Herbaspirillum seropedicae (DSM 6445, ATCC 35892, NCIB 12540)

Name: Herbaspirillum seropedicae (DSM 6445, ATCC 35892, NCIB 12540)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11353

Type strain

Strain Designation Z 67

Culture col. no. DSM 6445 ATCC 35892 NCIB 12540 CCUG 24564 LMG 6513 4 more

NCBI tax ID(s) 964

Special Collections DSMZ CCUG JCM

History DSMZ <- ATCC <- J. Döbereiner, Z 67 <- J.I. Baldani JCM <-- IAM 14977 <-- DSM 6445 <-- ATCC 35892 <-- J. Döbereiner Z 67 <-- J. I. Baldani.

Links

Herbaspirillum seropedicae Z 67 is a bacterium that was isolated from rice roots.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 3005

LMG 6513,ATCC 35892,LMG 10657,LMG 11131,NCIB 12540,DSM 6445,NCIMB 12540,CCUG 24564,IAM 14977,NCAIM B.01940,JCM 21448,NBRC 102524

@ref 20215

Last LPSN update 2026-05-29 08:27:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Herbaspirillum

Species Herbaspirillum seropedicae

Full scientific name Herbaspirillum seropedicae Baldani et al. 1986

BacDive ID	Other strains from **Herbaspirillum seropedicae** (4)	Type strain
11354	H. seropedicae Z 78, CCUG 24565, LMG 6514, LMG 7118, DSM ...
11355	H. seropedicae Z 152, DSM 6447, ATCC 35894
143180	H. seropedicae CCUG 17677, LMG 2284
144318	H. seropedicae CCUG 24563, LMG 6512, LMG 10656, LMG 11133

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.156

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2670	HERBASPIRILLUM MEDIUM (DSMZ Medium 538)		Medium recipe at MediaDive	Name: HERBASPIRILLUM MEDIUM (DSMZ Medium 538) Composition: Agar 15.0 g/l Na-malate 5.0 g/l KH2PO4 0.4 g/l MgSO4 x 7 H2O 0.2 g/l K2HPO4 0.1 g/l NaCl 0.1 g/l Yeast extract 0.05 g/l CaCl2 0.02 g/l FeCl2 x 6 H2O 0.01 g/l Na2MoO4 x 2 H2O 0.002 g/l Distilled water
2670	HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)		Medium recipe at MediaDive	Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2670	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.931

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

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
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
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
68382	trypsin	-	3.4.21.4	from API zym
68369	urease	+	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@ref

47973

Fatty acid	Percentage	ECL
C16:1 ω7c	42	15.819
C16:0	25	16
C18:1 ω7c /12t/9t	19.2	17.824
C14:0	4.2	14
C12:0 3OH	2.7	13.455
C17:0 CYCLO	2.2	16.888
C12:0 2OH	1.6	13.178
C14:0 2OH	1.2	15.205
C10:0 3OH	1.1	11.423
C18:0	0.9	18

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
47973	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
47973	+	-	-	+	+	-	-	+	+	+	+	+	+	-	+	+	-	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species
2670	rice roots
47973	Roots
67770	Oryza sativa root	Oryza sativa

Taxonmaps

69479

Global distribution of 16S sequence Y10146 (>99% sequence identity) for Herbaspirillum from Microbeatlas

Aquatic Samples	1120
Soil Samples	646
Animal Samples	1886
Plant Samples	1556
Total Samples	5208

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2670	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
67770	ASM104094v1 assembly for Herbaspirillum seropedicae Z67	complete	GCA_001040945	2636415568	964	99.28

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Herbaspirillum seropedicae gene for 16S rRNA, partial sequence, strain: NBRC 102524	AB681858	1458	964
20218	Herbaspirillum seropedicae 16S rRNA gene, strain Z67	AJ238361	1479	964
2670	H.seropedicae 16S rRNA gene	Y10146	1526	964

