Strain identifier

BacDive ID: 140361

Type strain: Yes

Species: Desulfosarcina alkanivorans

Strain Designation: PL12

Strain history: M. Watanabe; Hokkaido Univ., Japan; PL12.

NCBI tax ID(s): 571177 (species)

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General

@ref: 42968

BacDive-ID: 140361

DSM-Number: 103901

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

description: Desulfosarcina alkanivorans PL12 is an anaerobe, Gram-negative, motile bacterium that was isolated from oil-polluted marine sediment, p-xylene-degrading sulfate-reducing enrichment culture.

NCBI tax id

  • NCBI tax id: 571177
  • Matching level: species

strain history

@refhistory
42968<- M. Watanabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; PL12 <- Y. Higashioka {2008}
67770M. Watanabe; Hokkaido Univ., Japan; PL12.

doi: 10.13145/bacdive140361.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfobacterales
  • family: Desulfobacteraceae
  • genus: Desulfosarcina
  • species: Desulfosarcina alkanivorans
  • full scientific name: Desulfosarcina alkanivorans Watanabe et al. 2017

@ref: 42968

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulfosarcina

species: Desulfosarcina alkanivorans

full scientific name: Desulfosarcina alkanivorans Watanabe et al. 2017

strain designation: PL12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43887negative1.0-1.5 µm0.5 µmrod-shapedyes
69480yes97.12
69480negative99.999

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43887Basal mediumyesdefined bicarbonate-buffered, sulfate-reduced saltwater medium
42968DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)yesName: DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na-L-lactate 2.49252 g/l Na2CO3 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled waterhttps://mediadive.dsmz.de/medium/195c

culture temp

@refgrowthtypetemperaturerange
43887positivegrowth18-37
43887positiveoptimum30-34mesophilic
42968positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
43887positivegrowth6.5-7.3
43887positiveoptimum7.0-7.3

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43887anaerobe
69480anaerobe96.919

spore formation

@refspore formationconfidence
43887no
69481no100
69480no99.396

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4388716716benzene-carbon source
4388716150benzoate-carbon source
4388716947citrate-carbon source
4388716236ethanol-carbon source
4388717234glucose-carbon source
4388717790methanol-carbon source
4388715882phenol-carbon source
4388717578toluene-carbon source
4388727338xylene-carbon source
4388733403elemental sulfur-electron acceptor
4388729806fumarate-electron acceptor
4388717632nitrate-electron acceptor
4388716716benzene-electron donor
4388716150benzoate-electron donor
4388716947citrate-electron donor
4388716236ethanol-electron donor
4388717234glucose-electron donor
4388717790methanol-electron donor
4388715882phenol-electron donor
4388717578toluene-electron donor
4388727338xylene-electron donor
4388730089acetate+carbon source
4388717968butyrate+carbon source
4388741808decane+carbon source
4388715740formate+carbon source
4388729806fumarate+carbon source
4388729021hexane+carbon source
4388724996lactate+carbon source
4388717272propionate+carbon source
4388715361pyruvate+carbon source
4388730031succinate+carbon source
43887yeast extract+carbon source
4388716189sulfate+electron acceptor
4388717359sulfite+electron acceptor
4388716094thiosulfate+electron acceptor
4388730089acetate+electron donor
4388717968butyrate+electron donor
4388741808decane+electron donor
4388715740formate+electron donor
4388729806fumarate+electron donor
4388729021hexane+electron donor
4388724996lactate+electron donor
4388717272propionate+electron donor
4388715361pyruvate+electron donor
4388730031succinate+electron donor
4388716189sulfate+electron donor
43887yeast extract+electron donor
4388729806fumarate+fermentation
4388724996lactate+fermentation
4388725115malate+fermentation

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43887C15:0 anteiso11.6
    43887C14:09.4
    43887C15:021.3
    43887C15:0 DMA1.8
    43887C15:1ω6c5.9
    43887C16:017.8
    43887C16:1ω5c1.1
    43887C16:1ω7c7.6
    43887C17:05.9
    43887C17:1ω6c6
    43887C17:1ω8c4.7
    43887C17:1ω8c3.8
    43887C18:01.4
    43887C15:0 iso1.6
  • type of FA analysis: whole cell analysis
  • incubation medium: Basal medium, defined bicarbonate-buffered, sulfate-reduced saltwater medium
  • agar/liquid: agar
  • incubation temperature: 28
  • treatment: medium supplemented with 5mM fumarate
  • software version: Sherlock 6.0
  • library/peak naming table: MOORE6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
42968oil-polluted marine sediment, p-xylene-degrading sulfate-reducing enrichment cultureShuaibaKuwaitKWTAsia
43887p-xylene degarding sulfate-reducing enrichment culture established from petroleum-contaminated marine sediments of Shuaiba, KuwaitShuaibaKuwaitKWTAsia
67770Oil-polluted marine sediments of ShuaibaKuwaitKWTAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Engineered#Contamination#Oil (Fuel)
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_16088.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_127;96_1915;97_6501;98_12125;99_16088&stattab=map
  • Last taxonomy: Desulfosarcina alkanivorans subclade
  • 16S sequence: AB468588
  • Sequence Identity:
  • Total samples: 122
  • soil counts: 4
  • aquatic counts: 110
  • animal counts: 2
  • plant counts: 6

Safety information

risk assessment

  • @ref: 42968
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42968
  • description: Desulfosarcina alkanivorans gene for 16S ribosomal RNA, partial sequence
  • accession: AB468588
  • length: 1526
  • database: ena
  • NCBI tax ID: 571177

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfosarcina alkanivorans PL12GCA_009688945completencbi571177
66792Desulfosarcina alkanivorans strain PL12571177.3completepatric571177

GC content

  • @ref: 42968
  • GC-content: 57

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.582yes
flagellatedno66.449no
gram-positiveno98.983no
anaerobicyes96.737no
aerobicno95.28no
halophileno77.658no
spore-formingno89.733yes
glucose-utilyes51.882no
thermophileno99.702no
glucose-fermentno84.897no

External links

@ref: 42968

culture collection no.: DSM 103901, JCM 31728

straininfo link

  • @ref: 96659
  • straininfo: 400690

literature

  • topic: Phylogeny
  • Pubmed-ID: 28820122
  • title: Desulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment and emended description of the genus Desulfosarcina.
  • authors: Watanabe M, Higashioka Y, Kojima H, Fukui M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002062
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Hydrocarbons/*metabolism, Kuwait, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/classification/genetics/isolation & purification
  • topic2: Enzymology

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
42968Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103901Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103901)
43887Miho Watanabe, Yuriko Higashioka, Hisaya Kojima, Manabu FukuiDesulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment and emended description of the genus Desulfosarcina10.1099/ijsem.0.002062IJSEM 67: 2994-2997 201728820122
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
96659Reimer, 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-ID400690.1