The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY (한국해양학회지:바다)

The Korean Society of Oceanography (한국해양학회)
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Current Status and Prospects for the Data Quality Control in Terms of Diatom Analysis

돌말류 분석 자료 정도 관리의 현황 및 전망

  • KIM, HYESUK (Department of Convergence on the Ocean Science and Technology, Korea Maritime and Ocean University) ;
  • KHIM, JONGSEONG (School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University) ;
  • PARK, JINSOON (Department of Ocean Science and Department of Convergence on the Ocean Science and Technology, Korea Maritime and Ocean University)
  • 김혜숙 (한국해양대학교 해양과학기술전문대학원 해양과학기술융합학과) ;
  • 김종성 (서울대학교 자연과학대학 지구환경학부 및 해양연구소) ;
  • 박진순 (한국해양대학교 해양환경학과 및 해양과학기술전문대학원 해양과학기술융합학과)
  • Received : 2021.06.20
  • Accepted : 2021.08.25
  • Published : 2021.08.31
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Abstract

Diatoms are a type of microalgae which inhabits a wide variety of environments as one of the most important primary producers of freshwater and marine ecosystems. They have been widely used as bioindicators which represent the environmental characteristics, thus proper quality control of diatom data is very important to ensure for the researches from many scientists from various different regions to have scientific unity and objectivity. At present, diatom data analysis is primarily based both on morphological features and DNA sequences of given species. Challenge for the morphology-based analysis of diatoms is the consistent species identification among different taxonomists who interpret diatom community, while challenge for the molecular analysis of diatoms to secure reliable reference data. In the present study, we have reviewed the current status of data quality control of diatom analysis in Korea as well as the world. Finally, suggestions for the better data quality control for Korean marine diatoms have been also made.

돌말류는 미세조류의 일종으로서 담수 및 해양의 여러 다양한 환경의 수생태계에서 가장 중요한 1차 생산자 중 하나이다. 환경을 대표할 수 있는 생물 지표로서 널리 이용되고 있으며, 여러 지역에서 서로 다른 과학자들에 의한 연구 결과들이 과학적 통일성과 객관성을 갖추도록 하기 위해서는 돌말류 분석 자료의 정도 관리가 매우 중요하다. 현재 돌말류 분석은 형태적인 특징으로 분류하는 형태 기반의 분석과 DNA 서열로 종을 식별하는 DNA 바코드 분석이 사용되고 있다. 형태학 기반의 돌말류 분류는 분석 자료를 해석하는 분류학자들 간의 일관된 종 식별이 요구되는 한편 분자 분류 기반의 돌말류 분류는 신뢰성 있는 참조데이터가 필수적이다. 본 논문에서는 돌말류 분석 자료 정도관리의 국내외 현황을 우선 살펴보았으며, 그에 기반하여 국내 돌말류 분석 자료의 정도 관리에 대한 의견을 또한 제안하였다.

Keywords

Acknowledgement

본 연구는 2021년 해양수산부 재원으로 해양수산과학기술진흥원(과학기술기반 해역이용영향평가 기술개발, 20210427)의 지원을 받아 수행하였습니다.

