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)

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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Rhodocyclales*
	Family	*Rhodocyclaceae*
	Genus	*Rugosibacter*
	Species	**Rugosibacter aromaticivorans**
	Full Scientific Name (PNU)	Rugosibacter aromaticivorans Corteselli et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25209]	Gram stain	negative
[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

[Ref.: #25209]

Culture medium

sRB1-agar plates

[Ref.: #25209]

Culture medium growth

[Ref.: #25209]

Culture medium composition

expand / minimize

[Ref.: #24861]

Culture medium

RUGOSIBACTER MEDIUM (DSMZ Medium 1622)

[Ref.: #24861]

Culture medium growth

[Ref.: #24861]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #24861]

Culture medium composition

expand / minimize

[Ref.: #24861]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #24861]

Culture medium growth

[Ref.: #24861]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #24861]

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

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25209]

Oxygen tolerance

aerobe

[Ref.: #25209]

Nutrition type

heterotroph

	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 (bp)	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

Availability in culture collections External links

[Ref.: #24861]

Culture collection no.

DSM 103039, ATCC TSD-59

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) .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Rugosibacter aromaticivorans in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF