Herbaspirillum autotrophicum (DSM 732, ATCC 29984, CCUG 12808)

Name: Herbaspirillum autotrophicum (DSM 732, ATCC 29984, CCUG 12808)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11351

Type strain

Strain Designation SA 32, SA32

Culture col. no. DSM 732 ATCC 29984 CCUG 12808 LMG 4326 CIP 107295 8 more

NCBI tax ID(s) 180195

Special Collections DSMZ CCUG JCM CIP UCCCB

History <- M. Aragno, SA 32 IAM 14942 <-- IFO 15327 <-- LMG 4326 <-- M. Aragno SA 32. C. Schweizer and M. Aragno, Institute of Botany, University of Neuchâtel [Aquaspirillum autotrophicum Aragno and Schlegel 1978 (Approved Lists 1980) - homotypic synonym, validly published] CIP <- 2001, CCUG <- 1982, DSMZ <- M. Aragno: strain SA32

Links

Herbaspirillum autotrophicum SA 32 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from eutrophic lake water.

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

Name and taxonomic classification

SI-ID 891

LMG 4326,ATCC 29984,CCUG 12808,DSM 732,IFO 15327,VKM B-1394,IAM 14942,KCTC 2340,CIP 107295,NBRC 15327,JCM 21424

@ref 20215

Last LPSN update 2026-02-09 11:20:31

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Herbaspirillum

Species Herbaspirillum autotrophicum

Full scientific name Herbaspirillum autotrophicum (Aragno and Schlegel 1978) Ding and Yokota 2004

Synonyms (1)

Aquaspirillum autotrophicum

BacDive ID	Other strains from **Herbaspirillum autotrophicum** (1)	Type strain
11352	H. autotrophicum SA 33, CCUG 19112, LMG 7377, DSM 733

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
116653	negative	rod-shaped
125438	negative		98.9
125439	negative		99.8
125439			90.9

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
33759	MEDIUM 14 - Williams and Rittenberg medium for Aquaspirillum genus		Distilled water make up to (1000.000 ml);Agar (13.000 g);Yeast extract (3.000 g);Peptone (5.000 g);Beef extract (3.000 g)
377	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	Medium recipe at MediaDive	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
377	SPIRILLUM MEDIUM (DSMZ Medium 37)	Medium recipe at MediaDive	Name: SPIRILLUM MEDIUM (DSMZ Medium 37) Composition: Peptone 10.0 g/l (NH4)2SO4 1.0 g/l Succinic acid 1.0 g/l MgSO4 x 7 H2O 1.0 g/l FeCl3 x 6 H2O 0.002 g/l MnSO4 x H2O 0.002 g/l Distilled water
116653	CIP Medium 14	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
377	positive	growth	28
33759	positive	growth	25
45831	positive	growth	25-30
67770	positive	growth	30
67772	positive	minimum	35
67772	positive	optimum	28
67772	positive	maximum	10
116653	positive	growth	15-30
116653	negative	growth	5
116653	negative	growth	37
116653	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
45831	aerobe
116653	obligate aerobe
125439	obligate aerobe	99

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116653	NaCl	positive	growth	0-2 %
116653	NaCl		growth	4 %
116653	NaCl		growth	6 %
116653	NaCl		growth	8 %
116653	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116653	16947 ChEBI	citrate	+	carbon source
116653	4853 ChEBI	esculin	-	hydrolysis
116653	17234 ChEBI	glucose	-	fermentation
116653	17716 ChEBI	lactose	-	fermentation
116653	17632 ChEBI	nitrate	-	reduction
116653	17632 ChEBI	nitrate	-	respiration
116653	16301 ChEBI	nitrite	-	reduction
116653	132112 ChEBI	sodium thiosulfate	-	builds gas from

