Name: Paenibacillus azotifigens NF2-4-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 141156

Type strain:

Species: Paenibacillus azotifigens

Strain Designation: NF2-4-5

Culture col. no.: KACC 18967, LMG 29963, DSM 104138

Strain history: <- W.-T. Im, Hankyong National University, Anseong-si, Republic of Korea; NF2-4-5

NCBI tax ID(s): 2047734 (species)

SI-ID 403211

DSM 104138

Section

Paenibacillus azotifigens NF2-4-5 is an aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from paddy soil.

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Paenibacillus*
	Species	**Paenibacillus azotifigens**
	Full Scientific Name (LPSN)	Paenibacillus azotifigens Siddiqi et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #44077]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #44077]	Cell length	1.5-3 µm

[Ref.: #44077]	Cell width	0.5-1.2 µm

[Ref.: #44077]	Cell shape	rod-shaped

[Ref.: #44077]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.332

[Ref.: #44077]	Colony size	1.5-2.4 mm
[Ref.: #44077]	Colony color	milky-coloured
[Ref.: #44077]	Colony shape	circular
[Ref.: #44077]	Incubation period	2 days
[Ref.: #44077]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

NA agar

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

Dnase agar

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

MacConkey

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #44077]		optimum	30 °C
[Ref.: #44077]		growth	18-37 °C
[Ref.: #44077]	no	growth	15 °C
[Ref.: #44077]	no	growth	40 °C
[Ref.: #64983]		growth	30 °C

[Ref.: #44077]	Temperature range	mesophilic
[Ref.: #44077]	Temperature range	psychrophilic
[Ref.: #44077]	Temperature range	thermophilic
[Ref.: #64983]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #44077]			optimum	6.5-7.0
[Ref.: #44077]			growth	6.0-8.5

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #44077]	Spore description	ellipsoidal spores located subterminally in swollen sporangia
[Ref.: #44077]	Type of spore	endospore
[Ref.: #44077]	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

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44077]		NaCl		growth	0.5-2.0	%
[Ref.: #44077]		NaCl	no	growth	3	%

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Observation

nitrogen fixation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44077]	2-oxogluconate	+	assimilation
[Ref.: #44077]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #44077]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #44077]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #44077]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #44077]	acetate ChEBI	-	assimilation
[Ref.: #44077]	adipate ChEBI	-	assimilation
[Ref.: #44077]	citrate ChEBI	-	assimilation
[Ref.: #44077]	D-glucose ChEBI	+	assimilation
[Ref.: #44077]	D-mannitol ChEBI	+	assimilation
[Ref.: #44077]	D-mannose ChEBI	+	assimilation
[Ref.: #44077]	D-ribose ChEBI	+	assimilation
[Ref.: #44077]	D-sorbitol ChEBI	-	assimilation
[Ref.: #44077]	decanoate ChEBI	-	assimilation
[Ref.: #44077]	esculin ChEBI	+	hydrolysis
[Ref.: #44077]	gelatin ChEBI	-	hydrolysis
[Ref.: #44077]	gluconate ChEBI	+	assimilation
[Ref.: #44077]	glucose ChEBI	-	builds acid from
[Ref.: #44077]	glycogen ChEBI	+	assimilation
[Ref.: #44077]	itaconate ChEBI	-	assimilation
[Ref.: #44077]	L-alanine ChEBI	-	assimilation
[Ref.: #44077]	L-arabinose ChEBI	+	assimilation
[Ref.: #44077]	L-fucose ChEBI	-	assimilation
[Ref.: #44077]	L-histidine ChEBI	-	assimilation
[Ref.: #44077]	L-proline ChEBI	-	assimilation
[Ref.: #44077]	L-rhamnose ChEBI	-	assimilation
[Ref.: #44077]	L-serine ChEBI	-	assimilation
[Ref.: #44077]	lactate ChEBI	-	assimilation
[Ref.: #44077]	malate ChEBI	-	assimilation
[Ref.: #44077]	malonate ChEBI	-	assimilation
[Ref.: #44077]	maltose ChEBI	+	assimilation
[Ref.: #44077]	melibiose ChEBI	+	assimilation
[Ref.: #44077]	myo-inositol ChEBI	-	assimilation
[Ref.: #44077]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #44077]	nitrate ChEBI	+	reduction
[Ref.: #44077]	phenylacetate ChEBI	-	assimilation
[Ref.: #44077]	propionate ChEBI	-	assimilation
[Ref.: #44077]	salicin ChEBI	+	assimilation
[Ref.: #44077]	suberic acid ChEBI	-	assimilation
[Ref.: #44077]	sucrose ChEBI	+	assimilation
[Ref.: #44077]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #44077]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #44077]	acid phosphatase	+	3.1.3.2
[Ref.: #44077]	alkaline phosphatase	+	3.1.3.1
[Ref.: #44077]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #44077]	alpha-fucosidase	+	3.2.1.51
[Ref.: #44077]	alpha-galactosidase	+	3.2.1.22
[Ref.: #44077]	alpha-glucosidase	+	3.2.1.20
[Ref.: #44077]	alpha-mannosidase	+	3.2.1.24
[Ref.: #44077]	arginine dihydrolase	-	3.5.3.6
[Ref.: #44077]	beta-galactosidase	+	3.2.1.23
[Ref.: #44077]	beta-glucosidase	+	3.2.1.21
[Ref.: #44077]	beta-glucuronidase	-	3.2.1.31
[Ref.: #44077]	catalase	+	1.11.1.6
[Ref.: #44077]	cystine arylamidase	-	3.4.11.3
[Ref.: #44077]	cytochrome oxidase	+	1.9.3.1
[Ref.: #44077]	esterase	+
[Ref.: #44077]	esterase Lipase (C 8)	+
[Ref.: #44077]	leucine arylamidase	+	3.4.11.1
[Ref.: #44077]	lipase	-
[Ref.: #44077]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #44077]	trypsin	-	3.4.21.4
[Ref.: #44077]	urease	-	3.5.1.5
[Ref.: #44077]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #44077]	Sample type/isolated from	paddy soil
[Ref.: #44077]	Country	Republic of Korea
[Ref.: #44077]	Country ISO 3 Code	KOR
[Ref.: #44077]	Continent	Asia
[Ref.: #44077]	Enrichment culture	nitrogen-free medium (Cavalcante and Doëbereiner, 1988)
[Ref.: #44077]	Enrichment culture composition	composition g per litre of water: 2g sucrose, 5g dextrose, 3g mannitol, 1g malic acid, 1g citric acid, 1g sodium acetate, 0.2g K2HPO4, 0.6g KH2PO4 , 0.2g MgSO4 . 7H2O, 0.02g CaCl2 2H2O, 0.002g Na2 MoO4 and 1ml vitamin solution
[Ref.: #44077]	Enrichment culture duration	7 days
[Ref.: #44077]	Enrichment culture temperature	30 ̊C
[Ref.: #44077]	Isolation/enrichment procedure	One gram of soil was placed in 10ml (0.85% NaCl) sterile saline and stirred for 10min. An aqueous volume of 100µl of the mixture was spread on nitrogen-free medium

