Strain identifier

BacDive ID: 134263

Type strain: Yes

Species: Paracoccus marinus

Strain Designation: KKL-A5

Strain history: CIP <- 2004, NBRC <- S.T. Khan, Chiba, Japan: strain KKL-A5, "Paracoccus schoinia"

NCBI tax ID(s): 288426 (species)

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General

@ref: 32195

BacDive-ID: 134263

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Paracoccus marinus KKL-A5 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Environment, Sea water.

NCBI tax id

  • NCBI tax id: 288426
  • Matching level: species

strain history

  • @ref: 120819
  • history: CIP <- 2004, NBRC <- S.T. Khan, Chiba, Japan: strain KKL-A5, "Paracoccus schoinia"

doi: 10.13145/bacdive134263.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus marinus
  • full scientific name: Paracoccus marinus Khan et al. 2008

@ref: 32195

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus marinus

strain designation: KKL-A5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32195negative1 µm0.65 µmrod-shapedno
120819negativerod-shapedno

pigmentation

  • @ref: 32195
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40007Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120819CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
32195positivegrowth10-35
32195positiveoptimum30
40007positivegrowth22
120819positivegrowth22-25
120819nogrowth5
120819nogrowth10
120819nogrowth30
120819nogrowth37
120819nogrowth41

culture pH

@refabilitytypepHPH range
32195positivegrowth06-09alkaliphile
32195positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32195
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
32195NaClpositivegrowth<5 %
32195NaClpositiveoptimum2.5 %
120819NaClpositivegrowth2-4 %
120819NaClnogrowth0 %
120819NaClnogrowth6 %
120819NaClnogrowth8 %
120819NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3219522653asparagine+carbon source
3219528757fructose+carbon source
3219528260galactose+carbon source
3219517234glucose+carbon source
3219524996lactate+carbon source
3219515361pyruvate+carbon source
1208194853esculin-hydrolysis
12081917632nitrate-reduction
12081916301nitrite-reduction

metabolite production

  • @ref: 120819
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120819
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
32195catalase+1.11.1.6
32195cytochrome oxidase+1.9.3.1
120819oxidase+
120819beta-galactosidase-3.2.1.23
120819alcohol dehydrogenase-1.1.1.1
120819gelatinase-
120819amylase-
120819caseinase-3.4.21.50
120819catalase+1.11.1.6
120819tween esterase+
120819lecithinase-
120819lipase-
120819lysine decarboxylase-4.1.1.18
120819ornithine decarboxylase-4.1.1.17
120819phenylalanine ammonia-lyase-4.3.1.24
120819protease-
120819tryptophan deaminase-
120819urease-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
120819-+++-++---++--------

Isolation, sampling and environmental information

isolation

  • @ref: 120819
  • sample type: Environment, Sea water
  • geographic location: Chiba
  • country: Japan
  • origin.country: JPN
  • continent: Asia

taxonmaps

  • @ref: 69479
  • File name: preview.99_8336.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_3137;98_6069;99_8336&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: AB185957
  • Sequence Identity:
  • Total samples: 2123
  • soil counts: 44
  • aquatic counts: 415
  • animal counts: 1497
  • plant counts: 167

Safety information

risk assessment

  • @ref: 120819
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32195Paracoccus marinus gene for 16S ribosomal RNA, partial sequence, strain: KKL-A5AB1859571415nuccore288426
124043Paracoccus marinus gene for 16S rRNA, partial sequence, strain: NBRC 100637.AB6812091386nuccore288426
124043Paracoccus marinus NBRC 100637 gene for 16S rRNA, partial sequence.LC752394561nuccore288426

GC content

  • @ref: 32195
  • GC-content: 69

External links

@ref: 32195

culture collection no.: NBRC 100637, CIP 108500

straininfo link

  • @ref: 91850
  • straininfo: 133020

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218935Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay.Khan ST, Takaichi S, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.65103-02008Bacterial Typing Techniques, Carotenoids/*biosynthesis, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Glucosides/*biosynthesis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19329608Paracoccus aestuarii sp. nov., isolated from tidal flat sediment.Roh SW, Nam YD, Chang HW, Kim KH, Kim MS, Shin KS, Yoon JH, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65759-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny26971128Paracoccus cavernae sp. nov., isolated from a show cave.Dominguez-Monino I, Jurado V, Hermosin B, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijsem.0.0010182016*Air Microbiology, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Ubiquinone/chemistryTranscriptome
Phylogeny28933319Paracoccus sordidisoli sp. nov., isolated from an agricultural field contaminated with hexachlorocyclohexane isomers.Singh AK, Kohli P, Mahato NK, Lal RInt J Syst Evol Microbiol10.1099/ijsem.0.0022892017Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hexachlorocyclohexane/analysis, India, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*analysis, Ubiquinone/chemistryTranscriptome
Phylogeny31913112Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa.Rai A, N S, G S, A S, G D, Ch S, Ch V RInt J Syst Evol Microbiol10.1099/ijsem.0.0039622020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Indoleacetic Acids/chemistry, Nucleic Acid Hybridization, Orchidaceae/*microbiology, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
32195Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172843728776041
40007Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6130
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/
91850Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID133020.1
120819Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108500Collection of Institut Pasteur (CIP 108500)
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy