Strain identifier

BacDive ID: 158806

Type strain: Yes

Species: Neptunicoccus sediminis

Strain history: <- Yan-Jiao Zhang, Qingdao Agricultural Univ.

NCBI tax ID(s): 1892596 (species)

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General

@ref: 65568

BacDive-ID: 158806

keywords: 16S sequence, Bacteria, aerobe, halophilic, Gram-negative, coccus-shaped, colony-forming

description: Neptunicoccus sediminis CCTCC AB 2015430 is an aerobe, halophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface marine sediment.

NCBI tax id

  • NCBI tax id: 1892596
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Yan-Jiao Zhang, Qingdao Agricultural Univ.

doi: 10.13145/bacdive158806.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Neptunicoccus
  • species: Neptunicoccus sediminis
  • full scientific name: Neptunicoccus sediminis Zhang et al. 2018

@ref: 65568

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Neptunicoccus

species: Neptunicoccus sediminis

type strain: yes

Morphology

cell morphology

  • @ref: 65568
  • gram stain: negative
  • cell length: 0.8-1.8 µm
  • cell width: 0.5-1.6 µm
  • cell shape: coccus-shaped

colony morphology

  • @ref: 65568
  • colony size: 0.8-1.5 mm
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TYS

Culture and growth conditions

culture medium

  • @ref: 65568
  • name: TYS
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65568positivegrowth5-42
65568positiveoptimum35mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65568positivegrowth6-10alkaliphile
65568positiveoptimum8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65568aerobe
67771aerobe

halophily

@refhalophily levelsaltgrowthtested relationconcentration
65568halophilicNaClpositivegrowth0.5-9.0 %(w/v)
65568NaClpositiveoptimum1.5-3.0 %(w/v)
65568NaClnogrowth0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6556827613amygdalin-builds acid from
6556822599arabinose-assimilation
6556818305arbutin-builds acid from
6556827689decanoate-assimilation
65568casein-hydrolysis
6556817057cellobiose-builds acid from
6556816947citrate-assimilation
6556815963ribitol-builds acid from
6556817108D-arabinose-builds acid from
6556818333D-arabitol-builds acid from
6556815824D-fructose-builds acid from
6556828847D-fucose-builds acid from
6556812936D-galactose-builds acid from
6556817634D-glucose-builds acid from
6556862318D-lyxose-builds acid from
6556816899D-mannitol-builds acid from
6556816024D-mannose-builds acid from
6556816988D-ribose-builds acid from
6556817924D-sorbitol-builds acid from
6556816443D-tagatose-builds acid from
6556865327D-xylose-builds acid from
65568dipic acid-assimilation
6556816813galactitol-builds acid from
6556817113erythritol-builds acid from
65568esculin ferric citrate-builds acid from
6556828066gentiobiose-builds acid from
6556824265gluconate-assimilation
6556817234glucose-assimilation
6556817234glucose-builds acid from
6556817754glycerol-builds acid from
6556828087glycogen-builds acid from
6556817368hypoxanthine-hydrolysis
6556817268myo-inositol-builds acid from
6556815443inulin-builds acid from
6556830849L-arabinose-builds acid from
6556818403L-arabitol-builds acid from
6556818287L-fucose-builds acid from
6556862345L-rhamnose-builds acid from
6556817266L-sorbose-builds acid from
6556865328L-xylose-builds acid from
6556817716lactose-builds acid from
6556861995lecithin-hydrolysis
6556825115malate-assimilation
6556817306maltose-assimilation
6556817306maltose-builds acid from
6556829864mannitol-assimilation
6556837684mannose-assimilation
655686731melezitose-builds acid from
6556828053melibiose-builds acid from
65568320061methyl alpha-D-glucopyranoside-builds acid from
6556843943methyl alpha-D-mannoside-builds acid from
6556874863methyl beta-D-xylopyranoside-builds acid from
65568506227N-acetylglucosamine-assimilation
65568506227N-acetylglucosamine-builds acid from
6556817632nitrate-reduction
6556818401phenylacetate-assimilation
65568potassium 2-dehydro-D-gluconate-builds acid from
65568potassium 5-dehydro-D-gluconate-builds acid from
6556832032potassium gluconate-builds acid from
6556816634raffinose-builds acid from
6556817814salicin-builds acid from
6556828017starch-builds acid from
6556828017starch-hydrolysis
6556817992sucrose-builds acid from
6556827082trehalose-builds acid from
6556832528turanose-builds acid from
6556853423tween 40-hydrolysis
6556853425tween 60-hydrolysis
6556853426tween 80-hydrolysis
6556815318xanthine-hydrolysis
6556817151xylitol-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6556828077rifampicinyesyes5 µg (disc)
655682676amoxicillinyesyes10 µg (disc)
6556828971ampicillinyesyes10 µg (disc)
6556828669bacitracinyesyes10 Unit (disc)
6556818208penicillin gyesyes10 Unit (disc)
65568204928cefotaximeyesyes30 µg (disc)
65568209807cefoxitinyesyes30 µg (disc)
6556817698chloramphenicolyesyes30 µg (disc)
655687507neomycinyesyes30 µg (disc)
655683393carbenicillinyesyes100 µg (disc)
6556871415nitrofurantoinyesyes300 µg (disc)
655688309polymyxin byesyes300 Unit (disc)

