Strain identifier

BacDive ID: 133855

Type strain: Yes

Species: Neptunomonas qingdaonensis

Strain Designation: P10-2-4

NCBI tax ID(s): 1045558 (species)

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General

@ref: 30685

BacDive-ID: 133855

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

description: Neptunomonas qingdaonensis P10-2-4 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1045558
  • Matching level: species

doi: 10.13145/bacdive133855.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oceanospirillaceae
  • genus: Neptunomonas
  • species: Neptunomonas qingdaonensis
  • full scientific name: Neptunomonas qingdaonensis Liu et al. 2013

@ref: 30685

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Neptunomonas

species: Neptunomonas qingdaonensis

strain designation: P10-2-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30685negative1.5 µm0.75 µmrod-shapedyes
69480yes97.88
69480negative99.999

pigmentation

  • @ref: 30685
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30685positivegrowth04-33
30685positiveoptimum20psychrophilic

culture pH

@refabilitytypepH
30685positivegrowth6.5-8
30685positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30685
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

  • @ref: 30685
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 3.5 %

observation

  • @ref: 30685
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3068527689decanoate+carbon source
3068516947citrate+carbon source
3068525115malate+carbon source
3068518401phenylacetate+carbon source
3068517632nitrate+reduction

enzymes

@refvalueactivityec
30685acid phosphatase+3.1.3.2
30685alkaline phosphatase+3.1.3.1
30685catalase+1.11.1.6
30685cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 30685
  • sample type: marine sediment

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_89265.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_1716;97_3735;98_31648;99_89265&stattab=map
  • Last taxonomy: Neptunomonas qingdaonensis
  • 16S sequence: JF747202
  • Sequence Identity:
  • Total samples: 1144
  • soil counts: 42
  • aquatic counts: 1060
  • animal counts: 35
  • plant counts: 7

Sequence information

16S sequences

  • @ref: 30685
  • description: Neptunomonas qingdaonensis strain P10-2-4 16S ribosomal RNA gene, partial sequence
  • accession: JF747202
  • length: 1506
  • database: nuccore
  • NCBI tax ID: 1045558

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neptunomonas qingdaonensis CGMCC 1.10971GCA_900113275scaffoldncbi1045558
66792Neptunomonas qingdaonensis P10-2-4GCA_016082375contigncbi1045558
66792Neptunomonas qingdaonensis strain CGMCC 1.109711045558.5wgspatric1045558
66792Neptunomonas qingdaonensis CGMCC 1.109712663762747draftimg1045558

GC content

  • @ref: 30685
  • GC-content: 45.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.965yes
flagellatedyes93.676no
gram-positiveno98.882yes
anaerobicno98.769yes
aerobicyes66.5no
halophileyes73.664no
spore-formingno95.225no
glucose-fermentno86.447no
thermophileno99.639yes
glucose-utilyes66.19no

External links

@ref: 30685

culture collection no.: CGMCC 1.10971, KCTC 23686

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22904225Neptunomonas qingdaonensis sp. nov., isolated from intertidal sand.Liu A, Zhang XY, Chen CX, Xie BB, Qin QL, Liu C, Li GW, Li H, Xu Z, Chen XL, Zhou BC, Zhang YZInt J Syst Evol Microbiol10.1099/ijs.0.041970-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *Silicon DioxideGenetics
Phylogeny25487119Pelagitalea pacifica gen. nov., sp. nov., a new marine bacterium isolated from seawater.Lee H, Yoshizawa S, Kogure K, Kim HS, Yoon JCurr Microbiol10.1007/s00284-014-0750-12014Aquatic Organisms/classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Japan, Locomotion, Molecular Sequence Data, Oceanospirillaceae/*classification/genetics/*isolation & purification/physiology, Pacific Ocean, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAEnzymology

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
30685Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172701628776041
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/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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
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