Strain identifier

BacDive ID: 159643

Type strain: Yes

Species: Massilia armeniaca

Strain Designation: ZMN-3

Strain history: <- H. Huang; Tianjin Agricultural University, Tianjin, CHINA; ZMN-3<-H. Huang<-Y. Zhang;

NCBI tax ID(s): 2072590 (species)

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General

@ref: 66493

BacDive-ID: 159643

DSM-Number: 104676

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

description: Massilia armeniaca ZMN-3 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sandy desert soil.

NCBI tax id

  • NCBI tax id: 2072590
  • Matching level: species

strain history

  • @ref: 66493
  • history: <- H. Huang; Tianjin Agricultural University, Tianjin, CHINA; ZMN-3<-H. Huang<-Y. Zhang;

doi: 10.13145/bacdive159643.20230509.8.1

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 armeniaca
  • full scientific name: Massilia armeniaca Ren et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella armeniaca

@ref: 66493

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia armeniaca

full scientific name: Massilia armeniaca Ren et al. 2018

strain designation: ZMN-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
66589negative1.7-2.6 µm0.4-0.7 µmrod-shapedyesperitrichous
69480yes94.841
69480negative99.998

colony morphology

  • @ref: 66589
  • colony size: 3-4 mm
  • colony color: apricot
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Reasoner's 2A agar (R2A)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66493R2A 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
66589LB (Luria-Bertani) agarno
66589Nutrient agar (NA)yes
66589Reasoner's 2A agar (R2A)yes
66589tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
66493positivegrowth30mesophilic
66589positiveoptimum30mesophilic
66589positivegrowth10-45

culture pH

@refabilitytypepHPH range
66589positiveoptimum7
66589positivegrowth5-9alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 66589
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.993
69481no100

halophily

@refsaltgrowthtested relationconcentration
66589NaClpositivegrowth0-0.2 %(w/v)
66589NaClpositiveoptimum0.05 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6658917128adipate-assimilation
6658918401phenylacetate-assimilation
6658927689decanoate-assimilation
6658930797(S)-malic acid-assimilation
6658932032potassium gluconate-assimilation
6658953258sodium citrate-assimilation
6658959640N-acetylglucosamine-assimilation
6658916024D-mannose+assimilation
6658916899D-mannitol+assimilation
6658917306maltose+assimilation
6658917634D-glucose+assimilation
6658930849L-arabinose+assimilation
6658913705acetoacetate-carbon source
6658915740formate-carbon source
6658915748D-glucuronate-carbon source
6658916411acetic acid-carbon source
6658916467L-arginine-carbon source
6658916523D-serine-carbon source
6658916634raffinose-carbon source
6658916651(S)-lactate-carbon source
66589167632-oxobutanoate-carbon source
6658916865gamma-aminobutyric acid-carbon source
6658916977L-alanine-carbon source
6658917057cellobiose-carbon source
6658917115L-serine-carbon source
6658917164stachyose-carbon source
6658917268myo-inositol-carbon source
6658917272propionate-carbon source
6658917309pectin-carbon source
6658917464L-galactonic acid gamma-lactone-carbon source
6658917596inosine-carbon source
6658917716lactose-carbon source
6658917754glycerol-carbon source
6658917814salicin-carbon source
6658917924D-sorbitol-carbon source
66589181014-hydroxyphenylacetic acid-carbon source
6658918183L-pyroglutamic acid-carbon source
6658918287L-fucose-carbon source
6658918333D-arabitol-carbon source
6658926490quinate-carbon source
6658928053melibiose-carbon source
6658928066gentiobiose-carbon source
6658929985L-glutamate-carbon source
6658929990D-aspartate-carbon source
6658929991L-aspartate-carbon source
6658930612D-glucarate-carbon source
6658930796(R)-malic acid-carbon source
6658930797(S)-malic acid-carbon source
6658932528turanose-carbon source
6658935418n-acetylneuraminate-carbon source
66589370543-hydroxybutyrate-carbon source
6658948607lithium chloride-carbon source
6658951850methyl pyruvate-carbon source
6658953258citric acid-carbon source
6658953423tween 40-carbon source
6658959640N-acetylglucosamine-carbon source
6658962345L-rhamnose-carbon source
6658963153N-acetyl-D-mannosamine-carbon source
6658964103sodium butyrate-carbon source
66589645522-hydroxybutyrate-carbon source
6658970744glycine-proline-carbon source
6658971321fusidate-carbon source
6658973706bromosuccinate-carbon source
66589739183-O-methyl-D-glucose-carbon source
6658974611methyl (R)-lactate-carbon source
6658975229sodium bromate-carbon source
6658975248potassium tellurite-carbon source
66589100147nalidixic acid-carbon source
66589161680aztreonam-carbon source
665891 % sodium lactate-carbon source
66589168102-oxoglutarate-carbon source
665895291gelatin+carbon source
6658912936D-galactose+carbon source
6658914314D-glucose 6-phosphate+carbon source
6658915748D-glucuronate+carbon source
6658915824D-fructose+carbon source
6658915971L-histidine+carbon source
6658916024D-mannose+carbon source
6658916537galactarate+carbon source
6658916551D-trehalose+carbon source
6658916899D-mannitol+carbon source
6658917306maltose+carbon source
6658917925alpha-D-glucose+carbon source
6658917992sucrose+carbon source
6658918024D-galacturonic acid+carbon source
6658923652dextrin+carbon source
6658928800N-acetylgalactosamine+carbon source
6658928847D-fucose+carbon source
6658932323glucuronamide+carbon source
6658978697D-fructose 6-phosphate+carbon source
66589320055methyl beta-D-glucopyranoside+carbon source
6658928017starch-degradation
6658962968cellulose-degradation
665894853esculin+degradation
665895291gelatin+degradation
6658953426tween 80+degradation
66589casein+degradation
6658917234glucose+fermentation
6658917632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6658935581indoleyes
6658915688acetoinno
6658916136hydrogen sulfideno
6836935581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
6658917234glucose+
6658915688acetoin-
6836935581indole-

