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=== Genome Structure ===
=== Genome Structure ===
* The complete genome sequence of ''D. donghaensis DSW-1T'' can be accessed from [[GenBank]] under the accession number CP015125.<ref name=":2" /> The complete circular genome contains about 3,923,666 base pairs, 55 RNA genes, and 2,881 protein genes. The sequencing was established using the PacBio sequencing platform and funded by the National Research Foundation of Korea.<ref name=":2" />
* The complete genome sequence of ''D. donghaensis DSW-1T'' can be accessed from [[GenBank]] under the accession number CP015125.<ref name=":2" /> The complete circular genome contains about 3,923,666 base pairs, 55 RNA genes, and 2,881 protein genes. The sequencing was established using the PacBio sequencing platform and funded by the National Research Foundation of Korea.<ref name=":2" />
* As of March 2022, an additional nine species of Dokdonia have been added to core genomic databases such as Uniprot and Genbank but not all have undergone formal review.<ref>{{cite journal | vauthors = Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I | display-authors = 6 | title = NCBI Taxonomy: a comprehensive update on curation, resources and tools | journal = Database | volume = 2020 | pages = baaa062 | date = January 2020 | pmid = 32761142 | pmc = 7408187 | doi = 10.1093/database/baaa062 }}</ref>
* As of March 2022, an additional nine species of ''Dokdonia'' have been added to core genomic databases such as Uniprot and Genbank but not all have undergone formal review.<ref>{{cite journal | vauthors = Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I | display-authors = 6 | title = NCBI Taxonomy: a comprehensive update on curation, resources and tools | journal = Database | volume = 2020 | pages = baaa062 | date = January 2020 | pmid = 32761142 | pmc = 7408187 | doi = 10.1093/database/baaa062 }}</ref>


== Main members ==
== Main members ==
Line 128: Line 128:
=== Expression of proteorhodopsin encoding gene ===
=== Expression of proteorhodopsin encoding gene ===
* Light induce the expression fo PR gene.<ref name=":3" /><ref name=":8">{{Cite journal |last=Palovaara |first=Joakim |last2=Akram |first2=Neelam |last3=Baltar |first3=Federico |last4=Bunse |first4=Carina |last5=Forsberg |first5=Jeremy |last6=Pedrós-Alió |first6=Carlos |last7=González |first7=José M. |last8=Pinhassi |first8=Jarone |date=2014-09-02 |title=Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria |url=https://pnas.org/doi/full/10.1073/pnas.1402617111 |journal=Proceedings of the National Academy of Sciences |language=en |volume=111 |issue=35 |doi=10.1073/pnas.1402617111 |issn=0027-8424 |pmc=PMC4156726 |pmid=25136122}}</ref> There is a significant increase in the expression level of PR gene between light and dark conditions.<ref name=":8" />
* Light induce the expression fo PR gene.<ref name=":3" /><ref name=":8">{{Cite journal |last=Palovaara |first=Joakim |last2=Akram |first2=Neelam |last3=Baltar |first3=Federico |last4=Bunse |first4=Carina |last5=Forsberg |first5=Jeremy |last6=Pedrós-Alió |first6=Carlos |last7=González |first7=José M. |last8=Pinhassi |first8=Jarone |date=2014-09-02 |title=Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria |url=https://pnas.org/doi/full/10.1073/pnas.1402617111 |journal=Proceedings of the National Academy of Sciences |language=en |volume=111 |issue=35 |doi=10.1073/pnas.1402617111 |issn=0027-8424 |pmc=PMC4156726 |pmid=25136122}}</ref> There is a significant increase in the expression level of PR gene between light and dark conditions.<ref name=":8" />

== Behavior ==

* In the Tyrrhenian Sea off the coast of Naples, species of ''Dokdonia'' were found to be the most abundant in biofilms on plastic debris (4.76 ± 7.1% of genera belonged to ''Dokdonia''<ref>{{Cite journal |last=Basili |first=Marco |last2=Quero |first2=Grazia Marina |last3=Giovannelli |first3=Donato |last4=Manini |first4=Elena |last5=Vignaroli |first5=Carla |last6=Avio |first6=Carlo Giacomo |last7=De Marco |first7=Rocco |last8=Luna |first8=Gian Marco |date=2020-05-07 |title=Major Role of Surrounding Environment in Shaping Biofilm Community Composition on Marine Plastic Debris |url=https://www.frontiersin.org/article/10.3389/fmars.2020.00262/full |journal=Frontiers in Marine Science |volume=7 |pages=262 |doi=10.3389/fmars.2020.00262 |issn=2296-7745}}</ref>

