Paenibacillus rhizophilus (DSM 103168, CGMCC 1.15699, 7197)

Name: Paenibacillus rhizophilus (DSM 103168, CGMCC 1.15699, 7197)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159374

Type strain

Strain Designation 7197

Culture col. no. DSM 103168 CGMCC 1.15699 7197

NCBI tax ID(s) 1850366

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Paenibacillus rhizophilus 7197 is an aerobe, spore-forming, mesophilic prokaryote that forms circular colonies and was isolated from rhizosphere soil of wheat.

spore-forming Gram-variable motile rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404197

DSM 103168

@ref 20215

Last LPSN update 2025-12-16 10:08:14

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus rhizophilus

Full scientific name Paenibacillus rhizophilus Ripa et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
68134	variable	3.0-5.0 µm	0.5-0.6 µm	rod-shaped		polar

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
68134	0.5 mm	whey-coloured	circular	3 days	Reasoner's 2A agar (R2A)
68134	1.5-2.5 mm	cream-coloured	circular	3 days	Trypticase Soy Agar (TSA)

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66197	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66197	positive	growth	30	mesophilic
68134	positive	growth	20-40
68134	positive	optimum	30	mesophilic

Culture pH

@ref	Ability	Type	PH
68134	positive	optimum	7
68134	positive	growth	6.0-7.0

Physiology and metabolism

Oxygen tolerance

68134

Oxygen toleranceaerobe

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
68134	Ellipsoidal subterminal	endospore
125438				93.089

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68134	NaCl	positive	growth	1.0-3.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68134		1 % sodium lactate	+	growth
68134	17128 ChEBI	adipate	-	assimilation
68134	17925 ChEBI	alpha-D-glucose	+	growth
68134	27613 ChEBI	amygdalin	+	builds acid from
68134	18305 ChEBI	arbutin	+	builds acid from
68134	161680 ChEBI	aztreonam	+	growth
68134	17057 ChEBI	cellobiose	+	builds acid from
68134	18333 ChEBI	D-arabitol	-	builds acid from
68134	15824 ChEBI	D-fructose	+	builds acid from
68134	15824 ChEBI	D-fructose	+	growth
68134	28847 ChEBI	D-fucose	-	builds acid from
68134	12936 ChEBI	D-galactose	+	builds acid from
68134	12936 ChEBI	D-galactose	+	growth
68134	17634 ChEBI	D-glucose	+	builds acid from
68134	17634 ChEBI	D-glucose	-	assimilation
68134	62318 ChEBI	D-lyxose	-	builds acid from
68134	16899 ChEBI	D-mannitol	+	builds acid from
68134	16899 ChEBI	D-mannitol	-	assimilation
68134	16899 ChEBI	D-mannitol	+	growth
68134	16024 ChEBI	D-mannose	+	builds acid from
68134	16024 ChEBI	D-mannose	+	assimilation
68134	16024 ChEBI	D-mannose	+	growth
68134	17924 ChEBI	D-sorbitol	+	builds acid from
68134	16443 ChEBI	D-tagatose	-	builds acid from
68134	23652 ChEBI	dextrin	+	growth
68134	4853 ChEBI	esculin	+	hydrolysis
68134		esculin ferric citrate	+	builds acid from
68134	5291 ChEBI	gelatin	-	hydrolysis
68134	28066 ChEBI	gentiobiose	+	builds acid from
68134	17234 ChEBI	glucose	-	fermentation
68134	28087 ChEBI	glycogen	+	builds acid from
68134	17120 ChEBI	hexanoate	-	assimilation
68134	15443 ChEBI	inulin	+	builds acid from
68134	30849 ChEBI	L-arabinose	-	assimilation
68134	18403 ChEBI	L-arabitol	+/-	builds acid from
68134	18287 ChEBI	L-fucose	-	builds acid from
68134	17716 ChEBI	lactose	+	builds acid from
68134	25115 ChEBI	malate	-	assimilation
68134	17306 ChEBI	maltose	+	builds acid from
68134	17306 ChEBI	maltose	-	assimilation
68134	6731 ChEBI	melezitose	+	builds acid from
68134	28053 ChEBI	melibiose	+	builds acid from
68134	28053 ChEBI	melibiose	+	growth
68134	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
68134	43943 ChEBI	methyl alpha-D-mannoside	+	builds acid from
68134	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from
68134	37657 ChEBI	methyl D-glucoside	+	growth
68134	51850 ChEBI	methyl pyruvate	+	growth
68134	59640 ChEBI	N-acetylglucosamine	+	builds acid from
68134	59640 ChEBI	N-acetylglucosamine	-	assimilation
68134	100147 ChEBI	nalidixic acid	+	growth
68134	17632 ChEBI	nitrate	-	reduction
68134	17309 ChEBI	pectin	+	growth
68134	18401 ChEBI	phenylacetate	-	assimilation
68134		potassium 2-dehydro-D-gluconate	+	builds acid from
68134		potassium 5-dehydro-D-gluconate	+	builds acid from
68134		potassium 5-dehydro-D-gluconate	+	growth
68134	32032 ChEBI	potassium gluconate	+	builds acid from
68134	32032 ChEBI	potassium gluconate	-	assimilation
68134	16634 ChEBI	raffinose	+	builds acid from
68134	16634 ChEBI	raffinose	+	growth
68134	15963 ChEBI	ribitol	+	builds acid from
68134	17814 ChEBI	salicin	+	builds acid from
68134	64103 ChEBI	sodium butyrate	+	growth
68134	53258 ChEBI	sodium citrate	-	assimilation
68134	17164 ChEBI	stachyose	+	growth
68134	17992 ChEBI	sucrose	+	builds acid from
68134	17992 ChEBI	sucrose	+	growth
68134	27082 ChEBI	trehalose	+	builds acid from
68134	27082 ChEBI	trehalose	+	growth
68134	32528 ChEBI	turanose	+	builds acid from
68134	32528 ChEBI	turanose	+	growth
68134	17151 ChEBI	xylitol	+	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68134	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68134	6-phospho-beta-galactosidase	+	3.2.1.85
68134	acid phosphatase	+	3.1.3.2
68134	alkaline phosphatase	+	3.1.3.1
68134	alpha-chymotrypsin	+	3.4.21.1
68134	alpha-fucosidase	-	3.2.1.51
68134	alpha-galactosidase	+	3.2.1.22
68134	alpha-glucosidase	+	3.2.1.20
68134	alpha-mannosidase	-	3.2.1.24
68134	arginine dihydrolase	-	3.5.3.6
68134	beta-galactosidase	+	3.2.1.23
68134	beta-glucosidase	+	3.2.1.21
68134	beta-glucuronidase	-	3.2.1.31
68134	catalase	+	1.11.1.6
68134	cystine arylamidase	+	3.4.11.3
68134	cytochrome oxidase	-	1.9.3.1
68134	esterase (C 4)	+
68134	esterase Lipase (C 8)	+
68134	leucine arylamidase	+	3.4.11.1
68134	lipase (C 14)	-
68134	N-acetyl-beta-glucosaminidase	-	3.2.1.52
68134	naphthol-AS-BI-phosphohydrolase	+
68134	trypsin	+	3.4.21.4
68134	urease	-	3.5.1.5
68134	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