References

  1. Amato, A. and M. Montresor, 2008. Morphology, phylogeny, and sexual cycle of Pseudo-nitzschia mannii sp. nov. (Bacillariophyceae): a pseudo-cryptic species within the P. pseudodelicatissima complex. Phycologia, 47(5): 487-497. https://doi.org/10.2216/07-92.1
  2. Anonymous, 1703. Two Letters from a Gentleman in the Country, relating to Mr. Leuwenhoeck's Letter in Transaction, No. 283.Communicated by Mr. C. Phil Trans, 23(288): 1494-1501. https://doi.org/10.1098/rstl.1702.0065
  3. Archibald, R., 1984. Diatom illustrations-an appeal. Bacillaria, 7: 173-178.
  4. Benson, D.A., M. Cavanaugh, K. Clark, I. Karsch-Mizrachi, J. Ostell, K.D. Pruitt and E.W. Sayers, 2018. GenBank. Nucleic Acids Res, 46(D1): D41-D47. https://doi.org/10.1093/nar/gkx1094
  5. Coleman, C.O. and A. Radulovici, 2020. Challenges for the future of taxonomy: talents, databases and knowledge growth. Megataxa, 1(1): 28-34.
  6. Cox, E.J., 1987. Placoneis Mereschkowsky: the re-evaluation of a diatom genus originally characterized by its chloroplast type. Diatom Res., 2(2): 145-157. https://doi.org/10.1080/0269249X.1987.9704994
  7. Crawford, R.M., 1981. The siliceous components of the diatom cell wall and their morphological variation. In Silicon and siliceous structures in biological systems (pp. 129-156). Springer, New York, NY.
  8. Ehrenberg, C.G., 1838. Die Infusionsthierchen als vollkommene Organismen. Ein Blick in das tiefere organische Leben der Natur. Leipzig, Leopold Voss.
  9. Evans, K.M., A.H. Wortley and D.G. Mann, 2007. An assessment of potential diatom "barcode" genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist, 158: 349-364. https://doi.org/10.1016/j.protis.2007.04.001
  10. Evans, K.M., A.H. Wortley, G.E. Simpson, V.A. Chepurnov and D.G. Mann, 2008. A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta). J. Phycol., 44: 215-231. https://doi.org/10.1111/j.1529-8817.2007.00454.x
  11. Falciatore, A. and C. Bowler, 2002. Revealing the molecular secrets of marine diatoms. Annu. Rev. Plant Biol., 53(1): 109-130. https://doi.org/10.1146/annurev.arplant.53.091701.153921
  12. Falkowski, P.G., R.T. Barber and V. Smetacek, 1998. Biogeochemical controls and feedbacks on ocean primary production. Science, 281: 200-6. https://doi.org/10.1126/science.281.5374.200
  13. Fourtanier, E. and J.P. Kociolek, 1999. Catalogue of the diatom genera. Diatom Res., 14(1): 1-190. https://doi.org/10.1080/0269249X.1999.9705462
  14. Glockner, F.O., 2019. The SILVA database project: an ELIXIR core data resource for high-quality ribosomal RNA sequences. Biodivers. Inf. Sci. Stand., 3: e36125.
  15. Gmelin, J.F., 1791. Carolia Linne... Systema Naturae per regna tria naturae secundum classes, ordines, genera species cum characteribus, differentiis, synonymis, locis. Ed. 13, Tomus I. Pars VI. Vermes Infusoria. pp. 3021-3910. Lipsiae [Lepizig]: Georg Emanuel Beer.
  16. Gregory, W., 1857. On some new forms of marine Diatomaceae found in the Firth of Clyde and in Loch Fyne. Trans R Soc Edinb Earth Sci., 21: 473-542. https://doi.org/10.1017/S0080456800032269
  17. Greville, R.K., 1857. Description of some new diatomaceous forms from the West Indies. Quarterly Journal of Microscopical Science, London, 5: 7-12.
  18. Hamsher, S.E., K.M. Evans, D.G. Mann, A. Poulickova and G.W. Saunders, 2011. Barcoding diatoms: exploring alternatives to COI-5P. Protist, 162: 405-422. https://doi.org/10.1016/j.protis.2010.09.005
  19. Harris, D.J., 2003. Can you bank on GenBank? Trends Ecol. Evol., 18: 317-319. https://doi.org/10.1016/S0169-5347(03)00150-2
  20. Hebert, P.D., A. Cywinska, S.L. Ball and J.R. Dewaard, 2003. Biological identifications through DNA barcodes. Proc. Royal Soc. B, 270(1512): 313-321. https://doi.org/10.1098/rspb.2002.2218
  21. Hebert, P.D., M.Y. Stoeckle, T.S. Zemlak and C.M. Francis, 2004. Identification of birds through DNA barcodes. PLOS Biol., 2(10): e312. https://doi.org/10.1371/journal.pbio.0020312
