Strain identifier

BacDive ID: 13684

Type strain: Yes

Species: Sulfitobacter indolifex

Strain history: <- I. Wagner-Döbler; Hel45

NCBI tax ID(s): 225422 (species)

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General

@ref: 5583

BacDive-ID: 13684

DSM-Number: 14862

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

description: Sulfitobacter indolifex DSM 14862 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 225422
  • Matching level: species

strain history

  • @ref: 5583
  • history: <- I. Wagner-Döbler; Hel45

doi: 10.13145/bacdive13684.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Sulfitobacter
  • species: Sulfitobacter indolifex
  • full scientific name: Sulfitobacter indolifex (Wagner-Döbler et al. 2004) Liu et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Oceanibulbus indolifex

@ref: 5583

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Sulfitobacter

species: Sulfitobacter indolifex

full scientific name: Sulfitobacter indolifex (Wagner-Döbler et al. 2004) Liu et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30027negative4 µm2.15 µmrod-shapedno
43335negative3-5 µm1.8-2.5 µmrod-shaped

colony morphology

@refincubation periodcolony colorcolony shapemedium used
55832-3 days
433353 daysyellowycircularMarine agar 2216

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5583BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
43335Marine broth 2216yes
43335Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
5583positivegrowth28mesophilic
30027positivegrowth15-30
30027positiveoptimum27.5mesophilic
43335positiveoptimum25-30mesophilic
43335positivegrowth10-30

culture pH

@refabilitytypepHPH range
30027positivegrowth7.0-8.0
30027positiveoptimum7.5
43335positivegrowth7-9alkaliphile
43335positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30027aerobe
43335aerobe

spore formation

  • @ref: 30027
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30027NaClpositivegrowth1.0-7.0 %
30027NaClpositiveoptimum4 %
43335NaClpositivegrowth1-10 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3002717128adipate+carbon source
3002716449alanine+carbon source
3002722653asparagine+carbon source
3002735391aspartate+carbon source
3002716947citrate+carbon source
3002717234glucose+carbon source
3002729987glutamate+carbon source
3002717754glycerol+carbon source
3002724996lactate+carbon source
3002725115malate+carbon source
3002729864mannitol+carbon source
3002718257ornithine+carbon source
3002726271proline+carbon source
3002715361pyruvate+carbon source
3002717822serine+carbon source
3002730031succinate+carbon source
4333517634D-glucose+builds acid from
4333516899D-mannitol+builds acid from
4333517128adipate+builds acid from
4333525115malate+builds acid from
4333553258sodium citrate+builds acid from
4333518401phenylacetate+builds acid from
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
5583catalase+1.11.1.6
5583cytochrome-c oxidase+1.9.3.1
30027catalase+1.11.1.6
30027cytochrome oxidase+1.9.3.1
43335catalase+1.11.1.6
43335alkaline phosphatase+3.1.3.1
43335esterase (C 4)+
43335esterase Lipase (C 8)+
43335leucine arylamidase+3.4.11.1
43335valine arylamidase+
43335acid phosphatase+3.1.3.2
43335naphthol-AS-BI-phosphohydrolase+
43335lipase (C 14)+/-
43335cystine arylamidase+/-3.4.11.3
43335trypsin+/-3.4.21.4
43335alpha-chymotrypsin+/-3.4.21.1
43335alpha-galactosidase-3.2.1.22
43335beta-galactosidase-3.2.1.23
43335beta-glucuronidase-3.2.1.31
43335N-acetyl-beta-glucosaminidase-3.2.1.52
43335alpha-glucosidase-3.2.1.20
43335beta-glucosidase-3.2.1.21
43335alpha-mannosidase-3.2.1.24
43335alpha-fucosidase-3.2.1.51
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5583--------------------
5583--------++/-+/-+----+++++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
5583seawaterNorth Sea, offshore Helgoland, 54°08'N, 7°52'EGermanyDEUEurope54.13337.8667
43335North Sea water sampel from a depth of 10 m

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_703.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_252;97_275;98_565;99_703&stattab=map
  • Last taxonomy: Sulfitobacter
  • 16S sequence: AJ550939
  • Sequence Identity:
  • Total samples: 2624
  • soil counts: 83
  • aquatic counts: 2251
  • animal counts: 278
  • plant counts: 12

Safety information

risk assessment

  • @ref: 5583
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Oceanibulbus indolifex strain DSM14862 16S ribosomal RNA gene, partial sequenceDQ9156141307ena225422
5583Oceanibulbus indoliflex partial 16S rRNA gene, type strain Hel 45AJ5509391379ena391624

Genome sequences

  • @ref: 66792
  • description: Sulfitobacter indolifex DSM 14862
  • accession: GCA_022788655
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 225422

GC content

@refGC-contentmethod
3002760.1
4333559.5genome sequence analysis
558359.5sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno88.049yes
gram-positiveno98.154yes
anaerobicno98.129yes
aerobicyes94.64yes
halophileyes82.467no
spore-formingno96.515yes
motileyes64.49no
glucose-fermentno93.084yes
thermophileno98.992yes
glucose-utilyes77.508no

External links

@ref: 5583

culture collection no.: DSM 14862, MCCC 1A11773, NCIMB 13983, HEL Hel45, HEL 45

straininfo link

  • @ref: 82867
  • straininfo: 132794

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280288Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites.Wagner-Dobler I, Rheims H, Felske A, El-Ghezal A, Flade-Schroder D, Laatsch H, Lang S, Pukall R, Tindall BJInt J Syst Evol Microbiol10.1099/ijs.0.02850-02004Adaptation, Biological, Aerobiosis, Bacteriochlorophylls/biosynthesis, Base Composition, Cytoplasmic Granules, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Indoles/metabolism, Lipids/analysis/isolation & purification, Molecular Sequence Data, Movement, North Sea, Osmotic Pressure, Peptides, Cyclic/biosynthesis, Phenazines, Phylogeny, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/cytology/genetics/isolation & purification/*physiology, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Sodium Chloride, Temperature, Water MicrobiologyEnzymology
Phylogeny28693681Proposal for transfer of Oceanibulbus indolifex Wagner-Dobler et al. 2004 to the genus Sulfitobacter as Sulfitobacter indolifex comb. nov.Liu Y, Lai Q, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0019502017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification, Sequence Analysis, DNATranscriptome
Phylogeny33655407Sulfitobacter algicola sp. nov., isolated from green algae.Wang CN, Liu Y, Wang J, Du ZJ, Wang MYArch Microbiol10.1007/s00203-021-02213-w2021Bacterial Typing Techniques, Base Composition, China, Chlorophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/genetics, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
35456790Beyond the ABCs-Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW).Freese HM, Ringel V, Overmann J, Petersen JMicroorganisms10.3390/microorganisms100407382022

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
5583Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14862)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14862
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
30027Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126391
43335Yang Liu, Qiliang Lai, Zongze Shao10.1099/ijsem.0.001950Proposal for transfer of Oceanibulbus indolifex Wagner-Döbler et al. 2004 to the genus Sulfitobacter as Sulfitobacter indolifex comb. nov.IJSEM 67: 2328-2331 201728693681
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82867Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132794.1StrainInfo: A central database for resolving microbial strain identifiers