Paenibacillus azotifigens (KACC 18967, LMG 29963, DSM 104138)

Name: Paenibacillus azotifigens (KACC 18967, LMG 29963, DSM 104138)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141156

Type strain

Strain Designation NF2-4-5

Culture col. no. KACC 18967 LMG 29963 DSM 104138 NF2-4-5

NCBI tax ID(s) 2047734

Special Collections DSMZ Literature strains

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

Links

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

spore-forming Gram-positive motile rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403211

LMG 29963,DSM 104138

@ref 20215

Last LPSN update 2026-02-09 11:33:50

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus azotifigens

Full scientific name Paenibacillus azotifigens Siddiqi et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
44077	positive	1.5-3 µm	0.5-1.2 µm	rod-shaped
125439						91.3

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
44077	1.5-2.4 mm	milky-coloured	circular	2 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
44077	NA agar
44077	Reasoner's 2A agar (R2A)
44077	Trypticase Soy Agar (TSA)
64983	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
44077	Dnase agar
44077	LB (Luria-Bertani) MEDIUM
44077	MacConkey

Culture temp

@ref	Growth	Type	Temperature (°C)
44077	positive	optimum	30
44077	positive	growth	18-37
44077	negative	growth	15
44077	negative	growth	40
64983	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
44077	positive	optimum	6.5-7.0
44077	positive	growth	6.0-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44077	aerobe
125439	aerobe	91.7

Spore formation

@ref	Spore description	Type of spore	Confidence
44077	ellipsoidal spores located subterminally in swollen sporangia	endospore
125439			96.2
125438			90.375

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44077	NaCl	positive	growth	0.5-2.0 %
44077	NaCl		growth	3 %

Observation

44077

Observationnitrogen fixation

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44077		2-oxogluconate	+	assimilation
44077	16193 ChEBI	3-hydroxybenzoate	-	assimilation
44077	37054 ChEBI	3-hydroxybutyrate	-	assimilation
44077	17879 ChEBI	4-hydroxybenzoate	-	assimilation
44077	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
44077	30089 ChEBI	acetate	-	assimilation
44077	17128 ChEBI	adipate	-	assimilation
44077	16947 ChEBI	citrate	-	assimilation
44077	17634 ChEBI	D-glucose	+	assimilation
44077	16899 ChEBI	D-mannitol	+	assimilation
44077	16024 ChEBI	D-mannose	+	assimilation
44077	16988 ChEBI	D-ribose	+	assimilation
44077	17924 ChEBI	D-sorbitol	-	assimilation
44077	27689 ChEBI	decanoate	-	assimilation
44077	4853 ChEBI	esculin	+	hydrolysis
44077	5291 ChEBI	gelatin	-	hydrolysis
44077	24265 ChEBI	gluconate	+	assimilation
44077	17234 ChEBI	glucose	-	builds acid from
44077	28087 ChEBI	glycogen	+	assimilation
44077	17240 ChEBI	itaconate	-	assimilation
44077	16977 ChEBI	L-alanine	-	assimilation
44077	30849 ChEBI	L-arabinose	+	assimilation
44077	18287 ChEBI	L-fucose	-	assimilation
44077	15971 ChEBI	L-histidine	-	assimilation
44077	17203 ChEBI	L-proline	-	assimilation
44077	62345 ChEBI	L-rhamnose	-	assimilation
44077	17115 ChEBI	L-serine	-	assimilation
44077	24996 ChEBI	lactate	-	assimilation
44077	25115 ChEBI	malate	-	assimilation
44077	15792 ChEBI	malonate	-	assimilation
44077	17306 ChEBI	maltose	+	assimilation
44077	28053 ChEBI	melibiose	+	assimilation
44077	17268 ChEBI	myo-inositol	-	assimilation
44077	506227 ChEBI	N-acetylglucosamine	-	assimilation
44077	17632 ChEBI	nitrate	+	reduction
44077	18401 ChEBI	phenylacetate	-	assimilation
44077	17272 ChEBI	propionate	-	assimilation
44077	17814 ChEBI	salicin	+	assimilation
44077	9300 ChEBI	suberic acid	-	assimilation
44077	17992 ChEBI	sucrose	+	assimilation
44077	31011 ChEBI	valerate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
44077	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
44077	acid phosphatase	+	3.1.3.2
44077	alkaline phosphatase	+	3.1.3.1
44077	alpha-chymotrypsin	-	3.4.21.1
44077	alpha-fucosidase	+	3.2.1.51
44077	alpha-galactosidase	+	3.2.1.22
44077	alpha-glucosidase	+	3.2.1.20
44077	alpha-mannosidase	+	3.2.1.24
44077	arginine dihydrolase	-	3.5.3.6
44077	beta-galactosidase	+	3.2.1.23
44077	beta-glucosidase	+	3.2.1.21
44077	beta-glucuronidase	-	3.2.1.31
44077	catalase	+	1.11.1.6
44077	cystine arylamidase	-	3.4.11.3
44077	cytochrome oxidase	+	1.9.3.1
44077	esterase	+
44077	esterase Lipase (C 8)	+
44077	leucine arylamidase	+	3.4.11.1
44077	lipase	-
44077	naphthol-AS-BI-phosphohydrolase	+
44077	trypsin	-	3.4.21.4
44077	urease	-	3.5.1.5
44077	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure	Geographic location
44077	paddy soil	Republic of Korea	KOR	Asia	nitrogen-free medium (Cavalcante and Doëbereiner, 1988)	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	7 days	30	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
64983	paddy soil	Republic of Korea	KOR	Asia						Anseoung city

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64983	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
66792	ASM863580v1 assembly for Paenibacillus azotifigens LMG 29963	scaffold	GCA_008635805	2047734.6	2904120120	2047734
66792	Paenibacillus azotifigens strain LMG 29963	contig		2047734.3		2047734

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64983	Paenibacillus azotifigens strain NF2-4-5 16S ribosomal RNA gene, partial sequence	KX510118	1481		2047734

GC content

@ref	GC-content (mol%)	Method
64983	56.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus azotifigens LMG 29963
NCBI: GCA_008635805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	96.20	no
125439	motility	BacteriaNetⓘ	yes	91.30	no
125439	gram_stain	BacteriaNetⓘ	variable	88.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus azotifigens LMG 29963
NCBI: GCA_008635805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	67.00	yes
125438	anaerobic	anaerobicⓘ	no	91.29	yes
125438	aerobic	aerobicⓘ	yes	50.86	no
125438	spore-forming	spore-formingⓘ	yes	90.38	yes
125438	thermophilic	thermophileⓘ	no	94.91	no
125438	flagellated	motile2+ⓘ	yes	81.70	no

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) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Paenibacillus azotifigens (KACC 18967, LMG 29963, DSM 104138)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_008635805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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