Strain identifier
BacDive ID: 12823
Type strain:
Species: Pseudomonas citronellolis
Strain history: CIP <- 1995, DSM <- ATCC <- W. Seubert
NCBI tax ID(s): 1215097 (strain), 53408 (species)
General
@ref: 12711
BacDive-ID: 12823
DSM-Number: 50332
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Pseudomonas citronellolis DSM 50332 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil under pine trees.
NCBI tax id
NCBI tax id | Matching level |
---|---|
53408 | species |
1215097 | strain |
strain history
@ref | history |
---|---|
12711 | <- ATCC <- W. Seubert |
67770 | K. Komagata <-- R. Hugh 846 <-- ATCC 13674 <-- W. Seubert. |
118305 | CIP <- 1995, DSM <- ATCC <- W. Seubert |
doi: 10.13145/bacdive12823.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas citronellolis
- full scientific name: Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Pseudomonas humi
@ref: 12711
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas citronellolis
full scientific name: Pseudomonas citronellolis Seubert 1960 emend. Lang et al. 2007
type strain: yes
Morphology
cell morphology
- @ref: 118305
- gram stain: negative
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12711 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
40147 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
118305 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
118305 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12711 | positive | growth | 30 | mesophilic |
40147 | positive | growth | 30 | mesophilic |
46720 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
46720 | aerobe |
118305 | obligate aerobe |
compound production
@ref | compound |
---|---|
12711 | polyhydroxyalkanoic acids |
12711 | isoprene |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | + | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
118305 | 17632 | nitrate | + | reduction |
118305 | 16301 | nitrite | + | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
118305 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | + | 3.5.3.6 |
118305 | oxidase | + | |
118305 | catalase | + | 1.11.1.6 |
118305 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118305 | - | + | + | + | - | + | - | - | + | - | + | + | - | - | - | + | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12711 | + | - | - | + | - | - | - | - | + | - | - | - | - | - | + | + | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
12711 | soil under pine trees | Virginia | USA | USA | North America |
46720 | Soil under pine trees | USA | USA | North America | |
67770 | Soil under pine trees in northern Virginia | USA | USA | North America | |
118305 | Environment, Soil under pine trees |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Tree |
taxonmaps
- @ref: 69479
- File name: preview.99_854.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_203;97_221;98_250;99_854&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: Z76659
- Sequence Identity:
- Total samples: 112
- soil counts: 16
- aquatic counts: 31
- animal counts: 53
- plant counts: 12
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12711 | 1 | Risk group (German classification) |
118305 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pseudomonas citronellolis gene for 16S rRNA, strain: ATCC 13674 | AB021396 | 1499 | ena | 53408 |
12711 | P.citronellolis 16S rRNA gene | Z76659 | 1510 | ena | 53408 |
67770 | Pseudomonas citronellolis gene for 16S rRNA, partial sequence, strain: NBRC 103043 | AB681923 | 1462 | ena | 53408 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas citronellolis NBRC 103043 strain NBRC 103043 | 1215097.3 | wgs | patric | 1215097 |
66792 | Pseudomonas citronellolis strain DSM 50332 | 53408.24 | wgs | patric | 53408 |
66792 | Pseudomonas citronellolis strain LMG 18378 | 53408.9 | wgs | patric | 53408 |
66792 | Pseudomonas citronellolis LMG 18378 | 2663762793 | draft | img | 53408 |
67770 | Pseudomonas citronellolis NBRC 103043 | GCA_002091555 | contig | ncbi | 1215097 |
67770 | Pseudomonas citronellolis LMG 18378 | GCA_900112375 | scaffold | ncbi | 53408 |
67770 | Pseudomonas citronellolis DSM 50332 | GCA_004745455 | contig | ncbi | 53408 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 90.003 | no |
gram-positive | no | 98.353 | no |
anaerobic | no | 97.689 | yes |
aerobic | yes | 89.698 | yes |
halophile | no | 78.733 | no |
spore-forming | no | 94.889 | no |
thermophile | no | 99.702 | yes |
glucose-util | yes | 90.172 | yes |
flagellated | yes | 72.925 | no |
glucose-ferment | no | 89.272 | yes |
External links
@ref: 12711
culture collection no.: DSM 50332, ATCC 13674, CIP 104381, CCUG 17933, LMG 18378, NRRL B-2504, CFBP 5585, JCM 13426, BCRC 14345, IAM 15129, JCM 21587, KACC 10776, KCTC 12148, NBRC 103043, NCIMB 12783
straininfo link
- @ref: 82035
- straininfo: 11919
