Strain identifier

BacDive ID: 164191

Type strain: Yes

Species: Dongshaea marina

Strain Designation: DM2

Strain history: W. Y. Shieh; Inst. of Oceanogr., Natl. Taiwan Univ., Taiwan; DM2.

NCBI tax ID(s): 2047966 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 9.3 (current version)

General

@ref: 67770

BacDive-ID: 164191

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

description: Dongshaea marina DM2 is a facultative anaerobe, halophilic, chemoheterotroph bacterium that forms circular colonies and was isolated from Lagoon sediment sample of Dongsha Island.

NCBI tax id

  • NCBI tax id: 2047966
  • Matching level: species

strain history

  • @ref: 67770
  • history: W. Y. Shieh; Inst. of Oceanogr., Natl. Taiwan Univ., Taiwan; DM2.

doi: 10.13145/bacdive164191.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Dongshaea
  • species: Dongshaea marina
  • full scientific name: Dongshaea marina Huang et al. 2019

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Dongshaea

species: Dongshaea marina

full scientific name: Dongshaea marina Huang et al. 2019

strain designation: DM2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
67775negative1.4-2.2 µm1-1.2 µmrod-shapedno
67775yesmonotrichous
125439negative97.7
125438negative99.994

colony morphology

  • @ref: 67775
  • colony size: 2-4 mm
  • colony color: off-white
  • colony shape: circular
  • incubation period: 3-5 days
  • medium used: Peptone-yeast extract agar

Culture and growth conditions

culture temp

@refgrowthtypetemperature
67770positivegrowth30
67775positivegrowth15-35
67775positiveoptimum30
67775nogrowth4-10
67775nogrowth42

culture pH

@refabilitytypepHPH range
67775positivegrowth5-9alkaliphile
67775nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 67775
  • oxygen tolerance: facultative anaerobe

nutrition type

  • @ref: 67775
  • type: chemoheterotroph

spore formation

@reftype of sporespore formationconfidence
67775endosporeno
125438no91.691

halophily

@refhalophily levelsaltgrowthtested relationconcentration
67775halophilicNaClpositivegrowth1-5 %
67775NaClpositiveoptimum2-3 %
67775NaClnogrowth0 %
67775NaClnogrowth7-10 %

observation

@refobservation
67770quinones: Q-8
67775Nearly all cells are non-motile and non-flagellated, whereas a few of the cells exhibit motility and monotrichous flagella.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6777526710sodium chloride+required for growth
6777517634D-glucose+fermentation
6777517057cellobiose+builds acid from
6777512936D-galactose+builds acid from
6777516024D-mannose+builds acid from
6777517992sucrose+builds acid from
6777527082trehalose+builds acid from
6777565327D-xylose+builds acid from
6777517057cellobiose+builds gas from
6777512936D-galactose+builds gas from
6777516024D-mannose+builds gas from
6777517992sucrose+builds gas from
6777527082trehalose+builds gas from
6777565327D-xylose+builds gas from
6777517632nitrate+reduction
6777528017starch+hydrolysis
677752509agar-hydrolysis
67775casein-hydrolysis
6777516991dna-hydrolysis
677755291gelatin-hydrolysis

metabolite production

  • @ref: 67775
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
67775alkaline phosphatase+3.1.3.1
67775esterase (C 4)+
67775leucine arylamidase+3.4.11.1
67775acid phosphatase+3.1.3.2
67775N-acetyl-beta-glucosaminidase+3.2.1.52
67775valine arylamidase+
67775naphthol-AS-BI-phosphohydrolase+
67775beta-galactosidase+3.2.1.23
67775arginine dihydrolase+3.5.3.6
67775catalase-1.11.1.6
67775cytochrome oxidase-1.9.3.1
67775esterase Lipase (C 8)-
67775beta-glucuronidase-3.2.1.31
67775alpha-glucosidase-3.2.1.20
67775trypsin-3.4.21.4

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationenrichment culture temperatureisolation procedure
67770Lagoon sediment sample of Dongsha IslandTaiwan, Province of ChinaTWNAsia
67775lagoon sediment sampleTaiwan, Province of ChinaTWNAsiaDongsha Island25Some wet mass (2 g) of each sample was taken and vigorously shaken in 98 ml sterile NaCl-Tris buffer (30 g NaCl and 0.24 g Tris in 1 l deionized water, pH 8.0). The shaken solutions were decimally diluted with the same buffer. Aliquots (1 ml) of the dilutions (10-3 to 10-5) were transferred to rimless tubes containing PYG medium (5 ml) in triplicate. All cultures were set in anaerobic jars (Difco) and incubated at 25°C in the dark for 3-7 days. The air in each anaerobic jar was replaced by N2 before incubation. The gas replacement was performed by flushing the anaerobic jar 30 times with high-purity N2 (99.9 %). Oxygen-free or nearly oxygen-free conditions could be established in the culturesystem throughout such a gas replacement treatment. Cultures that developed visible turbidity were streaked (one loopful) onto the PY plate medium and the plates were incubated at 25°C in the dark for 2-3 days under aerobic conditions. Individual colonies appearing on the plates were picked off and purified by successive streaking on PY plates.

Sequence information

16S sequences

  • @ref: 67775
  • description: Dongshaea marina strain DM2 16S ribosomal RNA gene, partial sequence
  • accession: MG232375
  • length: 1471
  • database: nuccore
  • NCBI tax ID: 2047966

Genome sequences

  • @ref: 66792
  • description: Dongshaea marina DM2
  • accession: GCA_003072645
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2047966

GC content

@refGC-contentmethod
6777051genome sequence analysis
6777051.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.994yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.896yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no74.037yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.691yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes82.199no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno82
125439BacteriaNetmotilityAbility to perform movementyes78.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe62.7

External links

@ref: 67770

culture collection no.: JCM 32096, BCRC 81069

literature

  • topic: Phylogeny
  • Pubmed-ID: 30422104
  • title: Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production.
  • authors: Huang SP, Chen TY, Chen JS, Wang LT, Huang L, Lin ST, Wei CL, Lin S, Wang PL, Chen YM, Shieh WY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003080
  • year: 2019
  • mesh: Aeromonadaceae/*classification/isolation & purification, Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Gases, Geologic Sediments/*microbiology, Glucose/*metabolism, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry
  • 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/
67775Ssu-Po Huang, Tzu-Yin Chen, Jwo-Sheng Chen, Li-Ting Wang, Lina Huang, Shih-Ting Lin, Chih-Lin Wei, Saulwood Lin, Pei-Ling Wang, Yi-Min Chen, Wung Yang ShiehDongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production10.1099/ijsem.0.003080IJSEM 69: 3318-3325 2019
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG