Strain identifier

BacDive ID: 157768

Type strain: Yes

Species: Lysobacter silvestris

Strain Designation: AM20-91

Strain history: <- R. Margesin; University of Innsbruck, Innsbruck, AUSTRIA; AM20-91

NCBI tax ID(s): 1645665 (species)

« back to strain detail view
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 8.1 (current version)

General

@ref: 64340

BacDive-ID: 157768

DSM-Number: 104734

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, chemoorganotroph, mesophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Lysobacter silvestris AM20-91 is an obligate aerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from Forest soil.

NCBI tax id

  • NCBI tax id: 1645665
  • Matching level: species

strain history

  • @ref: 64340
  • history: <- R. Margesin; University of Innsbruck, Innsbruck, AUSTRIA; AM20-91

doi: 10.13145/bacdive157768.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter silvestris
  • full scientific name: Lysobacter silvestris Margesin et al. 2018

@ref: 64340

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter silvestris

full scientific name: Lysobacter silvestris Margesin et al. 2018

strain designation: AM20-91

type strain: yes

Morphology

cell morphology

  • @ref: 65560
  • gram stain: negative
  • cell length: 1.1-1.7 µm
  • cell width: 0.4-0.5 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: polar

colony morphology

  • @ref: 65560
  • colony color: light yellow
  • colony shape: circular
  • medium used: R2A

multimedia

  • @ref: 64340
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104734.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64340R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
65560Nutrient agar (NA)yes
65560Reasoner's 2A agar (R2A)yes
65560Trypticase Soy Agar (TSA)no

culture temp

@refgrowthtypetemperaturerange
64340positivegrowth25mesophilic
65560positivegrowth10-30
65560positiveoptimum25mesophilic
65560nogrowth0psychrophilic
65560nogrowth35mesophilic

culture pH

@refabilitytypepH
65560positivegrowth6-7
65560positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65560
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 65560
  • type: chemoorganotroph

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65560NaClpositivegrowth0-1.5 %(w/v)
65560NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6556016150benzoate-assimilation
6556085146carboxymethylcellulose-hydrolysis
6556017057cellobiose-assimilation
6556015824D-fructose-assimilation
6556065327D-xylose-assimilation
6556024996lactate-assimilation
6556029806fumarate-assimilation
6556028260galactose-assimilation
655605417glucosamine-assimilation
6556017234glucose-fermentation
6556017754glycerol-assimilation
6556030849L-arabinose-assimilation
6556017716lactose-assimilation
6556017306maltose+carbon source
6556017306maltose+energy source
65560506227N-acetylglucosamine+carbon source
65560506227N-acetylglucosamine+energy source
6556017632nitrate-reduction
6556015361pyruvate+carbon source
6556015361pyruvate+energy source
65560skimmed milk-hydrolysis
6556028017starch-hydrolysis
6556030031succinate+/-carbon source
6556030031succinate+/-energy source
6556017992sucrose-assimilation
6556027082trehalose+/-carbon source
6556027082trehalose+/-energy source
6556053426tween 80-hydrolysis
65560yeast extract+carbon source
65560yeast extract+energy source

metabolite production

  • @ref: 65560
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65560catalase+1.11.1.6
65560cytochrome oxidase+1.9.3.1
65560alkaline phosphatase+3.1.3.1
65560acid phosphatase+3.1.3.2
65560esterase Lipase (C 8)+
65560leucine arylamidase+3.4.11.1
65560valine arylamidase+
65560cystine arylamidase+/-3.4.11.3
65560trypsin+3.4.21.4
65560alpha-chymotrypsin+/-3.4.21.1
65560naphthol-AS-BI-phosphohydrolase+
65560alpha-glucosidase+3.2.1.20
65560beta-galactosidase+3.2.1.23
65560beta-glucosidase+3.2.1.21
65560N-acetyl-beta-glucosaminidase+3.2.1.52
65560lipase (C 14)-
65560gelatinase-
65560alpha-galactosidase-3.2.1.22
65560beta-glucuronidase-3.2.1.31
65560alpha-mannosidase-3.2.1.24
65560alpha-fucosidase-3.2.1.51
65560arginine dihydrolase-3.5.3.6
65560urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65560C10:0 iso0.3
    65560C11:0 iso13.3
    65560C11:0 anteiso0.9
    65560C10:0 3OH0.1
    65560C11:0 iso 3OH16.9
    65560C13:0 iso1.4
    65560C14:0 iso3.9
    65560C14:1ω5c0.2
    65560C14:00.8
    65560isoC15:1 F5.1
    65560C15:0 iso32.3
    65560C15:0 anteiso6.1
    65560C16:0 iso2.9
    65560C16:1ω6c / C16:1ω7c1.3
    65560C16:01
    65560C17:1 iso ω9c / C16:0 10-methyl9.3
    65560C17:0 iso2
    65560C16:0 3OH0.3
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 25
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: da Costa et al. 2011

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture compositionenrichment culture temperatureisolation procedure
64340Forest soilSouth Tyrol, MontigglItalyITAEurope
65560alpine forest soilMontiggl, South TyrolItalyITAEurope2014R2Awith cycloheximide20Ten grams of sample were shaken with 90 ml of sterile 0.1 % sodium pyrophosphate for 15 min at 150 rpm. Appropriate dilutions, prepared with sterile saline solution (0.9 %(w/v)), were plated.

isolation source categories

Cat1Cat2Cat3
#Climate#Cold#Alpine
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_161124.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_2841;97_3495;98_106059;99_161124&stattab=map
  • Last taxonomy: Lysobacter silvestris subclade
  • 16S sequence: KP899165
  • Sequence Identity:
  • Total samples: 781
  • soil counts: 227
  • aquatic counts: 213
  • animal counts: 301
  • plant counts: 40

Sequence information

16S sequences

  • @ref: 64340
  • description: Lysobacter silvestris strain AM20-91 16S ribosomal RNA gene, partial sequence
  • accession: KP899165
  • length: 1377
  • database: ena
  • NCBI tax ID: 1645665

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter silvestris AM20-91GCA_002895945contigncbi1645665
66792Lysobacter silvestris AM20-912834284710draftimg1645665

GC content

  • @ref: 65560
  • GC-content: 63.35
  • method: genome sequence analysis

External links

@ref: 64340

culture collection no.: DSM 104734, LMG 30011

straininfo link

  • @ref: 110623
  • straininfo: 407764

literature

  • topic: Phylogeny
  • Pubmed-ID: 29547093
  • title: Lysobacter silvestris sp. nov., isolated from alpine forest soil, and reclassification of Luteimonas tolerans as Lysobacter tolerans comb. nov.
  • authors: Margesin R, Zhang DC, Albuquerque L, Froufe HJC, Egas C, da Costa MS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002710
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Italy, Lysobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
64340Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104734Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104734)
65560Rosa Margesin, De-Chao Zhang, Luciana Albuquerque, Hugo J. C. Froufe, Conceição Egas and Milton S. da CostaLysobacter silvestris sp. nov., isolated from alpine forest soil, and reclassification of Luteimonas tolerans as Lysobacter tolerans comb. nov.10.1099/ijsem.0.002710IJSEM 68: 1571-1577 201829547093
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
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/
110623Reimer, 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-ID407764.1