Strain identifier

BacDive ID: 132358

Type strain: Yes

Species: Sulfurirhabdus autotrophica

Strain Designation: BiSO

Strain history: <- T. Watanabe, Univ. Hokkaido; BiSO <- T. Watanabe, Hokkaido University, Japan {2015}

NCBI tax ID(s): 1706046 (species)

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General

@ref: 24147

BacDive-ID: 132358

DSM-Number: 100309

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, rod-shaped

description: Sulfurirhabdus autotrophica BiSO is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from freshwater lake sediment.

NCBI tax id

  • NCBI tax id: 1706046
  • Matching level: species

strain history

  • @ref: 24147
  • history: <- T. Watanabe, Univ. Hokkaido; BiSO <- T. Watanabe, Hokkaido University, Japan {2015}

doi: 10.13145/bacdive132358.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Nitrosomonadales
  • family: Sulfuricellaceae
  • genus: Sulfurirhabdus
  • species: Sulfurirhabdus autotrophica
  • full scientific name: Sulfurirhabdus autotrophica Watanabe et al. 2016

@ref: 24147

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Sulfuricellales

family: Sulfuricellaceae

genus: Sulfurirhabdus

species: Sulfurirhabdus autotrophica

full scientific name: Sulfurirhabdus autotrophica Watanabe et al. 2016

strain designation: BiSO

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65216negative1.4-4.6 µm0.4-0.7 µmrod-shaped
69480yes98.594
69480negative99.997

Culture and growth conditions

culture medium

  • @ref: 24147
  • name: SULFURIFERULA MULTIVORANS MEDIUM (DSMZ Medium 1585)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1585
  • composition: Name: SULFURIFERULA MULTIVORANS MEDIUM (DSMZ Medium 1585) Composition: Na2S2O3 x 5 H2O 10.0 g/l Na2HPO4 x 12 H2O 3.0 g/l KH2PO4 1.8 g/l (NH4)2SO4 0.1 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.04 g/l MnSO4 x 5 H2O 0.03 g/l FeCl3 x 6 H2O 0.03 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24147positivegrowth15psychrophilic
65216positivegrowth0-32
65216positiveoptimum15-22psychrophilic

culture pH

@refabilitytypepH
65216positivegrowth5.2-8.1
65216positiveoptimum6.1-6.3

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.969

halophily

@refsaltgrowthtested relationconcentration
65216NaClpositivegrowth0-0.546 M
65216NaClpositiveoptimum0-0.066 M

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6521630089acetate-growth
6521622599arabinose-growth
6521616150benzoate-growth
65216casamino acids-growth
6521618276dihydrogen-growth
6521633403elemental sulfur-sulfur source
6521633403elemental sulfur+electron donor
6521633403elemental sulfur+oxidation
6521616236ethanol-growth
6521615740formate-growth
6521629806fumarate-growth
6521617234glucose-growth
6521624996lactate-growth
6521617716lactose-growth
6521625115malate-growth
6521637684mannose-growth
6521617632nitrate-growth
6521617632nitrate-reduction
6521616301nitrite-growth
65216peptone (0.01 %, w/v)-growth
6521615226tetrathionate+electron donor
6521615226tetrathionate+oxidation
6521616094thiosulfate+electron donor
6521616094thiosulfate+oxidation
6521616094thiosulfate+sulfur source
65216yeast extract (0.01 %, w/v)-growth

enzymes

@refvalueactivityec
65216catalase-1.11.1.6
65216cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65216C9:00.1
    65216C9:0 3-OH0.1
    65216C10:00.2
    65216C10:0 3OH5.4
    65216C12:00.5
    65216C14:01.1
    65216C15:1ω8c0.1
    65216C15:1ω6c0.2
    65216C16:1ω5c0.6
    65216C16:026.4
    65216C16:0 3OH0.2
    65216C17:00.2
    65216C17:1ω8c0.3
    65216C17:1ω6c0.4
    65216C18:1ω9c0.3
    65216C16:1ω7c and/or C16:1ω6c61.8
    65216C18:1ω7c and/or C18:1ω6c2
    65216C18:00.4
  • type of FA analysis: whole cell analysis
  • incubation medium: bicarbonate-buffered, low-salt de?ned medium modi?ed for aerobic cultivation
  • incubation temperature: 15
  • incubation pH: 7
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureenrichment culture compositionenrichment culture temperatureisolation procedure
24147freshwater lake sedimentShiga, Lake Biwa, station AJapanJPNAsia35.3833136.117
65216sediment samplecold anoxic hypolimnion of freshwater Lake BiwaJapanJPNAsia35.3833136.1172010-12bicarbonate-buffered low-salt defined medium(all l^-1): 0.2 g MgCl 2 .6H 2 O, 0.1 g CaCl 2 .2H 2 O, 0.1 g NH 4 Cl, 0.1 g KH 2 PO 4 , 0.1 g KCl, 1 ml trace element solution, 1 ml selenite-tungstate solution, 1 ml vitamin mixture solution, 1 ml vitamin B 12 solution, 1 ml thiamine solution, 30 ml NaHCO3 solution. Elemental sulfur (approximately 0.25 g l^-1) and sodium nitrate (20 mM). The headspace of the culture bottle was filled with N 2 /CO 2 (80 : 20, v/v).5incubation in the dark

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_76660.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_2539;97_41117;98_53596;99_76660&stattab=map
  • Last taxonomy: Sulfuricella
  • 16S sequence: LC076472
  • Sequence Identity:
  • Total samples: 173
  • soil counts: 30
  • aquatic counts: 141
  • animal counts: 2

Safety information

risk assessment

  • @ref: 24147
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24147
  • description: Sulfurirhabdus autotrophica gene for 16S ribosomal RNA, partial sequence
  • accession: LC076472
  • length: 1433
  • database: ena
  • NCBI tax ID: 1706046

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sulfurirhabdus autotrophica DSM 100309GCA_004346685contigncbi1706046
66792Sulfurirhabdus autotrophica strain DSM 1003091706046.4wgspatric1706046
66792Sulfurirhabdus autotrophica DSM 1003092788499826draftimg1706046

GC content

  • @ref: 24147
  • GC-content: 44
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.631no
gram-positiveno99.117yes
anaerobicno93.229no
aerobicno85.435no
halophileno91.555yes
spore-formingno95.29no
thermophileno92.945yes
glucose-utilno71.413yes
flagellatedyes65.65no
glucose-fermentno87.225no

External links

@ref: 24147

culture collection no.: DSM 100309, NBRC 110941

straininfo link

  • @ref: 90704
  • straininfo: 405628

literature

  • topic: Phylogeny
  • Pubmed-ID: 26475581
  • title: Sulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake.
  • authors: Watanabe T, Kojima H, Shinohara A, Fukui M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000679
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

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
24147Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100309Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100309)
65216Tomohiro Watanabe, Hisaya Kojima, Arisa Shinohara, Manabu FukuiSulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake10.1099/ijsem.0.000679IJSEM 66: 113-117 201626475581
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90704Reimer, 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-ID405628.1