* Given that ''Dokdonia'' was found on plastics but not in the sediment or water column, it is possible that the habitat in biofilms on plastics is preferable to planktonic growth for species of ''Dokdonia'' in the Mediterranean Sea 

== References ==
== References ==
{{Reflist}}
{{Reflist}}

Revision as of 07:16, 1 April 2022

Dokdonia
Scientific classification
Domain:
Bacteria
Phylum:
Bacteroidota
Order:
Flavobacteriia
Suborder:
Flavobacteriales
Family:
Flavobacteriaceae
Genus:
Dokdonia

Yoon et al. 2005[1]
Type species
Dokdonia donghaensis[1]
Species

D. diaphoros[1]
D. donghaensis[1]
D. eikasta[1]
D. genika[1]
D. pacifica[1]

Synonyms[2]
  • Dokdoa
  • Kitrinoberga
  • Krokinobacter Khan et al. 2006

Dokdonia is a genus of bacteria from the family of Flavobacteriaceae and phylum Bacteroidota.[1][3][2] Dokdonia is named after Dokdo, a Korean name for the Liancourt Rocks which sovereignty is disputed between Japan and Korea, at where the organisms were isolated.[4]

The general characteristics of this species is gram-negative, non-motile, non-spore-forming rods or elongated rods , aerobic, catalase- and oxidase-positive. It is considered relatively halophilic as it is cultivated optimally with 2% w/v NaCl.[5][6]

The International Committee on Systematics of Prokaryotes (ICSP) currently recognizes nine groups of Dokdonia described to species level.[7]

Research and Discovery

History of discovery

  • Isolated from seawater near Liancourt Rocks in the Sea of Japan between Japan and South Korea. In 2005, D. donghaensis was first cultivated in the lab by Yoon et. al.[8]
  • Dokdonia species have been found in surface seawater, marine sediment, and seaweed.[9][10][11][12][13]

Genome Structure

  • The complete genome sequence of D. donghaensis DSW-1T can be accessed from GenBank under the accession number CP015125.[8] The complete circular genome contains about 3,923,666 base pairs, 55 RNA genes, and 2,881 protein genes. The sequencing was established using the PacBio sequencing platform and funded by the National Research Foundation of Korea.[8]
  • As of March 2022, an additional nine species of Dokdonia have been added to core genomic databases such as Uniprot and Genbank but not all have undergone formal review.[14]

Main members

Dokdonia donghaensis[5][15]

  • Discovered by Yoon et al. in 2005 from seawater near Liancourt Rocks.
  • Gram-negative, non-motile, non-spore-forming, slightly halophilic.
  • Cells are 0·3–0·6×1·5–25·0 μm. Form circular, smooth, yellow colonies with diameter of 1 – 2 mm on marine agar after 3 days.
  • Optimum growth occurs at 30 °C, pH 7·0–8·0 and 2% (w/v) NaCl; No anaerobic growth on marine agar and no growth on marine agar supplemented with nitrate

Dokdonia aurantiaca[16]

  • Discovered by Choi et al. in 2018 from seaweed sample, Zostera marina, collected from East China Sea, Republic of Korea
  • Gram-negative, non-motile, aerobic, orange-coloured and rod-shaped
  • Cells are 0.68–0.76 µm in diameter and 1.76–3.04 µm in length. Form circular, convex, smooth, colonies with diameter of 1.5–2 mm on marine agar after 3 days
  • Optimum growth occurs with 4% (w/v) sea salts, at pH 7 and at 25 °C
  • Catalase-positive and oxidase-negative. Produce carotenoid pigments  

Dokdonia diaphoros[17][9]

  • Discovered by Khan et al. in 2006 from marine sediment at Kisarazu, Japan and classified as Krokinobacter diaphorus. In 2012, Yoon et al. reclassified this species as Dokdonia diaphoros as the 16S rRNA gene sequence analysis has shown that the genera Dokdonia and Krokinobacter under the family Flavobacteriaceae are phylogenetically closely related
  • Gram-negative, aerobic, flexirubin-negative rods with carotenioid pigments
  • Cells are 0.5 – 0.7 mm by 2.5 – 4.0 mm. Form slightly convex and yellowish colonies
  • Optimum growth occurs with 3% (w/v) sea salts at 20 °C
  • Catalase-positive and oxidase-positive; DNA G+C content is 33 mol%

Dokdonia eikasta [9]

  • Discovered by Khan et al. in 2006 and discribed as Krokinobacter eikastus from marine sediment of Kisarazu, Japan. In 2012, Yoon et al. reclassified this species as Dokdonia diaphoros
  • Gram-negative, aerobic, flexirubin-negative rods with carotenioid pigments
  • Cells are 0.5 – 0.7 mm by 2.5 – 4.0 mm. Form slightly convex and yellowish colonies
  • Optimum growth occurs with 3% (w/v) sea salts at 20 °C
  • Catalase-positive and oxidase-positive; DNA G+C content is 39 mol%

Dokdonia flava [10]

  • Discovered by Choi et al. from the seaweed Zostera marina from the Yellow Sea, Republic of Korea in 2018.
  • Gram-negative, aerobic, non-motile, rod-shape
  • Cell size of 0.80–0.89 µm in diameter and 2.24–3.84 µm in length. Form circular, convex, smooth, yellowish colonies with 1–2 mm in diameter on marine agar after 3 days.
  • Optimum growth occurs with 4% (w/v) sea salts at pH = 7 and  25 °C
  • Catalase-positive and oxidase-positive. No flexirubintype pigments but constraints carotenoid pigments; The DNA G+C content is 36 mol%.

Dokdonia genika [9]

  • Discovered by Khan et al. in 2006 from the marine sediment at Odawara, Japan and discribed as Krokinobacter genikus. In 2012, Yoon et al. reclassified this species as Dokdonia genika.
  • Gram-negative, aerobic, flexirubin-negative rods with carotenioid-type pigments
  • Cells are 0.5 – 0.7 mm by 2.5 – 4.0 mm. Form slightly convex and yellowish colonies
  • Optimum growth occurs with 3% (w/v) sea salts at 20 °C
  • Catalase-positive and oxidase-positive; DNA G+C content is 37-39 mol%

Dokdonia lutea [11]

  • Discovered by Choi et al. in 2017 from the brown alga Sargassum fulvellum collected from the East China Sea, Republic of Korea.
  • Gram-negative, aerobic, non-motile, rod-shaped with no flexirubintype pigments
  • Cells are  0.5 µm in diameter and 2.0–3.2 µm in length. Form circular, convex, smooth, and yellowish colonies that are 1.5–2 mm in diameter on marine agar after 3 days
  • Optimum growth occurs with 5% (w/v) sea salts at pH = 8 and at 25-30 °C
  • Catalase-positive and oxidase-negative; DNA G+C content is 35 mol%.

Dokdonia pacifica [12]

  • Discovered by Zhang et al. in 2015 from surface seawater collected from the South Pacific Gyre
  • Gram-negative, aerobic, non-flagellated, non-gliding, rod-shaped with no flexirubintype pigments
  • Cells are 1.2–1.5 mm in length, 0.3–0.4 mm in width. Form circular, convex, transparent, and yellow transparent, and yellow colonies that are 0.8–1.0 mm in diameter on marine agar after 3 days
  • Optimum growth occurs with 2-3% (w/v) sea salts at pH = 8 and at 28 °C
  • Catalase-positive and oxidase-positive; DNA G+C content is 36 mol%

Dokdonia sinensis [13]

  • Discovered by Zhou et al. in 2020 from from seawater collected around Xiaoshi Island, PR China.
  • Gram-negative, aerobic, non-motile, rod-shaped with no flexirubintype pigments
  • Cells are 1.0–3.0 µm in length and  0.5–0.8 µm in width. Form circular, convex, smooth, orange-pigmented colonies that are 1.0–1.5 mm in diameter on marine agar after 3 days
  • Optimum growth occurs with 3% (w/v) sea salts at pH = 7 and at 28 °C
  • Catalase-positive and oxidase-negative; DNA G+C content is 39.5 mol%

