Strain identifier

BacDive ID: 140593

Type strain: Yes

Species: Aquimarina rubra

Strain Designation: SS2-9

Strain history: <- Zongjun Du, Shandong Univ.

NCBI tax ID(s): 1920033 (species)

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General

@ref: 43262

BacDive-ID: 140593

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Aquimarina rubra SS2-9 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sediment collected from a pond for sea cucumber culture.

NCBI tax id

  • NCBI tax id: 1920033
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zongjun Du, Shandong Univ.

doi: 10.13145/bacdive140593.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aquimarina
  • species: Aquimarina rubra
  • full scientific name: Aquimarina rubra Han et al. 2017

@ref: 43262

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aquimarina

species: Aquimarina rubra

strain designation: SS2-9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43262negative1.5-6.0 µm0.3-0.5 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 43262
  • colony size: 1-2 mm
  • colony color: red
  • colony shape: circular
  • incubation period: 3 days
  • medium used: 2216E agar

pigmentation

  • @ref: 43262
  • production: no
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 43262
  • name: 2216E agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43262positiveoptimum28mesophilic
43262positivegrowth10-37
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepHPH range
43262positivegrowth6.5-8.5alkaliphile
43262positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43262facultative anaerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
43262NaClpositivegrowth0.5-6.0 %(w/v)
43262NaClpositiveoptimum2 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43262sodium(+)+required for growth
43262nitrate-reduction17632
43262tween 20+hydrolysis53424
43262tween 40+hydrolysis53423
43262tween 60+hydrolysis53425
43262alginate+hydrolysis58187
43262starch-hydrolysis28017
43262carboxymethylcellulose-hydrolysis85146
43262agar-hydrolysis2509
43262citrate+carbon source16947
43262D-xylose+builds acid from65327
43262D-glucose+builds acid from17634
43262amygdalin+builds acid from27613
43262esculin+builds acid from4853
43262cellobiose+builds acid from17057
43262maltose+builds acid from17306
43262trehalose+builds acid from27082
43262raffinose+builds acid from16634
43262glycogen+builds acid from28087
43262potassium 2-dehydro-D-gluconate+builds acid from
43262potassium 5-dehydro-D-gluconate+builds acid from
43262maltose+carbon source17306
43262cellobiose+carbon source17057
43262N-acetylgalactosamine+carbon source28037
43262dextrin+carbon source23652
43262raffinose+carbon source16634
43262alpha-D-glucose+carbon source17925
43262D-fructose+carbon source15824
43262acetoacetate+carbon source13705
43262acetate+carbon source30089
43262dna-hydrolysis16991
43262tween 80-hydrolysis53426
43262L-arabinose-builds acid from30849
43262D-fructose-builds acid from15824
43262sucrose-builds acid from17992

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4326231168acetylspiramycinyesyes30 µg
4326228971ampicillinyesyes10 µg
43262204928cefotaximeyesyes30 µg
4326229007ceftriaxoneyesyes30 µg
4326217698chloramphenicolyesyes30 µg
432623745clindamycinyesyes30 µg
4326248923erythromycinyesyes15 µg
4326217833gentamicinyesyes10 µg
432626104kanamycinyesyes30 µg
432626472lincomycinyesyes2 µg
43262100147nalidixic acidyesyes30 µg
432627507neomycinyesyes30 µg
43262100246norfloxacinyesyes10 µg
432627731ofloxacinyesyes5 µg
4326218208penicillin gyesyes10 µg
4326228077rifampicinyesyes5 µg
4326217076streptomycinyesyes10 µg
4326227902tetracyclineyesyes30 µg
4326228864tobramycinyesyes10 µg
4326228001vancomycinyesyes30 µg

metabolite production

@refChebi-IDmetaboliteproduction
4326235581indoleno
4326216136hydrogen sulfideno
4326215688acetoinyes

metabolite tests

  • @ref: 43262
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
43262catalase+1.11.1.6
43262cytochrome oxidase-1.9.3.1
43262gelatinase+
43262amylase+
43262arginine dihydrolase-3.5.3.6
43262lysine decarboxylase-4.1.1.18
43262ornithine decarboxylase-4.1.1.17
43262urease-3.5.1.5
43262tryptophan deaminase-4.1.99.1
43262alkaline phosphatase+3.1.3.1
43262esterase Lipase (C 8)+
43262leucine arylamidase+3.4.11.1
43262valine arylamidase+
43262cystine arylamidase+3.4.11.3
43262trypsin+3.4.21.4
43262alpha-chymotrypsin+3.4.21.1
43262acid phosphatase+3.1.3.2
43262esterase (C 4)-
43262naphthol-AS-BI-phosphohydrolase-
43262alpha-galactosidase-3.2.1.22
43262beta-galactosidase-3.2.1.23
43262alpha-glucosidase-3.2.1.20
43262N-acetyl-beta-glucosaminidase-3.2.1.52
43262beta-glucosidase-3.2.1.21
43262beta-glucuronidase-3.2.1.31
43262lipase (C 14)-
43262alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43262C15:1 iso G11
    43262C15:014.7
    43262C17:0 iso 3OH15.9
    43262C15:0 iso18
  • type of FA analysis: whole cell analysis
  • incubation medium: 2216E medium
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 4.5
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43262sediment collected from a pond for sea cucumber cultureRongcheng, Shandong province, ChinaChinaCHNAsia36122
67771From sediment, a pond for sea cucumber cultureRongcheng, Shandong provinceChinaCHNAsia36.9122.233

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#Sediment
#Host#Invertebrates (Other)#Echinodermata

taxonmaps

  • @ref: 69479
  • File name: preview.99_146763.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_3439;97_39456;98_97171;99_146763&stattab=map
  • Last taxonomy: Aquimarina rubra subclade
  • 16S sequence: KX262846
  • Sequence Identity:
  • Total samples: 47
  • aquatic counts: 45
  • animal counts: 2

Sequence information

16S sequences

  • @ref: 43262
  • description: 16S rRNA gene sequences
  • accession: KX262846
  • length: 1450
  • database: ena
  • NCBI tax ID: 1920033

GC content

  • @ref: 67771
  • GC-content: 34.5

External links

@ref: 43262

culture collection no.: KCTC 52274, MCCC 1H00142

literature

  • topic: Phylogeny
  • Pubmed-ID: 28598301
  • title: Aquimarina rubra sp. nov., isolated from sediment of a sea cucumber culture pond.
  • authors: Han JR, Fang DB, Xia HF, Chen GJ, Du ZJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001889
  • year: 2017
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Ponds/microbiology, RNA, Ribosomal, 16S/genetics, Sea Cucumbers/*microbiology, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/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
43262Ji-Ru Han, Dong-Bo Fang, Hai-Feng Xia, Guan-Jun Chen and Zong-Jun DuAquimarina rubra sp. nov., isolated from sediment of a sea cucumber culture pond10.1099/ijsem.0.001889IJSEM 67: 1932-1936 201728598301
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/