Strain identifier
BacDive ID: 1109
Type strain:
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)
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
@ref | history |
---|---|
3245 | <- NCIMB <- Novo Industri |
121987 | CIP <- 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
@ref synonym 20215 Alkalihalobacillus pseudofirmus 20215 Bacillus 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
@ref | name | growth | link | composition |
---|---|---|---|---|
3245 | ALKALINE NUTRIENT AGAR (DSMZ Medium 31) | yes | https://mediadive.dsmz.de/medium/31 | Name: 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 |
39253 | MEDIUM 113 - for Bacillus | yes | Distilled water make up to (900.000 ml);Columbia agar (39.000 g);Solution 1 - M00343 (100.000 ml) | |
121987 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
121987 | CIP Medium 113 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=113 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3245 | positive | growth | 30 | mesophilic |
39253 | positive | growth | 30 | mesophilic |
121987 | positive | growth | 10-45 | |
121987 | no | growth | 55 | thermophilic |
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
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | + | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
121987 | citrate | - | carbon source | 16947 |
121987 | esculin | - | hydrolysis | 4853 |
121987 | hippurate | - | hydrolysis | 606565 |
121987 | nitrate | - | reduction | 17632 |
121987 | nitrite | - | reduction | 16301 |
121987 | nitrate | - | respiration | 17632 |
metabolite production
- @ref: 121987
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
121987 | 15688 | acetoin | - | |
121987 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
121987 | oxidase | - | |
121987 | beta-galactosidase | + | 3.2.1.23 |
121987 | alcohol dehydrogenase | - | 1.1.1.1 |
121987 | gelatinase | + | |
121987 | amylase | - | |
121987 | DNase | - | |
121987 | caseinase | + | 3.4.21.50 |
121987 | catalase | + | 1.11.1.6 |
121987 | tween esterase | - | |
121987 | gamma-glutamyltransferase | - | 2.3.2.2 |
121987 | lysine decarboxylase | - | 4.1.1.18 |
121987 | ornithine decarboxylase | - | 4.1.1.17 |
121987 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121987 | - | - | + | + | - | + | - | - | - | + | - | + | - | - | - | + | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121987 | +/- | - | - | - | + | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | - | + | + | + | +/- | + | - | - | +/- | + | - | - | - | +/- | + | - | - | - | - | - | - | - | - | - | +/- | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
3245 | lake bank soil | Holstein | Germany | DEU | Europe |
121987 | Environment, 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
@ref | biosafety level | biosafety level comment |
---|---|---|
3245 | 1 | Risk group (German classification) |
121987 | 1 | Risk 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
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 88.831 | no |
flagellated | yes | 79.654 | no |
gram-positive | yes | 85.411 | no |
anaerobic | no | 97.42 | no |
aerobic | yes | 90.514 | no |
halophile | yes | 67.888 | no |
spore-forming | yes | 94.977 | no |
glucose-ferment | no | 93.564 | no |
thermophile | no | 98.796 | yes |
glucose-util | yes | 91.487 | no |
External links
@ref: 3245
culture collection no.: DSM 8715, ATCC 700159, NCIB 10283, CIP 105299, NCIMB 10283
straininfo link
- @ref: 70781
- straininfo: 10535
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10741833 | Reidentification of facultatively alkaliphilic Bacillus firmus OF4 as Bacillus pseudofirmus OF4. | Takami H, Krulwich TA | Extremophiles | 10.1007/s007920050003 | 2000 | Bacillus/*classification, DNA, Ribosomal/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Serotyping | Transcriptome |
Phylogeny | 15774682 | Bacillus bogoriensis sp. nov., a novel alkaliphilic, halotolerant bacterium isolated from a Kenyan soda lake. | Vargas VA, Delgado OD, Hatti-Kaul R, Mattiasson B | Int J Syst Evol Microbiol | 10.1099/ijs.0.63318-0 | 2005 | Bacillus/*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 Chloride | Genetics |
Phylogeny | 19700450 | Bacillus marmarensis sp. nov., an alkaliphilic, protease-producing bacterium isolated from mushroom compost. | Denizci AA, Kazan D, Erarslan A | Int J Syst Evol Microbiol | 10.1099/ijs.0.012369-0 | 2009 | *Agaricales, Bacillus/*classification/genetics/isolation & purification, Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil | Genetics |
Phylogeny | 24554634 | Bacillus 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 L | Int J Syst Evol Microbiol | 10.1099/ijs.0.058610-0 | 2014 | Bacillus/*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 Microbiology | Genetics |
Phylogeny | 26604103 | Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils. | Dou G, Liu H, He W, Ma Y | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0616-y | 2015 | Bacillus/*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 Microbiology | Metabolism |
Phylogeny | 28905696 | Paralkalibacillus 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 I | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002248 | 2017 | Bacillaceae/*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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3245 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8715) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8715 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
39253 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17303 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68371 | Automatically annotated from API 50CH acid | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
70781 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10535.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121987 | Curators of the CIP | Collection of Institut Pasteur (CIP 105299) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105299 |