Strain identifier

BacDive ID: 159837

Type strain: Yes

Species: Abyssibacter profundi

Strain Designation: OUC007

Strain history: <- Min Yu, Ocean Univ. of China

NCBI tax ID(s): 2182787 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 8.1 (current version)

General

@ref: 66716

BacDive-ID: 159837

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

description: Abyssibacter profundi OUC007 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from the seawater at a depth of 1000 m in the Mariana Trench at station MT1.

NCBI tax id

  • NCBI tax id: 2182787
  • Matching level: species

strain history

@refhistory
67770M. Yu; Coll. of Mar. Life Sci., Ocean Univ. of China, China; OUC007.
67771<- Min Yu, Ocean Univ. of China

doi: 10.13145/bacdive159837.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Nevskiales
  • family: Salinisphaeraceae
  • genus: Abyssibacter
  • species: Abyssibacter profundi
  • full scientific name: Abyssibacter profundi Zhou et al. 2018

@ref: 66716

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Nevskiales

family: Salinisphaeraceae

genus: Abyssibacter

species: Abyssibacter profundi

strain designation: OUC007

type strain: yes

Morphology

cell morphology

  • @ref: 66716
  • gram stain: negative
  • cell length: 1.7-1.9 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: polar

colony morphology

  • @ref: 66716
  • colony size: 1-2 mm
  • colony color: transparent
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Marine agar (MA)

Culture and growth conditions

culture medium

  • @ref: 66716
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66716positiveoptimum37mesophilic
66716positivegrowth10-45
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
66716positiveoptimum7.0-8.0
66716positivegrowth7.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66716aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
66716NaClpositivegrowth0-7 %(w/v)
66716NaClpositiveoptimum2-3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6671616024D-mannose-assimilation
6671616899D-mannitol-assimilation
6671617128adipate-assimilation
6671617306maltose-assimilation
6671617634D-glucose-assimilation
6671618401phenylacetate-assimilation
6671625115malate-assimilation
6671627689decanoate-assimilation
6671630849L-arabinose-assimilation
6671632032potassium gluconate-assimilation
6671653258sodium citrate-assimilation
6671659640N-acetylglucosamine-assimilation
667166731melezitose-builds acid from
6671612936D-galactose-builds acid from
6671615443inulin-builds acid from
6671615824D-fructose-builds acid from
6671615963ribitol-builds acid from
6671616024D-mannose-builds acid from
6671616443D-tagatose-builds acid from
6671616634raffinose-builds acid from
6671616813galactitol-builds acid from
6671616899D-mannitol-builds acid from
6671616988D-ribose-builds acid from
6671617057cellobiose-builds acid from
6671617108D-arabinose-builds acid from
6671617113erythritol-builds acid from
6671617151xylitol-builds acid from
6671617266L-sorbose-builds acid from
6671617268myo-inositol-builds acid from
6671617306maltose-builds acid from
6671617634D-glucose-builds acid from
6671617716lactose-builds acid from
6671617924D-sorbitol-builds acid from
6671618287L-fucose-builds acid from
6671618305arbutin-builds acid from
6671618333D-arabitol-builds acid from
6671618403L-arabitol-builds acid from
6671627082trehalose-builds acid from
6671627613amygdalin-builds acid from
6671628066gentiobiose-builds acid from
6671628087glycogen-builds acid from
6671628847D-fucose-builds acid from
6671630849L-arabinose-builds acid from
6671632528turanose-builds acid from
6671643943methyl alpha-D-mannoside-builds acid from
6671659640N-acetylglucosamine-builds acid from
6671662318D-lyxose-builds acid from
6671662345L-rhamnose-builds acid from
6671665327D-xylose-builds acid from
6671665328L-xylose-builds acid from
6671674863methyl beta-D-xylopyranoside-builds acid from
66716320061methyl alpha-D-glucopyranoside-builds acid from
66716esculin ferric citrate-builds acid from
66716potassium 2-dehydro-D-gluconate-builds acid from
66716potassium 5-dehydro-D-gluconate-builds acid from
6671617754glycerol+builds acid from
6671617814salicin+builds acid from
6671617992sucrose+builds acid from
6671628017starch+builds acid from
6671628053melibiose+builds acid from
6671632032potassium gluconate+builds acid from
667168295beta-hydroxybutyrate+carbon source
6671616383cis-aconitate+carbon source
66716167244-hydroxybutyrate+carbon source
6671621217L-alaninamide+carbon source
66716286442-oxopentanoate+carbon source
6671640585alpha-cyclodextrin+carbon source
6671651850methyl pyruvate+carbon source
6671653423tween 40+carbon source
6671653426tween 80+carbon source
6671675146monomethyl succinate+carbon source
6671616991dna-hydrolysis
6671617029chitin-hydrolysis
6671628017starch-hydrolysis
6671658187alginate-hydrolysis
6671662968cellulose-hydrolysis
66716casein-hydrolysis
667165291gelatin+hydrolysis
6671653423tween 40+hydrolysis
6671653424tween 20+hydrolysis
6671653426tween 80+hydrolysis