Metabolism

Metabolic processes used by Dokdonia

  • Dokdonia species are known to be chemoheterotrophs[18][19] that they acquire energy from organic molecules. They have maximum growth in high concentration of dissolved organic matter condition.[19] Dokdonia and other members of the Bacteroidetes phylum are important in the degradation of organic matters.[20]
  • Recent research has shown that some strains of Dokdonia are falcultative double mixotrophs as they can utilize both chemotrophic and phototrophic metabolism. [21] These strains contain proteorhodopsins (PRs) which act as light-dependent proton pumps.[19] [21] PRs allow cell to harvest energy from sunlight. When exposing to light, the protein pumps protons across membrane and build proton gradient that can be used to generate ATP and power other cellular functions.[20]
  • Dokdonia sp. strain MED134 contains proteorhodopsins which are predicted to be heptahelical integral membrane protein that pumps H+ across membrane to build proton gradient.[19][21] In the near surface, the maximum absorption wavelength of PR is 535 nm. In deeper water, the maximum absorption wavelength is 490 nm. [19]
  • Dokdonia sp. PRO95 has a light-driven sodium-motive pump Na+-rhodopsin (NaR) which pumps Na+ from cytoplasm to external medium. It can also pumps H+ when Na+ is absent.[22]

Ecological significance of proteorhodopsin-containing Dokdonia

  • The presence of PRs allow cells to grow better in light compare to darkness, especially when there is low or intermediate level of nutrients available.[19][21] Being able to harvest energy from light gives it an advantage during nutrient deficient period which is favored by natural selection.[19]

Expression of proteorhodopsin encoding gene

  • Light induce the expression fo PR gene.[19][21] There is a significant increase in the expression level of PR gene between light and dark conditions.[21]

Behavior

  • In the Tyrrhenian Sea off the coast of Naples, species of Dokdonia were found to be the most abundant in biofilms on plastic debris (4.76 ± 7.1% of genera belonged to Dokdonia[23]
  • Given that Dokdonia was found on plastics but not in the sediment or water column, it is possible that the habitat in biofilms on plastics is preferable to planktonic growth for species of Dokdonia in the Mediterranean Sea 

