Name: Paenibacillus azotofixans P3 L-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11504

Type strain:

Species: Paenibacillus azotofixans

Strain Designation: P3 L-5

Culture col. no.: DSM 5976, ATCC 35681, LMG 14658, CIP 104586

Strain history: CIP <- 1995, DSM <- ATCC <- L. Seldin: strain P3 L-5

NCBI tax ID(s): 44251 (species)

SI-ID 92131

LMG 9815, ATCC 35681, DSM 5976, LMG 14658, NCIMB 12093, NRRL B-14372, CCUG 28518, CIP 104586, KCTC 3740, BCRC 15905, CCRC 15905, CCT 4719, NCAIM B.01947

Section

Paenibacillus azotofixans P3 L-5 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from wheat roots.

motile
spore-forming
facultative anaerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus azotofixans**
	Full Scientific Name (LPSN)	Paenibacillus azotofixans (Seldin et al. 1984) Ash et al. 1994

Synonym

Bacillus azotofixans

Information on morphological and physiological properties Morphology

[Ref.: #116691]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #116691]	Cell shape	rod-shaped

[Ref.: #116691]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.825

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2403]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #2403]

Culture medium growth

[Ref.: #2403]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2403]

Culture medium composition

expand / minimize

[Ref.: #39058]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #39058]

Culture medium growth

[Ref.: #39058]

Culture medium composition

expand / minimize

[Ref.: #116691]

Culture medium

CIP Medium 3

[Ref.: #116691]

Culture medium growth

[Ref.: #116691]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #2403]		growth	30 °C
[Ref.: #39058]		growth	30 °C
[Ref.: #116691]		growth	30-37 °C
[Ref.: #116691]	no	growth	10 °C
[Ref.: #116691]	no	growth	45 °C
[Ref.: #116691]	no	growth	55 °C

[Ref.: #2403]	Temperature range	mesophilic
[Ref.: #39058]	Temperature range	mesophilic
[Ref.: #116691]	Temperature range	mesophilic
[Ref.: #116691]	Temperature range	psychrophilic
[Ref.: #116691]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #116691]			growth	6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #116691]

Oxygen tolerance

facultative anaerobe

[Ref.: #116691]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #116691]	citrate ChEBI	-	carbon source
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #116691]	nitrate ChEBI	-	reduction
[Ref.: #116691]	nitrate ChEBI	+	respiration
[Ref.: #116691]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116691]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #116691]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116691]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116691]	amylase	-
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116691]	caseinase	-	3.4.21.50
[Ref.: #116691]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #116691]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #116691]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116691]	lysine decarboxylase	+	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116691]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116691]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116691]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #116691]	9670	not determinedn.d.	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	+	-	+	+	-	+	-	+	+	+	+	+	+	-	+	+	+	+	+	+	+	+	-	+	+	-	-	-	-	-	-	+	+	+

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116691]	8055	-	-	+	+	-	-	-	-	-	-	+	+	+	-	-	+	+	-	-	-

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

[Ref.: #2403]	Sample type/isolated from	wheat roots

[Ref.: #116691]	Sample type/isolated from	Food, Wheat roots
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ251195 (>99% sequence identity) for Paenibacillus durus from Microbeatlas

Aquatic Samples	1
Soil Samples	2
Animal Samples	6
Plant Samples	3
Total Samples	12

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

[Ref.: #2403]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116691]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Paenibacillus durus gene for 16S rRNA, partial sequence	AB073195	1505	ENA	44251 tax ID	*
[Ref.: #20218]	Paenibacillus azotofixans 16S rRNA gene, strain ATCC 35681T, isolate P3L-5	AJ251192	1484	ENA	44251 tax ID	*
[Ref.: #20218]	Paenibacillus azotofixans 16S rRNA gene, strain LMG 14658T, isolate P3L-5	AJ251195	1484	ENA	44251 tax ID	*
[Ref.: #20218]	B.azotofixans 16S ribosomal RNA	X60608	1432	ENA	44251 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus durus ATCC 35681	GCA_000993825	complete	GenBank	1333534 tax ID	*
[Ref.: #66792]	Paenibacillus durus ATCC 35681	GCA_000520635	contig	GenBank	1333534 tax ID	*
[Ref.: #66792]	Paenibacillus azotofixans ATCC 35681	1333534.3	wgs	PATRIC	1333534 tax ID	*
[Ref.: #66792]	Paenibacillus durus ATCC 35681	1333534.5	complete	PATRIC	1333534 tax ID	*
[Ref.: #66792]	Paenibacillus durus ATCC 35681	2619619294	complete	JGI IMG/M	1333534 tax ID	*

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: Paenibacillus durus ATCC 35681 PATRIC: 1333534.5
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus durus ATCC 35681 ATCC 35681 NCBI: GCA_000993825.1
[Ref.: #69480]	motile	yes	84.282	no
[Ref.: #69480]	flagellated	yes	86.377	no
[Ref.: #69480]	gram-positive	yes	87.187	no
[Ref.: #69480]	anaerobic	no	83.401	no
[Ref.: #69480]	aerobic	no	51.854	no
[Ref.: #69480]	halophile	no	97.83	no
[Ref.: #69480]	spore-forming	yes	97.349	no
[Ref.: #69480]	thermophile	no	99.355	no
[Ref.: #69480]	glucose-util	yes	89.469	no
[Ref.: #69480]	glucose-ferment	no	83.092	no

Availability in culture collections External links

[Ref.: #2403]

Culture collection no.

DSM 5976, ATCC 35681, LMG 14658, CIP 104586

[Ref.: #80736]

SI-ID 92131

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genomic metrics analyses indicate that Paenibacillus azotofixans is not a later synonym of Paenibacillus durus.	Guella F, Porto RZ, Sant'Anna FH, Ambrosini A, Passaglia LMP	Int J Syst Evol Microbiol	10.1099/ijsem.0.003572	2019	*
Phylogeny	Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans.	Ma Y, Zhang J, Chen S	Int J Syst Evol Microbiol	10.1099/ijs.0.64652-0	2007	*
Phylogeny	Paenibacillus stellifer sp. nov., a cyclodextrin-producing species isolated from paperboard.	Suominen I, Sproer C, Kampfer P, Rainey FA, Lounatmaa K, Salkinoja-Salonen M	Int J Syst Evol Microbiol	10.1099/ijs.0.02277-0	2003	*

References

#2403

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5976

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#39058 ; Curators of the CIP;

#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) .

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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 )

#80736

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-ID92131.1 )

#116691 Collection of Institut Pasteur ; Curators of the CIP; CIP 104586
* These data were automatically processed and therefore are not curated

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Paenibacillus durus ATCC 35681

Paenibacillus durus ATCC 35681 ATCC 35681

Change proposal

Change proposal