Strain identifier

BacDive ID: 132627

Type strain: Yes

Species: Sphingomonas zeicaulis

Strain Designation: 541

Strain history: <- J.-L. Gao, Beijing Academy of Agriculture and Forestry Science; 541

NCBI tax ID(s): 1632740 (species)

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General

@ref: 24416

BacDive-ID: 132627

DSM-Number: 100587

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

description: Sphingomonas zeicaulis 541 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize.

NCBI tax id

  • NCBI tax id: 1632740
  • Matching level: species

strain history

  • @ref: 24416
  • history: <- J.-L. Gao, Beijing Academy of Agriculture and Forestry Science; 541

doi: 10.13145/bacdive132627.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas zeicaulis
  • full scientific name: Sphingomonas zeicaulis Gao et al. 2016

@ref: 24416

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas zeicaulis

full scientific name: Sphingomonas zeicaulis Gao et al. 2016

strain designation: 541

type strain: yes

Morphology

cell morphology

  • @ref: 43170
  • gram stain: negative
  • cell length: 0.9-1.9 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43170
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: LB agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24416TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
24416LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf
43170LB (Luria-Bertani) MEDIUMyes
43170tryptic soy agar (TSA)yes
24416NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43170positiveoptimum25mesophilic
43170positivegrowth5-45
24416positivegrowth28mesophilic

culture pH

@refabilitytypepH
43170positivegrowth6.0-8.0
43170positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43170
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43170NaClpositivegrowth0-2 %(w/v)
43170NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43170casein-hydrolysis
43170starch-hydrolysis28017
43170esculin+hydrolysis4853
43170beta-d-glucose+assimilation15903
43170L-arabinose+assimilation30849
43170potassium gluconate+assimilation32032
43170malate+assimilation25115
43170maltose+assimilation17306
43170D-trehalose+assimilation16551
43170cellobiose+assimilation17057
43170gentiobiose+assimilation28066
43170sucrose+assimilation17992
43170turanose+assimilation32528
43170alpha-lactose+assimilation36219
43170melibiose+assimilation28053
43170methyl beta-D-glucopyranoside+assimilation320055
43170salicin+assimilation17814
43170alpha-D-glucose+assimilation17925
43170D-mannose+assimilation16024
43170D-fructose+assimilation15824
43170D-galactose+assimilation12936
43170D-fucose+assimilation28847
43170L-fucose+assimilation18287
43170L-rhamnose+assimilation62345
43170sodium lactate+assimilation75228
43170rifamycin sv+assimilation29673
43170glycine-proline+assimilation70744
43170D-gluconate+assimilation8391
43170tetrazolium blue+assimilation75198
43170bromosuccinate+assimilation73706
43170nalidixic acid+assimilation100147
43170aztreonam+assimilation161680
43170tetrazolium violet-assimilation75193
43170dextrin-assimilation23652
43170gelatin-hydrolysis5291
43170nitrate-reduction17632

enzymes

@refvalueactivityec
43170catalase+1.11.1.6
43170cytochrome oxidase-1.9.3.1
43170beta-galactosidase+/-3.2.1.23
43170esterase (C 4)+
43170acid phosphatase+3.1.3.2
43170naphthol-AS-BI-phosphohydrolase+
43170alkaline phosphatase-3.1.3.1
43170esterase Lipase (C 8)-
43170leucine arylamidase-3.4.11.1
43170valine arylamidase-
43170cystine arylamidase-3.4.11.3
43170trypsin-3.4.21.4
43170alpha-glucosidase-3.2.1.20
43170N-acetyl-beta-glucosaminidase-3.2.1.52
43170lipase (C 14)-
43170alpha-chymotrypsin-3.4.21.1
43170alpha-galactosidase-3.2.1.22
43170beta-glucuronidase-3.2.1.31
43170beta-glucosidase-3.2.1.21
43170alpha-mannosidase-3.2.1.24
43170alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43170C14:02.1
    43170C14:0 2OH11.4
    43170C14:0 anteiso0.9
    43170C15:0 anteiso1.2
    43170C16:022
    43170C16:1ω5c1.3
    43170C18:1ω7c50.9
    43170C18:1ω7c 11-methyl4.4
    43170C15:0 iso 2OH / C16:1ω7c5.9
  • type of FA analysis: whole cell analysis
  • incubation medium: NK medium
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • instrument: model 6890, Hewlett Packard

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24416surface-sterilized root tissue of maizeBeijing, Fangshan DistrictChinaCHNAsia
43170surface-sterilized root tissue of maizeFangshan District, BeijingChinaCHNAsiaLB medium2-3 days21

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_90571.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_1204;97_1421;98_1729;99_90571&stattab=map
  • Last taxonomy: Sphingomonas zeicaulis
  • 16S sequence: KP172592
  • Sequence Identity:
  • Total samples: 26
  • soil counts: 9
  • aquatic counts: 8
  • animal counts: 7
  • plant counts: 2

Safety information

risk assessment

  • @ref: 24416
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24416
  • description: Sphingomonas zeicaulis strain 541 16S ribosomal RNA gene, complete sequence
  • accession: KP172592
  • length: 1445
  • database: ena
  • NCBI tax ID: 1632740

Genome sequences

  • @ref: 66792
  • description: Sphingomonas zeicaulis DSM 100587
  • accession: 2828417763
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1632740

GC content

  • @ref: 24416
  • GC-content: 64.7
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 24416

culture collection no.: DSM 100587, CGMCC 1.15008

straininfo link

  • @ref: 90941
  • straininfo: 405549

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
24416Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100587Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100587)
43170Jun-lian Gao, Pengbo Sun, Xu-ming Wang, Shoutao Cheng, Fanyang Lv, Tian-lei Qiu, Mei Yuan, Jian-guang SunSphingomonas zeicaulis sp. nov., an endophytic bacterium isolated from maize root10.1099/ijsem.0.001262IJSEM 66: 3755-3760 201627374123
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/
90941Reimer, 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-ID405549.1