Strain identifier

BacDive ID: 135100

Type strain: Yes

Species: Ruegeria denitrificans

Strain Designation: 5OM10

Strain history: CIP <- 2004, M.J. Pujalte, Burjasot, Spain: strain 5OM10

NCBI tax ID(s): 1715692 (species)

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General

@ref: 33961

BacDive-ID: 135100

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, mesophilic, Gram-negative, coccus-shaped, colony-forming

description: Ruegeria denitrificans 5OM10 is an aerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies.

NCBI tax id

  • NCBI tax id: 1715692
  • Matching level: species

strain history

@refhistory
339612004, M.J. Pujalte, Burjasot, Spain: strain 5OM10
33961CIP <- 2004, M.J. Pujalte, Burjasot, Spain: strain 5OM10

doi: 10.13145/bacdive135100.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Ruegeria
  • species: Ruegeria denitrificans
  • full scientific name: Ruegeria denitrificans Arahal et al. 2018

@ref: 33961

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Ruegeria

species: Ruegeria denitrificans

strain designation: 5OM10

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
66611negativecoccus-shapedno
69480negative99.993
33961negativerod-shapedyes

colony morphology

@refcolony shapemedium used
66611circularMarine agar (MA)
33961

pigmentation

  • @ref: 66611
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33961Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
66611Marine agar (MA)yes
33961CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
33961positivegrowth25mesophilic
66611nogrowth4psychrophilic
66611positiveoptimum15psychrophilic
66611positiveoptimum26mesophilic
66611nogrowth37mesophilic
33961positivegrowth15-30
33961nogrowth5psychrophilic
33961nogrowth37mesophilic
33961nogrowth41thermophilic
33961nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
66611positiveoptimum7
66611positivegrowth6-9alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 66611
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 66611
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
66611Marine saltspositivegrowth1.5-6 %
66611Marine saltspositiveoptimum3 %
66611Marine saltsnogrowth1 %
66611NaClnogrowth7 %
33961NaClnogrowth0 %
33961NaClnogrowth2 %
33961NaClnogrowth4 %
33961NaClnogrowth6 %
33961NaClnogrowth8 %
33961NaClnogrowth10 %

observation

@refobservation
66611Cells do not accumulate PHB.
66611unable to ferment carbohydrates
66611No growth without added salts; sodium and magnesium ions are required for growth.
66611Bacteriochlorophyll a is not produced, puf genes are absent.
66611Carbon monoxide oxidation genes are present.
66611Genes for cyanophycin synthesis and degradation (cyanophycin synthase, cyanophycinase and isoaspartyl dipeptidase) are also present.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6661112936D-galactose+carbon source
6661115603L-leucine+carbon source
6661115611sarcosine+carbon source
6661115708trans-aconitate+carbon source
6661115729L-ornithine+carbon source
6661116024D-mannose+carbon source
6661116349L-citrulline+carbon source
6661116467L-arginine+carbon source
6661116659D-glycerate+carbon source
6661116857L-threonine+carbon source
6661116899D-mannitol+carbon source
6661116977L-alanine+carbon source
6661116988D-ribose+carbon source
6661117115L-serine+carbon source
6661117148putrescine+carbon source
6661117268myo-inositol+carbon source
6661117272propionate+carbon source
6661117634D-glucose+carbon source
6661117754glycerol+carbon source
6661117895L-tyrosine+carbon source
6661117924D-sorbitol+carbon source
6661117968butyrate+carbon source
6661117992sucrose+carbon source
6661118019L-lysine+carbon source
6661125115malate+carbon source
6661129985L-glutamate+carbon source
6661129991L-aspartate+carbon source
66611305664-aminobutyrate+carbon source
6661132954sodium acetate+carbon source
66611370543-hydroxybutyrate+carbon source
6661150144sodium pyruvate+carbon source
6661153258sodium citrate+carbon source
6661159640N-acetylglucosamine+carbon source
6661162345L-rhamnose+carbon source
6661163675sodium succinate+carbon source
6661175228sodium lactate+carbon source
66611168102-oxoglutarate+carbon source
666118391D-gluconate-growth
6661115748D-glucuronate-growth
6661115971L-histidine-growth
6661117057cellobiose-growth
6661117716lactose-growth
6661117814salicin-growth
6661118024D-galacturonic acid-growth
6661127082trehalose-growth
6661127613amygdalin-growth
6661130612D-glucarate-growth
6661130849L-arabinose-growth
6661165327D-xylose-growth
6661115428glycine+/-growth
6661115824D-fructose+/-growth
6661117306maltose+/-growth
6661128053melibiose+/-growth
666114853esculin+hydrolysis
666115291gelatin+hydrolysis
6661116991dna+hydrolysis
6661128017starch+hydrolysis
6661153426tween 80+hydrolysis
66611902594-nitrophenyl beta-D-glucopyranoside+hydrolysis
66611casein+hydrolysis
6661117632nitrate+reduction
3396116947citrate-carbon source
339614853esculin-hydrolysis
33961606565hippurate-hydrolysis
3396117632nitrate+builds gas from
3396117632nitrate+reduction
3396116301nitrite+builds gas from
3396116301nitrite-reduction
3396115792malonate-assimilation
3396117234glucose+/-degradation

