Strain identifier

BacDive ID: 133384

Type strain: Yes

Species: Alcaligenes endophyticus

Strain Designation: AER 10, AER10

Strain history: <- W.-J. Li, YIM; AER10 <- X.-H. Shi

NCBI tax ID(s): 1929088 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 8.1 (current version)

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

@refnamegrowthlinkcomposition
64147NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
64147TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
25257LB mediumyes
64147CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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

@refgrowthtypetemperaturerange
25257positivegrowth10-45
64147positivegrowth30mesophilic
64147positivegrowth28mesophilic

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2525778697D-fructose 6-phosphate-respiration
2525728847D-fucose-respiration
2525730612D-glucarate-respiration
252578391D-gluconate-respiration
2525715748D-glucuronate-respiration
2525716523D-serine-respiration
2525723652dextrin-respiration
2525716865gamma-aminobutyric acid-respiration
252575291gelatin-hydrolysis
2525729991L-aspartate-respiration
2525715971L-histidine-respiration
2525717309pectin-respiration
2525728017starch-hydrolysis
2525753424tween 20-hydrolysis
2525753423tween 40-hydrolysis
2525753425tween 60-hydrolysis
2525753426tween 80-hydrolysis
2525716651(S)-lactate+respiration
2525715589L-malate+respiration
25257309162-oxoglutarate+respiration
25257370543-hydroxybutyrate+respiration
25257161680aztreonam+respiration
2525716947citrate+respiration
2525718024D-galacturonic acid+respiration
2525753071L-galactonate+respiration
2525729985L-glutamate+respiration
2525718183L-pyroglutamic acid+respiration
2525725000lactone+respiration
252576472lincomycin+respiration
2525751850methyl pyruvate+respiration
2525717632nitrate+reduction
2525717272propionate+respiration
2525729673rifamycin sv+respiration
25257skimmed milk+degradation
2525775198tetrazolium blue+respiration
2525775193tetrazolium violet+respiration
25257167632-oxobutanoate+/-respiration
25257181014-hydroxyphenylacetic acid+/-respiration
2525730089acetate+/-respiration
2525713705acetoacetate+/-respiration
2525773706bromosuccinate+/-respiration
25257370543-hydroxybutyrate+/-respiration
2525732323glucuronamide+/-respiration
2525716977L-alanine+/-respiration
2525718287L-fucose+/-respiration
2525725115malate+/-respiration
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2525716136hydrogen sulfideyes
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25257acid phosphatase+3.1.3.2
25257alkaline phosphatase+3.1.3.1
25257alpha-chymotrypsin+3.4.21.1
25257alpha-fucosidase-3.2.1.51
25257alpha-galactosidase-3.2.1.22
25257alpha-glucosidase-3.2.1.20
25257alpha-mannosidase-3.2.1.24
25257beta-galactosidase-3.2.1.23
25257beta-glucosidase-3.2.1.21
25257beta-glucuronidase-3.2.1.31
25257catalase+1.11.1.6
25257cystine arylamidase+3.4.11.3
25257cytochrome oxidase+1.9.3.1
25257esterase (C 4)+
25257esterase Lipase (C 8)+
25257leucine arylamidase+3.4.11.1
25257lipase (C 14)+
25257N-acetyl-beta-glucosaminidase-3.2.1.52
25257naphthol-AS-BI-phosphohydrolase+
25257trypsin+3.4.21.4
25257urease-3.5.1.5
25257valine arylamidase+
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25257C16:024.2
    25257C16:1ω7c / C16:1ω6c19.3
    25257C18:1ω7c25
    25257cyclo-C17:010.5
  • 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

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
64147-----------------++-
64147-----------------++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25257roots of Ammodendron bifolium obtained from Takeermohuer desertTakeermohuer desert (not found), Xinjiang Uygur Autonomous Region, northwest ChinaChinaCHNAsia
64147surface-sterilized roots of Ammodendron bifoliumXinjiang Uygur Autonomous Region, Takeermohuer desertChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#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

traitpredictionconfidencetraining_data
motileyes87.046yes
flagellatedyes64.461no
gram-positiveno98.144no
anaerobicno98.231no
aerobicyes80.75no
halophileno83.419no
spore-formingno95.873no
glucose-fermentno86.947no
thermophileno99.032yes
glucose-utilno76.551no

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

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25257C. 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 bifolium10.1099/ijsem.0.001719IJSEM 67: 939-943 201727959788
64147Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100498Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100498)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91424Reimer, 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 identifiers10.60712/SI-ID403250.1