Strain identifier

BacDive ID: 158614

Type strain: Yes

Species: Marinobacterium aestuarii

Strain Designation: ST58-10

Strain history: <- Kyunghwa Baek, MARINE BIODIVERSITY INSTITUTE OF KOREA

NCBI tax ID(s): 1821621 (species)

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General

@ref: 65336

BacDive-ID: 158614

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

description: Marinobacterium aestuarii ST58-10 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from estuarine sediment.

NCBI tax id

  • NCBI tax id: 1821621
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Kyunghwa Baek, MARINE BIODIVERSITY INSTITUTE OF KOREA

doi: 10.13145/bacdive158614.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacterium
  • species: Marinobacterium aestuarii
  • full scientific name: Marinobacterium aestuarii Bae et al. 2018

@ref: 65336

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacterium

species: Marinobacterium aestuarii

strain designation: ST58-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65336negative1.9-2.1 µm0.6-0.8 µmrod-shapedyes
69480yes95.965
69480negative99.997

colony morphology

  • @ref: 65336
  • colony size: 2 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: marine agar 2216

Culture and growth conditions

culture medium

  • @ref: 65336
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65336positivegrowth4-35
65336positiveoptimum20-25
65336nogrowth37mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
65336positivegrowth5-9alkaliphile
65336positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65336aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no99.962
69481no100

halophily

@refsaltgrowthtested relationconcentration
65336NaClpositivegrowth1-8 %(w/v)
65336NaClpositiveoptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65336645522-hydroxybutyrate-respiration
65336167632-oxobutanoate-respiration
65336309162-oxoglutarate+respiration
65336286442-oxopentanoate-respiration
65336620642,3-butanediol-respiration
65336370543-hydroxybutyrate+respiration
65336182404-hydroxy-L-proline-respiration
65336167244-hydroxybutyrate-respiration
65336181014-hydroxyphenylacetic acid-respiration
6533630089acetate-respiration
6533617128adipate-assimilation
6533615963ribitol-respiration
6533640585alpha-cyclodextrin-respiration
6533617925alpha-D-glucose+respiration
6533636219alpha-lactose-respiration
6533616716benzene+degradation
6533673706bromosuccinate-respiration
6533627689decanoate-assimilation
65336casein-hydrolysis
6533662968cellulose-hydrolysis
6533616383cis-aconitate+respiration
6533616947citrate+respiration
6533615570D-alanine+respiration
6533618333D-arabitol+respiration
6533617057cellobiose-respiration
6533615824D-fructose+respiration
6533615895D-galactonic acid lactone-respiration
6533612936D-galactose-respiration
6533618024D-galacturonic acid+respiration
6533630612D-glucarate-respiration
653368391D-gluconate+respiration
6533617784D-glucosaminic acid-respiration
6533617634D-glucose-assimilation
6533614314D-glucose 6-phosphate-respiration
6533615748D-glucuronate+respiration
6533617306maltose-assimilation
6533616899D-mannitol-assimilation
6533616899D-mannitol+respiration
6533616024D-mannose-assimilation
6533616024D-mannose-respiration
6533627605D-psicose-respiration
6533616523D-serine-respiration
6533617924D-sorbitol+respiration
6533623652dextrin-respiration
6533617126DL-carnitine+respiration
6533624996lactate+respiration
6533617113erythritol-respiration
653364853esculin-hydrolysis
6533616000ethanolamine-respiration
6533615740formate-respiration
6533616865gamma-aminobutyric acid-respiration
6533628066gentiobiose-respiration
6533629042glucose 1-phosphate-respiration
6533632323glucuronamide-respiration
6533617754glycerol+respiration
6533614336glycerol 1-phosphate-respiration
6533628087glycogen-respiration
6533673804glycyl L-aspartic acid-respiration
6533617596inosine-respiration
6533617240itaconate-respiration
6533621217L-alaninamide-respiration
6533616977L-alanine+respiration
6533673786L-alanylglycine-respiration
6533630849L-arabinose-assimilation
6533630849L-arabinose-respiration
6533617196L-asparagine+respiration
6533629991L-aspartate+respiration
6533618287L-fucose-respiration
6533629985L-glutamate+respiration
6533615971L-histidine-respiration
6533615603L-leucine-respiration
6533615729L-ornithine+respiration
6533617295L-phenylalanine-respiration
6533617203L-proline+respiration
6533618183L-pyroglutamic acid+respiration
6533662345L-rhamnose+respiration
6533617115L-serine-respiration
6533616857L-threonine-respiration
653366359lactulose-respiration
6533625115malate-assimilation
6533615792malonate-respiration
6533617306maltose-respiration
6533628053melibiose-respiration
65336320055methyl beta-D-glucopyranoside-respiration
6533651850methyl pyruvate-respiration
6533675146monomethyl succinate-respiration
6533617268myo-inositol+respiration
6533628037N-acetylgalactosamine-respiration
65336506227N-acetylglucosamine-assimilation
65336506227N-acetylglucosamine+respiration
6533673784glycyl-l-glutamate-respiration
6533618401phenylacetate-assimilation
6533650048phenylethylamine+respiration
6533632032potassium gluconate-assimilation
6533617272propionate-respiration
6533617148putrescine+respiration
6533626490quinate+respiration
6533616634raffinose-respiration
6533641865sebacic acid-respiration
6533653258sodium citrate-assimilation
6533628017starch-hydrolysis
65336143136succinamate+respiration
6533630031succinate+respiration
6533617992sucrose+respiration
6533617748thymidine-respiration
6533627082trehalose-respiration
6533632528turanose-respiration
6533653423tween 40-respiration
6533653426tween 80-hydrolysis
6533653426tween 80-respiration
6533616704uridine-respiration
6533627248urocanic acid-respiration
6533617151xylitol-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6533628001vancomycinyesyes30 µg (disc)
6533628077rifampicinyesyes5 µg (disc)
6533628971ampicillinyesyes10 µg (disc)
6533617833gentamicinyesyes10 µg (disc)
6533618208penicillin gyesyes10 µg (disc)
6533617076streptomycinyesyes10 µg (disc)
6533648923erythromycinyesyes15 µg (disc)
6533617698chloramphenicolyesyes30 µg (disc)
653366104kanamycinyesyes30 µg (disc)
65336100147nalidixic acidyesyes30 µg (disc)
6533627902tetracyclineyesyes30 µg (disc)

