Name: Paraburkholderia aromaticivorans BN5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158708

Type strain:

Species: Paraburkholderia aromaticivorans

Strain Designation: BN5

Culture col. no.: KACC 19419, JCM 32303

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; BN5.

NCBI tax ID(s): 2026199 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Paraburkholderia aromaticivorans BN5 is a facultative aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from gasoline-contaminated soil obtained near a gas station located in Yangju.

colony-forming
Gram-negative
motile
rod-shaped
facultative aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Paraburkholderia*
	Species	**Paraburkholderia aromaticivorans**
	Full Scientific Name (LPSN)	Paraburkholderia aromaticivorans Lee and Jeon 2018

Information on morphological and physiological properties Morphology

[Ref.: #65450]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98

[Ref.: #65450]	Cell length	1.1-1.3 µm

[Ref.: #65450]	Cell width	0.3-0.4 µm

[Ref.: #65450]	Cell shape	rod-shaped

[Ref.: #65450]	Motility	yes

[Ref.: #65450]	Flagellum arrangement	polar

[Ref.: #65450]	Colony color	white to cream
[Ref.: #65450]	Colony shape	circular
[Ref.: #65450]	Cultivation medium used	Reasoner's 2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65450]

Culture medium

Reasoner's 2A agar

[Ref.: #65450]

Culture medium growth

		Temperature
[Ref.: #65450]	growth	20-37 °C
[Ref.: #65450]	optimum	25-30 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #65450]			optimum	5-6
[Ref.: #65450]			growth	3-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65450]	Oxygen tolerance	facultative aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.1

[Ref.: #125439]

Ability of spore formation

no Confidence in %90.8

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65450]		NaCl		growth	0-2	%(w/v)
[Ref.: #65450]		NaCl		optimum	0	%(w/v)

[Ref.: #65450]	Observation	Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoamino lipid and two unidentified lipids are the major polar lipids, and three unidentified amino lipids and six unidentified lipids are the minor polar lip
[Ref.: #65450]	Observation	Q-8 is the predominant respiratory quinone

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65450]	adipate ChEBI	+	assimilation
[Ref.: #65450]	casein	-	hydrolysis
[Ref.: #65450]	D-glucose ChEBI	+	assimilation
[Ref.: #65450]	D-mannitol ChEBI	+	assimilation
[Ref.: #65450]	D-mannose ChEBI	+	assimilation
[Ref.: #65450]	decanoate ChEBI	+	assimilation
[Ref.: #65450]	esculin ChEBI	+	hydrolysis
[Ref.: #65450]	gelatin ChEBI	-	hydrolysis
[Ref.: #65450]	glucose ChEBI	+	fermentation
[Ref.: #65450]	L-arabinose ChEBI	+	assimilation
[Ref.: #65450]	malate ChEBI	+	assimilation
[Ref.: #65450]	maltose ChEBI	+	assimilation
[Ref.: #65450]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #65450]	nitrate ChEBI	-	reduction
[Ref.: #65450]	phenylacetate ChEBI	+	assimilation
[Ref.: #65450]	potassium gluconate ChEBI	+	assimilation
[Ref.: #65450]	sodium citrate ChEBI	+	assimilation
[Ref.: #65450]	starch ChEBI	-	hydrolysis
[Ref.: #65450]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65450]	tween 80 ChEBI	+	hydrolysis
[Ref.: #65450]	tyrosine ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65450]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #65450]	acid phosphatase	+	3.1.3.2
[Ref.: #65450]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65450]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65450]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65450]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65450]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65450]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65450]	arginine dihydrolase	+	3.5.3.6
[Ref.: #65450]	beta-galactopyranosidase	+
[Ref.: #65450]	beta-galactosidase	-	3.2.1.23
[Ref.: #65450]	beta-glucosidase	-	3.2.1.21
[Ref.: #65450]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65450]	catalase	+	1.11.1.6
[Ref.: #65450]	cystine arylamidase	-	3.4.11.3
[Ref.: #65450]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65450]	esterase (C 4)	-
[Ref.: #65450]	esterase Lipase (C 8)	+
[Ref.: #65450]	leucine arylamidase	+	3.4.11.1
[Ref.: #65450]	lipase (C 14)	-
[Ref.: #65450]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65450]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65450]	trypsin	-	3.4.21.4
[Ref.: #65450]	urease	-	3.5.1.5
[Ref.: #65450]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65450]

