Strain identifier

BacDive ID: 159839

Type strain: Yes

Species: Maribacter litoralis

Strain Designation: SDRB-Phe2

Strain history: B. S. Kim; Korea Univ., South Korea; SDRB-Phe2.

NCBI tax ID(s): 2059726 (species)

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General

@ref: 66725

BacDive-ID: 159839

DSM-Number: 106042

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

description: Maribacter litoralis SDRB-Phe2 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from a beach sediment during an investigation of polycyclic aromatic hydrocarbon-degrading bacteria on beach sediment contaminated by crude oil spill accident.

NCBI tax id

  • NCBI tax id: 2059726
  • Matching level: species

strain history

  • @ref: 67770
  • history: B. S. Kim; Korea Univ., South Korea; SDRB-Phe2.

doi: 10.13145/bacdive159839.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Maribacter
  • species: Maribacter litoralis
  • full scientific name: Maribacter litoralis Lee et al. 2018

@ref: 66725

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Maribacter

species: Maribacter litoralis

strain designation: SDRB-Phe2

type strain: yes

Morphology

cell morphology

  • @ref: 66725
  • gram stain: negative
  • cell length: 2.3-2.9 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 66725
  • colony size: 2-3 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: Marine agar (MA)

pigmentation

  • @ref: 66725
  • production: no
  • name: flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowthcomposition
66725ISP 2yes
66725Marine agar (MA)yes
66725Nutrient agar (NA)yessupplemented with artificial seawater
66725tryptic soy agar (TSA)yes
66725tryptic soy agar (TSA)yessupplemented with artificial seawater

culture temp

@refgrowthtypetemperaturerange
66725positiveoptimum20-30
66725positivegrowth4-37
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
66725positivegrowth5-11alkaliphile
66725positiveoptimum6.0-9.0

Physiology and metabolism

oxygen tolerance

  • @ref: 66725
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
66725NaClpositivegrowth0-9.0 %(w/v)
66725NaClpositiveoptimum0-3 %(w/v)

observation

@refobservation
66725cells produce capsular EPS
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6672516024D-mannose-assimilation
6672516899D-mannitol-assimilation
6672517128adipate-assimilation
6672517306maltose-assimilation
6672517634D-glucose-assimilation
6672518401phenylacetate-assimilation
6672525115malate-assimilation
6672527689decanoate-assimilation
6672530849L-arabinose-assimilation
6672532032potassium gluconate-assimilation
6672553258sodium citrate-assimilation
6672559640N-acetylglucosamine-assimilation
667256359lactulose-carbon source
667258391D-gluconate-carbon source
6672512936D-galactose-carbon source
6672514314D-glucose 6-phosphate-carbon source
6672514336glycerol 1-phosphate-carbon source
6672515570D-alanine-carbon source
6672515603L-leucine-carbon source
6672515729L-ornithine-carbon source
6672515740formate-carbon source
6672515748D-glucuronate-carbon source
6672515792malonate-carbon source
6672515895D-galactonic acid lactone-carbon source
6672515963ribitol-carbon source
6672515971L-histidine-carbon source
6672516000ethanolamine-carbon source
6672516383cis-aconitate-carbon source
6672516411acetic acid-carbon source
6672516523D-serine-carbon source
6672516634raffinose-carbon source
6672516704uridine-carbon source
66725167244-hydroxybutyrate-carbon source
66725167632-oxobutanoate-carbon source
6672516857L-threonine-carbon source
6672516865gamma-aminobutyric acid-carbon source
6672516899D-mannitol-carbon source
6672516977L-alanine-carbon source
6672517057cellobiose-carbon source
6672517113erythritol-carbon source
6672517115L-serine-carbon source
6672517126DL-carnitine-carbon source
6672517148putrescine-carbon source
6672517151xylitol-carbon source
6672517196L-asparagine-carbon source
6672517203L-proline-carbon source
6672517240itaconate-carbon source
6672517268myo-inositol-carbon source
6672517272propionate-carbon source
6672517295L-phenylalanine-carbon source
6672517306maltose-carbon source
6672517596inosine-carbon source
6672517716lactose-carbon source
6672517748thymidine-carbon source
6672517754glycerol-carbon source
6672517784D-glucosaminic acid-carbon source
6672517924D-sorbitol-carbon source
6672517992sucrose-carbon source
6672518024D-galacturonic acid-carbon source
6672518183L-pyroglutamic acid-carbon source
6672518287L-fucose-carbon source
6672518333D-arabitol-carbon source
6672521217L-alaninamide-carbon source
6672524741hydroxyproline-carbon source
6672524996lactate-carbon source
6672526490quinate-carbon source
6672527248urocanic acid-carbon source
6672527605D-psicose-carbon source
6672528053melibiose-carbon source
6672528066gentiobiose-carbon source
6672528087glycogen-carbon source
66725286442-oxopentanoate-carbon source
6672528800N-acetylgalactosamine-carbon source
6672529042glucose 1-phosphate-carbon source
6672529985L-glutamate-carbon source
6672529991L-aspartate-carbon source
6672530031succinate-carbon source
6672530612D-glucarate-carbon source
6672530849L-arabinose-carbon source
6672532323glucuronamide-carbon source
6672532528turanose-carbon source
66725370543-hydroxybutyrate-carbon source
6672537657methyl D-glucoside-carbon source
6672540585alpha-cyclodextrin-carbon source
6672550048phenylethylamine-carbon source
6672551850methyl pyruvate-carbon source
6672553258citric acid-carbon source
6672553426tween 80-carbon source
6672559640N-acetylglucosamine-carbon source
6672562345L-rhamnose-carbon source
66725645522-hydroxybutyrate-carbon source
6672573706bromosuccinate-carbon source
6672573784glycyl-L-glutamate-carbon source
6672573786L-alanylglycine-carbon source
6672573804glycyl L-aspartic acid-carbon source
66725143136succinamate-carbon source
66725620642,3-butanediol-carbon source
66725168102-oxoglutarate-carbon source
6672515824D-fructose+carbon source
6672516024D-mannose+carbon source
6672517925alpha-D-glucose+carbon source
66725181014-hydroxyphenylacetic acid+carbon source
6672523652dextrin+carbon source
6672527082trehalose+carbon source
6672541865sebacic acid+carbon source
6672553423tween 40+carbon source
6672575146monomethyl succinate+carbon source
667254853esculin+degradation
6672517234glucose-fermentation
667252509agar-hydrolysis
667255291gelatin-hydrolysis
6672515318xanthine-hydrolysis
6672516991dna-hydrolysis
6672517368hypoxanthine-hydrolysis
6672585146carboxymethylcellulose-hydrolysis
66725casein-hydrolysis
6672518186tyrosine+hydrolysis
6672517632nitrate-reduction

