Strain identifier

BacDive ID: 140989

Type strain: Yes

Species: Aquibium oceanicum

Strain Designation: B7

Strain history: <- Dildar, Zhejiang Univ.

NCBI tax ID(s): 1670800 (species)

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General

@ref: 43876

BacDive-ID: 140989

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

description: Aquibium oceanicum B7 is an aerobe, Gram-negative, oval-shaped bacterium that forms circular colonies and was isolated from From sea water from the East China Sea.

NCBI tax id

  • NCBI tax id: 1670800
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Dildar, Zhejiang Univ.

doi: 10.13145/bacdive140989.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Aquibium
  • species: Aquibium oceanicum
  • full scientific name: Aquibium oceanicum (Fu et al. 2017) Kim et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Mesorhizobium oceanicum

@ref: 43876

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Phyllobacteriaceae

genus: Mesorhizobium

species: Mesorhizobium oceanicum

strain designation: B7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43876negative0.8-1.0 µm0.4-0.6 µmoval-shapedno
69480negative99.985

colony morphology

  • @ref: 43876
  • colony size: 1.0-2.0 mm
  • colony color: light yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

@refnamegrowth
43876Marine agar (MA)yes
43876Yeast mannitol agaryes

culture temp

@refgrowthtypetemperaturerange
43876positivegrowth25-40
43876positiveoptimum35mesophilic
67771positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
43876positivegrowth5.5-9.0alkaliphile
43876positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43876aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
43876NaClpositivegrowth0-8 %(w/v)
43876NaClpositiveoptimum3 %(w/v)

observation

  • @ref: 43876
  • observation: quinone Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4387627689decanoate-assimilation
4387618401phenylacetate-assimilation
4387632032potassium gluconate-assimilation
43876casamino acids-carbon source
43876peptone-carbon source
43876tryptone-carbon source
4387617234glucose-fermentation
438764853esculin-hydrolysis
4387628017starch-hydrolysis
4387653424tween 20-hydrolysis
4387653426tween 80-hydrolysis
4387618186tyrosine-hydrolysis
4387616301nitrite-reduction
4387616947citrate+carbon source
4387617634D-glucose+carbon source
4387616899D-mannitol+carbon source
4387616024D-mannose+carbon source
4387630849L-arabinose+carbon source
4387625115malate+carbon source
4387617306maltose+carbon source
43876506227N-acetylglucosamine+carbon source
43876polypeptone+carbon source
43876soyton+carbon source
43876yeast extract+carbon source
43876casein+hydrolysis
4387653423tween 40+hydrolysis
4387653425tween 60+hydrolysis
4387616199urea+hydrolysis
4387617128adipate+/-carbon source
438765291gelatin+/-hydrolysis
4387617632nitrate+/-reduction

metabolite production

@refChebi-IDmetaboliteproduction
4387615688acetoinno
4387616136hydrogen sulfideno
4387635581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4387617234glucose-
4387615688acetoin-

enzymes

@refvalueactivityec
43876cytochrome oxidase+1.9.3.1
43876catalase+1.11.1.6
43876alkaline phosphatase+3.1.3.1
43876esterase (C 4)+
43876esterase Lipase (C 8)+
43876trypsin+3.4.21.4
43876acid phosphatase+/-3.1.3.2
43876naphthol-AS-BI-phosphohydrolase+/-
43876valine arylamidase+/-
43876chymotrypsin-3.4.4.5
43876cystine arylamidase-3.4.11.3
43876beta-D-fucosidase-3.2.1.38
43876alpha-galactosidase-3.2.1.22
438766-phospho-beta-galactosidase-3.2.1.85
43876alpha-glucosidase-3.2.1.20
43876beta-glucosidase-3.2.1.21
43876beta-glucuronidase-3.2.1.31
43876alpha-mannosidase-3.2.1.24
43876leucine arylamidase-3.4.11.1
43876lipase (C 14)-
43876N-acetyl-beta-glucosaminidase-3.2.1.52

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
67771From sea water from the East China SeaZhejiangChinaCHNAsia
43876deep seawater (at a depth of 1.0 km) in South China SeaSouth China SeaChinaCHNAsia2012-0815.2333117.283

isolation source categories

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

Sequence information

16S sequences

  • @ref: 43876
  • description: 16S rRNA gene sequence
  • accession: KT157593
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aquibium oceanicum B7GCA_001889605completencbi1670800
66792Mesorhizobium sp. B71670800.3completepatric1670800
66792Mesorhizobium oceanicum B72728369379completeimg1670800

GC content

  • @ref: 43876
  • GC-content: 65.1
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
flagellatedno80.957yes
gram-positiveno97.224yes
anaerobicno98.065yes
aerobicyes94.574yes
halophileno76.324no
spore-formingno96.279no
glucose-utilyes89.222yes
thermophileno96.474yes
motileyes77.185yes
glucose-fermentno91.417yes

External links

@ref: 43876

culture collection no.: KCTC 42783, MCCC 1K02305

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28853693Mesorhizobium oceanicum sp. nov., isolated from deep seawater.Fu GY, Yu XY, Zhang CY, Zhao Z, Wu D, Su Y, Wang RJ, Han SB, Wu M, Sun CInt J Syst Evol Microbiol10.1099/ijsem.0.0020092017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Mesorhizobium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny35038289Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov.Kim M, Kim W, Park WInt J Syst Evol Microbiol10.1099/ijsem.0.0052302022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mesorhizobium/classification/isolation & purification, *Microcystis, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

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
43876Ge-yi Fu, Xiao-yun Yu, Chong-ya Zhang, Zhe Zhao, Dildar Wu, Yue Su, Rui-jun Wang, Shuai-bo Han, Min Wu, Cong SunMesorhizobium oceanicum sp. nov., isolated from deep seawater10.1099/ijsem.0.002009IJSEM 67: 2739-2745 201728853693
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1