Strain identifier

BacDive ID: 159701

Type strain: Yes

Species: Marinicaulis flavus

Strain Designation: SY-3-19

Strain history: <- Xiao- Yun Yu, Zhejiang Univ.

NCBI tax ID(s): 2058213 (species)

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General

@ref: 66565

BacDive-ID: 159701

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

description: Marinicaulis flavus SY-3-19 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface water sample.

NCBI tax id

  • NCBI tax id: 2058213
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Xiao- Yun Yu, Zhejiang Univ.

doi: 10.13145/bacdive159701.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Parvularculales
  • family: Parvularculaceae
  • genus: Marinicaulis
  • species: Marinicaulis flavus
  • full scientific name: Marinicaulis flavus Yu et al. 2018

@ref: 66565

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Parvularculales

family: Parvularculaceae

genus: Marinicaulis

species: Marinicaulis flavus

strain designation: SY-3-19

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilitycell width
66565negative0.5-1 µmcoccus-shapedyes
66565negativeovoid-shapedyes
66565negative0.5-0.8 µmrod-shapedyes0.3-0.7 µm
66565negative2-5 µmspiral-shapedyes
66565negative2-5 µmcurved-shapedyes

colony morphology

  • @ref: 66565
  • colony size: 0.5-1 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: Marine agar (MA) 2216

Culture and growth conditions

culture medium

  • @ref: 66565
  • name: Marine agar (MA) 2216
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66565positiveoptimum28mesophilic
66565positivegrowth4-40
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
66565positivegrowth5-9alkaliphile
66565positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66565aerobe
67771aerobe

spore formation

  • @ref: 66565
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
66565NaClpositivegrowth0.5-16 %(w/v)
66565NaClpositiveoptimum4 %(w/v)

observation

@refobservation
66565Cells have three different morphologies with one to three flagella including: (1) coccoid-shaped or ovoid-shaped with one to six prosthecates; (2) short rod- or rod-shaped with no to one prosthecate; (3) spiral-shaped or curved rod-shaped with no prosthecate
66565Cells are flocculated in marine broth 2216

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6656517234glucose-fermentation
6656517234glucose+fermentation
665655291gelatin-hydrolysis
6656528017starch-hydrolysis
6656585146carboxymethylcellulose-hydrolysis
66565skimmed milk-hydrolysis
6656553423tween 40+hydrolysis
6656553424tween 20+hydrolysis
6656553425tween 60+hydrolysis
6656553426tween 80+hydrolysis
6656517632nitrate+reduction
6656526710sodium chloride+required for growth
665656359lactulose-respiration
665658391D-gluconate-respiration
6656512936D-galactose-respiration
6656514314D-glucose 6-phosphate-respiration
6656515570D-alanine-respiration
6656515963ribitol-respiration
6656516383cis-aconitate-respiration
66565167244-hydroxybutyrate-respiration
6656516899D-mannitol-respiration
6656517113erythritol-respiration
6656517126DL-carnitine-respiration
6656517151xylitol-respiration
6656517268myo-inositol-respiration
6656517295L-phenylalanine-respiration
6656517596inosine-respiration
6656517716lactose-respiration
6656517748thymidine-respiration
6656517924D-sorbitol-respiration
66565181014-hydroxyphenylacetic acid-respiration
6656518287L-fucose-respiration
6656518333D-arabitol-respiration
6656521217L-alaninamide-respiration
6656523652dextrin-respiration
6656527248urocanic acid-respiration
6656528053melibiose-respiration
6656528066gentiobiose-respiration
6656540585alpha-cyclodextrin-respiration
6656573784glycyl-L-glutamate-respiration
66565320055methyl beta-D-glucopyranoside-respiration
66565168102-oxoglutarate-respiration
6656514336glycerol 1-phosphate+respiration
6656515603L-leucine+respiration
6656515729L-ornithine+respiration
6656515740formate+respiration
6656515748D-glucuronate+respiration
6656515792malonate+respiration
6656515824D-fructose+respiration
6656515895D-galactonic acid lactone+respiration
6656515971L-histidine+respiration
6656516000ethanolamine+respiration
6656516024D-mannose+respiration
6656516411acetic acid+respiration
6656516523D-serine+respiration
6656516634raffinose+respiration
6656516704uridine+respiration
66565167632-oxobutanoate+respiration
6656516857L-threonine+respiration
6656516865gamma-aminobutyric acid+respiration
6656516977L-alanine+respiration
6656517057cellobiose+respiration
6656517115L-serine+respiration
6656517148putrescine+respiration
6656517196L-asparagine+respiration
6656517203L-proline+respiration
6656517240itaconate+respiration
6656517272propionate+respiration
6656517306maltose+respiration
6656517754glycerol+respiration
6656517784D-glucosaminic acid+respiration
6656517925alpha-D-glucose+respiration
6656517992sucrose+respiration
6656518024D-galacturonic acid+respiration
6656518183L-pyroglutamic acid+respiration
66565182404-hydroxy-L-proline+respiration
6656524996lactate+respiration
6656526490quinate+respiration
6656527082trehalose+respiration
6656527605D-psicose+respiration
6656528087glycogen+respiration
66565286442-oxopentanoate+respiration
6656528800N-acetylgalactosamine+respiration
6656529042glucose 1-phosphate+respiration
6656529985L-glutamate+respiration
6656529991L-aspartate+respiration
6656530031succinate+respiration
6656530612D-glucarate+respiration
6656530849L-arabinose+respiration
6656532323glucuronamide+respiration
6656532528turanose+respiration
66565370543-hydroxybutyrate+respiration
6656541865sebacic acid+respiration
6656550048phenylethylamine+respiration
6656551850methyl pyruvate+respiration
6656553258citric acid+respiration
6656553423tween 40+respiration
6656553426tween 80+respiration
6656559640N-acetylglucosamine+respiration
6656562345L-rhamnose+respiration
66565645522-hydroxybutyrate+respiration
6656573706bromosuccinate+respiration
6656573786L-alanylglycine+respiration
6656573804glycyl L-aspartic acid+respiration
6656575146monomethyl succinate+respiration
66565143136succinamate+respiration
66565620642,3-butanediol+respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6656517698chloramphenicolyesyes30 µg (disc)
6656548923erythromycinyesyes15 µg (disc)
6656517833gentamicinyesyes10 µg (disc)
665656104kanamycinyesyes30 µg (disc)
6656528077rifampicinyesyes5 µg (disc)
6656517076streptomycinyesyes10 µg (disc)
6656528001vancomycinyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6656516136hydrogen sulfideyes
6656515688acetoinno
6656535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6656517234glucose-
6656515688acetoin-

enzymes

@refvalueactivityec
66565alpha-fucosidase-3.2.1.51
66565alpha-galactosidase-3.2.1.22
66565alpha-mannosidase-3.2.1.24
66565arginine dihydrolase-3.5.3.6
66565beta-galactosidase-3.2.1.23
66565beta-glucosidase-3.2.1.21
66565beta-glucuronidase-3.2.1.31
66565chymotrypsin-3.4.4.5
66565cystine arylamidase-3.4.11.3
66565N-acetyl-beta-glucosaminidase-3.2.1.52
66565alpha-glucosidase+3.2.1.20
66565catalase+1.11.1.6
66565cytochrome oxidase+1.9.3.1
66565esterase (C 4)+
66565lipase (C 14)+
66565trypsin+3.4.21.4

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation dateisolation procedure
66565surface water sample2012-09-22South China SeaChinaCHNAsiamodified marine agar 2216202016-01-12standard dilution technique
67771From sea waterPacific Mariana TrenchChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Surface water

Sequence information

16S sequences

  • @ref: 66565
  • description: Aquisalinus sp. strain SY-3-19 16S ribosomal RNA gene, partial sequence
  • accession: KY861741
  • length: 1424
  • database: ena
  • NCBI tax ID: 2058213

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinicaulis flavus SY-3-19GCA_002943565contigncbi2058213
66792Marinicaulis flavus SY-3-192786546860draftimg2058213

GC content

  • @ref: 66565
  • GC-content: 60.9
  • method: genome sequence analysis

External links

@ref: 66565

culture collection no.: MCCC 1K03432, KCTC 62156

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29701576Marinicaulis flavus gen. nov., sp. nov., a novel stalked bacterium of the family Parvularculaceae.Yu XY, Yu XD, Fu GY, Zhao Z, Shen X, Sun C, Wu MInt J Syst Evol Microbiol10.1099/ijsem.0.0027952018Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny30084015Marinicaulis aureum sp. nov., isolated from a culture of the green alga Ulva prolifera, and emended description of the genus Marinicaulis.Wang Z, Zhang Z, Li C, Hu Z, Zhao H, Zhang YAntonie Van Leeuwenhoek10.1007/s10482-018-1139-02018Alphaproteobacteria/classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Ulva/*microbiologyEnzymology

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
66565Xiao-Yun Yu, Xiao-Dong Yu, Ge-Yi Fu, Zhe Zhao, Xia Shen, Cong Sun, Min WuMarinicaulis flavus gen. nov., sp. nov., a novel stalked bacterium of the family Parvularculaceae10.1099/ijsem.0.002795IJSEM 68: 2061-2067 201829701576
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc