Name: Stenotrophomonas bentonitica BII-R7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140359

Type strain:

Species: Stenotrophomonas bentonitica

Strain Designation: BII-R7

Culture col. no.: DSM 103927, CECT 9180, LMG 29893

Strain history: <- M. L. Merroun, University of Granada, Spain <- O. Fernández Sanfrancisco and M. López Fernández, University of Granada

NCBI tax ID(s): 1450134 (species)

SI-ID 400073

DSM 103927

Section

Stenotrophomonas bentonitica BII-R7 is an aerobe, psychrophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil, bentonitic formation.

colony-forming
Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Stenotrophomonas*
	Species	**Stenotrophomonas bentonitica**
	Full Scientific Name (LPSN)	Stenotrophomonas bentonitica Sánchez-Castro et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43476]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #43476]	Cell length	0.92-1.55 µm

[Ref.: #43476]	Cell width	0.45-0.65 µm

[Ref.: #43476]	Cell shape	rod-shaped

[Ref.: #43476]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %93.256

[Ref.: #43476]	Colony color	light yellow
[Ref.: #43476]	Colony shape	circular
[Ref.: #43476]	Incubation period	3 days
[Ref.: #43476]	Cultivation medium used	Luria Bertani agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43476]

Culture medium

LB (Luria-Bertani) MEDIUM

[Ref.: #43476]

Culture medium growth

[Ref.: #42966]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #42966]

Culture medium growth

[Ref.: #42966]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42966]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #42966]		growth	28 °C
[Ref.: #43476]	no	growth	4 °C
[Ref.: #43476]	no	growth	40 °C
[Ref.: #43476]		growth	15-37 °C
[Ref.: #43476]		optimum	28 °C

[Ref.: #42966]	Temperature range	mesophilic
[Ref.: #43476]	Temperature range	psychrophilic
[Ref.: #43476]	Temperature range	thermophilic
[Ref.: #43476]	Temperature range	mesophilic

	Kind of pH		pH
[Ref.: #43476]		optimum	7
[Ref.: #43476]	no	growth	12
[Ref.: #43476]		growth	5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43476]

Oxygen tolerance

aerobe

[Ref.: #43476]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43476]		NaCl	no	growth	5	%
[Ref.: #43476]		NaCl		growth	0-2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43476]	2-oxoglutarate ChEBI	-	assimilation
[Ref.: #43476]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43476]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #43476]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43476]	4-nitrophenyl alpha-D-glucopyranoside ChEBI	+	hydrolysis
[Ref.: #43476]	4-nitrophenyl beta-D-glucopyranoside ChEBI	+	hydrolysis
[Ref.: #43476]	4-nitrophenyl beta-D-glucuronide ChEBI	-	hydrolysis
[Ref.: #43476]	4-nitrophenyl beta-D-xylopyranoside ChEBI	+	hydrolysis
[Ref.: #43476]	acetate ChEBI	+	carbon source
[Ref.: #43476]	adipate ChEBI	-	assimilation
[Ref.: #43476]	arbutin ChEBI	+	assimilation
[Ref.: #43476]	azelaate ChEBI	-	assimilation
[Ref.: #43476]	beta-alanine ChEBI	-	assimilation
[Ref.: #43476]	bis-4-nitrophenyl phosphate ChEBI	+	hydrolysis
[Ref.: #43476]	bis-4-nitrophenyl-phosphorylcholine ChEBI	+	hydrolysis
[Ref.: #43476]	cellobiose ChEBI	-	builds acid from
[Ref.: #43476]	cellobiose ChEBI	+	assimilation
[Ref.: #43476]	cis-aconitate ChEBI	-	assimilation
[Ref.: #43476]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43476]	D-fructose ChEBI	-	assimilation
[Ref.: #43476]	D-galactose ChEBI	-	assimilation
[Ref.: #43476]	D-gluconate ChEBI	-	assimilation
[Ref.: #43476]	D-glucose ChEBI	+	builds acid from
[Ref.: #43476]	D-glucose ChEBI	+	carbon source
[Ref.: #43476]	D-mannitol ChEBI	-	assimilation
[Ref.: #43476]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43476]	D-mannose ChEBI	+	builds acid from
[Ref.: #43476]	D-mannose ChEBI	+	carbon source
[Ref.: #43476]	D-ribose ChEBI	+	carbon source
[Ref.: #43476]	D-xylose ChEBI	-	builds acid from
[Ref.: #43476]	D-xylose ChEBI	+	assimilation
[Ref.: #43476]	DL-2-gamma-aminobutyrate	-	assimilation
[Ref.: #43476]	esculin ChEBI	+	hydrolysis
[Ref.: #43476]	fumarate ChEBI	+	carbon source
[Ref.: #43476]	galactitol ChEBI	-	builds acid from
[Ref.: #43476]	glutaric acid ChEBI	+	assimilation
[Ref.: #43476]	itaconate ChEBI	-	assimilation
[Ref.: #43476]	L-alanine ChEBI	-	assimilation
[Ref.: #43476]	L-alanine 4-nitroanilide	+	hydrolysis
[Ref.: #43476]	L-arabinose ChEBI	-	assimilation
[Ref.: #43476]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43476]	L-aspartate ChEBI	-	assimilation
[Ref.: #43476]	L-glutamate-gamma-3-carboxy-4-nitroanilide	+	hydrolysis
[Ref.: #43476]	L-histidine ChEBI	-	assimilation
[Ref.: #43476]	L-leucine ChEBI	-	assimilation
[Ref.: #43476]	L-ornithine ChEBI	-	assimilation
[Ref.: #43476]	L-phenylalanine ChEBI	-	assimilation
[Ref.: #43476]	L-proline ChEBI	-	assimilation
[Ref.: #43476]	L-proline-4-nitroanilide	+	hydrolysis
[Ref.: #43476]	L-rhamnose ChEBI	-	assimilation
[Ref.: #43476]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43476]	L-serine ChEBI	-	assimilation
[Ref.: #43476]	L-tryptophan ChEBI	-	assimilation
[Ref.: #43476]	lactate ChEBI	+	carbon source
[Ref.: #43476]	lactose ChEBI	-	builds acid from
[Ref.: #43476]	malate ChEBI	+	carbon source
[Ref.: #43476]	maltitol ChEBI	-	assimilation
[Ref.: #43476]	maltose ChEBI	+	builds acid from
[Ref.: #43476]	maltose ChEBI	+	carbon source
[Ref.: #43476]	melibiose ChEBI	-	builds acid from
[Ref.: #43476]	melibiose ChEBI	+	assimilation
[Ref.: #43476]	mesaconate ChEBI	-	assimilation
[Ref.: #43476]	methyl D-glucoside ChEBI	-	builds acid from
[Ref.: #43476]	myo-inositol ChEBI	-	assimilation
[Ref.: #43476]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43476]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #43476]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #43476]	nitrate ChEBI	+	reduction
[Ref.: #43476]	O-nitrophenyl-beta-D-galactopyranosid	+	hydrolysis
[Ref.: #43476]	p-nitrophenyl phenyl phosphonate ChEBI	+	hydrolysis
[Ref.: #43476]	phenylacetate ChEBI	-	assimilation
[Ref.: #43476]	propionate ChEBI	+	carbon source
[Ref.: #43476]	putrescine ChEBI	-	assimilation
[Ref.: #43476]	pyruvate ChEBI	+	carbon source
[Ref.: #43476]	raffinose ChEBI	-	builds acid from
[Ref.: #43476]	ribitol ChEBI	-	assimilation
[Ref.: #43476]	ribitol ChEBI	-	builds acid from
[Ref.: #43476]	salicin ChEBI	+	carbon source
[Ref.: #43476]	sorbitol ChEBI	-	assimilation
[Ref.: #43476]	sorbitol ChEBI	-	builds acid from
[Ref.: #43476]	suberic acid ChEBI	-	assimilation
[Ref.: #43476]	sucrose ChEBI	-	assimilation
[Ref.: #43476]	trans-aconitate ChEBI	-	assimilation
[Ref.: #43476]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43476]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43476]	acid phosphatase	+	3.1.3.2
[Ref.: #43476]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43476]	beta-galactosidase	+/-	3.2.1.23
[Ref.: #43476]	catalase	+	1.11.1.6
[Ref.: #43476]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43476]	esterase	+
[Ref.: #43476]	esterase Lipase (C 8)	+
[Ref.: #43476]	leucine arylamidase	+	3.4.11.1
[Ref.: #43476]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43476]	protease	+
[Ref.: #43476]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43476]

Fatty acid	Percentage	ECL
C15:0 iso	23.8
C15:0 anteiso	19.4
C16:0	9.4
C16:1ω7c / C15:0 iso 2OH	9.2
C17:1 iso ω9c	7.5
C16:0 iso	4
C11:0 iso	3.7
C12:0 3OH	3.6
C13:0 iso 3OH	3.2
C17:0 iso	2.8
C16:1ω9c	2.3
C14:0	2.3
C11:0 iso 3OH	2
C13:0 2OH	1.7
cyclo-C17:0	1.7
C14:0 iso	1.4
C15:1 iso	1.1
Unknown ECL 11.799	1	11799
C15:0	0.9

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

[Ref.: #42966]	Sample type/isolated from	soil, bentonitic formation
[Ref.: #42966]	Geographic location (country and/or sea, region)	Almeria
[Ref.: #42966]	Country	Spain
[Ref.: #42966]	Country ISO 3 Code	ESP
[Ref.: #42966]	Continent	Europe

