Strain identifier

BacDive ID: 11379

Type strain: Yes

Species: Ammoniphilus oxalivorans

Strain Designation: RAOx-FS

Strain history: CIP <- 1998, G.M. Zaitsev, Juvegroup Oy Ltd., Rovaniemi, Finland: strain RAOx-FS

NCBI tax ID(s): 66864 (species)

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General

@ref: 4404

BacDive-ID: 11379

DSM-Number: 11537

keywords: 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Ammoniphilus oxalivorans RAOx-FS is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from rhizosphere of sorrel from a public garden.

NCBI tax id

  • NCBI tax id: 66864
  • Matching level: species

strain history

@refhistory
4404<- G. M. Zaitsev, RAOx-FS
121480CIP <- 1998, G.M. Zaitsev, Juvegroup Oy Ltd., Rovaniemi, Finland: strain RAOx-FS

doi: 10.13145/bacdive11379.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Ammoniphilus
  • species: Ammoniphilus oxalivorans
  • full scientific name: Ammoniphilus oxalivorans Zaitsev et al. 1998

@ref: 4404

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Ammoniphilus

species: Ammoniphilus oxalivorans

full scientific name: Ammoniphilus oxalivorans Zaitsev et al. 1998

strain designation: RAOx-FS

type strain: yes

Morphology

cell morphology

  • @ref: 121480
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_11537_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_11537_3.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4404OM-2 MEDIUM (DSMZ Medium 782)yeshttps://mediadive.dsmz.de/medium/782Name: OM-2 MEDIUM (DSMZ Medium 782) Composition: Agar 20.0 g/l NH4-oxalate 15.0 g/l NaHCO3 10.0 g/l NaH2PO4 x 2 H2O 10.0 g/l Na2S2O3 x 5 H2O 1.0 g/l NaCl 0.7 g/l KCl 0.57 g/l MgCl2 x 6 H2O 0.1 g/l CaCl2 x 2 H2O 0.01 g/l Distilled water
121480CIP Medium 282yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=282

culture temp

@refgrowthtypetemperaturerange
4404positivegrowth30mesophilic
121480positivegrowth10-37
121480nogrowth45thermophilic
121480nogrowth55thermophilic

Physiology and metabolism

spore formation

  • @ref: 121480
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121480606565hippurate-hydrolysis
12148017632nitrate-reduction
12148016301nitrite-reduction

metabolite production

  • @ref: 121480
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121480oxidase+
121480beta-galactosidase+3.2.1.23
121480gelatinase-
121480catalase+1.11.1.6
121480gamma-glutamyltransferase-2.3.2.2
121480tryptophan deaminase-
121480urease-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
121480--++-------+--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
4404rhizosphere of sorrel (Rumex acetosa) from a public gardenRumex acetosaHelsinkiFinlandFINEurope
121480Environment, Rhizosphere of sorrel, Rumex acetosaHelsinkiFinlandFINEurope1994

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Garden
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44041Risk group (German classification)
1214801Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Ammoniphilus oxalivorans 16S rRNA gene, strain RAOx-FS
  • accession: Y14580
  • length: 1497
  • database: ena
  • NCBI tax ID: 66864

External links

@ref: 4404

culture collection no.: DSM 11537, ATCC 700648, HAMBI 2284, CIP 105539

straininfo link

  • @ref: 80609
  • straininfo: 44055

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9542085New aerobic ammonium-dependent obligately oxalotrophic bacteria: description of Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov.Zaitsev GM, Tsitko IV, Rainey FA, Trotsenko YA, Uotila JS, Stackebrandt E, Salkinoja-Salonen MSInt J Syst Bacteriol10.1099/00207713-48-1-1511998Bacteria, Aerobic/*classification/genetics/metabolism, Bacterial Proteins/analysis, Bacteriological Techniques, DNA, Bacterial/analysis, Gram-Positive Endospore-Forming Rods/*classification/genetics/metabolism, Microscopy, Electron, Microscopy, Electron, Scanning, Molecular Sequence Data, Nitrogen/metabolism, Oxalates/*metabolism, Phylogeny, Quaternary Ammonium Compounds/*metabolism, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Spores, Bacterial/ultrastructure, Sulfur/metabolismMetabolism
Phylogeny27151144Ammoniphilus resinae sp. nov., an endospore-forming bacterium isolated from resin fragments.Lin SY, Wu YH, Hameed A, Liu YC, Young CCInt J Syst Evol Microbiol10.1099/ijsem.0.0011372016Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Indonesia, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Resins, Plant, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Spores, Bacterial, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4404Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11537)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11537
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
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
68382Automatically annotated from API zym
80609Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44055.1StrainInfo: A central database for resolving microbial strain identifiers
121480Curators of the CIPCollection of Institut Pasteur (CIP 105539)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105539