Name: Paenibacillus sonchi DSM 28159
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24281

Type strain:

Species: Paenibacillus sonchi

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

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

NCBI tax ID(s): 483937 (species)

SI-ID 365764

CECT 7330, CIP 110206, DSM 28159

Other strains from Paenibacillus sonchi

P. sonchi X19-5, CCBAU 83901, LMG 24727 (type strain)

Section

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

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

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 sonchi**
	Full Scientific Name (LPSN)	Paenibacillus sonchi Hong et al. 2009

Synonym

Paenibacillus riograndensis

Information on morphological and physiological properties Morphology

[Ref.: #29382]	Gram stain	variable
[Ref.: #29382]	Cell length	4.15 µm
[Ref.: #29382]	Cell width	0.72 µm
[Ref.: #29382]	Cell shape	rod-shaped
[Ref.: #29382]	Motility	yes

[Ref.: #122240]	Gram stain	negative
[Ref.: #122240]	Cell shape	rod-shaped
[Ref.: #122240]	Motility	yes

[Ref.: #29382]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20705]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #20705]

Culture medium growth

[Ref.: #20705]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20705]

Culture medium composition

expand / minimize

[Ref.: #40372]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #40372]

Culture medium growth

[Ref.: #40372]

Culture medium composition

expand / minimize

[Ref.: #122240]

Culture medium

CIP Medium 72

[Ref.: #122240]

Culture medium growth

[Ref.: #122240]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #20705]	growth	30 °C
[Ref.: #29382]	optimum	28 °C
[Ref.: #40372]	growth	30 °C

[Ref.: #20705]	Temperature range	mesophilic
[Ref.: #29382]	Temperature range	mesophilic
[Ref.: #40372]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29382]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29382]	Oxygen tolerance	facultative anaerobe
[Ref.: #122240]	Oxygen tolerance	facultative anaerobe

[Ref.: #29382]	Ability of spore formation	yes
[Ref.: #122240]	Ability of spore formation	yes

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29382]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose 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-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.: #29382]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29382]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29382]	glucose ChEBI	+	carbon source
[Ref.: #29382]	glycerol ChEBI	+	carbon source
[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-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29382]	lactose ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29382]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29382]	mannitol ChEBI	+	carbon source
[Ref.: #29382]	mannose ChEBI	+	carbon source
[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.: #122240]	nitrate ChEBI	+	reduction
[Ref.: #122240]	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.: #29382]	raffinose ChEBI	+	carbon source
[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.: #29382]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29382]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29382]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122240]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[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.: #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.: #122240]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122240]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122240]	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.: #122240]	11729	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.: #122240]	12439	-	-	+	+	-	+	-	-	-	-	-	+	+	+	-	+	+	-	-	-

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

[Ref.: #20705]	Sample type/isolated from	rhizosphere of Triticum aestivum
[Ref.: #20705]	Host species	Triticum aestivum
[Ref.: #20705]	Geographic location (country and/or sea, region)	Sao Borja
[Ref.: #20705]	Country	Brazil
[Ref.: #20705]	Country ISO 3 Code	BRA
[Ref.: #20705]	Continent	Middle and South America

[Ref.: #122240]	Sample type/isolated from	Environment, Triticum aestivum, rhizosphere
[Ref.: #122240]	Isolation date	2004
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #20705]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122240]	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.: #20705]	Paenibacillus riograndensis strain SBR5 16S ribosomal RNA gene, partial sequence	EU257201	1506	ENA	1073571 tax ID

[Ref.: #20705]

GC-content

55.1 mol%

Availability in culture collections External links

[Ref.: #20705]

Culture collection no.

DSM 28159, CCGB 1313, CECT 7330, SBR 5, CIP 110206

[Ref.: #88219]

SI-ID 365764

Literature:

Only first 10 entries are displayed. Click here to see all.

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	*
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	*
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	*
	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	*

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

#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 (see below)

#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 .

#88219

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-ID365764.1 )

#122240 Collection of Institut Pasteur ; Curators of the CIP; CIP 110206

#25790

IJSEM 128 2010 ( DOI 10.1099/ijs.0.011973-0 , PubMed 19648317 )

* These data were automatically processed and therefore are not curated

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