Strain identifier

BacDive ID: 134346

Type strain: Yes

Species: Marinobacter psychrophilus

Strain Designation: 20041

Strain history: D.-C. Zhang et al. 20041.

NCBI tax ID(s): 330734 (species)

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General

@ref: 32559

BacDive-ID: 134346

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

description: Marinobacter psychrophilus 20041 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 330734
  • Matching level: species

strain history

  • @ref: 67770
  • history: D.-C. Zhang et al. 20041.

doi: 10.13145/bacdive134346.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacter
  • species: Marinobacter psychrophilus
  • full scientific name: Marinobacter psychrophilus Zhang et al. 2008

@ref: 32559

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacter

species: Marinobacter psychrophilus

strain designation: 20041

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32559negative1.75 µm0.35 µmrod-shapedyes
125438negative99.5
125439negative99.2

pigmentation

  • @ref: 32559
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
32559positivegrowth0-22
32559positiveoptimum17
67770positivegrowth18

culture pH

@refabilitytypepHPH range
32559positivegrowth05-10alkaliphile
32559positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32559aerobe
125439obligate aerobe97.2

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.5

halophily

  • @ref: 32559
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 02-08 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3255922599arabinose+carbon source
3255917754glycerol+carbon source
3255917822serine+carbon source
3255917992sucrose+carbon source
3255917632nitrate+reduction

enzymes

@refvalueactivityec
32559alkaline phosphatase+3.1.3.1
32559catalase+1.11.1.6
32559cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typelatitudelongitude
32559seawater
67770Sea-ice samples collected off the Canadian Basin of the Arctic Ocean (78° 23' 14" N 149° 06' 55" W)78.3872-149.115

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_325.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_89;96_227;97_249;98_278;99_325&stattab=map
  • Last taxonomy: Marinobacter psychrophilus subclade
  • 16S sequence: DQ060402
  • Sequence Identity:
  • Total samples: 2059
  • soil counts: 171
  • aquatic counts: 1732
  • animal counts: 122
  • plant counts: 34

Sequence information

16S sequences

  • @ref: 32559
  • description: Marinobacter psychrophilus strain 20041 16S ribosomal RNA gene, partial sequence
  • accession: DQ060402
  • length: 1506
  • database: nuccore
  • NCBI tax ID: 330734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacter psychrophilus 20041GCA_001043175completencbi330734
66792Marinobacter psychrophilus 200412636415955completeimg330734

GC content

@refGC-contentmethod
3255955.4
6777055.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.781yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.347yes
125438spore-formingspore-formingAbility to form endo- or exosporesno86.623no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.824yes
125438motile2+flagellatedAbility to perform flagellated movementyes85.733no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.5
125439BacteriaNetmotilityAbility to perform movementyes84.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.2

External links

@ref: 32559

culture collection no.: CGMCC 1.6499, JCM 14643, BCRC 80070

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523195Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic.Zhang DC, Li HR, Xin YH, Chi ZM, Zhou PJ, Yu YInt J Syst Evol Microbiol10.1099/ijs.0.65690-02008Arctic Regions, Bacterial Typing Techniques, Base Composition, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Ice Cover/*microbiology, Marinobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny26908308Complete genome of Marinobacter psychrophilus strain 20041(T) isolated from sea-ice of the Canadian Basin.Song L, Ren L, Wang L, Yu Y, Wang X, Liu GMar Genomics10.1016/j.margen.2016.02.0012016Arctic Regions, Canada, *Genome, Bacterial, Ice Cover/*microbiology, Marinobacter/classification/*genetics, Phylogeny, Sequence Analysis, DNAGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
32559Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877728776041
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG