Strain identifier

BacDive ID: 141091

Type strain: Yes

Species: Psychroflexus planctonicus

Strain Designation: X15M-8

Strain history: Z.-P. Liu; Inst. of Microbiol., CAS, China; X15M-8.

NCBI tax ID(s): 1526575 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 43998

BacDive-ID: 141091

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

description: Psychroflexus planctonicus X15M-8 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from water sample.

NCBI tax id

  • NCBI tax id: 1526575
  • Matching level: species

strain history

  • @ref: 67770
  • history: Z.-P. Liu; Inst. of Microbiol., CAS, China; X15M-8.

doi: 10.13145/bacdive141091.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Psychroflexus
  • species: Psychroflexus planctonicus
  • full scientific name: Psychroflexus planctonicus Zhong et al. 2016

@ref: 43998

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Psychroflexus

species: Psychroflexus planctonicus

strain designation: X15M-8

type strain: yes

Morphology

cell morphology

  • @ref: 43998
  • gram stain: negative
  • cell length: 1.2-2.2 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43998
  • colony size: 0.5-2.0 mm
  • colony color: orange-red
  • incubation period: 4 days
  • medium used: marine agar 2216

Culture and growth conditions

culture medium

  • @ref: 43998
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43998positivegrowth4-35
43998positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43998positivegrowth6.5-10.0alkaliphile
43998positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43998
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43998NaClpositivegrowth0.5-14.0 %
43998NaClpositiveoptimum3 %

observation

@refobservation
43998glistening after cultivation on MA
43998positive for carotenoid pigments
43998major respiratory quinone is MK-6
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4399827613amygdalin-carbon source
4399817057cellobiose-carbon source
4399815963ribitol-carbon source
4399817108D-arabinose-carbon source
4399818333D-arabitol-carbon source
4399815824D-fructose-carbon source
4399828847D-fucose-carbon source
4399862318D-lyxose-carbon source
4399816899D-mannitol-carbon source
4399816024D-mannose-carbon source
4399816988D-ribose-carbon source
4399817924D-sorbitol-carbon source
4399816443D-tagatose-carbon source
4399865327D-xylose-carbon source
4399816813galactitol-carbon source
4399817113erythritol-carbon source
4399828066gentiobiose-carbon source
4399817754glycerol-carbon source
4399828087glycogen-carbon source
4399817268myo-inositol-carbon source
4399815443inulin-carbon source
4399830849L-arabinose-carbon source
4399818403L-arabitol-carbon source
4399818287L-fucose-carbon source
4399862345L-rhamnose-carbon source
4399817266L-sorbose-carbon source
4399865328L-xylose-carbon source
4399817716lactose-carbon source
439986731melezitose-carbon source
4399828053melibiose-carbon source
43998320061methyl alpha-D-glucopyranoside-carbon source
4399843943methyl alpha-D-mannoside-carbon source
4399874863methyl beta-D-xylopyranoside-carbon source
43998506227N-acetylglucosamine-carbon source
43998potassium 2-dehydro-D-gluconate-carbon source
43998potassium 5-dehydro-D-gluconate-carbon source
4399832032potassium gluconate-carbon source
4399816634raffinose-carbon source
4399827082trehalose-carbon source
4399832528turanose-carbon source
4399817151xylitol-carbon source
43998casein-hydrolysis
4399816467L-arginine-hydrolysis
4399817895L-tyrosine-hydrolysis
4399853423tween 40-hydrolysis
4399853425tween 60-hydrolysis
4399853426tween 80-hydrolysis
4399816199urea-hydrolysis
4399817632nitrate-reduction
4399812936D-galactose+carbon source
4399818305arbutin+carbon source
4399817634D-glucose+carbon source
43998esculin ferric citrate+carbon source
4399817306maltose+carbon source
4399828017starch+carbon source
4399817992sucrose+carbon source
4399817634D-glucose+fermentation
439984853esculin+hydrolysis
439985291gelatin+hydrolysis
4399828017starch+hydrolysis
4399853424tween 20+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4399835581indoleno
4399816136hydrogen sulfideyes

enzymes

@refvalueactivityec
43998cytochrome oxidase+1.9.3.1
43998catalase+1.11.1.6
43998alkaline phosphatase+3.1.3.1
43998esterase (C 4)+
43998esterase Lipase (C 8)+
43998leucine arylamidase+3.4.11.1
43998valine arylamidase+
43998trypsin+3.4.21.4
43998acid phosphatase+3.1.3.2
43998naphthol-AS-BI-phosphohydrolase+
43998beta-glucosidase+3.2.1.21
43998lipase (C 14)-
43998cystine arylamidase-3.4.11.3
43998alpha-chymotrypsin-3.4.21.1
43998alpha-galactosidase-3.2.1.22
43998beta-galactosidase-3.2.1.23
43998beta-glucuronidase-3.2.1.31
43998alpha-glucosidase-3.2.1.20
43998N-acetyl-beta-glucosaminidase-3.2.1.52
43998alpha-mannosidase-3.2.1.24
43998alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43998C15:0 anteiso17.3
    43998C15:1 anteiso A1.2
    43998C15:0 2OH5.9
    43998C15:0 3OH3.5
    43998C15:1ω6c6.1
    43998C17:0 2OH5.5
    43998C17:1ω6c1.5
    4399810-methyl C18:01.2
    43998C14:0 iso1.1
    43998C15:0 iso11.9
    43998C15:0 iso 3OH2.7
    43998C15:1 iso G6.1
    43998C16:0 iso 3OH5.2
    43998C16:1 iso H1.4
    43998C17:0 iso 3OH11.2
  • type of FA analysis: whole cell analysis
  • incubation medium: marine agar 2216/marine broth 2216
  • incubation temperature: 25
  • incubation time: 3
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43998water sampleLake Xiaochaidan in Qaidam basin, Qinghai ProvinceChinaCHNAsia
67770Lake Xiaochaidan, a salt lake in Qaidam basinQinghai ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_127320.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_423;96_42397;97_64034;98_85393;99_127320&stattab=map
  • Last taxonomy: Psychroflexus planctonicus subclade
  • 16S sequence: KJ782429
  • Sequence Identity:
  • Total samples: 152
  • soil counts: 27
  • aquatic counts: 120
  • animal counts: 5

Sequence information

16S sequences

  • @ref: 43998
  • description: 16S rRNA gene sequence
  • accession: KJ782429
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychroflexus planctonicus CGMCC 1.12931GCA_014640195scaffoldncbi1526575
66792Psychroflexus planctonicus strain CGMCC 1.129311526575.3wgspatric1526575

GC content

@refGC-contentmethod
4399835
6777035thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.533yes
gram-positiveno98.013yes
anaerobicno98.282yes
aerobicyes85.364yes
halophileyes59.77no
spore-formingno94.788no
glucose-utilyes87.012no
thermophileno97.913yes
motileno90.445yes
glucose-fermentno84.443yes

External links

@ref: 43998

culture collection no.: CGMCC 1.12931, JCM 30616

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26475261Psychroflexus salis sp. nov. and Psychroflexus planctonicus sp. nov., isolated from a salt lake.Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZPInt J Syst Evol Microbiol10.1099/ijsem.0.0006872015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny32453683Mesohalobacter halotolerans gen. nov., sp. nov., isolated from a marine solar saltern.Feng X, Zhang JY, Sang J, Mu DS, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0041432020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome

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
43998Zhi-Ping Zhong, Ying Liu, Fang Wang, Yu-Guang Zhou, Hong-Can Liu, Zhi-Pei LiuPsychroflexus salis sp. nov. and Psychroflexus planctonicus sp. nov., isolated from a salt lake10.1099/ijsem.0.000687IJSEM 66: 125-131 201626475261
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/