Name: Herbaspirillum lusitanum P6-12
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11364

Type strain:

Species: Herbaspirillum lusitanum

Strain Designation: P6-12, Strain P6-12

Culture col. no.: DSM 17154, CCUG 48869, CECT 5661, LMG 21710, UCCCB3, CIP 108242

Strain history: CIP <- 2004, CECT <- A. Valverde: strain P6-12

NCBI tax ID(s): 213312 (species)

SI-ID 88963

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

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Herbaspirillum*
	Species	**Herbaspirillum lusitanum**
	Full Scientific Name (LPSN)	Herbaspirillum lusitanum Valverde et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #120680]	Gram stain	negative

[Ref.: #120680]	Cell shape	rod-shaped

[Ref.: #120680]	Motility	yes

[Ref.: #120680]	Pigment production	no
[Ref.: #120680]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6795]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #6795]

Culture medium growth

[Ref.: #6795]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6795]

Culture medium composition

expand / minimize

[Ref.: #33924]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #33924]

Culture medium growth

[Ref.: #33924]

Culture medium composition

expand / minimize

[Ref.: #120680]

Culture medium

CIP Medium 72

[Ref.: #120680]

Culture medium growth

[Ref.: #120680]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #120680]

Culture medium

CIP Medium 583

[Ref.: #120680]

Culture medium growth

[Ref.: #120680]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6795]		growth	28 °C
[Ref.: #33924]		growth	30 °C
[Ref.: #67772]		optimum	28 °C
[Ref.: #120680]		growth	10-30 °C
[Ref.: #120680]	no	growth	5 °C
[Ref.: #120680]	no	growth	37 °C
[Ref.: #120680]	no	growth	41 °C

[Ref.: #6795]	Temperature range	mesophilic
[Ref.: #33924]	Temperature range	mesophilic
[Ref.: #67772]	Temperature range	mesophilic
[Ref.: #120680]	Temperature range	psychrophilic
[Ref.: #120680]	Temperature range	mesophilic
[Ref.: #120680]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #67772]			maximum	8.0
[Ref.: #67772]			minimum	5.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120680]

Oxygen tolerance

obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #120680]	NaCl		growth	0-2	%
[Ref.: #120680]	NaCl	no	growth	4	%
[Ref.: #120680]	NaCl	no	growth	6	%
[Ref.: #120680]	NaCl	no	growth	8	%
[Ref.: #120680]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120680]	citrate ChEBI	-	carbon source
[Ref.: #120680]	esculin ChEBI	-	hydrolysis
[Ref.: #120680]	nitrate ChEBI	-	reduction
[Ref.: #120680]	nitrate ChEBI	-	respiration
[Ref.: #120680]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120680]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120680]	alcohol dehydrogenase	-	1.1.1.1
[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.: #120680]	amylase	-
[Ref.: #120680]	beta-galactosidase	-	3.2.1.23
[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.: #120680]	caseinase	-	3.4.21.50
[Ref.: #120680]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120680]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120680]	gelatinase	-
[Ref.: #120680]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120680]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120680]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120680]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120680]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120680]	tryptophan deaminase	-
[Ref.: #120680]	tween esterase	-
[Ref.: #120680]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	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
[Ref.: #120680]	2667	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.: #120680]	11018	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #6795]	Sample type/isolated from	root nodules of Phaseolus vulgaris plants grown in a soil from Sierra da Peneda
[Ref.: #6795]	Host species	Phaseolus vulgaris
[Ref.: #6795]	Country	Portugal
[Ref.: #6795]	Country ISO 3 Code	PRT
[Ref.: #6795]	Continent	Europe

[Ref.: #58368]	Sample type/isolated from	Root nodules,Phaseolus vulgaris
[Ref.: #58368]	Sampling date	2000
[Ref.: #58368]	Geographic location (country and/or sea, region)	Sierra da Penada
[Ref.: #58368]	Country	Portugal
[Ref.: #58368]	Country ISO 3 Code	PRT
[Ref.: #58368]	Continent	Europe

[Ref.: #67772]	Sample type/isolated from	Phaseolus vulgaris, root nodules
[Ref.: #67772]	Sampling date	2000
[Ref.: #67772]	Geographic location (country and/or sea, region)	Alto-Minho, Arcos de Valdevez
[Ref.: #67772]	Country	Portugal
[Ref.: #67772]	Country ISO 3 Code	PRT
[Ref.: #67772]	Continent	Europe
[Ref.: #67772]	Geographic location	41.8500°/-8.4167°

[Ref.: #120680]	Sample type/isolated from	Plant, Endophyllous
[Ref.: #120680]	Geographic location (country and/or sea, region)	Arcos de Valdevez
[Ref.: #120680]	Country	Portugal
[Ref.: #120680]	Country ISO 3 Code	PRT
[Ref.: #120680]	Continent	Europe
[Ref.: #120680]	Isolation date	2000
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #6795]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #67772]	Biosafety level	1
[Ref.: #120680]	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.: #6795]	Herbaspirillum lusitanum 16S ribosomal RNA gene, complete sequence	AF543312	1524	ENA	1161913 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67772]	Herbaspirillum lusitanum P6-12	GCA_000256565	contig	GenBank	1161913 tax ID
[Ref.: #66792]	Herbaspirillum lusitanum P6-12	1161913.3	wgs	PATRIC	1161913 tax ID	*
[Ref.: #66792]	Herbaspirillum lusitanum P6-12	2548876994	draft	JGI IMG/M	1161913 tax ID	*

[Ref.: #6795]

GC-content

57.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Herbaspirillum lusitanum P6-12 PATRIC: 1161913.3
[Ref.: #69480]	motile	yes	92.1	no
[Ref.: #69480]	gram-positive	no	98.974	no
[Ref.: #69480]	anaerobic	no	98.125	no
[Ref.: #69480]	aerobic	yes	90.299	no
[Ref.: #69480]	halophile	no	96.611	no
[Ref.: #69480]	spore-forming	no	94.647	no
[Ref.: #69480]	flagellated	yes	56.799	no
[Ref.: #69480]	thermophile	no	99.386	yes
[Ref.: #69480]	glucose-util	yes	86.864	no
[Ref.: #69480]	glucose-ferment	no	90.731	no

Availability in culture collections External links

[Ref.: #6795]

Culture collection no.

DSM 17154, CCUG 48869, CECT 5661, LMG 21710, UCCCB3, CIP 108242

[Ref.: #80595]

SI-ID 88963

Literature:

	Title	Authors	Journal	DOI	Year
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	*
	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	*

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

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#80595

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-ID88963.1 )

#120680 Collection of Institut Pasteur ; Curators of the CIP; CIP 108242
* These data were automatically processed and therefore are not curated

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