metabolite production

  • @ref: 65568
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65568catalase+1.11.1.6
65568cytochrome oxidase+1.9.3.1
65568alkaline phosphatase+3.1.3.1
65568esterase (C 4)+
65568esterase Lipase (C 8)+
65568leucine arylamidase+3.4.11.1
65568valine arylamidase+
65568cystine arylamidase+3.4.11.3
65568acid phosphatase+3.1.3.2
65568naphthol-AS-BI-phosphohydrolase+
65568lipase (C 14)-
65568trypsin-3.4.21.4
65568alpha-chymotrypsin-3.4.21.1
65568alpha-galactosidase-3.2.1.22
65568beta-galactosidase-3.2.1.23
65568beta-glucuronidase-3.2.1.31
65568alpha-glucosidase-3.2.1.20
65568beta-glucosidase-3.2.1.21
65568N-acetyl-beta-glucosaminidase-3.2.1.52
65568alpha-mannosidase-3.2.1.24
65568alpha-fucosidase-3.2.1.51
65568arginine dihydrolase-3.5.3.6
65568urease-3.5.1.5
65568gelatinase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65568C16:010.6
    65568C18:1ω7c57.6
    6556811-methyl C18:1ω7c22.8
    65568unknown 11.7995
  • type of FA analysis: whole cell analysis
  • incubation medium: TYS
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedurecountryorigin.countrycontinent
65568surface marine sediment2014-11-19Site B26, Yellow Sea37.69121.98TYMcontaining 0.5 % tryptone, 0.1 % yeast extract, 0.5 % skim milk, 1.5 % agar and artificial seawater, pH 7.515 days15approximately 1 g (wet weight) sediment was mixed with 99 ml sterilized artificial seawater (ASW) and 16 g glass beads (diameter 6-8 mm). The mixture was shaken at 15 °C and 150 rpm for 0.5 h and serially diluted (to 10-6) in artifical seawater. 70 µl aliquots were spread onto TYM
67771From the sediments of the Yellow Sea.ChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7549.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3523;97_4322;98_5533;99_7549&stattab=map
  • Last taxonomy: Neptunicoccus sediminis subclade
  • 16S sequence: KY777997
  • Sequence Identity:
  • Total samples: 905
  • soil counts: 48
  • aquatic counts: 743
  • animal counts: 105
  • plant counts: 9

Sequence information

16S sequences

  • @ref: 65568
  • description: 16S rRNA gene sequence
  • accession: KY777997
  • database: nuccore

GC content

  • @ref: 65568
  • GC-content: 57.5
  • method: genome sequence analysis

External links

@ref: 65568

culture collection no.: CCTCC AB 2015430, KCTC 42985, NBRC 111872, MCCC 1K03518, CY 02

literature

  • topic: Phylogeny
  • Pubmed-ID: 29580372
  • title: Neptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea.
  • authors: Zhang YJ, Liu XF, Kuang BZ, Zhang XY, Zhou MY, Chen S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002728
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/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
65568Yan-Jiao Zhang, Xu-Feng Liu, Bao-Zhi Kuang, Xi-Ying Zhang, Ming-Yang Zhou and Shiyong ChenNeptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea10.1099/ijsem.0.002728IJSEM 68: 1702-1706 201829580372
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/