Name: Neorhizobium petrolearium SL-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24484

Type strain:

Species: Neorhizobium petrolearium

Strain Designation: SL-1

Culture col. no.: DSM 26482, ACCC 11238, KCTC 23288

Strain history: <- KCTC <- R. Jiang, Chinese Academy of Agriculture Sci., Beijing, China; SL-1

NCBI tax ID(s): 515361 (species)

SI-ID 405059

DSM 26482

Section

Neorhizobium petrolearium SL-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil-contaminated soil.

Gram-negative
motile
rod-shaped
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Neorhizobium*
	Species	**Neorhizobium petrolearium**
	Full Scientific Name (LPSN)	Neorhizobium petrolearium (Zhang et al. 2012) Kuzmanovi? et al. 2022

Synonym

Rhizobium petrolearium

Information on morphological and physiological properties Morphology

[Ref.: #29927]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #29927]	Cell length	1.75 µm

[Ref.: #29927]	Cell width	0.75 µm

[Ref.: #29927]	Cell shape	rod-shaped

[Ref.: #29927]	Motility	yes

[Ref.: #21030]

Incubation period

2-3 days

[Ref.: #29927]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21030]

Culture medium

RHIZOBIUM MEDIUM (DSMZ Medium 98)

[Ref.: #21030]

Culture medium growth

[Ref.: #21030]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21030]

Culture medium composition

expand / minimize

[Ref.: #21030]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #21030]

Culture medium growth

[Ref.: #21030]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21030]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21030]	growth	30 °C
[Ref.: #29927]	growth	10-40 °C
[Ref.: #29927]	optimum	30 °C

[Ref.: #21030]	Temperature range	mesophilic
[Ref.: #29927]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29927]			optimum	7.5
[Ref.: #29927]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29927]

Oxygen tolerance

aerobe

[Ref.: #29927]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29927]		NaCl		growth	<3	%
[Ref.: #29927]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29927]	alanine ChEBI	+	carbon source
[Ref.: #29927]	arabinose ChEBI	+	carbon source
[Ref.: #29927]	arginine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29927]	aspartate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29927]	dextrin ChEBI	+	carbon source
[Ref.: #29927]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #29927]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #29927]	glucose ChEBI	+	carbon source
[Ref.: #29927]	glutamate ChEBI	+	carbon source
[Ref.: #29927]	glycine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29927]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #29927]	mannitol ChEBI	+	carbon source
[Ref.: #29927]	melibiose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #29927]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #29927]	phenylalanine ChEBI	+	carbon source
[Ref.: #29927]	rhamnose ChEBI	+	carbon source
[Ref.: #29927]	sorbitol ChEBI	+	carbon source
[Ref.: #29927]	sucrose ChEBI	+	carbon source
[Ref.: #29927]	threonine ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #29927]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #21030]	catalase	+	1.11.1.6
[Ref.: #29927]	catalase	+	1.11.1.6
[Ref.: #29927]	cytochrome oxidase	+	1.9.3.1
[Ref.: #21030]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #21030]	23945	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	+/-	-	+/-	-	not determinedn.d.

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

[Ref.: #21030]	Sample type/isolated from	oil-contaminated soil
[Ref.: #21030]	Geographic location (country and/or sea, region)	Shandong
[Ref.: #21030]	Country	China
[Ref.: #21030]	Country ISO 3 Code	CHN
[Ref.: #21030]	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 EU556969 (>99% sequence identity) for Rhizobium from Microbeatlas

Aquatic Samples	68
Soil Samples	73
Animal Samples	62
Plant Samples	108
Total Samples	311

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

[Ref.: #21030]

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.: #21030]	Rhizobium petrolearium strain SL-1 16S ribosomal RNA gene, partial sequence	EU556969	1444	ENA	515361 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Neorhizobium petrolearium DSM 26482	GCA_017873175	contig	GenBank	515361 tax ID	*
[Ref.: #66792]	Rhizobium petrolearium strain DSM 26482	515361.4	wgs	PATRIC	515361 tax ID	*
[Ref.: #66792]	Rhizobium petrolearium DSM 26482	2738541324	draft	JGI IMG/M	515361 tax ID	*
[Ref.: #66792]	Rhizobium petrolearium DSM 26482	2913319810	draft	JGI IMG/M	515361 tax ID	*

[Ref.: #29927]

GC-content

62.2 mol%

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: Rhizobium petrolearium strain DSM 26482 PATRIC: 515361.4
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium petrolearium strain DSM 26482 PATRIC: 515361.4
[Ref.: #69480]	gram-positive	no	98.459	no
[Ref.: #69480]	anaerobic	no	97.994	yes
[Ref.: #69480]	halophile	no	88.61	no
[Ref.: #69480]	spore-forming	no	95.311	no
[Ref.: #69480]	glucose-util	yes	90.858	no
[Ref.: #69480]	aerobic	yes	87.062	yes
[Ref.: #69480]	thermophile	no	99.03	no
[Ref.: #69480]	flagellated	no	82.062	no
[Ref.: #69480]	motile	yes	86.248	yes
[Ref.: #69480]	glucose-ferment	no	90.733	yes

Availability in culture collections External links

[Ref.: #21030]

Culture collection no.

DSM 26482, ACCC 11238, KCTC 23288

[Ref.: #88345]

SI-ID 405059

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass.	Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ	J Appl Microbiol	10.1111/jam.13401	2017	*
Phylogeny	Rhizobium rhizosphaerae sp. nov., a novel species isolated from rice rhizosphere.	Zhao JJ, Zhang J, Zhang RJ, Zhang CW, Yin HQ, Zhang XX	Antonie Van Leeuwenhoek	10.1007/s10482-017-0831-9	2017	*
Metabolism	Biodegradation of phenanthrene by Rhizobium petrolearium SL-1.	Huang X, Shi J, Cui C, Yin H, Zhang R, Ma X, Zhang X	J Appl Microbiol	10.1111/jam.13292	2016	*
Phylogeny	Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei.	Boonsnongcheep P, Prathanturarug S, Takahashi Y, Matsumoto A	Int J Syst Evol Microbiol	10.1099/ijsem.0.000863	2015	*
Phylogeny	Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil.	Zhang X, Li B, Wang H, Sui X, Ma X, Hong Q, Jiang R	Int J Syst Evol Microbiol	10.1099/ijs.0.026880-0	2011	*

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 )

#21030

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26482

#29927

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 #26298 (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) .

#68369

Automatically annotated from API 20NE .

#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 .

#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 )

#88345

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-ID405059.1 )

#26298

IJSEM 1871 2012 ( DOI 10.1099/ijs.0.026880-0 , PubMed 21984664 )

* These data were automatically processed and therefore are not curated

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Rhizobium petrolearium strain DSM 26482

Rhizobium petrolearium strain DSM 26482

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