[Ref.: #64983]	Sample type/isolated from	paddy soil
[Ref.: #64983]	Geographic location (country and/or sea, region)	Anseoung city
[Ref.: #64983]	Country	Republic of Korea
[Ref.: #64983]	Country ISO 3 Code	KOR
[Ref.: #64983]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

What are isolation sources categories?

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

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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.: #64983]	Paenibacillus azotifigens strain NF2-4-5 16S ribosomal RNA gene, partial sequence	KX510118	1481	ENA	2047734 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paenibacillus azotifigens LMG 29963	GCA_008635805	scaffold	GenBank	2047734 tax ID	*
[Ref.: #66792]	Paenibacillus azotifigens strain LMG 29963	2047734.3	wgs	PATRIC	2047734 tax ID	*
[Ref.: #66792]	Paenibacillus azotifigens LMG 29963	2904120120	draft	JGI IMG/M	2047734 tax ID	*

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GC-content

56.3 mol%

high performance liquid chromatography (HPLC)

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 azotifigens LMG 29963 NCBI: GCA_008635805.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paenibacillus azotifigens LMG 29963 NCBI: GCA_008635805.1
[Ref.: #69480]	motile	yes	87.426	yes
[Ref.: #69480]	flagellated	yes	81.249	no
[Ref.: #69480]	gram-positive	yes	88.222	no
[Ref.: #69480]	anaerobic	no	95.49	no
[Ref.: #69480]	aerobic	yes	86.402	yes
[Ref.: #69480]	halophile	no	94.994	no
[Ref.: #69480]	spore-forming	yes	95.748	yes
[Ref.: #69480]	thermophile	no	99.91	no
[Ref.: #69480]	glucose-util	yes	91.03	yes
[Ref.: #69480]	glucose-ferment	no	80.937	no

Availability in culture collections External links

[Ref.: #64983]

Culture collection no.

KACC 18967, LMG 29963, DSM 104138

[Ref.: #96871]

SI-ID 403211

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus helianthi sp. nov., a nitrogen fixing species isolated from the rhizosphere of Helianthus annuus L.	Ambrosini A, Sant'Anna FH, Heinzmann J, de Carvalho Fernandes G, Bach E, Passaglia LMP	Antonie Van Leeuwenhoek	10.1007/s10482-018-1135-4	2018	*
Phylogeny	Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.	Siddiqi MZ, Choi GM, Choi KD, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.002269	2017	*
Phylogeny	Description of Paenibacillus yunnanensis sp. nov., Isolated from a Tepid Spring.	Narsing Rao MP, Dong ZY, Amoolya S, Neelavar S, Liu BB, Guo SX, Hozzein W, Li WJ	Curr Microbiol	10.1007/s00284-020-02087-z	2020	*
Phylogeny	Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring.	Narsing Rao MP, Dong ZY, Kan Y, Dong L, Li S, Xiao M, Kang YQ, Zhang K, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004004	2020	*

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 )

#44077

Muhammad Zubair Siddiqi, Gyu-Min Choi, Kang Duk Choi and Wan-Taek Im: Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil. IJSEM 67: 4917 - 4922 2017 ( DOI 10.1099/ijsem.0.002269 , PubMed 29039306 )

#64983

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104138

#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) .

#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 )

#96871

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-ID403211.1 )

* These data were automatically processed and therefore are not curated

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Paenibacillus azotifigens LMG 29963

Paenibacillus azotifigens LMG 29963

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