Name: Allorhizobium borbori DN316
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13641

Type strain:

Species: Allorhizobium borbori

Strain Designation: DN316

Culture col. no.: DSM 26385, CICC 10378, HAMBI 3454, LMG 23925

Strain history: <- LMG <- G. Sun <- R. Suizhou, Guangdong Inst. Microbiology, China

NCBI tax ID(s): 485907 (species)

SI-ID 377102

LMG 23925, DSM 22790, LMG 25371

Section

Allorhizobium borbori DN316 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of a textile-printing wastewater-treatment plant.

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	*Allorhizobium*
	Species	**Allorhizobium borbori**
	Full Scientific Name (LPSN)	Allorhizobium borbori (Zhang et al. 2011) Mousavi et al. 2016

	Synonym	"Ectorhizobium* borbori"*
	Synonym	Rhizobium borbori

Information on morphological and physiological properties Morphology

[Ref.: #29839]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #29839]	Cell shape	rod-shaped

[Ref.: #29839]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %90.769

[Ref.: #18209]	Type of hemolysis	gamma
[Ref.: #18209]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18209]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #18209]

Culture medium growth

[Ref.: #18209]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18209]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18209]	growth	30 °C
[Ref.: #29839]	growth	4.0-37 °C
[Ref.: #29839]	optimum	28 °C

[Ref.: #18209]	Temperature range	mesophilic
[Ref.: #29839]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29839]			optimum	6.9
[Ref.: #29839]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29839]

Oxygen tolerance

aerobe

[Ref.: #29839]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29839]		NaCl		growth	0.0-0.5	%
[Ref.: #29839]		NaCl		optimum	0.25	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29839]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29839]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29839]	cellobiose 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.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #29839]	fructose ChEBI	+	carbon source
[Ref.: #29839]	fucose ChEBI	+	carbon source
[Ref.: #29839]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29839]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #29839]	L-arabitol ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #29839]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #29839]	mannitol ChEBI	+	carbon source
[Ref.: #29839]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #29839]	propionate ChEBI	+	carbon source
[Ref.: #29839]	sorbitol ChEBI	+	carbon source
[Ref.: #29839]	sucrose ChEBI	+	carbon source
[Ref.: #29839]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
	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.: #18209]	catalase	+	1.11.1.6
[Ref.: #18209]	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.: #18209]	23932	+	-	-	-	+	+	-	+	+	+	+	+	-	+	-	-	-	+	+	-	not determinedn.d.

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

[Ref.: #18209]	Sample type/isolated from	activated sludge of a textile-printing wastewater-treatment plant
[Ref.: #18209]	Geographic location (country and/or sea, region)	Guangzhou
[Ref.: #18209]	Country	China
[Ref.: #18209]	Country ISO 3 Code	CHN
[Ref.: #18209]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Industrial wastewater
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF125187 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	179
Soil Samples	162
Animal Samples	35
Plant Samples	105
Total Samples	481

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

[Ref.: #18209]

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.: #18209]	Rhizobium borbori strain DN316 16S ribosomal RNA gene, partial sequence	EF125187	1353	ENA	485907 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Allorhizobium borbori DSM 26385	GCA_014196535	scaffold	GenBank	485907 tax ID	*
[Ref.: #66792]	Rhizobium borbori strain DSM 26385	485907.3	wgs	PATRIC	485907 tax ID	*
[Ref.: #66792]	Rhizobium borbori DSM 26385	2829903426	draft	JGI IMG/M	485907 tax ID	*
[Ref.: #66792]	Rhizobium borbori LMG 23925	2739367697	draft	JGI IMG/M	485907 tax ID	*

[Ref.: #18209]

GC-content

60.9 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 borbori DSM 26385 NCBI: GCA_014196535.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium borbori DSM 26385 NCBI: GCA_014196535.1
[Ref.: #69480]	flagellated	no	72.855	no
[Ref.: #69480]	gram-positive	no	98.199	yes
[Ref.: #69480]	anaerobic	no	94.471	no
[Ref.: #69480]	aerobic	yes	82.828	yes
[Ref.: #69480]	halophile	no	93.788	no
[Ref.: #69480]	spore-forming	no	95.998	yes
[Ref.: #69480]	glucose-util	yes	92.354	yes
[Ref.: #69480]	motile	yes	89.073	yes
[Ref.: #69480]	glucose-ferment	no	90.881	yes
[Ref.: #69480]	thermophile	no	98.824	yes

Availability in culture collections External links

[Ref.: #18209]

Culture collection no.

DSM 26385, CICC 10378, HAMBI 3454, LMG 23925

[Ref.: #82824]

SI-ID 377102

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.	Rozahon M, Ismayil N, Hamood B, Erkin R, Abdurahman M, Mamtimin H, Abdukerim M, Lal R, Rahman E	Int J Syst Evol Microbiol	10.1099/ijs.0.061416-0	2014	*
Phylogeny	Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis).	Kittiwongwattana C, Thawai C	Int J Syst Evol Microbiol	10.1099/ijs.0.051888-0	2013	*
Phylogeny	Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand.	Ramana CV, Parag B, Girija KR, Ram BR, Ramana VV, Sasikala C	Int J Syst Evol Microbiol	10.1099/ijs.0.041442-0	2012	*
Phylogeny	Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge.	Zhang GX, Ren SZ, Xu MY, Zeng GQ, Luo HD, Chen JL, Tan ZY, Sun GP	Int J Syst Evol Microbiol	10.1099/ijs.0.022228-0	2010	*

References

#18209

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26385

#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 )

#29839

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 #26215 (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 )

#82824

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-ID377102.1 )

#26215

IJSEM 816 2011 ( DOI 10.1099/ijs.0.022228-0 , PubMed 20453105 )

* These data were automatically processed and therefore are not curated

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Rhizobium borbori DSM 26385

Rhizobium borbori DSM 26385

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