Fatty acid	Percentage
C16:0	24.2
cyclo-C19:0ω8c	7.9
C18:1ω7c and/or C18:1ω6c	7.4
C16:0 3OH	4.7
C12:0	4.1
C14:0 3OH and/or C16:1 iso I	4.1
cyclo-C17:0	3.9
C19:0	3.5
anteiso-C18:0 and/or C18:2ω6,9c	3.4
C14:0	3.2
C18:1 2OH	3.2
C20:2ω6,8c	2.5
C12:1	2.3
C16:1 2OH	2.2
C13:0 3-OH and/or iso-C15:1 H	2.1
C16:1ω7c and/or C16:1ω6c	2
C11:0 iso 3OH	1.9
C16:0 2OH	1.8
C17:0 iso	1.8
C19:1ω7c and/or C19:1ω6c	1.7
C18:0	1.4
C15:0 anteiso	1.2
C10:0	1.2
C10:0 iso	1.1
C17:0 anteiso	1.1
C17:1 iso ω5c	1

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

[Ref.: #65450]	Sample type/isolated from	gasoline-contaminated soil obtained near a gas station located in Yangju
[Ref.: #65450]	Geographic location (country and/or sea, region)	Kyeonggi province
[Ref.: #65450]	Country	Republic of Korea
[Ref.: #65450]	Country ISO 3 Code	KOR
[Ref.: #65450]	Continent	Asia
[Ref.: #65450]	Geographic location	37.8393°/126.9940°
[Ref.: #65450]	Enrichment culture temperature	25 ̊C
[Ref.: #65450]	Isolation/enrichment procedure	To enrich aromatic hydrocarbon-degrading bacteria, soil extract broth was prepared by resuspending 800 g gasoline-contaminated soil in 2 l distilled water. The supernatant from the resuspended soil mixture was centrifuged (3745 g , 10 min) and filtered using a 0.45 µm membrane filter (Millipore). Approximately 10 g gasoline-contaminated soil sample was added to a cotton-plugged 500 ml Erlenmeyer flask containing 100 ml soil extract broth and 1 ml benzene, toluene, ethylbenzene and o-, m-, p-xyle

[Ref.: #67770]	Sample type/isolated from	Gasoline-contaminated soil near a gas station in Yangju
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kyeonggi Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MF817715 (>99% sequence identity) for Paraburkholderia from Microbeatlas

Aquatic Samples	44
Soil Samples	579
Animal Samples	56
Plant Samples	43
Total Samples	722

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence database
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 16S ribosomal RNA gene, partial sequence	MF817715	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 chromosome 1, complete sequence	CP022989	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 chromosome 2, complete sequence	CP022990	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 plasmid pBN1, complete sequence	CP022991	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 plasmid pBN2, complete sequence	CP022992	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 plasmid pBN3, complete sequence	CP022993	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 plasmid pBN4, complete sequence	CP022994	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 plasmid pBN5, complete sequence	CP022995	GenBank ENA
[Ref.: #65450]	Paraburkholderia aromaticivorans strain BN5 plasmid pBN6, complete sequence	CP022996	GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Paraburkholderia aromaticivorans strain BN5 chromosome 2, complete sequence	CP022990		GenBank ENA	2026199 tax ID
[Ref.: #66792]	Paraburkholderia aromaticivorans BN5	GCA_002278075	complete	GenBank ENA	2026199 tax ID	*
[Ref.: #66792]	Paraburkholderia aromaticivorans BN5	2775506701	complete	JGI IMG/M	2026199 tax ID	*

[Ref.: #65450]

GC-content

62.93 mol%

sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia aromaticivorans BN5 NCBI: GCA_002278075.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.36	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.407	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.699	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.424	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	86.676	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia aromaticivorans BN5 NCBI: GCA_002278075
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	90.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	59.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	87
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.1

Availability in culture collections External links

[Ref.: #65450]

Culture collection no.

KACC 19419, JCM 32303

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil.	Lee Y, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002661	2018	*

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 )

#65450

Yunho Lee, Che Ok Jeon: Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil. IJSEM 68: 1251 - 1257 2018 ( DOI 10.1099/ijsem.0.002661 , PubMed 29461181 )

#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;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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 .

* These data were automatically processed and therefore are not curated

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