Paenibacillus sonchi (DSM 28159, CCGB 1313, CECT 7330)

Name: Paenibacillus sonchi (DSM 28159, CCGB 1313, CECT 7330)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24281

Type strain

Culture col. no. DSM 28159 CCGB 1313 CECT 7330 SBR 5 CIP 110206

NCBI tax ID(s) 483937

Special Collections DSMZ Literature strains CIP

History <- CECT <- A. Beneduzi CIP <- 2010, CECT <- A. Beneduzi, Rio Grande Univ., Porto Algere, Brazil: strain SBR5

Links

Paenibacillus sonchi DSM 28159 is a facultative anaerobe, spore-forming, Gram-variable bacterium that was isolated from rhizosphere of Triticum aestivum.

spore-forming Gram-variable motile rod-shaped facultative anaerobe 16S sequence Bacteria

Name and taxonomic classification

SI-ID 365764

CECT 7330,CIP 110206,DSM 28159

@ref 20215

Last LPSN update 2026-02-09 11:23:56

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus sonchi

Full scientific name Paenibacillus sonchi Hong et al. 2009

Synonyms (1)

Paenibacillus riograndensis

BacDive ID	Other strains from **Paenibacillus sonchi** (1)	Type strain
133511	P. sonchi X19-5, CCBAU 83901, LMG 24727 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29382	variable	4.15 µm	0.72 µm	rod-shaped
122240	negative			rod-shaped

Pigmentation

29382

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
20705	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40372	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122240	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
20705	positive	growth	30
29382	positive	optimum	28
40372	positive	growth	30

Culture pH

@ref	Ability	Type	PH
29382	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29382	facultative anaerobe
122240	facultative anaerobe

Spore formation

@ref	Spore formation
29382
122240

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
29382	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
29382	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
29382	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
29382	17234 ChEBI	glucose	+	carbon source
29382	17754 ChEBI	glycerol	+	carbon source
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	+	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
29382	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
29382	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
29382	29864 ChEBI	mannitol	+	carbon source
29382	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	+	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
122240	17632 ChEBI	nitrate	+	reduction
122240	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	+	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
29382	16634 ChEBI	raffinose	+	carbon source
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
29382	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
29382	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
29382	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122240	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122240	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122240	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
122240	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122240	-	-	+	+	-	+	-	-	-	-	-	+	+	+	-	+	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122240	not determinedn.d.	+	-	+/-	+	+/-	+	-	-	+	+	+	+	+	-	+/-	-	-	+	+/-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+/-	+	+	-	-	-	+/-	-	-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
20705	rhizosphere of Triticum aestivum	Triticum aestivum	Sao Borja	Brazil	BRA	Middle and South America
122240	Environment, Triticum aestivum, rhizosphere						2004

Taxonmaps

69479

Global distribution of 16S sequence EU257201 (>99% sequence identity) for Paenibacillus from Microbeatlas

Aquatic Samples	22
Soil Samples	152
Animal Samples	13
Plant Samples	15
Total Samples	202

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20705	1	Risk group (German classification)
122240	1	Risk group (French classification)

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20705	Paenibacillus riograndensis strain SBR5 16S ribosomal RNA gene, partial sequence	EU257201	1506		1073571

GC content

20705

GC-content (mol%)55.1

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Metabolic Engineering of Corynebacterium glutamicum for Sustainable Production of the Aromatic Dicarboxylic Acid Dipicolinic Acid.	Schwardmann LS, Dransfeld AK, Schaffer T, Wendisch VF	Microorganisms	10.3390/microorganisms10040730	2022
Phylogeny	Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification.	Sant'Anna FH, Ambrosini A, de Souza R, de Carvalho Fernandes G, Bach E, Balsanelli E, Baura V, Brito LF, Wendisch VF, de Oliveira Pedrosa F, de Souza EM, Passaglia LMP	Front Microbiol	10.3389/fmicb.2017.01849	2017
	Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions.	Brito LF, Lopez MG, Straube L, Passaglia LMP, Wendisch VF	Front Microbiol	10.3389/fmicb.2020.588605	2020
Enzymology	CRISPR interference-based gene repression in the plant growth promoter Paenibacillus sonchi genomovar Riograndensis SBR5.	Brito LF, Schultenkamper K, Passaglia LMP, Wendisch VF	Appl Microbiol Biotechnol	10.1007/s00253-020-10571-6	2020
Transcriptome	Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.	Brito LF, Irla M, Kalinowski J, Wendisch VF	BMC Genomics	10.1186/s12864-017-4235-z	2017
Metabolism	Glutamine synthetase stabilizes the binding of GlnR to nitrogen fixation gene operators.	Fernandes GC, Hauf K, Sant'Anna FH, Forchhammer K, Passaglia LM	FEBS J	10.1111/febs.14021	2017
Cultivation	How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier.	Bach E, de Carvalho Fernandes G, Passaglia LMP	J Microbiol Methods	10.1016/j.mimet.2016.10.012	2016
Metabolism	Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5.	Sperb ER, Tadra-Sfeir MZ, Sperotto RA, Fernandes Gde C, Pedrosa Fde O, de Souza EM, Passaglia LM	Res Microbiol	10.1016/j.resmic.2016.04.007	2016
Genetics	Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.	Brito LF, Bach E, Kalinowski J, Ruckert C, Wibberg D, Passaglia LM, Wendisch VF	J Biotechnol	10.1016/j.jbiotec.2015.04.025	2015
Metabolism	Alternative nitrogenase and pseudogenes: unique features of the Paenibacillus riograndensis nitrogen fixation system.	Fernandes Gde C, Trarbach LJ, de Campos SB, Beneduzi A, Passaglia LM	Res Microbiol	10.1016/j.resmic.2014.06.002	2014
Genetics	Genome sequence of the diazotrophic Gram-positive rhizobacterium Paenibacillus riograndensis SBR5(T).	Beneduzi A, Campos S, Ambrosini A, de Souza R, Granada C, Costa P, Arruda L, Moreira F, Vargas LK, Weiss V, Tieppo E, Faoro H, de Souza EM, Pedrosa FO, Passaglia LM	J Bacteriol	10.1128/JB.06100-11	2011
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	Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens.	Jin HJ, Zhou YG, Liu HC, Chen SF	Int J Syst Evol Microbiol	10.1099/ijs.0.025056-0	2010
Phylogeny	Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum.	Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH, Passaglia LMP	Int J Syst Evol Microbiol	10.1099/ijs.0.011973-0	2009

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 )
#20705	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28159
#25790	IJSEM 128 2010 ( DOI 10.1099/ijs.0.011973-0 , PubMed 19648317 )
#29382	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 #25790
#40372	; Curators of the CIP;
#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 .
#122240	Collection of Institut Pasteur ; Curators of the CIP; CIP 110206
#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 sonchi (DSM 28159, CCGB 1313, CECT 7330)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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