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116653	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116653	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
116653	15688 ChEBI	acetoin	-
116653	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
116653	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
116653	amylase	-
116653	beta-galactosidase	-	3.2.1.23
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
116653	caseinase	-	3.4.21.50
116653	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
116653	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
116653	gamma-glutamyltransferase	+	2.3.2.2
116653	gelatinase	-
116653	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116653	lipase	-
68382	lipase (C 14)	-		from API zym
116653	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
116653	ornithine decarboxylase	-	4.1.1.17
116653	oxidase	+
116653	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
116653	tryptophan deaminase	-
116653	tween esterase	-
116653	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
116653	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
116653	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	+	-	-	+	-	-	+	+	-	-	+	-	+	+	-	+	-	-	-	-	-	-	-	-	-	+	+	+	-	+	+	+	+	-	-	-	+	+	+	+	+	+	-	+	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
377	eutrophic lake water			Switzerland	CHE	Europe
45831	Eutrophic lake water			Switzerland	CHE	Europe
67770	Eutrophic lake water
67772	Eutrophic lake water	1976	Neuchâtel, Saint-Blaise	Switzerland	CHE	Europe	47.0167	6.98333 47.0167/6.98333
116653	Environment, Eutrophic lake water			Switzerland	CHE	Europe

Taxonmaps

69479

Global distribution of 16S sequence AB074524 (>99% sequence identity) for Herbaspirillum autotrophicum from Microbeatlas

Aquatic Samples	22
Soil Samples	6
Animal Samples	12
Plant Samples	13
Total Samples	53

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
377	1	Risk group (German classification) According to TRBA 466
67772	1
116653	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	Score
67770	ASM118991v1 assembly for Herbaspirillum autotrophicum IAM 14942	contig	GCA_001189915	180195.5	2654587661	180195	52.75

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Herbaspirillum autotrophicum gene for 16S rRNA, partial sequence, strain: NBRC 15327	AB680836	1458		180195
377	Aquaspirillum autotrophicum gene for 16S rRNA, partial sequence	AB074524	1489		180195

GC content

377

GC-content (mol%)61.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Herbaspirillum autotrophicum IAM 14942
NCBI: GCA_001189915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	yes	90.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Herbaspirillum autotrophicum strain IAM 14942
PATRIC: 180195.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.90	no
125438	anaerobic	anaerobicⓘ	no	96.25	yes
125438	spore-forming	spore-formingⓘ	no	85.90	no
125438	aerobic	aerobicⓘ	yes	80.60	no
125438	thermophilic	thermophileⓘ	no	98.49	yes
125438	flagellated	motile2+ⓘ	yes	83.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Bacterial Small RNAs in the Genus Herbaspirillum spp.	Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaco LM, Graf H.	Int J Mol Sci	10.3390/ijms20010046	2018
	Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.	Wang D, Duan Y, He L, Jiang J, Xian J, Yuan K, Zhang R, Zhang H, Wang J, Li N, Huang M, Hu C, Lu S, Luo Z, Deng T, Zhang Z, Chen B, Li W.	Commun Biol	10.1038/s42003-025-08234-1	2025
	Distinct microbial signatures of liquid biopsy samples during gastric carcinogenesis and insights from extracellular vesicle analysis.	You HS, Park JY, Seo H, Kim BJ, Kim JG.	Korean J Intern Med	10.3904/kjim.2024.339	2025
Genetics	Impact of scented candle use on indoor air quality and airborne microbiome.	Yun H, Seo JH, Kim YG, Yang J.	Sci Rep	10.1038/s41598-025-95010-0	2025
	Biological removal of benzalkonium chlorides from wastewater by immobilized cells of Pseudomonas sp. BIOMIG1 in an up-flow packed bed reactor.	Sakarya FK, Haznedaroglu BZ, Tezel U.	J Hazard Mater	10.1016/j.jhazmat.2021.126210	2021
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
Enzymology	Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A.	Bueche M, Wunderlin T, Roussel-Delif L, Junier T, Sauvain L, Jeanneret N, Junier P.	Appl Environ Microbiol	10.1128/aem.01376-13	2013
Enzymology	Localization and stability of hydrogenases from aerobic hydrogen bacteria.	Schneider K, Schlegel HG	Arch Microbiol	10.1007/BF00413086	1977
Phylogeny	Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.	Ding L, Yokota A.	Int J Syst Evol Microbiol	10.1099/ijs.0.02975-0	2004
Phylogeny	Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil.	Anandham R, Kim SJ, Moon JY, Weon HY, Kwon SW	J Microbiol	10.1007/s12275-013-2563-5	2013

References

#377	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 732
#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 )
#33759	; Curators of the CIP;
#45831	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12808
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#116653	Collection of Institut Pasteur ; Curators of the CIP; CIP 107295
#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 autotrophicum (DSM 732, ATCC 29984, CCUG 12808)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

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_001189915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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