enzymes

@refvalueactivityec
66716acid phosphatase-3.1.3.2
66716alpha-galactosidase-3.2.1.22
66716alpha-glucosidase-3.2.1.20
66716alpha-mannosidase-3.2.1.24
66716beta-glucosidase-3.2.1.21
66716beta-glucuronidase-3.2.1.31
66716catalase-1.11.1.6
66716N-acetyl-beta-glucosaminidase-3.2.1.52
66716trypsin-3.4.21.4
66716valine arylamidase-
66716alkaline phosphatase+3.1.3.1
66716alpha-fucosidase+3.2.1.51
66716beta-galactosidase+3.2.1.23
66716cytochrome oxidase+1.9.3.1
66716esterase (C 4)+
66716esterase Lipase (C 8)+
66716gelatinase+
66716leucine arylamidase+3.4.11.1
66716naphthol-AS-BI-phosphohydrolase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66716C19:1 w6c / C19:0 cyclo1.03
    66716C10:01.05
    66716C11:01.22
    66716C20:1 w7c1.24
    66716C16:1 w5c1.27
    66716C17:0 10-methyl1.94
    66716C17:02.54
    66716C16:04.03
    66716C17:1 w6c4.25
    66716C18:1 w6c / C18:1 w7c58.3
    66716C18:06.57
    66716C12:0 3OH6.81
    66716C12:07.22
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture temperatureisolation procedure
66716the seawater at a depth of 1000 m in the Mariana Trench at station MT12015-111000 m in the Mariana Trench at station MT1 in the western Pacific Ocean, an average of 200 km to the east of the Mariana Islands, in the Western PacificPhilippinesPHLAsia11.3839142.5marine agar28The seawater samples were spread on marine agar 2216E plates and incubated atroom temperature (approximately 28°C) on board and 28°C in the laboratory.
67770Seawater at a depth of 1000 m in the Mariana Trench
67771From 1000m sea waterMarianas Trench of Pacific OceanInternational waters

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_68188.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16084;96_28507;97_35926;98_46423;99_68188&stattab=map
  • Last taxonomy: Abyssibacter profundi subclade
  • 16S sequence: KY612316
  • Sequence Identity:
  • Total samples: 649
  • soil counts: 2
  • aquatic counts: 620
  • animal counts: 26
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 66716
  • description: Oceanococcus sp. strain OUC007 16S ribosomal RNA gene, partial sequence
  • accession: KY612316
  • length: 1502
  • database: ena
  • NCBI tax ID: 2182787

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Abyssibacter profundi OUC0072831460164draftimg2182787
67770Abyssibacter profundi OUC007GCA_003151135contigncbi2182787

GC content

  • @ref: 66716
  • GC-content: 63.1
  • method: genome sequence analysis

External links

@ref: 66716

culture collection no.: KCTC 52933, MCCC 1K03450, JCM 32025

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30204582Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench.Zhou S, Ren Q, Li Y, Liu J, Wang X, Wu Y, Zhang Y, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0029992018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Pacific Ocean, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyTranscriptome
Phylogeny33034549Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes.Parada-Pinilla MP, Diaz-Cardenas C, Lopez G, Diaz-Riano JI, Gonzalez LN, Restrepo S, Trujillo ME, Baena SInt J Syst Evol Microbiol10.1099/ijsem.0.0044902020Bacterial Typing Techniques, Base Composition, Colombia, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Genome Size, Geologic Sediments/microbiology, *Mining, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, 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
66716Shun Zhou, Qiaomeng Ren, Yuying Li, Jiwen Liu, Xiaolei Wang, Yanhong Wu, Yulin Zhang, Xiao-hua ZhangAbyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench10.1099/ijsem.0.002999IJSEM 68: 3423-3429 201830204582
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/