68134

Fatty acid	Percentage
C15:0 anteiso	52.3
C16:0	15.7
C15:0 iso	14.1
C16:0 iso	5.7
C14:0	3.1
C17:0 iso	2.8
C17:0 anteiso	2.7
C14:0 iso	2.3
C12:0	1.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
66197	rhizosphere soil of wheat	Inner Mongulia	China	CHN	Asia
68134	Rhizosphere of wheat	Yakeshi County, Inner Mongolia	China	CHN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68134	ASM385496v1 assembly for Paenibacillus rhizophilus 7197	contig	GCA_003854965	1850366.3	2881636855	1850366	69.18
124043	ASM4268070v1 assembly for Paenibacillus rhizophilus CGMCC 1.15699	scaffold	GCA_042680705			1850366	65.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66197	Paenibacillus rhizophilus strain 7197 16S ribosomal RNA gene, partial sequence	KX132137	1515		1850366
68134	Paenibacillus rhizophilus strain 7197 16S ribosomal RNA gene, partial sequence	KX132137.2	1515		1850366

GC content

@ref	GC-content (mol%)	Method
68134	51.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus rhizophilus 7197
NCBI: GCA_003854965.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	59.63	yes
125438	anaerobic	anaerobicⓘ	no	84.53	yes
125438	aerobic	aerobicⓘ	no	53.69	yes
125438	spore-forming	spore-formingⓘ	yes	93.09	yes
125438	thermophilic	thermophileⓘ	no	95.72	yes
125438	flagellated	motile2+ⓘ	yes	82.15	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paenibacillus rhizophilus sp. nov., a nitrogen-fixing bacterium isolated from the rhizosphere of wheat (Triticum aestivum L.).	Ripa FA, Tong S, Cao WD, Wang ET, Wang T, Liu HC, Gao JL, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.003472	2019

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 )
#66197	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103168
#68134	Farhana Alam Ripa, Shuai Tong, Wei-dong Cao, En Tao Wang, Tianyu Wang, Hong Can Liu, Jun-lian Gao and Jian-guang Sun: Paenibacillus rhizophilus sp. nov., a nitrogen-fixing bacterium isolated from the rhizosphere of wheat (Triticum aestivum L.). IJSEM 69: 3689 - 3695 2019 ( DOI 10.1099/ijsem.0.003472 )
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )
#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 rhizophilus (DSM 103168, CGMCC 1.15699, 7197)

Name and taxonomic classification