Strain identifier

BacDive ID: 11351

Type strain: Yes

Species: Herbaspirillum autotrophicum

Strain Designation: SA 32, SA32

Strain history: CIP <- 2001, CCUG <- 1982, DSMZ <- M. Aragno: strain SA32

NCBI tax ID(s): 180195 (species)

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General

@ref: 377

BacDive-ID: 11351

DSM-Number: 732

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Herbaspirillum autotrophicum SA 32 is an aerobe, mesophilic, motile bacterium that was isolated from eutrophic lake water.

NCBI tax id

  • NCBI tax id: 180195
  • Matching level: species

strain history

@refhistory
377<- M. Aragno, SA 32
67770IAM 14942 <-- IFO 15327 <-- LMG 4326 <-- M. Aragno SA 32.
67772C. Schweizer and M. Aragno, Institute of Botany, University of Neuchâtel [Aquaspirillum autotrophicum Aragno and Schlegel 1978 (Approved Lists 1980) - homotypic synonym, validly published]
116653CIP <- 2001, CCUG <- 1982, DSMZ <- M. Aragno: strain SA32

doi: 10.13145/bacdive11351.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • 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

    • @ref: 20215
    • synonym: Aquaspirillum autotrophicum

@ref: 377

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum autotrophicum

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

strain designation: SA 32, SA32

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.36
6948099.995negative
116653nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33759MEDIUM 14 - Williams and Rittenberg medium for Aquaspirillum genusyesDistilled 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)
377MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yesName: 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 waterhttps://mediadive.dsmz.de/medium/81
377SPIRILLUM MEDIUM (DSMZ Medium 37)yesName: 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 waterhttps://mediadive.dsmz.de/medium/37
116653CIP Medium 14yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=14

culture temp

@refgrowthtypetemperaturerange
377positivegrowth28mesophilic
33759positivegrowth25mesophilic
45831positivegrowth25-30mesophilic
67770positivegrowth30mesophilic
67772positivemaximum10psychrophilic
67772positiveoptimum28mesophilic
67772positiveminimum35mesophilic
116653positivegrowth15-30
116653nogrowth5psychrophilic
116653nogrowth37mesophilic
116653nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45831aerobe
116653obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
116653NaClpositivegrowth0-2 %
116653NaClnogrowth4 %
116653NaClnogrowth6 %
116653NaClnogrowth8 %
116653NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11665316947citrate+carbon source
1166534853esculin-hydrolysis
11665317234glucose-fermentation
11665317716lactose-fermentation
11665317632nitrate-reduction
11665316301nitrite-reduction
116653132112sodium thiosulfate-builds gas from
11665317632nitrate-respiration

antibiotic resistance

  • @ref: 116653
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116653
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11665315688acetoin-
11665317234glucose-

enzymes

@refvalueactivityec
116653oxidase+
116653beta-galactosidase-3.2.1.23
116653alcohol dehydrogenase-1.1.1.1
116653gelatinase-
116653amylase-
116653DNase-
116653caseinase-3.4.21.50
116653catalase+1.11.1.6
116653tween esterase-
116653gamma-glutamyltransferase+2.3.2.2
116653lecithinase-
116653lipase-
116653lysine decarboxylase-4.1.1.18
116653ornithine decarboxylase-4.1.1.17
116653phenylalanine ammonia-lyase-4.3.1.24
116653tryptophan deaminase-
116653urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116653--+--+--------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116653----------------------------------------------+-+++--+--++--+-++-+---------+++-++++---++++++-+-++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationlatitudelongitude
377eutrophic lake waterSwitzerlandCHEEurope
45831Eutrophic lake waterSwitzerlandCHEEurope
67770Eutrophic lake water
67772Eutrophic lake waterSwitzerlandCHEEurope1976Neuchâtel, Saint-Blaise47.01676.98333
116653Environment, Eutrophic lake waterSwitzerlandCHEEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7248.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_2888;99_7248&stattab=map
  • Last taxonomy: Herbaspirillum autotrophicum
  • 16S sequence: AB074524
  • Sequence Identity:
  • Total samples: 53
  • soil counts: 6
  • aquatic counts: 22
  • animal counts: 12
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
3771Risk group (German classification)
677721
1166531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herbaspirillum autotrophicum gene for 16S rRNA, partial sequence, strain: NBRC 15327AB6808361458ena180195
377Aquaspirillum autotrophicum gene for 16S rRNA, partial sequenceAB0745241489ena180195

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum autotrophicum strain IAM 14942180195.5wgspatric180195
66792Herbaspirillum autotrophicum IAM 149422654587661draftimg180195
67770Herbaspirillum autotrophicum IAM 14942GCA_001189915contigncbi180195

GC content

  • @ref: 377
  • GC-content: 61.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.795no
gram-positiveno98.876no
anaerobicno98.666no
aerobicyes93.001yes
halophileno93.652no
spore-formingno93.831no
glucose-utilyes75.089no
flagellatedyes66.438no
thermophileno99.394yes
glucose-fermentno88.795no

External links

@ref: 377

culture collection no.: DSM 732, ATCC 29984, CCUG 12808, LMG 4326, CIP 107295, IAM 14942, NBRC 15327, JCM 21424, IFO 15327, VKM B-1394, UCCCB7

straininfo link

  • @ref: 80583
  • straininfo: 891

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology871226Localization and stability of hydrogenases from aerobic hydrogen bacteria.Schneider K, Schlegel HGArch Microbiol10.1007/BF004130861977Aerobiosis, Alcaligenes/enzymology, Bacteria/*enzymology, Corynebacterium/enzymology, Cytosol/enzymology, Drug Stability, Hydrogen, Oxidoreductases/*analysis, Paracoccus denitrificans/enzymology, Pseudomonas/enzymology, Spirillum/enzymology, Subcellular Fractions/enzymology
Phylogeny23625231Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil.Anandham R, Kim SJ, Moon JY, Weon HY, Kwon SWJ Microbiol10.1007/s12275-013-2563-52013Base Composition, Fatty Acids/metabolism, Molecular Sequence Data, Oxalobacteraceae/classification/genetics/*isolation & purification/metabolism, Phylogeny, Republic of Korea, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
377Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 732)https://www.dsmz.de/collection/catalogue/details/culture/DSM-732
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33759Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4714
45831Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12808)https://www.ccug.se/strain?id=12808
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80583Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID891.1StrainInfo: A central database for resolving microbial strain identifiers
116653Curators of the CIPCollection of Institut Pasteur (CIP 107295)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107295