Strain identifier

BacDive ID: 11870

Type strain: Yes

Species: Hoeflea phototrophica

Strain Designation: DFL-43

Strain history: <- H. Biebl <- M. Allgaier

NCBI tax ID(s): 244596 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6735

BacDive-ID: 11870

DSM-Number: 17068

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

description: Hoeflea phototrophica DFL-43 is an aerobe, mesophilic, motile bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 244596
  • Matching level: species

strain history

  • @ref: 6735
  • history: <- H. Biebl <- M. Allgaier

doi: 10.13145/bacdive11870.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Hoeflea
  • species: Hoeflea phototrophica
  • full scientific name: Hoeflea phototrophica Biebl et al. 2006

@ref: 6735

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Hoeflea

species: Hoeflea phototrophica

full scientific name: Hoeflea phototrophica Biebl et al. 2006

strain designation: DFL-43

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stainconfidence
316440.7-2 µm0.3-0.5 µmrod-shapedyes
69480negative99.94

pigmentation

  • @ref: 31644
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17068_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17068_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17068_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17068_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17068_504.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17068_505.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 6735
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
6735positivegrowth30mesophilic
31644positivegrowth0-33
31644positiveoptimum31mesophilic

culture pH

@refabilitytypepHPH range
31644positivegrowth06-09alkaliphile
31644positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31644
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31644no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31644NaClpositivegrowth0.5-7 %
31644NaClpositiveoptimum0.5-7 %

observation

  • @ref: 31644
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3164430089acetate+carbon source
3164416947citrate+carbon source
3164428757fructose+carbon source
3164417234glucose+carbon source
3164429987glutamate+carbon source
3164417754glycerol+carbon source
3164424996lactate+carbon source
3164425115malate+carbon source
3164415361pyruvate+carbon source
3164430031succinate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typesampling date
31644marine sediment
62154Cultured cells of Alexandrium ostenfeldii2002-04-01

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 6735
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 31644
  • description: Hoeflea phototrophica DFL-43 partial 16S rRNA gene, strain DFL-43
  • accession: AJ582088
  • length: 800
  • database: nuccore
  • NCBI tax ID: 411684

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hoeflea phototrophica DFL-43GCA_000154705chromosomencbi411684
66792Hoeflea phototrophica DFL-43411684.3wgspatric411684
66792Hoeflea phototrophica DFL-432663763045completeimg411684

GC content

  • @ref: 31644
  • GC-content: 59.3

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 6735

culture collection no.: DSM 17068, CIP 109233, CCUG 59890, NCIMB 14078

straininfo link

@refstraininfo
81087402271
81088411216

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585702Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a.Biebl H, Tindall BJ, Pukall R, Lunsdorf H, Allgaier M, Wagner-Dobler IInt J Syst Evol Microbiol10.1099/ijs.0.63958-02006Aerobiosis, Alphaproteobacteria/*classification/cytology/*isolation & purification/physiology, Bacteriochlorophyll A/*biosynthesis/metabolism, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiologyGenetics
Phylogeny19820094Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis.Klassen JLJ Bacteriol10.1128/JB.01060-092009Bacteria/*genetics/*metabolism, Biosynthetic Pathways/*genetics, Carotenoids/*biosynthesis, Computational Biology/methods, DNA, Bacterial/genetics, *Evolution, Molecular, *Gene Transfer, Horizontal, Mutation, Missense, Phylogeny, Point Mutation, *Selection, Genetic, Sequence Analysis, DNATranscriptome
Phylogeny23064857Lentilitoribacter donghaensis gen. nov., sp. nov., a slowly-growing alphaproteobacterium isolated from coastal seawater.Park S, Lee JS, Lee KC, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-012-9825-92012Aerobiosis, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysisGenetics
Phylogeny23159752Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.Chung EJ, Park JA, Pramanik P, Bibi F, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.045484-02012Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny23314912Hoeflea halophila sp. nov., a novel bacterium isolated from marine sediment of the East Sea, Korea.Jung MY, Shin KS, Kim S, Kim SJ, Park SJ, Kim JG, Cha IT, Kim MN, Rhee SKAntonie Van Leeuwenhoek10.1007/s10482-013-9876-62013Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phyllobacteriaceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysis, alpha-Galactosidase/metabolismGenetics
24019991Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)).Fiebig A, Pradella S, Petersen J, Michael V, Pauker O, Rohde M, Goker M, Klenk HP, Wagner-Dobler IStand Genomic Sci10.4056/sigs.34869822013
Transcriptome26126731Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail.Avraham O, Meir A, Fish A, Bayer EA, Livnah OJ Struct Biol10.1016/j.jsb.2015.06.0202015Amino Acid Sequence, Avidin/*chemistry, Bacterial Proteins/*chemistry, Binding Sites, Crystallography, X-Ray, Dimerization, Models, Molecular, Phyllobacteriaceae/*chemistry, Protein Engineering, Sequence Alignment, Sequence Analysis, Protein, Thermodynamics
Enzymology29744634Characterization of a new nitrilase from Hoeflea phototrophica DFL-43 for a two-step one-pot synthesis of (S)-beta-amino acids.Zhang ZJ, Cai RF, Xu JHAppl Microbiol Biotechnol10.1007/s00253-018-9057-72018Alphaproteobacteria/*enzymology, Amino Acids/*biosynthesis, Aminohydrolases/*metabolism, Biocatalysis, Escherichia coli/genetics/metabolism, Kinetics, Stereoisomerism, beta-Alanine/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6735Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17068)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17068
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
31644Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2792728776041
62154Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59890)https://www.ccug.se/strain?id=59890
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81087Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402271.1StrainInfo: A central database for resolving microbial strain identifiers
81088Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID411216.1StrainInfo: A central database for resolving microbial strain identifiers