Strain identifier

BacDive ID: 13124

Type strain: Yes

Species: Pseudomonas azotifigens

Strain Designation: 6H33b

Strain history: CIP <- 2005, JCM <- 2004, A. Nakamura, Tsukuba Univ., Ibaraki, Japan: strain 6H33b

NCBI tax ID(s): 1292027 (strain), 291995 (species)

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General

@ref: 6972

BacDive-ID: 13124

DSM-Number: 17556

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

description: Pseudomonas azotifigens 6H33b is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from hyperthermal compost material.

NCBI tax id

NCBI tax idMatching level
1292027strain
291995species

strain history

@refhistory
6972<- A. Nakamura <- K. Hatayama; 6H33b
67770A. Nakamura 6H33b.
116688CIP <- 2005, JCM <- 2004, A. Nakamura, Tsukuba Univ., Ibaraki, Japan: strain 6H33b

doi: 10.13145/bacdive13124.20230509.8.1

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 azotifigens
  • full scientific name: Pseudomonas azotifigens Hatayama et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Stutzerimonas azotifigens

@ref: 6972

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas azotifigens

full scientific name: Pseudomonas azotifigens Hatayama et al. 2005

strain designation: 6H33b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31448negative3.5 µm0.5 µmrod-shapedyes
69480yes98.066
69480negative99.996
116688negativerod-shapedyes

pigmentation

@refproductionname
31448no
116688noPyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6972REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
6972LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
38348MEDIUM 368 - for Luria bertaniyesDistilled water make up to (1000.000 ml);Sodium chloride (10.000 g);Agar(15.000 g);Yeast extract (5.000 g);Tryptone (10.000 g)
116688CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368

culture temp

@refgrowthtypetemperaturerange
6972positivegrowth30mesophilic
31448positivegrowth28-41
31448positiveoptimum34.5mesophilic
38348positivegrowth30mesophilic
60054positivegrowth30mesophilic
67770positivegrowth30mesophilic
116688positivegrowth25-41
116688nogrowth5psychrophilic
116688nogrowth10psychrophilic

culture pH

@refabilitytypepHPH range
31448positivegrowth6.1-9.8alkaliphile
31448positiveoptimum7.95

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31448microaerophile
60054aerobe
116688obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.977

halophily

@refsaltgrowthtested relationconcentration
31448NaClpositivegrowth2.5-5 %
31448NaClpositiveoptimum3.75 %
116688NaClpositivegrowth0-6 %
116688NaClnogrowth8 %
116688NaClnogrowth10 %

observation

  • @ref: 31448
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3144830089acetate+carbon source
3144821217L-alaninamide+carbon source
3144816449alanine+carbon source
31448286442-oxopentanoate+carbon source
3144818403L-arabitol+carbon source
3144822653asparagine+carbon source
3144835391aspartate+carbon source
3144816947citrate+carbon source
3144815740formate+carbon source
3144824265gluconate+carbon source
3144829987glutamate+carbon source
3144828087glycogen+carbon source
31448182404-hydroxy-L-proline+carbon source
3144817240itaconate+carbon source
3144824996lactate+carbon source
3144825017leucine+carbon source
3144829864mannitol+carbon source
3144851850methyl pyruvate+carbon source
3144826271proline+carbon source
3144817272propionate+carbon source
3144817822serine+carbon source
3144830031succinate+carbon source
3144826986threonine+carbon source
3144853423tween 40+carbon source
3144853426tween 80+carbon source
11668816947citrate+carbon source
1166884853esculin-hydrolysis
11668817632nitrate-reduction
11668816301nitrite-reduction
11668817632nitrate-respiration

