Strain identifier
BacDive ID: 133384
Type strain:
Species: Alcaligenes endophyticus
Strain Designation: AER 10, AER10
Strain history: <- W.-J. Li, YIM; AER10 <- X.-H. Shi
NCBI tax ID(s): 1929088 (species)
General
@ref: 64147
BacDive-ID: 133384
DSM-Number: 100498
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, motile, rod-shaped, colony-forming
description: Alcaligenes endophyticus AER 10 is a Gram-negative, motile, rod-shaped bacterium that forms circular colonies and was isolated from roots of Ammodendron bifolium obtained from Takeermohuer desert.
NCBI tax id
- NCBI tax id: 1929088
- Matching level: species
strain history
- @ref: 64147
- history: <- W.-J. Li, YIM; AER10 <- X.-H. Shi
doi: 10.13145/bacdive133384.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Alcaligenaceae
- genus: Alcaligenes
- species: Alcaligenes endophyticus
- full scientific name: Alcaligenes endophyticus Lu et al. 2017
@ref: 64147
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Alcaligenes
species: Alcaligenes endophyticus
full scientific name: Alcaligenes endophyticus Lu et al. 2017
strain designation: AER 10, AER10
type strain: yes
Morphology
cell morphology
- @ref: 25257
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: peritrichous
colony morphology
- @ref: 25257
- colony color: pale yellow
- colony shape: circular
- medium used: LB medium
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
64147 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf | |
64147 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
25257 | LB medium | yes | ||
64147 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
25257 | positive | growth | 10-45 | |
64147 | positive | growth | 30 | mesophilic |
64147 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 25257
- ability: positive
- type: growth
- pH: 5.0-9.0
- PH range: alkaliphile
Physiology and metabolism
halophily
- @ref: 25257
- salt: NaCl
- tested relation: maximum
- concentration: 10 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25257 | 78697 | D-fructose 6-phosphate | - | respiration |
25257 | 28847 | D-fucose | - | respiration |
25257 | 30612 | D-glucarate | - | respiration |
25257 | 8391 | D-gluconate | - | respiration |
25257 | 15748 | D-glucuronate | - | respiration |
25257 | 16523 | D-serine | - | respiration |
25257 | 23652 | dextrin | - | respiration |
25257 | 16865 | gamma-aminobutyric acid | - | respiration |
25257 | 5291 | gelatin | - | hydrolysis |
25257 | 29991 | L-aspartate | - | respiration |
25257 | 15971 | L-histidine | - | respiration |
25257 | 17309 | pectin | - | respiration |
25257 | 28017 | starch | - | hydrolysis |
25257 | 53424 | tween 20 | - | hydrolysis |
25257 | 53423 | tween 40 | - | hydrolysis |
25257 | 53425 | tween 60 | - | hydrolysis |
25257 | 53426 | tween 80 | - | hydrolysis |
25257 | 16651 | (S)-lactate | + | respiration |
25257 | 15589 | L-malate | + | respiration |
25257 | 30916 | 2-oxoglutarate | + | respiration |
25257 | 37054 | 3-hydroxybutyrate | + | respiration |
25257 | 161680 | aztreonam | + | respiration |
25257 | 16947 | citrate | + | respiration |
25257 | 18024 | D-galacturonic acid | + | respiration |
25257 | 53071 | L-galactonate | + | respiration |
25257 | 29985 | L-glutamate | + | respiration |
25257 | 18183 | L-pyroglutamic acid | + | respiration |
25257 | 25000 | lactone | + | respiration |
25257 | 6472 | lincomycin | + | respiration |
25257 | 51850 | methyl pyruvate | + | respiration |
25257 | 17632 | nitrate | + | reduction |
25257 | 17272 | propionate | + | respiration |
25257 | 29673 | rifamycin sv | + | respiration |
25257 | skimmed milk | + | degradation | |
25257 | 75198 | tetrazolium blue | + | respiration |
25257 | 75193 | tetrazolium violet | + | respiration |
25257 | 16763 | 2-oxobutanoate | +/- | respiration |
25257 | 18101 | 4-hydroxyphenylacetic acid | +/- | respiration |
25257 | 30089 | acetate | +/- | respiration |
25257 | 13705 | acetoacetate | +/- | respiration |
25257 | 73706 | bromosuccinate | +/- | respiration |
25257 | 37054 | 3-hydroxybutyrate | +/- | respiration |
25257 | 32323 | glucuronamide | +/- | respiration |
25257 | 16977 | L-alanine | +/- | respiration |
25257 | 18287 | L-fucose | +/- | respiration |
25257 | 25115 | malate | +/- | respiration |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
25257 | 16136 | hydrogen sulfide | yes |
68369 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
