Strain identifier
BacDive ID: 2954
Type strain: 
Species: Delftia lacustris
Strain Designation: 332
Strain history: <- N. O. G. Jorgensen, Dept. Agriculture and Ecology, Fac. Life Sci., Univ. Copenhagen, Frederiksberg, Denmark
NCBI tax ID(s): 558537 (species)
version 8.1 (current version)
General
@ref: 15591
BacDive-ID: 2954
DSM-Number: 21246
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Delftia lacustris 332 is a mesophilic, Gram-negative, motile bacterium that was isolated from mesotrophic lake water.
NCBI tax id
- NCBI tax id: 558537
- Matching level: species
strain history
- @ref: 15591
- history: <- N. O. G. Jorgensen, Dept. Agriculture and Ecology, Fac. Life Sci., Univ. Copenhagen, Frederiksberg, Denmark
doi: 10.13145/bacdive2954.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Delftia
- species: Delftia lacustris
- full scientific name: Delftia lacustris Jørgensen et al. 2009
@ref: 15591
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Delftia
species: Delftia lacustris
full scientific name: Delftia lacustris Jørgensen et al. 2009
strain designation: 332
type strain: yes
Morphology
cell morphology
- @ref: 23085
- gram stain: negative
- cell length: 1.6-3.0 µm
- cell width: 0.6-0.8 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 15591
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15591 | positive | growth | 28 | mesophilic |
| 23085 | positive | growth | 3.0-37.0 | |
| 23085 | positive | optimum | 25.0 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 23085 | positive | growth | 5.0-10.0 | alkaliphile |
| 23085 | positive | optimum | 6.0-7.0 |
Physiology and metabolism
spore formation
- @ref: 23085
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 23085 | NaCl | positive | growth | 0.0-6.0 g/L |
| 23085 | NaCl | optimum | 1.0 g/L |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23085 | 17115 | L-serine | - | carbon source |
| 23085 | 17115 | L-serine | - | growth |
| 23085 | 15588 | D-malate | + | carbon source |
| 23085 | 16724 | 4-hydroxybutyrate | + | carbon source |
| 23085 | 15895 | D-galactonic acid lactone | + | carbon source |
| 23085 | 8391 | D-gluconate | + | carbon source |
| 23085 | 16899 | D-mannitol | + | carbon source |
| 23085 | 15588 | D-malate | + | growth |
| 23085 | 16724 | 4-hydroxybutyrate | + | growth |
| 23085 | 15895 | D-galactonic acid lactone | + | growth |
| 23085 | 8391 | D-gluconate | + | growth |
| 23085 | 16899 | D-mannitol | + | growth |
| 23085 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23085 | acid phosphatase | + | 3.1.3.2 |
| 23085 | alkaline phosphatase | + | 3.1.3.1 |
| 23085 | alpha-glucosidase | + | 3.2.1.20 |
| 23085 | beta-glucosidase | + | 3.2.1.21 |
| 23085 | chitinase | + | 3.2.1.14 |
| 23085 | esterase (C 4) | + | |
| 23085 | esterase lipase (C 8) | + | |
| 23085 | leucine arylamidase | + | 3.4.11.1 |
| 23085 | lysozyme | + | 3.2.1.17 |
| 23085 | naphthol-AS-BI-phosphohydrolase | + | |
| 23085 | valine arylamidase | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
|---|---|---|---|---|---|---|---|---|---|
| 15591 | mesotrophic lake water | northern Zealand, Sjælsø | Denmark | DNK | Europe | ||||
| 23085 | mesotrophic Lake Sjælsø, northern Zealand | microcosms | supplemented with PG from Bacillus sp. strain A6 (final concentration 2 mg l-1) | 7 days | 20.0 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Lake (large)
taxonmaps
- @ref: 69479
- File name: preview.99_701.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_431;97_492;98_563;99_701&stattab=map
- Last taxonomy: Delftia
- 16S sequence: EU888308
- Sequence Identity:
- Total samples: 58111
- soil counts: 6069
- aquatic counts: 15249
- animal counts: 31574
- plant counts: 5219
Safety information
risk assessment
- @ref: 15591
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15591
- description: Delftia lacustris strain 332 16S ribosomal RNA gene, partial sequence
- accession: EU888308
- length: 1534
- database: ena
- NCBI tax ID: 558537
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Delftia lacustris LMG 24775 | GCA_900107225 | contig | ncbi | 558537 |
| 66792 | Delftia lacustris strain LMG 24775 | 558537.5 | wgs | patric | 558537 |
| 66792 | Delftia lacustris LMG 24775 | 2675903026 | draft | img | 558537 |
GC content
- @ref: 15591
- GC-content: 65.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 98.502 | yes |
| anaerobic | no | 98.87 | no |
| halophile | no | 96.047 | yes |
| spore-forming | no | 93.505 | no |
| glucose-util | no | 57.307 | no |
| aerobic | yes | 93.345 | no |
| motile | yes | 90.186 | yes |
| flagellated | yes | 62.255 | no |
| thermophile | no | 99.577 | yes |
| glucose-ferment | no | 88.882 | no |
External links
@ref: 15591
culture collection no.: DSM 21246, LMG 24775
straininfo link
- @ref: 72476
- straininfo: 359262
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19605727 | Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium. | Jorgensen NO, Brandt KK, Nybroe O, Hansen M | Int J Syst Evol Microbiol | 10.1099/ijs.0.008375-0 | 2009 | Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, Chitinases/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Delftia/*classification/genetics/*isolation & purification/metabolism, Denmark, Fatty Acids/analysis, Fresh Water/*microbiology, Locomotion, Molecular Sequence Data, Muramidase/metabolism, Nucleic Acid Hybridization, Peptidoglycan/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| Phylogeny | 25842037 | Delftia deserti sp. nov., isolated from a desert soil sample. | Li CT, Yan ZF, Chu X, Hussain F, Xian WD, Yunus Z, Hozzein WN, Abaydulla G, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0440-4 | 2015 | Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Delftia/*classification/genetics/*isolation & purification/physiology, Desert Climate, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 15591 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21246) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21246 | |||
| 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 | |||
| 23085 | Niels O. G. Jorgensen,Kristian K. Brandt,Ole Nybroe,Michael Hansen | 10.1099/ijs.0.008375-0 | Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium | IJSEM 59: 2195-2199 2009 | 19605727 | |
| 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) | |||
| 69479 | João 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 | |||
| 72476 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID359262.1 | StrainInfo: A central database for resolving microbial strain identifiers |