enzymes

@refvalueactivityec
66589alpha-galactosidase-3.2.1.22
66589alpha-glucosidase-3.2.1.20
66589alpha-mannosidase-3.2.1.24
66589beta-D-fucosidase-3.2.1.38
66589beta-galactosidase-3.2.1.23
66589beta-glucosidase-3.2.1.21
66589beta-glucuronidase-3.2.1.31
66589chymotrypsin-3.4.4.5
66589cystine arylamidase-3.4.11.3
66589cytochrome oxidase-1.9.3.1
66589esterase (C 4)-
66589esterase Lipase (C 8)-
66589lipase (C 14)-
66589N-acetyl-beta-glucosaminidase-3.2.1.52
66589trypsin-3.4.21.4
66589acid phosphatase+3.1.3.2
66589alkaline phosphatase+3.1.3.1
66589catalase+1.11.1.6
66589leucine arylamidase+3.4.11.1
66589naphthol-AS-BI-phosphohydrolase+
66589valine arylamidase+
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
66493+----++-+++--++-----+
66493+----+++------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66493sandy desert soilInner Mongolia, Wengniute county, Ongniod QiChinaCHNAsia43.0219119.021
66589desert soil sampleOngniod Qi, Inner MongoliaChinaCHNAsia43.0219119.021TJA medium(per litre: 15 g sucrose, 0.5 g peptone, 0.5 g yeast extract, 1.5 g NaNO3, K2HPO4 0.5 g, 0.2 g MgSO4, 0.005 g FeSO4, 15 g agar; pH 7.0)3 days30standard dilution plating method

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 66589
  • description: Massilia sp. strain ZMN-3 16S ribosomal RNA gene, partial sequence
  • accession: KY432691
  • length: 1406
  • database: ena
  • NCBI tax ID: 2072590

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella armeniaca ZMN-3GCA_003028855completencbi2072590
66792Massilia armeniaca ZMN-32788500515completeimg2072590

GC content

  • @ref: 66589
  • GC-content: 66.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes83.089yes
gram-positiveno98.678yes
anaerobicno98.95no
halophileno95.784yes
spore-formingno92.615no
glucose-utilyes92.637yes
aerobicyes91.248no
thermophileno99.222yes
motileyes90.306no
glucose-fermentno86.934no

External links

@ref: 66493

culture collection no.: DSM 104676, CGMCC 1.16209

straininfo link

  • @ref: 112117
  • straininfo: 404091

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29786497Massilia armeniaca sp. nov., isolated from desert soil.Ren M, Li X, Zhang Y, Jin Y, Li S, Huang HInt J Syst Evol Microbiol10.1099/ijsem.0.0028362018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, 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

@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
66493Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104676Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104676)
66589Mengnan Ren, Xiaoyan Li, Yueqi Zhang, Yu Jin, Siqi Li, Haidong HuangMassilia armeniaca sp. nov., isolated from desert soil10.1099/ijsem.0.002836IJSEM 68: 2319-2324 201829786497
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
68369Automatically annotated from API 20NE
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
112117Reimer, 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-ID404091.1