Name: Rugosibacter aromaticivorans Ca6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133073

Type strain:

Species: Rugosibacter aromaticivorans

Strain Designation: Ca6

Culture col. no.: DSM 103039, ATCC TSD-59

Strain history: <- E. Corteselli, University of North Carolina, Gillings School of Global Public Health, Environmental Sciences and Engineering, Chapel Hill, USA; Ca6 <- D. R. Singleton, Univ. of North Carolina

NCBI tax ID(s): 1565605 (species)

SI-ID 402305

DSM 103039

Section

Rugosibacter aromaticivorans Ca6 is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from PAH contaminated soil from a former manufactured gas plant.

colony-forming
Gram-negative
rod-shaped
aerobe
heterotroph
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Rhodocyclales*
	Family	*Rhodocyclaceae*
	Genus	*Rugosibacter*
	Species	**Rugosibacter aromaticivorans**
	Full Scientific Name (LPSN)	Rugosibacter aromaticivorans Corteselli et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25209]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #25209]	Cell length	0.77-1.15 µm

[Ref.: #25209]	Cell width	0.23-0.27 µm

[Ref.: #25209]	Cell shape	rod-shaped

[Ref.: #25209]	Motility	no

[Ref.: #25209]	Colony size	0.5-0.8 mm
[Ref.: #25209]	Colony color	yellow-white
[Ref.: #25209]	Colony shape	circular
[Ref.: #25209]	Incubation period	14 days
[Ref.: #25209]	Cultivation medium used	sRB1-agar plates

Information on culture and growth conditions Culture and growth conditions

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Culture medium

sRB1-agar plates

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Culture medium growth

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Culture medium composition

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Culture medium

RUGOSIBACTER MEDIUM (DSMZ Medium 1622)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #24861]	growth	28 °C
[Ref.: #25209]	growth	20.0-35.0 °C
[Ref.: #25209]	optimum	30.0-34.0 °C

[Ref.: #24861]	Temperature range	mesophilic
[Ref.: #25209]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25209]			optimum	6.5
[Ref.: #25209]			growth	6.5-7.5

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Nutrition type

heterotroph

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25209]	gelatin ChEBI	-	hydrolysis
[Ref.: #25209]	nitrate ChEBI	-	reduction
[Ref.: #25209]	nitrate ChEBI	+	nitrogen source
[Ref.: #25209]	starch ChEBI	-	hydrolysis

	Enzyme	Enzyme activity	EC number
[Ref.: #25209]	catalase	-	1.11.1.6
[Ref.: #25209]	cellulase	-	3.2.1.4
[Ref.: #25209]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25209]	lipase	+
[Ref.: #25209]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25209]

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	42.5
C16:0	36.7
Cyclo C17:0	6.5
C18:1ω7c	4.9
C10:0 3OH	3.9
C12:0	3

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	nitrate assimilation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	60	9 of 15
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	pyrimidine metabolism	55.56	25 of 45
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24861]	Sample type/isolated from	PAH contaminated soil from a former manufactured gas plant
[Ref.: #24861]	Geographic location (country and/or sea, region)	Charlotte, North Carolina
[Ref.: #24861]	Country	USA
[Ref.: #24861]	Country ISO 3 Code	USA
[Ref.: #24861]	Continent	North America
[Ref.: #24861]	Geographic location	35.1940°/-80.8370°

[Ref.: #25209]	Sample type/isolated from	(polycyclic aromatic hydrocarbon) PAH-contaminated soil
[Ref.: #25209]	Enrichment culture	modified sk43HT isolation medium
[Ref.: #25209]	Enrichment culture composition	contained 5 mM sodium-potassium phosphate buffer (pH 7.0) and 5 mM NH4NO3, 1 mM MgSO4.7H2O, 1 mM CaCl2.2H2O, 1 ml trace element solution l-1 [containing per litre; 12.5 ml HCl (25 %), 2.1g FeSO4.7H2O, 30 mg H3BO3 , 100 mg MnCl2.4H2O, 190 mg CoCl2.6H2O, 24 mg NaCl2.6H2O, 2 mg CuCl2.2H2O, 144 mg ZnSO4.7H2O, 36 mg Na2MoO4.2H2O] and 1 ml selenium-tungsten solution l-1 (containing per litre; 0.4 g NaOH, 6 mg Na2SeO3.5H2O, 8 mg Na2WO4.2H2O). After autoclaving following filter-sterilized solutions (0.
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Engineered	#Industrial	#Plant (Factory)
#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.: #24861]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rugosibacter aromaticivorans Ca6	GCA_000934545	complete	GenBank	1565605 tax ID	*

[Ref.: #25209]	GC-content	55.14 mol%	genome sequence analysis
[Ref.: #24861]	GC-content	55.14 mol%	sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rugosibacter aromaticivorans Ca6 NCBI: GCA_000934545.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rugosibacter aromaticivorans Ca6 NCBI: GCA_000934545.1
[Ref.: #69480]	motile	no	83.408	yes
[Ref.: #69480]	flagellated	no	91.892	no
[Ref.: #69480]	gram-positive	no	98.63	yes
[Ref.: #69480]	anaerobic	no	94.667	yes
[Ref.: #69480]	aerobic	no	51.381	yes
[Ref.: #69480]	halophile	no	95.672	no
[Ref.: #69480]	spore-forming	no	94.803	no
[Ref.: #69480]	glucose-util	no	68.44	no
[Ref.: #69480]	thermophile	no	91.467	yes
[Ref.: #69480]	glucose-ferment	no	93.464	no

Availability in culture collections External links

[Ref.: #24861]

Culture collection no.

DSM 103039, ATCC TSD-59

[Ref.: #91338]

SI-ID 402305

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds.	Corteselli EM, Aitken MD, Singleton DR	Int J Syst Evol Microbiol	10.1099/ijsem.0.001622	2017	*

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 )

#24861

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103039

#25209

E. M. A. Corteselli, M. D.,Singleton, D. R.: Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds. IJSEM 67: 311 - 318 2017 ( DOI 10.1099/ijsem.0.001622 , PubMed 27902243 )

#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 )

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91338

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-ID402305.1 )

* These data were automatically processed and therefore are not curated

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