Strain identifier

BacDive ID: 1109

Type strain: Yes

Species: Alkalihalophilus pseudofirmus

Strain Designation: C 324, PN 3

Strain history: CIP <- 1997, DSMZ <- NCIMB <- Novo Indust.: strain C 324

NCBI tax ID(s): 79885 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3245

BacDive-ID: 1109

DSM-Number: 8715

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Alkalihalophilus pseudofirmus C 324 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from lake bank soil.

NCBI tax id

  • NCBI tax id: 79885
  • Matching level: species

strain history

@refhistory
3245<- NCIMB <- Novo Industri
121987CIP <- 1997, DSMZ <- NCIMB <- Novo Indust.: strain C 324

doi: 10.13145/bacdive1109.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Alkalihalophilus
  • species: Alkalihalophilus pseudofirmus
  • full scientific name: Alkalihalophilus pseudofirmus (Nielsen et al. 1995) Joshi et al. 2022
  • synonyms

    @refsynonym
    20215Alkalihalobacillus pseudofirmus
    20215Bacillus pseudofirmus

@ref: 3245

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Alkalihalophilus

species: Alkalihalophilus pseudofirmus

full scientific name: Alkalihalophilus pseudofirmus (Nielsen et al. 1995) Joshi et al. 2022

strain designation: C 324, PN 3

type strain: yes

Morphology

cell morphology

  • @ref: 121987
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3245ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
39253MEDIUM 113 - for BacillusyesDistilled water make up to (900.000 ml);Columbia agar (39.000 g);Solution 1 - M00343 (100.000 ml)
121987CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121987CIP Medium 113yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=113

culture temp

@refgrowthtypetemperaturerange
3245positivegrowth30mesophilic
39253positivegrowth30mesophilic
121987positivegrowth10-45
121987nogrowth55thermophilic

culture pH

  • @ref: 121987
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 121987
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 121987
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
121987citrate-carbon source16947
121987esculin-hydrolysis4853
121987hippurate-hydrolysis606565
121987nitrate-reduction17632
121987nitrite-reduction16301
121987nitrate-respiration17632

metabolite production

  • @ref: 121987
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12198715688acetoin-
12198717234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
121987oxidase-
121987beta-galactosidase+3.2.1.23
121987alcohol dehydrogenase-1.1.1.1
121987gelatinase+
121987amylase-
121987DNase-
121987caseinase+3.4.21.50
121987catalase+1.11.1.6
121987tween esterase-
121987gamma-glutamyltransferase-2.3.2.2
121987lysine decarboxylase-4.1.1.18
121987ornithine decarboxylase-4.1.1.17
121987urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121987--++-+---+-+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121987+/----+-----+++--------+-++++/-+--+/-+---+/-+---------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3245lake bank soilHolsteinGermanyDEUEurope
121987Environment, Lake bank soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5186.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2523;97_3081;98_3867;99_5186&stattab=map
  • Last taxonomy: Alkalihalobacillus pseudofirmus
  • 16S sequence: X76439
  • Sequence Identity:
  • Total samples: 5930
  • soil counts: 1074
  • aquatic counts: 1398
  • animal counts: 3124
  • plant counts: 334

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32451Risk group (German classification)
1219871Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bacillus pseudofirmus DSM 8715, 16S rRNA gene
  • accession: X76439
  • length: 1506
  • database: ena
  • NCBI tax ID: 79885

Genome sequences

  • @ref: 66792
  • description: Alkalihalophilus pseudofirmus DSM 8715
  • accession: GCA_029094545
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 79885

GC content

  • @ref: 3245
  • GC-content: 39.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.831no
flagellatedyes79.654no
gram-positiveyes85.411no
anaerobicno97.42no
aerobicyes90.514no
halophileyes67.888no
spore-formingyes94.977no
glucose-fermentno93.564no
thermophileno98.796yes
glucose-utilyes91.487no

External links

@ref: 3245

culture collection no.: DSM 8715, ATCC 700159, NCIB 10283, CIP 105299, NCIMB 10283

straininfo link

  • @ref: 70781
  • straininfo: 10535

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10741833Reidentification of facultatively alkaliphilic Bacillus firmus OF4 as Bacillus pseudofirmus OF4.Takami H, Krulwich TAExtremophiles10.1007/s0079200500032000Bacillus/*classification, DNA, Ribosomal/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, SerotypingTranscriptome
Phylogeny15774682Bacillus bogoriensis sp. nov., a novel alkaliphilic, halotolerant bacterium isolated from a Kenyan soda lake.Vargas VA, Delgado OD, Hatti-Kaul R, Mattiasson BInt J Syst Evol Microbiol10.1099/ijs.0.63318-02005Bacillus/*classification/genetics/growth & development/isolation & purification, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Hydrogen-Ion Concentration, Kenya, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium ChlorideGenetics
Phylogeny19700450Bacillus marmarensis sp. nov., an alkaliphilic, protease-producing bacterium isolated from mushroom compost.Denizci AA, Kazan D, Erarslan AInt J Syst Evol Microbiol10.1099/ijs.0.012369-02009*Agaricales, Bacillus/*classification/genetics/isolation & purification, Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *SoilGenetics
Phylogeny24554634Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai LInt J Syst Evol Microbiol10.1099/ijs.0.058610-02014Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny26604103Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils.Dou G, Liu H, He W, Ma YAntonie Van Leeuwenhoek10.1007/s10482-015-0616-y2015Bacillus/*classification/genetics/*isolation & purification/metabolism, Base Sequence, Cell Wall/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/metabolism, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism/pharmacology, Soil/chemistry, *Soil MicrobiologyMetabolism
Phylogeny28905696Paralkalibacillus indicireducens gen., nov., sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor used for dyeing.Hirota K, Nishita M, Matsuyama H, Yumoto IInt J Syst Evol Microbiol10.1099/ijsem.0.0022482017Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Coloring Agents, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Fermentation, *Indigo Carmine, Japan, Nucleic Acid Hybridization, *Phylogeny, Polygonum, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3245Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8715)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8715
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
39253Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17303
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)
68371Automatically annotated from API 50CH acid
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
70781Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10535.1StrainInfo: A central database for resolving microbial strain identifiers
121987Curators of the CIPCollection of Institut Pasteur (CIP 105299)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105299