Strain identifier

BacDive ID: 11962

Type strain: Yes

Species: Planococcus rifietoensis

Strain Designation: M8

Strain history: CIP <- 2004, A. Gambacorta, ICB Istituto di Chimica Biomolecolare, Naples, Italy: strain M8

NCBI tax ID(s): 200991 (species)

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General

@ref: 5693

BacDive-ID: 11962

DSM-Number: 15069

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Planococcus rifietoensis M8 is an obligate aerobe, mesophilic, motile bacterium that was isolated from sulfurous mineral water spring, algal mat.

NCBI tax id

  • NCBI tax id: 200991
  • Matching level: species

strain history

@refhistory
5693<- A. Gambacorta; M8
339232004, A. Gambacorta, ICB, Napoli, Italy: strain M8
122237CIP <- 2004, A. Gambacorta, ICB Istituto di Chimica Biomolecolare, Naples, Italy: strain M8

doi: 10.13145/bacdive11962.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Planococcus
  • species: Planococcus rifietoensis
  • full scientific name: Planococcus rifietoensis corrig. Romano et al. 2003

  • synonyms

    • @ref: 20215
    • synonym: Planococcus rifietensis

@ref: 5693

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus rifietoensis

full scientific name: Planococcus rifietoensis Romano et al. 2003

strain designation: M8

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.117
69480100positive
122237nopositiveovoid-shaped

colony morphology

  • @ref: 122237

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5693NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: NaCl 100.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33923MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122237CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122237CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
5693positivegrowth28mesophilic
33923positivegrowth37mesophilic
122237positivegrowth10-37
122237nogrowth41thermophilic
122237nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122237
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.724

halophily

@refsaltgrowthtested relationconcentration
122237NaClnogrowth0 %
122237NaClnogrowth2 %
122237NaClnogrowth4 %
122237NaClnogrowth6 %
122237NaClnogrowth8 %
122237NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
122237606565hippurate+hydrolysis
12223717632nitrate-reduction
12223716301nitrite-reduction

antibiotic resistance

  • @ref: 122237
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122237
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122237
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
122237oxidase-
122237beta-galactosidase+3.2.1.23
122237alcohol dehydrogenase-1.1.1.1
122237gelatinase-
122237amylase-
122237DNase+
122237caseinase-3.4.21.50
122237catalase+1.11.1.6
122237tween esterase-
122237gamma-glutamyltransferase+2.3.2.2
122237lysine decarboxylase-4.1.1.18
122237ornithine decarboxylase-4.1.1.17
122237phenylalanine ammonia-lyase-4.3.1.24
122237tryptophan deaminase-
122237urease-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
122237-+++-+-+---+-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5693sulfurous mineral water spring, algal matSavignano Irpino, CampinaItalyITAEurope
122237Algal mat, sulphurous mineral water springItalyITAEurope2002

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Spring
#Host#Algae
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_129.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_75;99_129&stattab=map
  • Last taxonomy: Planococcus
  • 16S sequence: AJ493659
  • Sequence Identity:
  • Total samples: 12884
  • soil counts: 6586
  • aquatic counts: 2240
  • animal counts: 2949
  • plant counts: 1109

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56931Risk group (German classification)
1222371Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5693
  • description: Planococcus rifitiensis 16S rRNA gene, strain M8
  • accession: AJ493659
  • length: 1531
  • database: ena
  • NCBI tax ID: 200991

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planococcus rifietoensis M8GCA_001465795completencbi200991
66792Planococcus rifietoensis M82687453186completeimg200991

GC content

  • @ref: 5693
  • GC-content: 47.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes72no
flagellatedno51.735no
flagellatedno51.735no
gram-positiveyes92.887no
gram-positiveyes92.887no
anaerobicno99.172no
anaerobicno99.172no
aerobicyes95.504no
aerobicyes95.504no
halophileyes86.32no
halophileyes86.32no
spore-formingyes54.794no
spore-formingyes54.794no
glucose-utilyes89.191no
glucose-utilyes89.191no
motileyes73.653no
motileyes73.653no
thermophileno99.691yes
thermophileno99.691yes
glucose-fermentno87.653no
glucose-fermentno87.653no

External links

@ref: 5693

culture collection no.: DSM 15069, ATCC BAA 790, CIP 108240

straininfo link

  • @ref: 81174
  • straininfo: 128005

literature

  • topic: Genetics
  • Pubmed-ID: 26808870
  • title: Complete genome of Planococcus rifietoensis M8(T), a halotolerant and potentially plant growth promoting bacterium.
  • authors: See-Too WS, Convey P, Pearce DA, Lim YL, Ee R, Yin WF, Chan KG
  • journal: J Biotechnol
  • DOI: 10.1016/j.jbiotec.2016.01.026
  • year: 2016
  • mesh: Bacterial Proteins/genetics/pharmacology, Base Composition, Genome Size, *Genome, Bacterial, Italy, Planococcaceae/genetics/*isolation & purification, Plant Development/drug effects, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5693Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15069)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15069
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
33923Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5841
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic 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.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)
81174Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128005.1StrainInfo: A central database for resolving microbial strain identifiers
122237Curators of the CIPCollection of Institut Pasteur (CIP 108240)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108240