[Ref.: #43476]	Sample type/isolated from	Bentonite formations
[Ref.: #43476]	Geographic location (country and/or sea, region)	Southern Spain
[Ref.: #43476]	Country	Spain
[Ref.: #43476]	Country ISO 3 Code	ESP
[Ref.: #43476]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LT622838 (>99% sequence identity) for Stenotrophomonas from Microbeatlas

Aquatic Samples	14518
Soil Samples	24235
Animal Samples	31589
Plant Samples	10577
Total Samples	80919

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

[Ref.: #42966]

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.: #42966]	Stenotrophomonas sp. BIIR7 partial 16S rRNA gene, isolate BIIR7	LT622838	1385	ENA	1904462 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Stenotrophomonas bentonitica DSM 103927	GCA_013185915	scaffold	GenBank	1450134 tax ID	*
[Ref.: #66792]	Stenotrophomonas bentonitica strain DSM 103927	1450134.7	wgs	PATRIC	1450134 tax ID	*

[Ref.: #43476]	GC-content	66.5 mol%
[Ref.: #42966]	GC-content	66.5 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: Stenotrophomonas bentonitica DSM 103927 NCBI: GCA_013185915.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Stenotrophomonas bentonitica DSM 103927 NCBI: GCA_013185915.1
[Ref.: #69480]	flagellated	no	86.557	yes
[Ref.: #69480]	gram-positive	no	98.076	yes
[Ref.: #69480]	anaerobic	no	98.43	yes
[Ref.: #69480]	aerobic	yes	91.397	yes
[Ref.: #69480]	halophile	no	95.879	no
[Ref.: #69480]	spore-forming	no	95.003	no
[Ref.: #69480]	glucose-util	yes	89.972	yes
[Ref.: #69480]	thermophile	no	99.522	no
[Ref.: #69480]	motile	yes	84.738	yes
[Ref.: #69480]	glucose-ferment	no	91.276	no

Availability in culture collections External links

[Ref.: #42966]

Culture collection no.

DSM 103927, CECT 9180, LMG 29893

[Ref.: #96657]

SI-ID 400073

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Stenotrophomonas nematodicola sp. nov., isolated from Caenorhabditis elegans.	Wei X, Lei S, Deng Y, Zhang Y, Zhang L, Niu Q	Arch Microbiol	10.1007/s00203-021-02586-y	2021	*
Transcriptome	Multisystem combined uranium resistance mechanisms and bioremediation potential of Stenotrophomonas bentonitica BII-R7: Transcriptomics and microscopic study.	Pinel-Cabello M, Jroundi F, Lopez-Fernandez M, Geffers R, Jarek M, Jauregui R, Link A, Vilchez-Vargas R, Merroun ML	J Hazard Mater	10.1016/j.jhazmat.2020.123858	2020	*
Phylogeny	Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations.	Sanchez-Castro I, Ruiz-Fresneda MA, Bakkali M, Kampfer P, Glaeser SP, Busse HJ, Lopez-Fernandez M, Martinez-Rodriguez P, Merroun ML	Int J Syst Evol Microbiol	10.1099/ijsem.0.002016	2017	*
Genetics	Draft Genome Sequence of Stenotrophomonas bentonitica BII-R7(T), a Selenite-Reducing Bacterium Isolated from Spanish Bentonites.	Sanchez-Castro I, Bakkali M, Merroun ML	Genome Announc	10.1128/genomeA.00719-17	2017	*
Biotechnology	Genetic mechanisms for Se(VI) reduction and synthesis of trigonal 1-D nanostructures in Stenotrophomonas bentonitica: Perspectives in eco-friendly nanomaterial production and bioremediation.	Pinel-Cabello M, Jauregui R, Jroundi F, Geffers R, Jarek M, Link A, Vilchez-Vargas R, Merroun ML	Sci Total Environ	10.1016/j.scitotenv.2022.160635	2022	*
	Delineation of cellular stages and identification of key proteins for reduction and biotransformation of Se(IV) by Stenotrophomonas bentonitica BII-R7.	Pinel-Cabello M, Chapon V, Ruiz-Fresneda MA, Alpha-Bazin B, Berthomieu C, Armengaud J, Merroun ML	J Hazard Mater	10.1016/j.jhazmat.2021.126150	2021	*

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 )

#42966

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103927

#43476

Ivan Sanchez-Castro, Miguel Angel Ruiz-Fresneda, Mohammed Bakkali, Peter Kaempfer, Stefanie P. Glaeser, Hans Jürgen Busse, Margarita López-Fern andez, Pablo Martínez-Rodríguez, Mohamed Larbi Merroun: Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations. IJSEM 67: 2779 - 2786 2017 ( DOI 10.1099/ijsem.0.002016 , PubMed 28820086 )

#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) .

#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 )

#96657

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-ID400073.1 )

* These data were automatically processed and therefore are not curated

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Stenotrophomonas bentonitica DSM 103927

Stenotrophomonas bentonitica DSM 103927

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