25257 | acid phosphatase | + | 3.1.3.2 |
25257 | alkaline phosphatase | + | 3.1.3.1 |
25257 | alpha-chymotrypsin | + | 3.4.21.1 |
25257 | alpha-fucosidase | - | 3.2.1.51 |
25257 | alpha-galactosidase | - | 3.2.1.22 |
25257 | alpha-glucosidase | - | 3.2.1.20 |
25257 | alpha-mannosidase | - | 3.2.1.24 |
25257 | beta-galactosidase | - | 3.2.1.23 |
25257 | beta-glucosidase | - | 3.2.1.21 |
25257 | beta-glucuronidase | - | 3.2.1.31 |
25257 | catalase | + | 1.11.1.6 |
25257 | cystine arylamidase | + | 3.4.11.3 |
25257 | cytochrome oxidase | + | 1.9.3.1 |
25257 | esterase (C 4) | + | |
25257 | esterase Lipase (C 8) | + | |
25257 | leucine arylamidase | + | 3.4.11.1 |
25257 | lipase (C 14) | + | |
25257 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
25257 | naphthol-AS-BI-phosphohydrolase | + | |
25257 | trypsin | + | 3.4.21.4 |
25257 | urease | - | 3.5.1.5 |
25257 | valine arylamidase | + | |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
fatty acid profile
fatty acids
@ref fatty acid percentage 25257 C16:0 24.2 25257 C16:1ω7c / C16:1ω6c 19.3 25257 C18:1ω7c 25 25257 cyclo-C17:0 10.5 - type of FA analysis: whole cell analysis
- incubation medium: TSB
- agar/liquid: liquid
- incubation temperature: 30
- software version: Sherlock 6.1
- library/peak naming table: TSBA 6
- system: MIS MIDI
- method/protocol: Sasser 1990
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
64147 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | |
64147 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
25257 | roots of Ammodendron bifolium obtained from Takeermohuer desert | Takeermohuer desert (not found), Xinjiang Uygur Autonomous Region, northwest China | China | CHN | Asia |
64147 | surface-sterilized roots of Ammodendron bifolium | Xinjiang Uygur Autonomous Region, Takeermohuer desert | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Desert |
#Host | #Plants | #Shrub (Scrub) |
#Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_64920.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_894;97_1043;98_45880;99_64920&stattab=map
- Last taxonomy: Alcaligenes endophyticus subclade
- 16S sequence: KR967368
- Sequence Identity:
- Total samples: 1717
- soil counts: 134
- aquatic counts: 341
- animal counts: 1158
- plant counts: 84
Safety information
risk assessment
- @ref: 64147
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64147
- description: Alcaligenes endophyticus strain AER10 16S ribosomal RNA gene, partial sequence
- accession: KR967368
- length: 1560
- database: ena
- NCBI tax ID: 1929088
Genome sequences
- @ref: 66792
- description: Alcaligenes endophyticus DSM 100498
- accession: GCA_026344035
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1929088
GC content
- @ref: 64147
- GC-content: 53.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 87.046 | yes |
flagellated | yes | 64.461 | no |
gram-positive | no | 98.144 | no |
anaerobic | no | 98.231 | no |
aerobic | yes | 80.75 | no |
halophile | no | 83.419 | no |
spore-forming | no | 95.873 | no |
glucose-ferment | no | 86.947 | no |
thermophile | no | 99.032 | yes |
glucose-util | no | 76.551 | no |
External links
@ref: 64147
culture collection no.: DSM 100498, KCTC 42688
straininfo link
- @ref: 91424
- straininfo: 403250
literature
- topic: Phylogeny
- Pubmed-ID: 27959788
- title: Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium.
- authors: Lu CY, Li YQ, Tian Y, Han MX, Rao MPN, Li YR, Zhu ZN, Wei DQ, An DD, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001719
- year: 2017
- mesh: Alcaligenes/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Desert Climate, Fabaceae/*microbiology, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | 10.1099/ijsem.0.004332 | |||
25257 | C. Y. L. Lu, Y. Q.,Tian, Y.,Han, M. X.,Rao, M. P. N.,Li, Y. R.,Zhu, Z. N.,Wei, D. Q.,An, D. D.,Li, W. J. | Alcaligenes endophyticus sp. nov., isolated from roots of Ammodendron bifolium | 10.1099/ijsem.0.001719 | IJSEM 67: 939-943 2017 | 27959788 | |
64147 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100498 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100498) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
68369 | Automatically annotated from API 20NE | |||||
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 | https://microbeatlas.org/ | |||
91424 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID403250.1 |