Name: Immundisolibacter cernigliae TR3.2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133093

Type strain:

Species: Immundisolibacter cernigliae

Strain Designation: TR3.2

Culture col. no.: DSM 103040, ATCC TSD-58

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

NCBI tax ID(s): 1810504 (species)

SI-ID 400010

DSM 103040

Section

Immundisolibacter cernigliae TR3.2 is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from polycyclic aromatic hydrocarbon-contaminated and bioreactor treated soil from the site of a former manufactured gas plant.

colony-forming
Gram-negative
oval-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	*Gammaproteobacteria*
	Order	*Immundisolibacterales*
	Family	*Immundisolibacteraceae*
	Genus	*Immundisolibacter*
	Species	**Immundisolibacter cernigliae**
	Full Scientific Name (LPSN)	Immundisolibacter cernigliae Corteselli et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25270]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #25270]	Cell length	0.56 µm

[Ref.: #25270]	Cell width	0.35 µm

[Ref.: #25270]	Cell shape	oval-shaped

[Ref.: #25270]	Motility	no

[Ref.: #25270]	Colony size	0.5-0.75 mm
[Ref.: #25270]	Colony color	yellow-orange
[Ref.: #25270]	Colony shape	circular
[Ref.: #25270]	Cultivation medium used	sRB2 agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

sRB2 agar

[Ref.: #25270]

Culture medium growth

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Culture medium composition

expand / minimize

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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

[Ref.: #24881]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24881]	growth	28 °C
[Ref.: #25270]	growth	20-36 °C
[Ref.: #25270]	optimum	28-30 °C

[Ref.: #24881]	Temperature range	mesophilic
[Ref.: #25270]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25270]			optimum	7
[Ref.: #25270]			growth	6.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25270]

Oxygen tolerance

aerobe

[Ref.: #25270]

Nutrition type

heterotroph

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.975

	Salt		Salt conc.
[Ref.: #25270]	NaCl	maximum	1	%(w/v)
[Ref.: #25270]	NaCl	growth	0-1	%(w/v)
[Ref.: #25270]	NaCl	optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25270]	2-oxobutanoate ChEBI	+	assimilation
[Ref.: #25270]	ammonia ChEBI	+	nitrogen source
[Ref.: #25270]	anthracene ChEBI	+	carbon source
[Ref.: #25270]	fluorene ChEBI	+	carbon source
[Ref.: #25270]	gelatin ChEBI	-	hydrolysis
[Ref.: #25270]	nitrate ChEBI	+	nitrogen source
[Ref.: #25270]	phenanthrene ChEBI	+	carbon source
[Ref.: #25270]	pyrene ChEBI	+	carbon source
[Ref.: #25270]	starch ChEBI	-	hydrolysis
[Ref.: #25270]	tetraphene ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #25270]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25270]	catalase	+	1.11.1.6
[Ref.: #25270]	cellulase	-	3.2.1.4
[Ref.: #25270]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25270]	lipase	+
[Ref.: #25270]	skimmed milk protease	-
[Ref.: #25270]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25270]

Fatty acid	Percentage
C17:0 cyclo	32.1
C16:0	29.6
C16:1ω7c / C16:1ω6c	12
C19:0 cyclo ω8c	8.3
C12:0 3OH	6.4
C12:0	2
C18:1ω7c / C18:1ω6c	1.9
C18:0 anteiso / C18:2ω6,9c	1.6
C14:0	1.4
C10:0	1.4

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	heme 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]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	3-phenylpropionate degradation	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	flavin biosynthesis	53.33	8 of 15
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	41.76	38 of 91
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		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.: #24881]	Sample type/isolated from	polycyclic aromatic hydrocarbon-contaminated and bioreactor treated soil from the site of a former manufactured gas plant
[Ref.: #24881]	Geographic location (country and/or sea, region)	North Carolina, Salisbury
[Ref.: #24881]	Country	USA
[Ref.: #24881]	Country ISO 3 Code	USA
[Ref.: #24881]	Continent	North America
[Ref.: #24881]	Geographic location	35.6667°/-80.4500°

[Ref.: #25270]	Sample type/isolated from	aerobic bioreactor-treated, PAH-contaminated soil from a former manufactured gas plant
[Ref.: #25270]	Isolation/enrichment procedure	serial dilution method
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#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.: #24881]

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]	Immundisolibacter cernigliae TR3.2	GCA_001697225	complete	GenBank	1810504 tax ID	*
[Ref.: #66792]	Immundisolibacter cernigliae TR3.2	2775507249	complete	JGI IMG/M	1810504 tax ID	*

[Ref.: #25270]	GC-content	67.79 mol%	genome sequence analysis
[Ref.: #24881]	GC-content	67.79 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: Immundisolibacter cernigliae TR3.2 NCBI: GCA_001697225.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Immundisolibacter cernigliae TR3.2 NCBI: GCA_001697225.1
[Ref.: #69480]	flagellated	no	85.264	yes
[Ref.: #69480]	gram-positive	no	98.378	yes
[Ref.: #69480]	anaerobic	no	96.403	yes
[Ref.: #69480]	halophile	no	94.432	yes
[Ref.: #69480]	spore-forming	no	91.155	no
[Ref.: #69480]	glucose-util	no	53.446	no
[Ref.: #69480]	aerobic	yes	64.928	no
[Ref.: #69480]	thermophile	no	79.396	no
[Ref.: #69480]	motile	yes	72.705	no
[Ref.: #69480]	glucose-ferment	no	89.059	no

Availability in culture collections External links

[Ref.: #24881]

Culture collection no.

DSM 103040, ATCC TSD-58

[Ref.: #91358]

SI-ID 400010

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.	Duarte M, Nielsen A, Camarinha-Silva A, Vilchez-Vargas R, Bruls T, Wos-Oxley ML, Jauregui R, Pieper DH	Environ Microbiol	10.1111/1462-2920.13756	2017	*
Phylogeny	Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.	Corteselli EM, Aitken MD, Singleton DR	Int J Syst Evol Microbiol	10.1099/ijsem.0.001714	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 )

#24881

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103040

#25270

E. M. A. Corteselli, M. D.,Singleton, D. R.: Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov. IJSEM 67: 925 - 931 2017 ( DOI 10.1099/ijsem.0.001714 , PubMed 27926817 )

#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 )

#91358

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-ID400010.1 )

* These data were automatically processed and therefore are not curated

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