Strain identifier

BacDive ID: 11327

Type strain: Yes

Species: Massilia plicata

Strain Designation: 76

Strain history: CIP <- 2006, KCTC

NCBI tax ID(s): 321984 (species)

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General

@ref: 7027

BacDive-ID: 11327

DSM-Number: 17505

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

description: Massilia plicata 76 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from heavy-metal-polluted farm soil.

NCBI tax id

  • NCBI tax id: 321984
  • Matching level: species

strain history

@refhistory
7027<- W.-J- Li, Yunnan University, China
332812006, KCTC
121871CIP <- 2006, KCTC

doi: 10.13145/bacdive11327.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Massilia
  • species: Massilia plicata
  • full scientific name: Massilia plicata Zhang et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella plicata

@ref: 7027

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia plicata

full scientific name: Massilia plicata Zhang et al. 2006

strain designation: 76

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31701negative2-2.5 µm0.6-0.7 µmrod-shapedyes
69480yes95.978
69480negative99.999
121871negativerod-shapedyes

colony morphology

@refincubation period
70271-2 days
121871

pigmentation

  • @ref: 31701
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7027R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33281MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121871CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7027positivegrowth30mesophilic
31701positivegrowth10-45
31701positiveoptimum28-30mesophilic
33281positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31701positivegrowth6.5-8.5alkaliphile
31701positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31701aerobe
121871facultative anaerobe

spore formation

@refspore formationconfidence
31701no
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
31701NaClpositivegrowth0-1 %
31701NaClpositiveoptimum0-1 %

observation

  • @ref: 31701
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170117234glucose+carbon source
3170115792malonate+carbon source
3170117992sucrose+carbon source
3170117632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12187117632nitrate-reduction
12187116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12187135581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
7027catalase+1.11.1.6
7027cytochrome-c oxidase+1.9.3.1
31701catalase+1.11.1.6
31701urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121871oxidase+
121871alcohol dehydrogenase-1.1.1.1
121871catalase+1.11.1.6
121871lysine decarboxylase-4.1.1.18
121871ornithine decarboxylase-4.1.1.17
121871urease-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
121871-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7027-----+++/-+++--++/---+/---+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7027----+-+---++-+-+/---------+/-+-++---+---++-+-------+/---
121871------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7027heavy-metal-polluted farm soilNanjing, Jiangsu provinceChinaCHNAsia
121871Environment, Heavy metal, polluted farm soilNanjing, JiangsuChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Contamination#Heavy metal
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70271Risk group (German classification)
1218711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7027
  • description: Massilia plicata strain 76 16S ribosomal RNA gene, partial sequence
  • accession: AY966000
  • length: 1471
  • database: ena
  • NCBI tax ID: 321984

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella plicata KCTC 12344GCA_014651435scaffoldncbi321984
66792Pseudoduganella plicata DSM 17505GCA_004421005completencbi321984
66792Massilia plicata strain DSM 17505321984.3completepatric321984
66792Massilia plicata strain KCTC 12344321984.4wgspatric321984
66792Massilia plicata DSM 175052847005498completeimg321984

GC content

@refGC-content
702765
3170165.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.599yes
flagellatedyes79.752no
gram-positiveno98.683no
anaerobicno98.987yes
aerobicyes94.617yes
halophileno94.711yes
spore-formingno93.19yes
glucose-utilyes90.559no
thermophileno99.101yes
glucose-fermentno89.449yes

External links

@ref: 7027

culture collection no.: DSM 17505, CCTCC AB 204072, KCTC 12344, CIP 109191

straininfo link

  • @ref: 80560
  • straininfo: 232831

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449458Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China.Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y, Xu LH, Jiang CL, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.64083-02006Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/*genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23087170Massilia lurida sp. nov., isolated from soil.Luo X, Xie Q, Wang J, Pang H, Fan J, Zhang JInt J Syst Evol Microbiol10.1099/ijs.0.047068-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26846918Massilia humi sp. nov. isolated from soil in Incheon, South Korea.Du J, Yin CSArch Microbiol10.1007/s00203-016-1195-72016Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Ubiquinone/metabolismTranscriptome
Phylogeny28933315Massilia buxea sp. nov., isolated from a rock surface.Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WYInt J Syst Evol Microbiol10.1099/ijsem.0.0023012017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny32601835Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China.Lu HB, Deng TC, Xu MYCurr Microbiol10.1007/s00284-020-02104-12020Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, Nucleic Acid Hybridization, Oxalobacteraceae, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rivers, Sequence Analysis, DNA, *UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7027Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17505
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
31701Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797828776041
33281Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6904
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)
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
80560Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232831.1StrainInfo: A central database for resolving microbial strain identifiers
121871Curators of the CIPCollection of Institut Pasteur (CIP 109191)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109191