metabolite production

  • @ref: 116688
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31448catalase+1.11.1.6
31448cytochrome oxidase+1.9.3.1
116688oxidase+
116688beta-galactosidase-3.2.1.23
116688alcohol dehydrogenase-1.1.1.1
116688gelatinase-
116688amylase+
116688DNase-
116688caseinase-3.4.21.50
116688catalase+1.11.1.6
116688tween esterase+
116688lecithinase-
116688lipase-
116688lysine decarboxylase-4.1.1.18
116688ornithine decarboxylase-4.1.1.17
116688protease-
116688tryptophan deaminase-
116688urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116688-+++-+--+-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6972hyperthermal compost materialMotobu, Okinawa prefectureJapanJPNAsia
60054Compost pileJapanJPNAsia
67770Compost pileJapanJPNAsia
116688Environment, Compost pileJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_39822.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_18646;97_23071;98_29098;99_39822&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB189452
  • Sequence Identity:
  • Total samples: 1247
  • soil counts: 270
  • aquatic counts: 389
  • animal counts: 494
  • plant counts: 94

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69721Risk group (German classification)
1166881Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6972
  • description: Pseudomonas azotifigens gene for 16S rRNA
  • accession: AB189452
  • length: 1458
  • database: ena
  • NCBI tax ID: 291995

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas azotifigens DSM 175561292027.3wgspatric1292027
66792Pseudomonas azotifigens DSM 175562523533560draftimg1292027
67770Stutzerimonas azotifigens DSM 17556GCA_000425625scaffoldncbi1292027

GC content

@refGC-contentmethod
3144866.3
6777066.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.528yes
gram-positiveno98.771yes
anaerobicno98.406yes
aerobicyes93.011no
halophileno67.254no
spore-formingno95.077no
thermophileno99.685yes
glucose-utilyes83.458no
flagellatedyes84.977no
glucose-fermentno90.189no

External links

@ref: 6972

culture collection no.: DSM 17556, ATCC BAA 1049, JCM 12708, CCUG 53885, CIP 108866, TBRC 7232

straininfo link

  • @ref: 82332
  • straininfo: 265400

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014478Pseudomonas azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from a compost pile.Hatayama K, Kawai S, Shoun H, Ueda Y, Nakamura AInt J Syst Evol Microbiol10.1099/ijs.0.63586-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, *Nitrogen Fixation/genetics, Nucleic Acid Hybridization, Oxidoreductases/genetics, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S, Refuse Disposal/methods, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Genetics24179119Draft Genome Sequence of Pseudomonas azotifigens Strain DSM 17556T (6H33bT), a Nitrogen Fixer Strain Isolated from a Compost Pile.Busquets A, Pena A, Gomila M, Mulet M, Mayol J, Garcia-Valdes E, Bennasar A, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Palaniappan K, Ivanova N, Schaumberg A, Pati A, Reddy TB, Nordberg H, Woyke T, Klenk HP, Kyrpides N, Lalucat JGenome Announc10.1128/genomeA.00893-132013Phylogeny
Phylogeny25525124Pseudomonas matsuisoli sp. nov., isolated from a soil sample.Lin SY, Hameed A, Hung MH, Liu YC, Hsu YH, Young LS, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.0000352014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Taiwan, Ubiquinone/chemistryGenetics
Phylogeny28984556Pseudomonas tarimensis sp. nov., an endophytic bacteria isolated from Populus euphratica.Anwar N, Rozahon M, Zayadan B, Mamtimin H, Abdurahman M, Kurban M, Abdurusul M, Mamtimin T, Abdukerim M, Rahman EInt J Syst Evol Microbiol10.1099/ijsem.0.0022952017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Stems/*microbiology, Populus/*microbiology, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny30950783Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia.Zou Y, He S, Sun Y, Zhang X, Liu Y, Cheng QInt J Syst Evol Microbiol10.1099/ijsem.0.0033902019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny31429815Pseudomonas mangiferae sp. nov., isolated from bark of mango tree in Thailand.Anurat P, Duangmal K, Srisuk NInt J Syst Evol Microbiol10.1099/ijsem.0.0036572019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Mangifera/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6972Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17556)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17556
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
31448Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2775128776041
38348Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6543
60054Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53885)https://www.ccug.se/strain?id=53885
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
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
82332Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265400.1StrainInfo: A central database for resolving microbial strain identifiers
116688Curators of the CIPCollection of Institut Pasteur (CIP 108866)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108866