Strain identifier
BacDive ID: 11870
Type strain:
Species: Hoeflea phototrophica
Strain Designation: DFL-43
Strain history: <- H. Biebl <- M. Allgaier
NCBI tax ID(s): 244596 (species)
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
@ref | cell length | cell width | cell shape | motility | gram stain | confidence |
---|---|---|---|---|---|---|
31644 | 0.7-2 µm | 0.3-0.5 µm | rod-shaped | yes | ||
69480 | negative | 99.94 |
pigmentation
- @ref: 31644
- production: yes
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_17068_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17068_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17068_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17068_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17068_504.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17068_505.jpg | electron 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
6735 | positive | growth | 30 | mesophilic |
31644 | positive | growth | 0-33 | |
31644 | positive | optimum | 31 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31644 | positive | growth | 06-09 | alkaliphile |
31644 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31644
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31644 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31644 | NaCl | positive | growth | 0.5-7 % |
31644 | NaCl | positive | optimum | 0.5-7 % |
observation
- @ref: 31644
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31644 | 30089 | acetate | + | carbon source |
31644 | 16947 | citrate | + | carbon source |
31644 | 28757 | fructose | + | carbon source |
31644 | 17234 | glucose | + | carbon source |
31644 | 29987 | glutamate | + | carbon source |
31644 | 17754 | glycerol | + | carbon source |
31644 | 24996 | lactate | + | carbon source |
31644 | 25115 | malate | + | carbon source |
31644 | 15361 | pyruvate | + | carbon source |
31644 | 30031 | succinate | + | carbon source |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date |
---|---|---|
31644 | marine sediment | |
62154 | Cultured cells of Alexandrium ostenfeldii | 2002-04-01 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Hoeflea phototrophica DFL-43 | GCA_000154705 | chromosome | ncbi | 411684 |
66792 | Hoeflea phototrophica DFL-43 | 411684.3 | wgs | patric | 411684 |
66792 | Hoeflea phototrophica DFL-43 | 2663763045 | complete | img | 411684 |
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
@ref | straininfo |
---|---|
81087 | 402271 |
81088 | 411216 |
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16585702 | Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a. | Biebl H, Tindall BJ, Pukall R, Lunsdorf H, Allgaier M, Wagner-Dobler I | Int J Syst Evol Microbiol | 10.1099/ijs.0.63958-0 | 2006 | Aerobiosis, Alphaproteobacteria/*classification/cytology/*isolation & purification/physiology, Bacteriochlorophyll A/*biosynthesis/metabolism, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology | Genetics |
Phylogeny | 19820094 | Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis. | Klassen JL | J Bacteriol | 10.1128/JB.01060-09 | 2009 | Bacteria/*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, DNA | Transcriptome |
Phylogeny | 23064857 | Lentilitoribacter donghaensis gen. nov., sp. nov., a slowly-growing alphaproteobacterium isolated from coastal seawater. | Park S, Lee JS, Lee KC, Yoon JH | Antonie Van Leeuwenhoek | 10.1007/s10482-012-9825-9 | 2012 | Aerobiosis, 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/analysis | Genetics |
Phylogeny | 23159752 | Hoeflea 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 YR | Int J Syst Evol Microbiol | 10.1099/ijs.0.045484-0 | 2012 | Bacterial 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/analysis | Genetics |
Phylogeny | 23314912 | Hoeflea 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 SK | Antonie Van Leeuwenhoek | 10.1007/s10482-013-9876-6 | 2013 | Base 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/metabolism | Genetics |
24019991 | Genome 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 I | Stand Genomic Sci | 10.4056/sigs.3486982 | 2013 | |||
Transcriptome | 26126731 | Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail. | Avraham O, Meir A, Fish A, Bayer EA, Livnah O | J Struct Biol | 10.1016/j.jsb.2015.06.020 | 2015 | Amino 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 | |
Enzymology | 29744634 | Characterization 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 JH | Appl Microbiol Biotechnol | 10.1007/s00253-018-9057-7 | 2018 | Alphaproteobacteria/*enzymology, Amino Acids/*biosynthesis, Aminohydrolases/*metabolism, Biocatalysis, Escherichia coli/genetics/metabolism, Kinetics, Stereoisomerism, beta-Alanine/metabolism | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
6735 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17068) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17068 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
31644 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27927 | 28776041 | ||
62154 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 59890) | https://www.ccug.se/strain?id=59890 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
81087 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402271.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
81088 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID411216.1 | StrainInfo: A central database for resolving microbial strain identifiers |