  22. Im, A., J.S. Khim and J. Park, 2020. Taxonomy and distribution of two small Tryblionella (Bacillariophyceae) species from the Northeast Asian tidal flats. J. Species Res., 9(3): 191-197. https://doi.org/10.12651/JSR.2020.9.3.191
  23. Johns, G.C. and G.C. Avise, 1998. A comparative summary of genetic distances in the vertebrates from themitochondrial cytochrome b gene. Mol. Biol. Evol., 15: 1481-1490. https://doi.org/10.1093/oxfordjournals.molbev.a025875
  24. Kawecka, B. and M. Olech, 1993. Diatom communities in the Vanishing and Ornithologist Creek, King George Island, South Shetlands, Antarctica. Hydrobiologia, 269-270, 327-333. https://doi.org/10.1007/BF00028031
  25. Kermarrec, L., A. Franc, F. Rimet, P. Chaumeil, J.F. Humbert and A. Bouchez, 2013. Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Mol Ecol Resour, 13(4): 607-619. https://doi.org/10.1111/1755-0998.12105
  26. Kim, H., J.S. Khim and J. Park, 2020. First Report of Navicula spartinetensis (Bacillariophyceae) from Korean Tidal Flats Along with Its Distribution in Northeast Asia. J. Korean Soc. Oceanogr., 25(4): 97-105.
  27. Kusber, W.H. and R. Jahn, 2007. AlgaTerra Information System: Types data and data types. In Proceedings of the 1st Central European Diatom Meeting, pp. 97-100.
  28. Kutzing, F.T., 1833. Synopsis Diatomacearum oder Versuch einer systematischen Zusammenstellung der Diatomeen. Linnaea, 8: 529-620.
  29. Kutzing, F.T., 1844. Die Kieselschaligen BacilLarien oder Diatomeen. W. Kohne Nordhausen. 152 pp.
  30. Lavoie, I., P.B. Hamilton, Y.K. Wang, P.J. Dillon and S. Campeau, 2009. A comparison of stream bioassessment in Quebec (Canada) using six European and North American diatom-based indices. Nova Hedwigia, 135: 37-56.
  31. Luddington, I.A., I. Kaczmarska and C. Lovejoy, 2012. Distance and characterbased evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS ONE, 7: e45664. https://doi.org/10.1371/journal.pone.0045664
  32. MacGillivary, M.L. and I. Kaczmarska, 2011. Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms. J. Eukaryot. Microbiol., 58: 529-536. https://doi.org/10.1111/j.1550-7408.2011.00585.x
  33. Mann, D.G., 1999. The species concept in diatoms. Phycologia, 38: 437-495. https://doi.org/10.2216/i0031-8884-38-6-437.1
  34. Mann, D.G., R.M. Crawford and F.E. Round, 2017. "Bacillariophyta." Handbook of the Protists, Springer, Cham: 1657.
  35. Mann, D.G., S. Sato, R. Trobajo, P. Vanormelngen and C. Souffreau, 2010. DNA barcoding for species identification and discovery in diatoms. Cryptogam., Algol., 31: 557-577.
  36. Meiklejohn, K.A., N. Damaso and J.M. Robertson, 2019. Assessment of BOLD and GenBank-Their accuracy and reliability for the identification of biological materials. PLoS ONE, 14(6): e0217084. https://doi.org/10.1371/journal.pone.0217084
  37. Moniz, M.B. and I. Kaczmarska, 2009. Barcoding diatoms: Is there a good marker?. Mol Ecol Resour, 9: 65-74. https://doi.org/10.1111/j.1755-0998.2009.02633.x
  38. Mora, C., D.P. Tittensor, S. Adl, A.G. Simpson and B. Worm, 2011. How many species are there on Earth and in the ocean?. PLOS Biol., 9(8): e1001127. https://doi.org/10.1371/journal.pbio.1001127
  39. Morrow, A.C., T.R. Deason and D. Clayton, 1981. A NEW SPECIES OF THE DIATOM GENUS EUNOTIA 1. J. Phycol., 17(3): 265-270. https://doi.org/10.1111/j.0022-3646.1981.00265.x
  40. Park, J. and C.-H. Koh, 2012. Taxonomic studies on Korean marine benthic diatoms LM and SEM observations of the diatom genus Amphora from Korean tidal flats. Ocean Sci. J., 47: 101-112. https://doi.org/10.1007/s12601-012-0011-9
  41. Park, J., B.-O. Kwon, M. Kim, S. Hong, J. Ryu, S.J. Song and J.S. Khim, 2014. Microphytobenthos of Korean tidal flats: A review and analysis on floral distribution and tidal dynamics. Ocean Coast Manag, 102: 471-482. https://doi.org/10.1016/j.ocecoaman.2014.07.007
  42. Pecnikar, Z.F. and E.V. Buzan, 2014. 20 years since the introduction of DNA barcoding: from theory to application. J. Appl. Genet., 55(1): 43-52. https://doi.org/10.1007/s13353-013-0180-y
