Strain identifier

BacDive ID: 164505

Type strain: Yes

Species: Shewanella maritima

Strain Designation: D4-2

Strain history: S. S. Bae; Natl. Mar. Biodivers. Inst. of Korea, South Korea; D4-2.

NCBI tax ID(s): 2520507 (species)

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General

@ref: 67770

BacDive-ID: 164505

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

description: Shewanella maritima D4-2 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Coastal seawater.

NCBI tax id

  • NCBI tax id: 2520507
  • Matching level: species

strain history

  • @ref: 67770
  • history: S. S. Bae; Natl. Mar. Biodivers. Inst. of Korea, South Korea; D4-2.

doi: 10.13145/bacdive164505.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella maritima
  • full scientific name: Shewanella maritima Bae et al. 2020

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella maritima

full scientific name: Shewanella maritima Bae et al. 2020

strain designation: D4-2

type strain: yes

Morphology

cell morphology

  • @ref: 69681
  • gram stain: negative
  • cell length: 1.0-3.7 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 69681
  • colony color: light brown
  • colony shape: circular
  • medium used: Marine agar (MA)

Culture and growth conditions

culture medium

  • @ref: 69681
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth30mesophilic
69681positivegrowth10-36
69681positiveoptimum29-32mesophilic

culture pH

@refabilitytypepH
69681positivegrowth6-9
69681positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 69681
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
69681NaClpositivegrowth1-6 %(w/v)
69681NaClpositiveoptimum2 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-7, Q-8, MK-7, MMK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6968117128adipate-assimilation
6968117120hexanoate-assimilation
6968116947citrate-assimilation
6968117634D-glucose-assimilation
6968116899D-mannitol-assimilation
6968116024D-mannose-assimilation
6968130849L-arabinose-assimilation
6968125115malate-assimilation
6968117306maltose-assimilation
69681506227N-acetylglucosamine-assimilation
6968118401phenylacetate-assimilation
69681potassium 5-dehydro-D-gluconate-assimilation
6968117634D-glucose-builds acid from
6968117234glucose-fermentation
6968158187alginate-hydrolysis
6968185146carboxymethylcellulose-hydrolysis
69681casein-hydrolysis
696815291gelatin-hydrolysis
6968128017starch-hydrolysis
6968118186tyrosine-hydrolysis
6968116199urea-hydrolysis
6968165327D-xylose+assimilation
696814853esculin+assimilation
6968116991dna+hydrolysis
6968153424tween 20+hydrolysis
6968153425tween 60+hydrolysis
6968153426tween 80+hydrolysis
6968117632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6968128971ampicillinyesyes10 µg (disc)
6968117698chloramphenicolyesyes30 µg (disc)
6968148923erythromycinyesyes15 µg (disc)
69681100147nalidixic acidyesyes30 µg (disc)
6968118208penicillin gyesyes10 µg (disc)
6968128077rifampicinyesyes30 µg (disc)
6968117833gentamicinyesyes10 µg (disc)
696816104kanamycinyesyes30 µg (disc)
6968117076streptomycinyesyes10 µg (disc)
6968127902tetracyclineyesyes30 µg (disc)
6968128001vancomycinyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6968135581indoleno
6968116136hydrogen sulfideyes

enzymes

@refvalueactivityec
69681catalase+1.11.1.6
69681cytochrome oxidase+1.9.3.1
69681arginine dihydrolase-3.5.3.6
69681beta-galactosidase-3.2.1.23
69681urease-3.5.1.5
69681alkaline phosphatase+3.1.3.1
69681esterase (C 4)+
69681esterase Lipase (C 8)+
69681leucine arylamidase+3.4.11.1
69681valine arylamidase+/-
69681cystine arylamidase+/-3.4.11.3
69681trypsin+/-3.4.21.4
69681alpha-chymotrypsin+3.4.21.1
69681acid phosphatase+3.1.3.2
69681naphthol-AS-BI-phosphohydrolase+/-
69681N-acetyl-beta-glucosaminidase+3.2.1.52

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    69681anteiso-C15:0/iso-C15:00.9
    69681C12:03.3
    69681C12:0 3OH1.4
    69681C12:0 aldehyde2.3
    69681C13:02
    69681C14:02.2
    69681C15:1 w6c0.9
    69681C15:1 w8c0.8
    69681C16:08.9
    69681C16:1 w7c/C16:1 w6c16.5
    69681C17:01.7
    69681C17:1 w6c1.4
    69681C17:1 w8c8
    69681C18:02
    69681C18:1 w7c/C18:1 w6c5.1
    69681C18:1 w9c1.2
    69681iso-C13:06.1
    69681iso-C13:0 3OH3.9
    69681iso-C14:01.5
    69681iso-C15:024
    69681iso-C15:1 H / C13:0 3OH1.3
    69681iso-C16:00.6
    69681iso-C17:02
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine Agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: HP6890; Hewlett Packard
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
67770Coastal seawater
69681seawaterDong-do marina, Dokdo IslandRepublic of KoreaKORAsia37.2333131.867

taxonmaps

  • @ref: 69479
  • File name: preview.99_171111.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_215;97_74906;98_112117;99_171111&stattab=map
  • Last taxonomy: Shewanella maritima subclade
  • 16S sequence: MK212917
  • Sequence Identity:
  • Total samples: 438
  • soil counts: 17
  • aquatic counts: 296
  • animal counts: 123
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 67770
  • description: Shewanella sp. strain D4-2 16S ribosomal RNA gene, partial sequence
  • accession: MK212917
  • length: 1350
  • database: ena
  • NCBI tax ID: 2520507

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella sp. D4-22520507.3completepatric2520507
67770Shewanella maritima D4-2GCA_004295345completencbi2520507
69681Whole genome shotgunCP036200ncbi2520507

GC content

  • @ref: 67770
  • GC-content: 44.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.193no
gram-positiveno98.99no
anaerobicno96.356no
aerobicyes60.222no
halophileyes55.5no
spore-formingno96.399no
glucose-utilyes90.154no
flagellatedyes87.569no
thermophileno99.089no
glucose-fermentno75.719no

External links

@ref: 67770

culture collection no.: JCM 33294, KCTC 72040

literature

  • topic: Phylogeny
  • Pubmed-ID: 31778351
  • title: Shewanella maritima sp. nov., a facultative anaerobic marine bacterium isolated from seawater, and emended description of Shewanella intestini.
  • authors: Bae SS, Jung YH, Baek K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003916
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
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
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/
69681Seung Seob Bae, Yoon-hee Jung, Kyunghwa BaekShewanella maritima sp. nov., a facultative anaerobic marine bacterium isolated from seawater, and emended description of Shewanella intestini10.1099/ijsem.0.003916IJSEM 70: 1288-1293 2020