Strain identifier

BacDive ID: 159712

Type strain: Yes

Species: Pseudomonas abyssi

Strain Designation: MT5

NCBI tax ID(s): 170540 (species)

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General

@ref: 66559

BacDive-ID: 159712

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

description: Pseudomonas abyssi MT5 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from deep seawater .

NCBI tax id

  • NCBI tax id: 170540
  • Matching level: species

doi: 10.13145/bacdive159712.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas abyssi
  • full scientific name: Pseudomonas abyssi Wei et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Neopseudomonas abyssi

@ref: 66559

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas abyssi

strain designation: MT5

type strain: yes

Morphology

cell morphology

  • @ref: 66559
  • gram stain: negative
  • cell length: 2.4-2.8 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 66559
  • colony color: whitish
  • colony shape: circular
  • medium used: Marine agar (MA) 2216

Culture and growth conditions

culture medium

  • @ref: 66559
  • name: Marine agar (MA) 2216
  • growth: yes

culture temp

  • @ref: 66559
  • growth: positive
  • type: growth
  • temperature: 4-45

culture pH

  • @ref: 66559
  • ability: positive
  • type: growth
  • pH: 4-11
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 66559
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
66559NaClpositivegrowth0-18 %(w/v)
66559NaClpositiveoptimum3-7 %(w/v)

observation

  • @ref: 66559
  • observation: motile by one or two flagella

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6655916024D-mannose-assimilation
6655916899D-mannitol-assimilation
6655917128adipate-assimilation
6655917306maltose-assimilation
6655917634D-glucose-assimilation
6655918401phenylacetate-assimilation
6655925115malate-assimilation
6655930849L-arabinose-assimilation
6655932032potassium gluconate-assimilation
6655959640N-acetylglucosamine-assimilation
6655927689decanoate+assimilation
6655953258sodium citrate+assimilation
6655917634D-glucose-fermentation
665594853esculin-hydrolysis
665595291gelatin-hydrolysis
6655928017starch-hydrolysis
6655953424tween 20+hydrolysis
6655917632nitrate+reduction
6655916383cis-aconitate+respiration
6655916977L-alanine+respiration
6655917196L-asparagine+respiration
6655917203L-proline+respiration
6655917272propionate+respiration
6655924996lactate+respiration
6655929985L-glutamate+respiration
66559370543-hydroxybutyrate+respiration
6655941865sebacic acid+respiration
6655951850methyl pyruvate+respiration
6655953258citric acid+respiration
6655953423tween 40+respiration
6655953426tween 80+respiration

metabolite production

  • @ref: 66559
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66559alpha-chymotrypsin-3.4.21.1
66559alpha-fucosidase-3.2.1.51
66559alpha-galactosidase-3.2.1.22
66559alpha-glucosidase-3.2.1.20
66559alpha-mannosidase-3.2.1.24
66559arginine dihydrolase-3.5.3.6
66559beta-galactosidase-3.2.1.23
66559beta-glucosidase-3.2.1.21
66559beta-glucuronidase-3.2.1.31
66559cystine arylamidase-3.4.11.3
66559esterase (C 4)-
66559esterase Lipase (C 8)-
66559N-acetyl-beta-glucosaminidase-3.2.1.52
66559trypsin-3.4.21.4
66559acid phosphatase+3.1.3.2
66559alkaline phosphatase+3.1.3.1
66559catalase+1.11.1.6
66559cytochrome oxidase+1.9.3.1
66559leucine arylamidase+3.4.11.1
66559lipase (C 14)+
66559naphthol-AS-BI-phosphohydrolase+
66559urease+3.5.1.5
66559valine aminopeptidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    6655911-methyl C18:1 w7c0.1
    66559C11:0 iso 3OH0.1
    6655910-m C16:0 and/or C17:1 w9c0.1
    66559C15:0 anteiso0.2
    66559C11:0 2OH0.2
    66559C16:1 w5c0.2
    66559C13:0 iso0.2
    66559C15:0 iso0.2
    66559C11:00.3
    66559C10:00.4
    66559C13:00.4
    66559C15:1 w6c0.4
    66559C11:0 3OH0.7
    66559C17:00.9
    66559C18:01.1
    66559C14:01.2
    66559C17:1 w6c1.2
    66559C17:1 w8c1.4
    66559C16:015.9
    66559C16:1 w7c and/or C16:1 w6c24.1
    66559C10:0 3OH3.4
    66559C12:0 3OH3.6
    66559C18:1 w7c and/or C18:1 w6c35.3
    66559C12:07.2
  • type of FA analysis: whole cell analysis
  • incubation medium: marine broth
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 66559
  • sample type: deep seawater (5000m depth)
  • sampling date: 2016-12-25
  • geographic location: Mariana Trench
  • country: Northwest Pacific
  • latitude: 11.43
  • longitude: 142.36
  • enrichment culture: marine agar 2216
  • enrichment culture duration: 3 days
  • enrichment culture temperature: 28
  • isolation procedure: serially diluted

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7672.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_1501;97_4381;98_5610;99_7672&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: MF962536
  • Sequence Identity:
  • Total samples: 2691
  • soil counts: 83
  • aquatic counts: 2395
  • animal counts: 169
  • plant counts: 44

Sequence information

16S sequences

  • @ref: 66559
  • description: Pseudomonas sp. strain MT5 16S ribosomal RNA gene, partial sequence
  • accession: MF962536
  • length: 1407
  • database: ena
  • NCBI tax ID: 170540

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas abyssi MT5GCA_002307495contigncbi170540
66792Pseudomonas abyssi MT52882363878draftimg170540

GC content

  • @ref: 66559
  • GC-content: 61.2
  • method: genome sequence analysis

External links

@ref: 66559

culture collection no.: KCTC 62295, MCCC 1K03351

literature

  • topic: Phylogeny
  • Pubmed-ID: 29927369
  • title: Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench.
  • authors: Wei Y, Mao H, Xu Y, Zou W, Fang J, Blom J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002785
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
66559Yuli Wei, Haiyan Mao, Yunping Xu, Wencai Zou, Jiasong Fang, Jochen BlomPseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench10.1099/ijsem.0.002785IJSEM 68: 2462-2467 201829927369
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
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/