enzymes

@refvalueactivityec
65336catalase+1.11.1.6
65336cytochrome oxidase+1.9.3.1
65336alkaline phosphatase+3.1.3.1
65336esterase Lipase (C 8)+
65336leucine arylamidase+3.4.11.1
65336naphthol-AS-BI-phosphohydrolase+
65336esterase (C 4)-
65336lipase (C 14)-
65336valine arylamidase-
65336cystine arylamidase-3.4.11.3
65336alpha-chymotrypsin-3.4.21.1
65336trypsin-3.4.21.4
65336acid phosphatase-3.1.3.2
65336alpha-galactosidase-3.2.1.22
65336beta-galactosidase-3.2.1.23
65336beta-glucuronidase-3.2.1.31
65336alpha-glucosidase-3.2.1.20
65336beta-glucosidase-3.2.1.21
65336N-acetyl-beta-glucosaminidase-3.2.1.52
65336alpha-mannosidase-3.2.1.24
65336alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65336C12:04.2
    65336C14:03.7
    65336C16:018.5
    65336C18:00.6
    65336C10:0 3OH7.4
    65336C16:1ω7c/C16:1ω6c38.6
    65336C18:1ω7c/C18:1ω6c22.4
  • type of FA analysis: whole cell analysis
  • incubation medium: marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 1
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation proceduregeographic location
65336estuarine sedimentRepublic of KoreaKORAsia34.9363128.299marine agar 22167 days25fresh estuarine sediment was resuspended and serially diluted in 2 % (w/v) NaCl. The diluted samples were spread on marine agar 2216 and incubated at 25°C for 7 days under aerobic conditions
67771From seawaterRepublic of KoreaKORAsiaByeongsan-ri, Samsan-myeon, Goseong-gun, Gyeongsangnam-do

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Estuary
#Environmental#Aquatic#Sediment
#Environmental#Aquatic#Brackish

taxonmaps

  • @ref: 69479
  • File name: preview.99_1615.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_914;97_1064;98_1273;99_1615&stattab=map
  • Last taxonomy: Marinobacterium
  • 16S sequence: KU886021
  • Sequence Identity:
  • Total samples: 1629
  • soil counts: 153
  • aquatic counts: 1066
  • animal counts: 375
  • plant counts: 35

Sequence information

16S sequences

  • @ref: 65336
  • description: 16S rRNA gene sequence
  • accession: KU886021
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacterium aestuarii ST58-10GCA_001651805completencbi1821621
66792Marinobacterium aestuarii ST58-102687453330completeimg1821621

GC content

  • @ref: 65336
  • GC-content: 58.78
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes85.005no
gram-positiveno99.014no
anaerobicno98.835yes
halophileyes70.064no
spore-formingno95.927no
glucose-utilyes92.005no
motileyes90.854no
aerobicyes93.712yes
thermophileno99.504yes
glucose-fermentno84.5no

External links

@ref: 65336

culture collection no.: KCTC 52193, NBRC 112103

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29303694Marinobacterium aestuarii sp. nov., a benzene-degrading marine bacterium isolated from estuary sediment.Bae SS, Jung J, Chung D, Baek KInt J Syst Evol Microbiol10.1099/ijsem.0.0025612018Bacterial Typing Techniques, Base Composition, Benzene, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Oceanospirillaceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Genetics30533631Complete Genome Sequence of Marinobacterium aestuarii ST58-10(T), a Benzene-Degrading Bacterium Isolated from Estuarine Sediment.Baek K, Bae SS, Jung J, Chung DMicrobiol Resour Announc10.1128/MRA.00971-182018Phylogeny

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
65336Seung Seob Bae, Jaejoon Jung, Dawoon Chung, Kyunghwa BaekMarinobacterium aestuarii sp. nov., a benzene-degrading marine bacterium isolated from estuary sediment10.1099/ijsem.0.002561IJSEM 68: 651-656 201829303694
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
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