Name: Pseudarthrobacter phenanthrenivorans Sphe3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7622

Type strain:

Species: Pseudarthrobacter phenanthrenivorans

Strain Designation: Sphe3

Culture col. no.: DSM 18606, LMG 23796, JCM 16027

Strain history: LMG 23796 <-- A. Kallimanis et al. Sphe3.

NCBI tax ID(s): 361575 (species)

SI-ID 323911

LMG 23796, DSM 18606, JCM 16027

Section

Pseudarthrobacter phenanthrenivorans Sphe3 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from creosote-contaminated soil.

coccus-shaped
Gram-positive
aerobe
mesophilic
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	*Micrococcaceae*
	Genus	*Pseudarthrobacter*
	Species	**Pseudarthrobacter phenanthrenivorans**
	Full Scientific Name (LPSN)	Pseudarthrobacter phenanthrenivorans (Kallimanis et al. 2009) Busse 2016

Synonym

Arthrobacter phenanthrenivorans

Information on morphological and physiological properties Morphology

[Ref.: #28902]	Gram stain	positive

[Ref.: #28902]	Cell length	3.25 µm

[Ref.: #28902]	Cell width	1.25 µm

[Ref.: #28902]	Cell shape	coccus-shaped

[Ref.: #28902]	Motility	no

[Ref.: #18324]	Colony color	Beige (1001)
[Ref.: #18324]	Incubation period	10-14 days
[Ref.: #18324]	Cultivation medium used	ISP 2

[Ref.: #18324]	Colony color	Oyster white (1013)
[Ref.: #18324]	Incubation period	10-14 days
[Ref.: #18324]	Cultivation medium used	ISP 3

[Ref.: #18324]	Colony color	Beige (1001)
[Ref.: #18324]	Incubation period	10-14 days
[Ref.: #18324]	Cultivation medium used	ISP 4

[Ref.: #18324]	Colony color	Beige (1001)
[Ref.: #18324]	Incubation period	10-14 days
[Ref.: #18324]	Cultivation medium used	ISP 5

[Ref.: #18324]	Colony color	Beige (1001)
[Ref.: #18324]	Incubation period	10-14 days
[Ref.: #18324]	Cultivation medium used	ISP 6

[Ref.: #18324]	Colony color	Beige (1001)
[Ref.: #18324]	Incubation period	10-14 days
[Ref.: #18324]	Cultivation medium used	ISP 7

[Ref.: #28902]

Pigment production

yes

[Ref.: #18324]	Multicellular complex forming ability	no
[Ref.: #18324]	Medium Name (multicellularity)	ISP 2

[Ref.: #18324]	Multicellular complex forming ability	no
[Ref.: #18324]	Medium Name (multicellularity)	ISP 3

[Ref.: #18324]	Multicellular complex forming ability	no
[Ref.: #18324]	Medium Name (multicellularity)	ISP 4

[Ref.: #18324]	Multicellular complex forming ability	no
[Ref.: #18324]	Medium Name (multicellularity)	ISP 5

[Ref.: #18324]	Multicellular complex forming ability	no
[Ref.: #18324]	Medium Name (multicellularity)	ISP 6

[Ref.: #18324]	Multicellular complex forming ability	no
[Ref.: #18324]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7620]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #7620]

Culture medium growth

[Ref.: #7620]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7620]

Culture medium composition

expand / minimize

[Ref.: #18324]

Culture medium

ISP 2

[Ref.: #18324]

Culture medium growth

[Ref.: #18324]

Culture medium composition

expand / minimize

[Ref.: #18324]

Culture medium

ISP 3

[Ref.: #18324]

Culture medium growth

[Ref.: #18324]

Culture medium composition

expand / minimize

[Ref.: #18324]

Culture medium

ISP 4

[Ref.: #18324]

Culture medium growth

[Ref.: #18324]

Culture medium composition

expand / minimize

[Ref.: #18324]

Culture medium

ISP 5

[Ref.: #18324]

Culture medium growth

[Ref.: #18324]

Culture medium composition

expand / minimize

[Ref.: #18324]

Culture medium

ISP 6

[Ref.: #18324]

Culture medium growth

[Ref.: #18324]

Culture medium composition

expand / minimize

[Ref.: #18324]

Culture medium

ISP 7

[Ref.: #18324]

Culture medium growth

[Ref.: #18324]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7620]	growth	28 °C
[Ref.: #18324]	optimum	28 °C
[Ref.: #28902]	growth	04-37 °C
[Ref.: #28902]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #7620]	Temperature range	mesophilic
[Ref.: #18324]	Temperature range	mesophilic
[Ref.: #28902]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28902]			optimum	7.25
[Ref.: #28902]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28902]

Oxygen tolerance

aerobe

[Ref.: #28902]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8, MK-9(H₂), MK-9(H₂), MK-8(H₂), MK-10(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #28902]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym, 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.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #28902]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[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]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[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.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #18324]	19	-	-	-	-	-	+	+	-	-	+	+	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.: #18324]	34	not determinedn.d.	-	-	-	-	+	-	-	+	-	-	-	+	+	-	+	-	-	+	-

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

[Ref.: #7620]	Sample type/isolated from	creosote-contaminated soil
[Ref.: #7620]	Geographic location (country and/or sea, region)	Ioannina
[Ref.: #7620]	Country	Greece
[Ref.: #7620]	Country ISO 3 Code	GRC
[Ref.: #7620]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Creosote-contaminated soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Epirus
[Ref.: #67770]	Country	Greece
[Ref.: #67770]	Country ISO 3 Code	GRC
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #7620]