GC content

@ref	GC-content (mol%)	Method
2670	66.7	high performance liquid chromatography (HPLC)
67770	64.4	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: ASM104094v1 assembly for Herbaspirillum seropedicae Z67
NCBI: GCA_001040945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	99.16	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	66.22	no
125439	motility	BacteriaNetⓘ	yes	84.81	no
125439	spore_formation	BacteriaNetⓘ	no	99.93	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon.	Kuang W, Sanow S, Kelm JM, Muller Linow M, Andeer P, Kohlheyer D, Northen T, Vogel JP, Watt M, Arsova B.	J Exp Bot	10.1093/jxb/erac184	2022
Enzymology	Microfluidic-Assisted Evolution of a Robust NAD⁺-Dependent Enzyme with Improved Isobutanol Tolerance at Elevated Temperatures.	Teshima M, Genth R, Bayaraa T, Doring M, Beer B, Schenk G, Sieber V.	ChemSusChem	10.1002/cssc.202501120	2025
Metabolism	Characterization of highly active 2-keto-3-deoxy-L-arabinonate and 2-keto-3-deoxy-D-xylonate dehydratases in terms of the biotransformation of hemicellulose sugars to chemicals.	Sutiono S, Siebers B, Sieber V.	Appl Microbiol Biotechnol	10.1007/s00253-020-10742-5	2020
	Quantification of natural populations of Gluconacetobacter diazotrophicus and Herbaspirillum spp. In sugar cane (Saccharum spp.) Using differente polyclonal antibodies.	da Silva-Froufe LG, Boddey RM, Reis VM.	Braz J Microbiol	10.1590/s1517-838220090004000018	2009
Enzymology	New molecular screening tools for analysis of free-living diazotrophs in soil.	Burgmann H, Widmer F, Von Sigler W, Zeyer J.	Appl Environ Microbiol	10.1128/aem.70.1.240-247.2004	2004
	Diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils.	Selesi D, Schmid M, Hartmann A.	Appl Environ Microbiol	10.1128/aem.71.1.175-184.2005	2005
	A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV.	OMICS	10.1089/omi.2009.0100	2010
Biotechnology	Fusarium Oxysporum f. sp. Cannabis Isolated from Cannabis Sativa L.: In Vitro and In Planta Biocontrol by a Plant Growth Promoting-Bacteria Consortium.	Pellegrini M, Ercole C, Gianchino C, Bernardi M, Pace L, Del Gallo M.	Plants (Basel)	10.3390/plants10112436	2021
	A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.	Pinheiro Y, Faria da Mota F, Peixoto RS, van Elsas JD, Lins U, Mazza Rodrigues JL, Rosado AS.	Commun Biol	10.1038/s42003-023-04617-4	2023
Metabolism	Development of a direct isolation procedure for free-living diazotrophs under controlled hypoxic conditions.	Mirza BS, Rodrigues JL.	Appl Environ Microbiol	10.1128/aem.00714-12	2012
Enzymology	Recovery of Herbaspirillum species from persons with cystic fibrosis.	Spilker T, Uluer AZ, Marty FM, Yeh WW, Levison JH, Vandamme P, Lipuma JJ.	J Clin Microbiol	10.1128/jcm.00460-08	2008
Phylogeny	Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest.	Mirza BS, Potisap C, Nusslein K, Bohannan BJ, Rodrigues JL.	Appl Environ Microbiol	10.1128/aem.02362-13	2014
Metabolism	L-arabinose metabolism in Herbaspirillum seropedicae.	Mathias AL, Rigo LU, Funayama S, Pedrosa FO.	J Bacteriol	10.1128/jb.171.9.5206-5209.1989	1989
Phylogeny	Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10.	Tanaka Y, Tamaki H, Matsuzawa H, Nigaya M, Mori K, Kamagata Y.	Microbes Environ	10.1264/jsme2.me11288	2012
Phylogeny	Effects of the inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice.	Govindarajan M, Balandreau J, Kwon SW, Weon HY, Lakshminarasimhan C	Microb Ecol	10.1007/s00248-007-9247-9	2007
Metabolism	Heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to Herbaspirillum seropedicae Z67.	Wagh J, Shah S, Bhandari P, Archana G, Kumar GN	Appl Microbiol Biotechnol	10.1007/s00253-014-5610-1	2014
Phylogeny	Herbaspirillum canariense sp. nov., Herbaspirillum aurantiacum sp. nov. and Herbaspirillum soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus Herbaspirillum.	Carro L, Rivas R, Leon-Barrios M, Gonzalez-Tirante M, Velazquez E, Valverde A	Int J Syst Evol Microbiol	10.1099/ijs.0.031336-0	2011

References

#2670	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6445
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#47973	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 24564
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#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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Herbaspirillum seropedicae (DSM 6445, ATCC 35892, NCIB 12540)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001040945

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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