  43. Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies and F.O. Glockner, 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res, 41: D590-D596. https://doi.org/10.1093/nar/gks1219
  44. Ratnasingham, S. and P.D. Hebert, 2007. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Notes, 7(3): 355-364. https://doi.org/10.1111/j.1471-8286.2007.01678.x
  45. Rimet, F., P.Chaumeil, F. Keck, L. Kermarrec, V. Vasselon, M. Kahlert and A. Bouchez, 2016. R-Syst:: diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.
  46. Round, F.E., R.M., Crawford and D.G. Mann, 1990. The Diatoms. Cambridge, New York. 747 pp.
  47. Sato, S., W.H. Kooistra, T. Watanabe, S. Matsumoto and L.K. Medlin, 2008. A new araphid diatom genus Psammoneis gen. nov.(Plagiogrammaceae, Bacillariophyta) with three new species based on SSU and LSU rDNA sequence data and morphology. Phycologia, 47(5): 510-528. https://doi.org/10.2216/08-04.1
  48. Shen, Y.Y., X. Chen and R.W. Murphy, 2013. Assessing DNA barcoding as a tool for species identification and data quality control. PLoS ONE, 8(2): e57125. https://doi.org/10.1371/journal.pone.0057125
  49. Skvortzow, B.W., 1929. Freshwater diatoms from Korea, Japan. hilipp J. Sci., 38: 283-291.
  50. Smith, W., 1853. A synopsis of the British Diatomaceae, vol. 1. London, J. van Voorst.
  51. Smith, W., 1856. A synopsis of the British Diatomaceae, vol. 2. London, J. van Voorst.
  52. Sogin, M.L., H.G. Morrison, J.A. Huber, D.M. Welch, S.M. Huse, P.R. Neal, J.M. Arrieta and G.J. Herndl, 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci., 103: 12115-12120. https://doi.org/10.1073/pnas.0605127103
  53. Treguer, P., D.M. Nelson, A.J. Van Bennekom, D.J. DeMaster, A. Leynaert and B. Queguiner, 1995. The silica balance in the world ocean: A reestimate, Science, 268: 375-379. https://doi.org/10.1126/science.268.5209.375
  54. Underwood, G.J.C. and J. Kromkamp, 1999. Primary production by phytoplankton and microphytobenthos in estuaries. Adv. Ecol. Res., 29: 93-153. https://doi.org/10.1016/S0065-2504(08)60192-0
  55. Valentin, V., R. Frederic, D. Isabelle, M. Olivier, R. Yorick and B. Agnes, 2019. Assessing pollution of aquatic environments with diatoms' DNA metabarcoding: experience and developments from France Water Framework Directive networks. Metabarcoding Metagenom., 3: e39646. https://doi.org/10.3897/mbmg.3.39646
  56. Valentini, A., F. Pompanon and P. Taberlet, 2009. DNA barcoding for ecologists. Trends Ecol. Evol., 24: 110-117. https://doi.org/10.1016/j.tree.2008.09.011.
  57. Ward, R.D., T.S. Zemlak, B.H. Innes, P.R. Last and P.D. Hebert, 2005. DNA barcoding Australia's fish species. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 360(1462): 1847-1857. https://doi.org/10.1098/rstb.2005.1716
  58. Wesche, P.L., D.J. Gaffney and P.D. Keightley, 2004. DNA sequence error rates in Genbank records estimated using the mouse genome as a reference. Dna Sequence, 15(5-6): 362-364. https://doi.org/10.1080/10425170400008972
  59. Yilmaz, P., L.W. Parfrey, P . Yarza, J . Gerken, E. Pruesse, C. Quast, T. Schweer, J. Peplies, W. Ludwig and F.O. Glockner, 2014. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res, 42: D643-D648. https://doi.org/10.1093/nar/gkt1209
  60. Yool, A. and T. Tyrrell, 2003. Role of diatoms in regulating the ocean's silicon cycle. Global Biogeochem Cycles, 17: 1103.
  61. Zemlak, T.S., R.D. Ward, A.D. Connell, B.H. Holmes, and P.D. Hebert, 2009. DNA barcoding reveals overlooked marine fishes. Mol Ecol Resour, 9: 237-242. https://doi.org/10.1111/j.1755-0998.2009.02649.x
  62. Zimmermann, J., R. Jahn and B. Gemeinholzer, 2011. Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Org. Divers. Evol., 11: 173-192. https://doi.org/10.1007/s13127-011-0050-6
  63. Zimmermann, J., G. Glockner, R. Jahn, N. Enke and B. Gemeinholzer, 2015. Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Mol Ecol Resour, 15(3): 526-542. https://doi.org/10.1111/1755-0998.12336