References

  1. ^ a b c d e f g h Parte AC. "Dokdonia". LPSN.
  2. ^ a b "Dokdonia". www.uniprot.org.
  3. ^ Parker CT, Garrity GM (2012). "Nomenclature Abstract for Dokdonia Yoon et al. 2005 emend. Yoon et al. 2012". The NamesforLife Abstracts. doi:10.1601/nm.9754.
  4. ^ Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB, eds. (2011). Bergey's Manual of Systematic Bacteriology: Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer Science & Business Media. ISBN 9780387685724.
  5. ^ a b Yoon JH, Kang SJ, Lee CH, Oh TK (November 2005). "Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water". International Journal of Systematic and Evolutionary Microbiology. 55 (Pt 6): 2323–2328. doi:10.1099/ijs.0.63817-0. PMID 16280490.
  6. ^ Yoon JH, Kang SJ, Park S, Oh TK (August 2012). "Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005". International Journal of Systematic and Evolutionary Microbiology. 62 (Pt 8): 1896–1901. doi:10.1099/ijs.0.035253-0. PMID 21984677.
  7. ^ "Genus: Dokdonia". lpsn.dsmz.de. Retrieved 2022-02-20.
  8. ^ a b c Kim K, Kwon SK, Yoon JH, Kim JF (August 2016). "Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea)". Genome Announcements. 4 (4): e00804–16. doi:10.1128/genomeA.00804-16. PMID 27491981.
  9. ^ a b c d Khan ST, Nakagawa Y, Harayama S (February 2006). "Krokinobacter gen. nov., with three novel species, in the family Flavobacteriaceae". International Journal of Systematic and Evolutionary Microbiology. 56 (Pt 2): 323–328. doi:10.1099/ijs.0.63841-0. PMID 16449433.
  10. ^ a b Choi S, Kang JW, Yoon JH, Seong CN (March 2018). "Dokdonia flava sp. nov., isolated from the seaweed Zostera marina". International Journal of Systematic and Evolutionary Microbiology. 68 (3): 899–904. doi:10.1099/ijsem.0.002607. PMID 29458481.
  11. ^ a b Choi S, Kang JW, Lee JH, Seong CN (November 2017). "Dokdonia lutea sp. nov., isolated from Sargassum fulvellum seaweed". International Journal of Systematic and Evolutionary Microbiology. 67 (11): 4482–4486. doi:10.1099/ijsem.0.002317. PMID 28933321.
  12. ^ a b Zhang Z, Gao X, Wang L, Zhang XH (July 2015). "Dokdonia pacifica sp. nov., isolated from seawater". International Journal of Systematic and Evolutionary Microbiology. 65 (7): 2222–2226. doi:10.1099/ijs.0.000252. PMID 25862384.
  13. ^ a b Zhou LY, Meng X, Zhong YL, Li GY, Du ZJ, Mu DS (March 2020). "Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater". International Journal of Systematic and Evolutionary Microbiology. 70 (3): 1617–1622. doi:10.1099/ijsem.0.003949. PMID 32228747.
  14. ^ Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. (January 2020). "NCBI Taxonomy: a comprehensive update on curation, resources and tools". Database. 2020: baaa062. doi:10.1093/database/baaa062. PMC 7408187. PMID 32761142.
  15. ^ "Taxonomy of the genus Dokdonia Yoon et al. 2005 emend. Yoon et al. 2012". NamesForLife. doi:10.1601/tx.9754.
  16. ^ Choi S, Kang JW, Kim MS, Yoon JH, Seong CN (May 2018). "Dokdonia aurantiaca sp. nov., isolated from seaweed Zostera marina". International Journal of Systematic and Evolutionary Microbiology. 68 (5): 1697–1701. doi:10.1099/ijsem.0.002730. PMID 29570445.
  17. ^ Yoon JH, Kang SJ, Park S, Oh TK (August 2012). "Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005". International Journal of Systematic and Evolutionary Microbiology. 62 (Pt 8): 1896–1901. doi:10.1099/ijs.0.035253-0. PMID 21984677.
  18. ^ Posacka AM, Semeniuk DM, Maldonado MT (2019-02-05). "Effects of Copper Availability on the Physiology of Marine Heterotrophic Bacteria". Frontiers in Marine Science. 5: 523. doi:10.3389/fmars.2018.00523. ISSN 2296-7745.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  19. ^ a b c d e f g h Gómez-Consarnau L, González JM, Coll-Lladó M, Gourdon P, Pascher T, Neutze R, et al. (January 2007). "Light stimulates growth of proteorhodopsin-containing marine Flavobacteria". Nature. 445 (7124): 210–213. doi:10.1038/nature05381. PMID 17215843.
  20. ^ a b González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, et al. (December 2011). "Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134". Applied and Environmental Microbiology. 77 (24): 8676–8686. doi:10.1128/AEM.06152-11. PMC 3233072. PMID 22003006.
  21. ^ a b c d e f Palovaara, Joakim; Akram, Neelam; Baltar, Federico; Bunse, Carina; Forsberg, Jeremy; Pedrós-Alió, Carlos; González, José M.; Pinhassi, Jarone (2014-09-02). "Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria". Proceedings of the National Academy of Sciences. 111 (35). doi:10.1073/pnas.1402617111. ISSN 0027-8424. PMC 4156726. PMID 25136122.{{cite journal}}: CS1 maint: PMC format (link)
  22. ^ Bogachev, Alexander V.; Bertsova, Yulia V.; Verkhovskaya, Marina L.; Mamedov, Mahir D.; Skulachev, Vladimir P. (2016-02-11). "Real-time kinetics of electrogenic Na+ transport by rhodopsin from the marine flavobacterium Dokdonia sp. PRO95". Scientific Reports. 6 (1): 21397. doi:10.1038/srep21397. ISSN 2045-2322. PMC 4749991. PMID 26864904.{{cite journal}}: CS1 maint: PMC format (link)
  23. ^ Basili, Marco; Quero, Grazia Marina; Giovannelli, Donato; Manini, Elena; Vignaroli, Carla; Avio, Carlo Giacomo; De Marco, Rocco; Luna, Gian Marco (2020-05-07). "Major Role of Surrounding Environment in Shaping Biofilm Community Composition on Marine Plastic Debris". Frontiers in Marine Science. 7: 262. doi:10.3389/fmars.2020.00262. ISSN 2296-7745.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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