metabolite production

@refChebi-IDmetaboliteproduction
6661135581indoleno
3396135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3396115688acetoin-
3396117234glucose-

enzymes

@refvalueactivityec
66611arginine dihydrolase-3.5.3.6
66611urease-3.5.1.5
66611acid phosphatase+3.1.3.2
66611alkaline phosphatase+3.1.3.1
66611catalase+1.11.1.6
33961oxidase+
33961beta-galactosidase+3.2.1.23
33961alcohol dehydrogenase-1.1.1.1
33961gelatinase+/-
33961amylase-
33961caseinase-3.4.21.50
33961catalase+1.11.1.6
33961tween esterase-
33961gamma-glutamyltransferase+2.3.2.2
33961lecithinase-
33961lipase-
33961lysine decarboxylase-4.1.1.18
33961ornithine decarboxylase-4.1.1.17
33961phenylalanine ammonia-lyase-4.3.1.24
33961protease-
33961tryptophan deaminase-
33961urease-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
33961-+++-++---++-+------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typesampling datelatitudelongitudeenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation date
33961ValenciaSpainESPEurope
66611Western Mediterranean coastSpainESPEuropeoysters on the coast of VinarozMay, 199040.45660.5266The strain was isolated from homogenized, seawater-diluted oyster meat, inoculated on the surface of a marine agar (MA, Difco) plate.10 days28
33961ValenciaSpainESPEuropeAnimal, Oyster meat1990

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Host#Invertebrates (Other)#Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_5032.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_588;97_688;98_803;99_5032&stattab=map
  • Last taxonomy: Ruegeria
  • 16S sequence: MH023307
  • Sequence Identity:
  • Total samples: 5251
  • soil counts: 60
  • aquatic counts: 4771
  • animal counts: 398
  • plant counts: 22

Safety information

risk assessment

  • @ref: 33961
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
66611Ruegeria sp. CECT 5091 16S ribosomal RNA gene, partial sequenceMH0233071419ena1715692
66611Ruegeria denitrificans strain CECT 5091, whole genome shotgun sequencing projectCYUD0000000042ena1715692

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruegeria denitrificans CECT 5091GCA_001458295contigncbi1715692
66792Ruegeria sp. CECT 50911715692.3wgspatric1715692
66792Ruegeria denitrificans CECT 50912713896969draftimg1715692

GC content

  • @ref: 66611
  • GC-content: 56.70
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno62.101yes
gram-positiveno98.182no
anaerobicno98.538yes
aerobicyes91.09yes
halophileyes79.922no
spore-formingno95.767no
glucose-utilyes69.929yes
flagellatedno81.679no
thermophileno96.146yes
glucose-fermentno91.827no

External links

@ref: 33961

culture collection no.: CIP 108403, CECT 5091, LMG 29896

literature

  • topic: Phylogeny
  • Pubmed-ID: 29944092
  • title: Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis.
  • authors: Arahal DR, Lucena T, Rodrigo-Torres L, Pujalte MJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002867
  • year: 2018
  • mesh: Animals, Bacterial Proteins/biosynthesis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Mediterranean Sea, Nucleic Acid Hybridization, Ostreidae/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Spain
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
33961Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108403Collection of Institut Pasteur (CIP 108403)
66611David R. Arahal, Teresa Lucena, Lidia Rodrigo-Torres, Maria J. PujalteRuegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis10.1099/ijsem.0.002867IJSEM 68: 2515-2522 201829944092
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1