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 8526489 | Microbial degradation of monoterpenes in the absence of molecular oxygen. | Harder J, Probian C | Appl Environ Microbiol | 10.1128/aem.61.11.3804-3808.1995 | 1995 | Anaerobiosis, Bacteria, Anaerobic/isolation & purification/metabolism, Biodegradation, Environmental, Environmental Pollutants/metabolism, Molecular Structure, Nitric Acid/metabolism, Oxidation-Reduction, Pseudomonas/growth & development/metabolism, Terpenes/chemistry/*metabolism | Enzymology |
Metabolism | 11718820 | Intracellular degradation of two structurally different polyhydroxyalkanoic acids accumulated in Pseudomonas putida and Pseudomonas citronellolis from mixtures of octanoic acid and 5-phenylvaleric acid. | Chung DM, Choi MH, Song JJ, Yoon SC, Kang IK, Huh NE | Int J Biol Macromol | 10.1016/s0141-8130(01)00172-6 | 2001 | Calorimetry, Differential Scanning, Caprylates/*chemistry, Carbon/metabolism, Carboxylic Acids/*metabolism, Culture Media, Kinetics, Pentanoic Acids/*chemistry, Polyesters/chemistry, Protein Binding, Pseudomonas/*metabolism, Pseudomonas putida/*metabolism, Temperature, Time Factors | Cultivation |
Phylogeny | 12656147 | Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. | Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.02326-0 | 2003 | Agriculture, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Genetics |
Enzymology | 14499938 | Molecular cloning of the carboxylesterase gene and biochemical characterization of the encoded protein from Pseudomonas citronellolis ATCC 13674. | Chao YP, Fu H, Wang YL, Huang WB, Wang JY | Res Microbiol | 10.1016/S0923-2508(03)00144-X | 2003 | Amino Acid Sequence, Base Sequence, Carboxylesterase/*genetics/*metabolism, *Cloning, Molecular, Escherichia coli/enzymology/genetics, Gene Expression Regulation, Bacterial, Genomic Library, Molecular Sequence Data, Protein Folding, Pseudomonas/*enzymology/genetics, Sequence Analysis, DNA, Temperature | Genetics |
Metabolism | 15284892 | Pyrimidine nucleotide synthesis in Pseudomonas citronellolis. | West TP | Can J Microbiol | 10.1139/w04-028 | 2004 | Aspartate Carbamoyltransferase/metabolism, Enzyme Repression, Gene Expression Regulation, Bacterial, Pseudomonas/enzymology/genetics/*metabolism, Pyrimidine Nucleotides/*biosynthesis | Enzymology |
16349378 | Polyester Biosynthesis Characteristics of Pseudomonas citronellolis Grown on Various Carbon Sources, Including 3-Methyl-Branched Substrates. | Choi MH, Yoon SC | Appl Environ Microbiol | 10.1128/aem.60.9.3245-3254.1994 | 1994 | |||
Phylogeny | 17329778 | Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. | Prakash O, Kumari K, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.64456-0 | 2007 | Acyclic Monoterpenes, *Carbon, Coal Ash, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Monoterpenes/metabolism, *Particulate Matter, Phenanthrenes/metabolism, Phylogeny, *Power Plants, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 17329787 | Pseudomonas knackmussii sp. nov. | Stolz A, Busse HJ, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.64761-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/genetics | Genetics |
Phylogeny | 18523175 | Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site. | Gupta SK, Kumari R, Prakash O, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65401-0 | 2008 | Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species Specificity | Genetics |
Metabolism | 29040817 | Potential for mcl-PHA production from nonanoic and azelaic acids. | Gillis J, Ko K, Ramsay JA, Ramsay BA | Can J Microbiol | 10.1139/cjm-2017-0554 | 2017 | Acyltransferases/metabolism, Biomass, Caprylates/*metabolism, Carbon/metabolism, Dicarboxylic Acids/*metabolism, Fatty Acids/*metabolism, Polyhydroxyalkanoates/*biosynthesis, Pseudomonas/growth & development/*metabolism | Biotechnology |
Phylogeny | 30478729 | Pseudomonas humi sp. nov., isolated from leaf soil. | Akita H, Kimura ZI, Hoshino T | Arch Microbiol | 10.1007/s00203-018-1588-x | 2018 | Fatty Acids/chemistry, Japan, Multilocus Sequence Typing, Phylogeny, Plant Leaves, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Ubiquinone/analysis | Enzymology |
32260526 | Preparation and Characterization of Films Based on a Natural P(3HB)/mcl-PHA Blend Obtained through the Co-culture of Cupriavidus Necator and Pseudomonas Citronellolis in Apple Pulp Waste. | Rebocho AT, Pereira JR, Neves LA, Alves VD, Sevrin C, Grandfils C, Freitas F, Reis MAM | Bioengineering (Basel) | 10.3390/bioengineering7020034 | 2020 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
12711 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50332) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-50332 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
40147 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16283 | ||||
46720 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 17933) | https://www.ccug.se/strain?id=17933 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
82035 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID11919.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118305 | Curators of the CIP | Collection of Institut Pasteur (CIP 104381) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104381 |