metabolite production

  • @ref: 66725
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66725alpha-chymotrypsin-3.4.21.1
66725alpha-fucosidase-3.2.1.51
66725arginine dihydrolase-3.5.3.6
66725beta-galactosidase-3.2.1.23
66725beta-glucuronidase-3.2.1.31
66725lipase (C 14)-
66725trypsin-3.4.21.4
66725urease-3.5.1.5
66725acid phosphatase+3.1.3.2
66725alkaline phosphatase+3.1.3.1
66725alpha-galactosidase+3.2.1.22
66725alpha-glucosidase+3.2.1.20
66725alpha-mannosidase+3.2.1.24
66725beta-glucosidase+3.2.1.21
66725catalase+1.11.1.6
66725cystine arylamidase+3.4.11.3
66725esterase (C 4)+
66725esterase Lipase (C 8)+
66725leucine arylamidase+3.4.11.1
66725N-acetyl-beta-glucosaminidase+3.2.1.52
66725naphthol-AS-BI-phosphohydrolase+
66725valine arylamidase+
66725cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66725a beach sediment during an investigation of polycyclic aromatic hydrocarbon-degrading bacteria on beach sediment contaminated by crude oil spill accident2016-07-24Sinduri beach in TaeanRepublic of KoreaKORAsia35.9833126.6mineral salts basal (MSB) medium20.0 g NaCl, 7.0 g Na2HPO4 12HO, 1 g KH2PO4 , 10 mg CaCl2 2H2O, 1 mg FeCl3 , 20 mg MgSO4 7H2O, 1 g (NH4)2SO4 and 1000 ml distilled water; pH 7.0) supplemented with 20 mg of naphthalene, phenanthrene or pyrene7 days28A beach sediment sample was collected from Sinduri beach in Taean, Republic of Korea in 24 July 2016. The sediment sample was inoculated into separate Erlenmeyer flasks containing 100 ml modified mineral salts basal medium (20.0 g NaCl, 7.0 g Na2HPO4 12HO, 1 g KH2PO4 , 10 mg CaCl2 2H2O, 1 mg FeCl3 , 20 mg MgSO4 7H2O, 1 g (NH4)2SO4 and 1000 ml distilled water; pH 7.0) supplemented with 20 mg of naphthalene, phenanthrene or pyrene as the sole carbon source. After incubation for 7 days with shaking (200 r.p.m) at 28°C, 10 ml culture broth was transferred into 100 ml fresh MSB medium for an additional 7 days of enrichment. Subsequently, enrichment cultures were diluted and spread onto marine agar, and the plates were incubated for 3 days at 28°C.
67770Sinduri beach sediment in TaeanRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_48070.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_141;96_1222;97_1664;98_2415;99_48070&stattab=map
  • Last taxonomy: Maribacter litoralis
  • 16S sequence: MG456900
  • Sequence Identity:
  • Total samples: 243
  • soil counts: 1
  • aquatic counts: 230
  • animal counts: 6
  • plant counts: 6

Sequence information

16S sequences

  • @ref: 66725
  • description: Maribacter sp. SDRB-Phe2 16S ribosomal RNA gene, partial sequence
  • accession: MG456900
  • length: 1442
  • database: ena
  • NCBI tax ID: 2059726

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Maribacter litoralis SDRB-Phe22834232880draftimg2059726
67770Maribacter litoralis SDRB-Phe2GCA_003075045scaffoldncbi2059726

GC content

  • @ref: 66725
  • GC-content: 36.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 66725

culture collection no.: JCM 32373, KCTC 62273, DSM 106042

literature

  • topic: Phylogeny
  • Pubmed-ID: 30222095
  • title: Maribacter litoralis sp. nov. a marine bacterium isolated from seashore.
  • authors: Lee DW, Lee H, Kwon BO, Khim JS, Yim UH, Park H, Park B, Choi IG, Kim BS, Kim JJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003011
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, 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
66725Dong Wan Lee, Hanbyul Lee, Bong-Oh Kwon, Jong Seong Khim, Un Hyuk Yim, Hongjae Park, Byeonghyeok Park, In-Geol Choi, Beom Seok Kim, Jae-Jin KimMaribacter litoralis sp. nov. a marine bacterium isolated from seashore10.1099/ijsem.0.003011IJSEM 68: 3471-3478 201830222095
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/