Strain identifier

BacDive ID: 133173

Type strain: Yes

Species: Massilia psychrophila

Strain Designation: B1555-1

Strain history: Y. Liu; Inst. of Tibetan Plateau Res., CAS, China; B1555-1.

NCBI tax ID(s): 1603353 (species)

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General

@ref: 24949

BacDive-ID: 133173

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

description: Massilia psychrophila B1555-1 is an aerobe, spore-forming, psychrophilic bacterium that forms circular colonies and was isolated from ice core which was drilled from Ulugh Muztagh Glacier.

NCBI tax id

  • NCBI tax id: 1603353
  • Matching level: species

strain history

  • @ref: 67770
  • history: Y. Liu; Inst. of Tibetan Plateau Res., CAS, China; B1555-1.

doi: 10.13145/bacdive133173.20230509.8.1

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 psychrophila
  • full scientific name: Massilia psychrophila Guo et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Mokoshia psychrophila

@ref: 24949

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia psychrophila

strain designation: B1555-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24949negative1.2-1.3 µm0.7-0.8 µmrod-shapedyes
69480yes96.443
69480negative99.999

colony morphology

  • @ref: 24949
  • colony color: yellow
  • colony shape: circular
  • incubation period: 4-5 days
  • medium used: R2A agar (Reasoner's 2A agar)

Culture and growth conditions

culture medium

  • @ref: 24949
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
24949positiveoptimum15psychrophilic
24949positivegrowth10.0-25.0
67770positivegrowth15psychrophilic

culture pH

@refabilitytypepHPH range
24949positiveoptimum7
24949positivegrowth6.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 24949
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
24949yes
69481yes96
69480no99.999

halophily

@refsalttested relationconcentrationgrowth
24949NaCloptimum1 %
24949NaClgrowth0.0-2.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2494917128adipate-assimilation
2494922599arabinose-assimilation
2494916947citrate-assimilation
2494927689decanoate-assimilation
2494924265gluconate-assimilation
2494917234glucose-assimilation
2494925115malate-assimilation
2494917306maltose-assimilation
2494929864mannitol-assimilation
2494937684mannose-assimilation
24949506227N-acetylglucosamine-assimilation
2494917632nitrate-reduction
2494917309pectin-hydrolysis
2494918401phenylacetate-assimilation
2494928017starch-hydrolysis
2494953426tween 80-hydrolysis
249494853esculin+hydrolysis
249495291gelatin+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2494916136hydrogen sulfideno
2494935581indoleno

enzymes

@refvalueactivityec
24949acid phosphatase+3.1.3.2
24949alkaline phosphatase+3.1.3.1
24949alpha-fucosidase-3.2.1.51
24949alpha-galactosidase-3.2.1.22
24949alpha-glucosidase+3.2.1.20
24949alpha-mannosidase-3.2.1.24
24949beta-galactosidase-3.2.1.23
24949beta-glucosidase-3.2.1.21
24949catalase+1.11.1.6
24949chymotrypsin+3.4.4.5
24949cystine arylamidase-3.4.11.3
24949cytochrome oxidase+1.9.3.1
24949esterase (C 4)+
24949esterase lipase (C 8)+
24949leucine arylamidase+3.4.11.1
24949lipase (C 14)-
24949N-acetyl-beta-glucosaminidase-3.2.1.52
24949naphthol-AS-BI-phosphohydrolase+
24949trypsin-3.4.21.4
24949urease-3.5.1.5
24949valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
24949ice core which was drilled from Ulugh Muztagh Glacierice cap Ulugh Muztagh (highest part of the central Kunlun Mountains)Republic of ChinaCHNAsia3587R2A agar (Reasoner's 2A agar)30 days4
67770Ice core drilled from Ulugh Muztagh GlacierChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Aquatic#Ice
#Environmental#Terrestrial#Core sample

Sequence information

16S sequences

  • @ref: 24949
  • description: Massilia sp. B1555-1 16S ribosomal RNA gene, partial sequence
  • accession: KM873051
  • length: 1415
  • database: nuccore
  • NCBI tax ID: 1603353

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Massilia psychrophila CGMCC 1.15196GCA_014641415contigncbi1603353
66792Massilia psychrophila strain CGMCC 1.151961603353.4wgspatric1603353
66792Massilia psychrophila strain JCM 308131603353.3wgspatric1603353
66792Massilia psychrophila JCM 308132791355047draftimg1603353
67770Massilia psychrophila JCM 30813GCA_002760665contigncbi1603353

GC content

@refGC-contentmethod
2494966
6777066thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
motileyes90.191no
gram-positiveno98.585yes
anaerobicno98.041no
aerobicyes86.145yes
halophileno96.15no
spore-formingno86.911yes
thermophileno98.939yes
glucose-utilno55.663yes
flagellatedyes73.9no
glucose-fermentno92.135no

External links

@ref: 24949

culture collection no.: CGMCC 1.15196, JCM 30813

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27432318Massilia psychrophila sp. nov., isolated from an ice core.Guo B, Liu Y, Gu Z, Shen L, Liu K, Wang N, Xing T, Liu H, Zhou Y, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0013152016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29851375Massilia violaceinigra sp. nov., a novel purple-pigmented bacterium isolated from glacier permafrost.Wang H, Zhang X, Wang S, Zhao B, Lou K, Xing XHInt J Syst Evol Microbiol10.1099/ijsem.0.0028262018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Permafrost/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
24949B. L. Guo, Yongqin,Gu, Zhengquan,Shen, Liang,Liu, Keshao,Wang, Ningliang,Xing, Tingting,Liu, Hongcan,Zhou, Yuguang,Li, JiuleMassilia psychrophila sp. nov., isolated from an ice core10.1099/ijsem.0.001315IJSEM 66: 4088-4093 201627432318
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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