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.: #7620]	Arthrobacter phenanthrenivorans partial 16S rRNA gene, type strain Sphe3T	AM176541	1520	ENA	930171 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudarthrobacter phenanthrenivorans Sphe3	GCA_000189535	complete	GenBank	930171 tax ID	*
[Ref.: #66792]	Pseudarthrobacter phenanthrenivorans Sphe3	930171.23	plasmid	PATRIC	930171 tax ID	*
[Ref.: #66792]	Pseudarthrobacter phenanthrenivorans Sphe3	930171.24	plasmid	PATRIC	930171 tax ID	*
[Ref.: #66792]	Pseudarthrobacter phenanthrenivorans Sphe3	650377905	complete	JGI IMG/M	930171 tax ID	*

[Ref.: #7620]	GC-content	65.7±0.2 mol%	fluorimetric
[Ref.: #28902]	GC-content	65.7 mol%
[Ref.: #67770]	GC-content	65.5-65.9 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	65.6 mol%	genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudarthrobacter phenanthrenivorans Sphe3 Sphe3 NCBI: GCA_000189535.1
[Ref.: #69480]	motile	no	88.943	yes
[Ref.: #69480]	flagellated	no	96.269	yes
[Ref.: #69480]	gram-positive	yes	92.853	no
[Ref.: #69480]	anaerobic	no	99.678	yes
[Ref.: #69480]	aerobic	yes	95.448	yes
[Ref.: #69480]	halophile	no	83.99	no
[Ref.: #69480]	spore-forming	no	87.001	no
[Ref.: #69480]	glucose-util	yes	86.349	no
[Ref.: #69480]	thermophile	no	98.798	yes
[Ref.: #69480]	glucose-ferment	no	84.905	no

Availability in culture collections External links

[Ref.: #7620]

Culture collection no.

DSM 18606, LMG 23796, JCM 16027

[Ref.: #77066]

SI-ID 323911

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation and Characterization of Levoglucosan-Metabolizing Bacteria.	Arya AS, Hang MTH, Eiteman MA	Appl Environ Microbiol	10.1128/AEM.01868-21	2021	*
Metabolism	Characterization of Protocatechuate 4,5-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and In Situ Reaction Monitoring in the NMR Tube.	Tsagogiannis E, Vandera E, Primikyri A, Asimakoula S, Tzakos AG, Gerothanassis IP, Koukkou AI	Int J Mol Sci	10.3390/ijms22179647	2021	*
Genetics	Draft Genome Sequence of Pseudarthrobacter phenanthrenivorans Strain MHSD1, a Bacterial Endophyte Isolated From the Medicinal Plant Pellaea calomelanos.	Tshishonga K, Serepa-Dlamini MH	Evol Bioinform Online	10.1177/1176934320913257	2020	*
Phylogeny	Reclassification of Arthrobacter enclensis as Pseudarthrobacter enclensis comb. nov., and emended descriptions of the genus Pseudarthrobacter, and the species Pseudarthrobacter phenanthrenivorans and Pseudarthrobacter scleromae.	Busse HJ, Schumann P	Int J Syst Evol Microbiol	10.1099/ijsem.0.003652	2019	*
Enzymology	Cold-active and NaCl-tolerant exo-inulinase from a cold-adapted Arthrobacter sp. MN8 and its potential for use in the production of fructose at low temperatures.	Zhou J, Lu Q, Peng M, Zhang R, Mo M, Tang X, Li J, Xu B, Ding J, Huang Z	J Biosci Bioeng	10.1016/j.jbiosc.2014.08.003	2014	*
Metabolism	Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose.	Vandera E, Samiotaki M, Parapouli M, Panayotou G, Koukkou AI	J Proteomics	10.1016/j.jprot.2014.08.018	2014	*
Phylogeny	Arthrobacter siccitolerans sp. nov., a highly desiccation-tolerant, xeroprotectant-producing strain isolated from dry soil.	SantaCruz-Calvo L, Gonzalez-Lopez J, Manzanera M	Int J Syst Evol Microbiol	10.1099/ijs.0.052902-0	2013	*
Enzymology	Heterologous expression and characterization of two 1-hydroxy-2-naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans.	Vandera E, Kavakiotis K, Kallimanis A, Kyrpides NC, Drainas C, Koukkou AI	Appl Environ Microbiol	10.1128/AEM.07137-11	2011	*
Genetics	Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3).	Kallimanis A, Labutti KM, Lapidus A, Clum A, Lykidis A, Mavromatis K, Pagani I, Liolios K, Ivanova N, Goodwin L, Pitluck S, Chen A, Palaniappan K, Markowitz V, Bristow J, Velentzas AD, Perisynakis A, Ouzounis CC, Kyrpides NC, Koukkou AI, Drainas C	Stand Genomic Sci	10.4056/sigs.1393494	2011	*
Phylogeny	Arthrobacter phenanthrenivorans sp. nov., to accommodate the phenanthrene-degrading bacterium Arthrobacter sp. strain Sphe3.	Kallimanis A, Kavakiotis K, Perisynakis A, Sproer C, Pukall R, Drainas C, Koukkou AI	Int J Syst Evol Microbiol	10.1099/ijs.0.000984-0	2009	*

References

#7620

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18606

#18324

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 )

#28902

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 #25342 (see below)

#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;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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) .

#77066

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-ID323911.1 )

#25342

IJSEM 275 2009 ( DOI 10.1099/ijs.0.000984-0 , PubMed 19196765 )

* These data were automatically processed and therefore are not curated

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Pseudarthrobacter phenanthrenivorans Sphe3 Sphe3

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