Strain identifier

BacDive ID: 164440

Type strain: Yes

Species: Glycocaulis profundi

Strain Designation: ZYF765

Strain history: M. Yu; Coll. of Mar. Life Sci., Ocean Univ. of China, China; ZYF765.

NCBI tax ID(s): 2518983 (species)

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General

@ref: 67770

BacDive-ID: 164440

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

description: Glycocaulis profundi ZYF765 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Seawater sampled at a depth of 4000 m in the Mariana Trench.

NCBI tax id

  • NCBI tax id: 2518983
  • Matching level: species

strain history

  • @ref: 67770
  • history: M. Yu; Coll. of Mar. Life Sci., Ocean Univ. of China, China; ZYF765.

doi: 10.13145/bacdive164440.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Maricaulaceae
  • genus: Glycocaulis
  • species: Glycocaulis profundi
  • full scientific name: Glycocaulis profundi Sun et al. 2020

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Caulobacterales

family: Maricaulaceae

genus: Glycocaulis

species: Glycocaulis profundi

full scientific name: Glycocaulis profundi Sun et al. 2020

strain designation: ZYF765

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell lengthcell widthcell shapemotility
69480negative98.796
69525negative0.5-2.0 µm0.2-0.3 µmrod-shapedno

colony morphology

  • @ref: 69525
  • colony size: 0.5-1.0 mm
  • colony color: faint yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA 2216E

Culture and growth conditions

culture medium

  • @ref: 69525
  • name: MA 2216E
  • growth: yes

culture temp

@refgrowthtypetemperature
67770positivegrowth30
69525positivegrowth16.0-37.0
69525positiveoptimum28

culture pH

@refabilitytypepH
69525positivegrowth6.0-10.0
69525positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 69525
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
69525NaClpositivegrowth1.0-15.0 %(w/v)
69525NaClpositiveoptimum4 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6952558187alginate-hydrolysis
6952562968cellulose-hydrolysis
6952517029chitin-hydrolysis
6952516991dna-hydrolysis
695255291gelatin-hydrolysis
6952528017starch-hydrolysis
69525esculin ferric citrate+builds acid from
69525casein+hydrolysis
6952553424tween 20+hydrolysis
6952553423tween 40+hydrolysis
6952553426tween 80+hydrolysis

metabolite production

  • @ref: 69525
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

enzymes

@refvalueactivityec
69525cytochrome oxidase+1.9.3.1
69525catalase+1.11.1.6
69525alkaline phosphatase+3.1.3.1
69525esterase (C 4)+
69525leucine arylamidase+3.4.11.1
69525valine arylamidase+
69525trypsin+3.4.21.4
69525alpha-chymotrypsin+3.4.21.1
69525acid phosphatase+3.1.3.2
69525naphthol-AS-BI-phosphohydrolase+
69525cystine arylamidase+/-3.4.11.3
69525esterase Lipase (C 8)+/-
69525lipase (C 14)-
69525alpha-galactosidase-3.2.1.22
69525beta-galactosidase-3.2.1.23
69525beta-glucuronidase-3.2.1.31
69525beta-glucosidase-3.2.1.21
69525N-acetyl-beta-glucosaminidase-3.2.1.52
69525alpha-mannosidase-3.2.1.24
69525beta-fucosidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    6952511-methyl C18:1 w7c4.3
    69525C12:03.5
    69525C12:0 3OH0.2
    69525C14:00.4
    69525C16:01.5
    69525C16:1 w7c / C16:1 w6c3.2
    69525C17:08.5
    69525C17:1 w6c3.9
    69525C18:014.1
    69525C18:1 w7c46.2
    69525C19:0 cyclo w8c9.7
    69525ECL 18.846 / C19:1 w6c0.4
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine Agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.10
  • library/peak naming table: RTSBA6.00
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountrylatitudelongitudeenrichment cultureenrichment culture temperature
67770Seawater sampled at a depth of 4000 m in the Mariana Trench
69525deepsea water sample from 4000m depth2016-09-02Station L9 Mariana TrenchPacific Ocean11.3333142.192MA 2216E28

taxonmaps

  • @ref: 69479
  • File name: preview.99_64951.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_331;96_2611;97_3197;98_4014;99_64951&stattab=map
  • Last taxonomy: Glycocaulis profundi
  • 16S sequence: MH010196
  • Sequence Identity:
  • Total samples: 464
  • soil counts: 95
  • aquatic counts: 102
  • animal counts: 250
  • plant counts: 17

Sequence information

16S sequences

  • @ref: 67770
  • description: Glycocaulis profundi 16S ribosomal RNA gene, partial sequence
  • accession: MH010196
  • length: 1429
  • database: nuccore
  • NCBI tax ID: 2518983

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Glycocaulis profundi ZYF765GCA_007050995contigncbi2518983
69525genome sequenceVJOU00000000ncbi2518983

GC content

  • @ref: 67770
  • GC-content: 67.7
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.796no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.245no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.274yes
69480spore-formingspore-formingAbility to form endo- or exosporesno88.53no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.396yes
69480flagellatedmotile2+Ability to perform flagellated movementyes72.693no

External links

@ref: 67770

culture collection no.: JCM 33028, MCCC 1K03554

literature

  • topic: Phylogeny
  • Pubmed-ID: 31675288
  • title: Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench.
  • authors: Sun H, Hu Y, Zhou S, Zheng Y, Zhang XH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003830
  • year: 2020
  • mesh: Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/url
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
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/
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
69525Hao Sun, Yuyao Hu, Shun Zhou, Yanfen Zheng, Xiao-Hua ZhangGlycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench10.1099/ijsem.0.003830