerol	+	carbon source
30474	17596 ChEBI	inosine	+	carbon source
30474	25115 ChEBI	malate	+	carbon source
30474	17306 ChEBI	maltose	+	carbon source
30474	29864 ChEBI	mannitol	+	carbon source
30474	37684 ChEBI	mannose	+	carbon source
30474	28053 ChEBI	melibiose	+	carbon source
30474	51850 ChEBI	methyl pyruvate	+	carbon source
30474	15361 ChEBI	pyruvate	+	carbon source
30474	16634 ChEBI	raffinose	+	carbon source
30474	17822 ChEBI	serine	+	carbon source
30474	17992 ChEBI	sucrose	+	carbon source
30474	53423 ChEBI	tween 40	+	carbon source
30474	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30474	acid phosphatase	+	3.1.3.2
30474	alkaline phosphatase	+	3.1.3.1
30474	alpha-galactosidase	+	3.2.1.22
30474	catalase	+	1.11.1.6
30474	gelatinase	+
30474	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17726	rhizosphere soil, cypress tree (Cupressus sempervirens)	Cupressus sempervirens	Sichuan province, Mianyang	China	CHN	Asia
67770	Rhizosphere soil of a cypress tree (Cupressus sempervirens)	Cupressus sempervirens	Mianyang, Sichuan Province	China	CHN	Asia
118819	Environment, Rhizosphere soil, cypress tree, Cupressus sempervirens		Sichuan Province, Mianyang, China	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17726	1	Risk group (German classification) According to TRBA 466
118819	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1340990v1 assembly for Arthrobacter cupressi DSM 24664	contig	GCA_013409905	1045773.10	2844849076	1045773	78.46
67770	IMG-taxon 2663762744 annotated assembly for Arthrobacter cupressi CGMCC 1.10783	scaffold	GCA_900099975	1045773.8	2663762744	1045773	70.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17726	Arthrobacter cupressi strain D48 16S ribosomal RNA gene, partial sequence	HQ657321	1491		1045773

GC content

@ref	GC-content (mol%)	Method
17726	65.0	thermal denaturation, midpoint method (Tm)
30474	65
67770	65	thermal denaturation, midpoint method (Tm)
67770	67	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arthrobacter cupressi CGMCC 1.10783
NCBI: GCA_900099975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.30	no
125439	gram_stain	BacteriaNetⓘ	positive	88.40	no
125439	motility	BacteriaNetⓘ	no	63.40	no
125439	spore_formation	BacteriaNetⓘ	no	55.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arthrobacter cupressi strain CGMCC 1.10783
PATRIC: 1045773.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.20	yes
125438	anaerobic	anaerobicⓘ	no	97.19	yes
125438	spore-forming	spore-formingⓘ	no	65.93	no
125438	aerobic	aerobicⓘ	yes	89.17	no
125438	thermophilic	thermophileⓘ	no	98.47	yes
125438	flagellated	motile2+ⓘ	no	91.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance.	Rosas-Diaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sanchez-Reyes A, Pardo-Lopez L.	Front Microbiol	10.3389/fmicb.2021.713702	2021
Phylogeny	Arthrobacter celericrescens sp. nov., isolated from forest soil.	Yan R, Liu D, Fu Y, Zhang Y, Ju H, Zhao J, Wang X, Zhang J, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.003597	2019
Phylogeny	Arthrobacter silvisoli sp. nov., isolated from forest soil.	Yan R, Fu Y, Liu D, Jiang S, Ju H, Guo X, Guo X, Wang X, Zhang J, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.003085	2018
Phylogeny	Arthrobacter cupressi sp. nov., an actinomycete isolated from the rhizosphere soil of Cupressus sempervirens.	Zhang J, Ma Y, Yu H	Int J Syst Evol Microbiol	10.1099/ijs.0.036889-0	2012

References

#17726	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24664
#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 )
#26809	IJSEM 2731 2012 ( DOI 10.1099/ijs.0.036889-0 , PubMed 22228666 )
#30474	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26809
#41616	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#118819	Collection of Institut Pasteur ; Curators of the CIP; CIP 110640
#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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Arthrobacter cupressi (DSM 24664, CGMCC 1.10783, CIP 110640)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013409905

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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