Herbaspirillum lusitanum (DSM 17154, CCUG 48869, CECT 5661)

Name: Herbaspirillum lusitanum (DSM 17154, CCUG 48869, CECT 5661)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11364

Type strain

Strain Designation P6-12, Strain P6-12

Culture col. no. DSM 17154 CCUG 48869 CECT 5661 LMG 21710 P6-12 3 more

NCBI tax ID(s) 213312

Special Collections DSMZ CCUG CIP UCCCB

History <- E. Velázquez, Univ. Salamanca, Spain; P6-12 <- A. Valverde, Dept. Producción Vegetal, Inst. Recursos Naturales y Agrobiol., Consejo Superior de Investigaciones Científicas, Spain Valverde, A., Consejo Superior de Investigaciones Científicas CIP <- 2004, CECT <- A. Valverde: strain P6-12

Links

Herbaspirillum lusitanum P6-12 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from root nodules of Phaseolus vulgaris plants grown in a soil from Sierra da Peneda.

Gram-negative motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 88963

LMG 21710,CECT 5661,CCUG 48869,CIP 108242,DSM 17154

@ref 20215

Last LPSN update 2026-02-09 11:20:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Herbaspirillum

Species Herbaspirillum lusitanum

Full scientific name Herbaspirillum lusitanum Valverde et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120680	negative	rod-shaped
125438	negative		97.5
125439	negative		99.9
125439			90.1

Pigmentation

@ref	Production	Name
120680		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6795	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33924	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120680	CIP Medium 72	Medium recipe at CIP
120680	CIP Medium 583	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6795	positive	growth	28
33924	positive	growth	30
67772	positive	optimum	28
120680	positive	growth	10-30
120680	negative	growth	5
120680	negative	growth	37
120680	negative	growth	41

Culture pH

@ref	Ability	Type	PH
67772	positive	maximum	8.0
67772	positive	minimum	5.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120680	obligate aerobe
125439	obligate aerobe	95.9

Spore formation

@ref	Spore formation	Confidence
125439		99.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120680	NaCl	positive	growth	0-2 %
120680	NaCl		growth	4 %
120680	NaCl		growth	6 %
120680	NaCl		growth	8 %
120680	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120680	16947 ChEBI	citrate	-	carbon source
120680	4853 ChEBI	esculin	-	hydrolysis
120680	17632 ChEBI	nitrate	-	reduction
120680	17632 ChEBI	nitrate	-	respiration
120680	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120680	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120680	alcohol dehydrogenase	-	1.1.1.1
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
120680	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120680	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120680	caseinase	-	3.4.21.50
120680	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120680	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120680	gelatinase	-
120680	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120680	lipase	-
68382	lipase (C 14)	-		from API zym
120680	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120680	ornithine decarboxylase	-	4.1.1.17
120680	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120680	tryptophan deaminase	-
120680	tween esterase	-
120680	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
120680	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
120680	not determinedn.d.	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	+	+	-	+	+	-	-	-	+	-	+	-	-	-	+	-	+	-	-	-	+	+	+	+	-	+	+	+	-	+	+	+	+	+	+	-	+	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	+	+	-	-	+	+	-	+	-	-	-	-	+	+	+	+	+	+	+	+	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Host species	Isolation date
6795	root nodules of Phaseolus vulgaris plants grown in a soil from Sierra da Peneda			Portugal	PRT	Europe			Phaseolus vulgaris
58368	Root nodules,Phaseolus vulgaris	2000	Sierra da Penada	Portugal	PRT	Europe
67772	Phaseolus vulgaris, root nodules	2000	Alto-Minho, Arcos de Valdevez	Portugal	PRT	Europe	41.85	-8.41667 41.85/-8.41667
120680	Plant, Endophyllous		Arcos de Valdevez	Portugal	PRT	Europe				2000

Taxonmaps

69479

Global distribution of 16S sequence AF543312 (>99% sequence identity) for Herbaspirillum from Microbeatlas

Aquatic Samples	4
Soil Samples	3
Animal Samples	11
Plant Samples	3
Total Samples	21

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6795	1	Risk group (German classification) According to TRBA 466
67772	1
120680	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
67772	Asm2.0 assembly for Herbaspirillum lusitanum P6-12	contig	GCA_000256565	1161913.3	2548876994	1161913

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6795	Herbaspirillum lusitanum 16S ribosomal RNA gene, complete sequence	AF543312	1524		1161913

GC content

6795

GC-content (mol%)57.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Herbaspirillum lusitanum P6-12
NCBI: GCA_000256565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	yes	90.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbaspirillum lusitanum P6-12
PATRIC: 1161913.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	98.49	no
125438	spore-forming	spore-formingⓘ	no	86.57	no
125438	aerobic	aerobicⓘ	yes	88.37	yes
125438	thermophilic	thermophileⓘ	no	95.99	yes
125438	flagellated	motile2+ⓘ	yes	81.26	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The genome of the endophytic bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum genus to interact with plants.	Straub D, Rothballer M, Hartmann A, Ludewig U.	Front Microbiol	10.3389/fmicb.2013.00168	2013
	Whole-cell electric sensor for determination of sodium dodecyl sulfate.	Velichko NS, Guliy OI, Kanevsky MV, Kupryashina MA, Fedonenko YP	World J Microbiol Biotechnol	10.1007/s11274-022-03309-1	2022
Metabolism	Characterization of biopolymers produced by planktonic and biofilm cells of Herbaspirillum lusitanum P6-12.	Velichko NS, Grinev VS, Fedonenko YP	J Appl Microbiol	10.1111/jam.14647	2020
Genetics	Draft genome sequence of Herbaspirillum lusitanum P6-12, an endophyte isolated from root nodules of Phaseolus vulgaris.	Weiss VA, Faoro H, Tadra-Sfeir MZ, Raittz RT, de Souza EM, Monteiro RA, Cardoso RL, Wassem R, Chubatsu LS, Huergo LF, Muller-Santos M, Steffens MB, Rigo LU, Pedrosa Fde O, Cruz LM	J Bacteriol	10.1128/JB.00657-12	2012
Phylogeny	Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots.	Rothballer M, Schmid M, Klein I, Gattinger A, Grundmann S, Hartmann A	Int J Syst Evol Microbiol	10.1099/ijs.0.64031-0	2006
Phylogeny	Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris.	Valverde A, Velazquez E, Gutierrez C, Cervantes E, Ventosa A, Igual JM	Int J Syst Evol Microbiol	10.1099/ijs.0.02677-0	2003

References

#6795	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17154
#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 )
#33924	; Curators of the CIP;
#58368	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48869
#67772	The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;
#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 .
#120680	Collection of Institut Pasteur ; Curators of the CIP; CIP 108242
#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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Herbaspirillum lusitanum (DSM 17154, CCUG 48869, CECT 5661)

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

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000256565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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