Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
권호 표지
DOI QR코드

DOI QR Code

Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea

  • Received : 2020.09.16
  • Accepted : 2020.11.27
  • Published : 2021.02.28
Download PDF
⟨ Previous Next ⟩

Abstract

Diatoms have been used in examining water quality and environmental change in freshwater systems. Here, we analyzed molecular profiling of seasonal diatoms in the Han River, Korea, using the hypervariable region of 18S V1-V3 rRNA and pyrosequencing. Physicochemical data, such as temperature, DO, pH, and nutrients showed the typical seasonal pattern in a temperate region. In addition, cell counts and chlorophyll-a, were recorded at high levels in spring compared to other seasons, due to the diatom bloom. Metagenomic analysis showed a seasonal variation in the phytoplankton community composition, with diatoms as the most frequently detected in spring (83.8%) and winter (69.7%). Overall, diatom genera such as Stephanodiscus, Navicula, Cyclotella, and Discostella were the most frequent in the samples. However, a large number of unknown Thalassiosirales diatoms were found in spring (35.5%) and winter (36.3%). Our molecular profiling revealed a high number of diatom taxa compared to morphological observation. This is the first study of diatoms in the Han River using molecular approaches, providing a valuable reference for future study on diatoms-basis environmental molecular monitoring and ecology.

Keywords

References

  1. Adenan, N.S., F.M. Yusoff and M. Shariff. 2013. Effect of salinity and temperature on the growth of diatoms and green algae. Journal of Fisheries and Aquatic Science 8(2):397. https://doi.org/10.3923/jfas.2013.397.404
  2. Alverson, A.J., R.K. Jansen and E.C. Theriot. 2007. Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Molecular Phylogenetics and Evolution 45(1):193-210. https://doi.org/10.1016/j.ympev.2007.03.024
  3. Baek, S.H., S.W. Jung and K. Shin. 2011. Effects of temperature and salinity on growth of Thalassiosira pseudonana (Bacillariophyceae) isolated from ballast water. Journal of Freshwater Ecology 26(4):547-552.
  4. Banerji, A., M. Bagley, M. Elk, E. Pilgrim, J. Martinson and J. Santo Domingo. 2018. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. Hydrobiologia 818(1):71-86. https://doi.org/10.1007/s10750-018-3593-0
  5. Boopathi, T. and J.S. Ki. 2016. Unresolved diversity and monthly dynamics of eukaryotic phytoplankton in a temperate freshwater reservoir explored by pyrosequencing. Marine and Freshwater Research 67(11):1680-1691. https://doi.org/10.1071/MF15136
  6. Boopathi, T., D.G. Faria, M.D. Lee, J. Lee, M. Chang and J.S. Ki. 2015. A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79 N) in summer by using next-generation sequencing. Polar Biology 38(2):179-187. https://doi.org/10.1007/s00300-014-1576-9
  7. Chou, H.H. and M.H. Holmes. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17(12):1093-1104. https://doi.org/10.1093/bioinformatics/17.12.1093
  8. Dixit, S.S., J.P. Smol, J.C. Kingston and D.F. Charles. 1992. Diatoms: powerful indicators of environmental change. Environmental Science and Technology 26(1):22-33. https://doi.org/10.1021/es00025a002
  9. Ebenezer, V., L.K. Medlin and J.S. Ki. 2012. Molecular detection, quantification, and diversity evaluation of microalgae. Marine Biotechnology 14(2):129-142. https://doi.org/10.1007/s10126-011-9427-y
  10. Eiler, A., F. Heinrich and S. Bertilsson. 2012. Coherent dynamics and association networks among lake bacterioplankton taxa. The ISME Journal 6(2):330-342. https://doi.org/10.1038/ismej.2011.113
  11. Eiler, A., S. Drakare, S. Bertilsson, J. Pernthaler, S. Peura, C. Rofner and E.S. Lindstrom. 2013. Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach. PLoS One 8(1):e53516. https://doi.org/10.1371/journal.pone.0053516
  12. Faria, D.G., M.D. Lee, J.B. Lee, J. Lee, M. Chang, S.H. Youn and J.S. Ki. 2014. Molecular diversity of phytoplankton in the East China Sea around Jeju Island (Korea), unraveled by pyrosequencing. Journal of Oceanography 70(1):11-23. https://doi.org/10.1007/s10872-013-0208-2
  13. Ghiglione, J.F. and A.E. Murray. 2012. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environmental Microbiology 14(3):617-629. https://doi.org/10.1111/j.1462-2920.2011.02601.x
  14. Graham, L.E., J.M. Graham and W.W. Lee. 2009. Algae.- Second edition, Benjamin Cummings, New York.
  15. Grigorszky, I., K. Tihamer Kiss, G. Por, G. Devai, A.S. Nagy, I. Somlyai and E. Acs. 2017. Temperature and growth strategies as the essential factors influencing the occurrence of Stephanodiscus minutulus(Kutzing) Cleve and Moller and Palatinus apiculatus(Ehrenberg) Craveiro, Calado, Daugbjerg and Moestrup. Fundamental and Applied Limnology/Archiv fur Hydrobiologie 189(2):167-175. https://doi.org/10.1127/fal/2016/0941
  16. Gugger, M., C. Lyra, P. Henriksen, A. Coute, J.F. Humbert and K. Sivonen. 2002. Phylogenetic comparison of the cyanobacterial gen era Anabaena and Aphanizomenon. International Journal of Systematic and Evolutionary Microbiology 52(5):1867-1880. https://doi.org/10.1099/ijs.0.02270-0
  17. Ha, K., H.W. Kim and G.J. Joo. 1998. The phytoplankton succession in the lower part of hypertrophic Nakdong River (Mulgum), South Korea.- In Pytoplankton and Trophic Gradients Springer, Dordrecht(pp. 217-227).
  18. Hakansson, H. and H. Kling. 1994. Cyclotella agassizensis nov. sp. and its relationship to C. quillensis Bailey and other prairie Cyclotella species. Diatom Research 9(2):289-301. https://doi.org/10.1080/0269249X.1994.9705308
  19. Hammer, O., D.A. Harper and P.D. Ryan. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4(1):9.
  20. Harder, T., S.C. Lau, S. Dobretsov, T.K. Fang and P.Y. Qian. 2003. A distinctive epibiotic bacterial community on the soft coral Dendronephthya sp. and antibacterial activity of coral tissue extracts suggest a chemical mechanism against bacterial epibiosis. FEMS Microbiology Ecology 43(3):337-347. https://doi.org/10.1016/S0168-6496(02)00434-8
  21. Hilaluddin, F., F.M. Yusoff and T. Toda. 2020. Shifts in Diatom Dominance Associated with Seasonal Changes in an Estuarine-Mangrove Phytoplankton Community. Journal of Marine Science and Engineering 8(7):528. https://doi.org/10.3390/jmse8070528
  22. Hwang, S.J., N.Y. Kim, S.A. Yoon, B.H. Kim, M.H. Park, K.A. You, and O.M. Lee. 2011. Distribution of benthic diatoms in Korean rivers and streams in relation to environmental variables. In Annales de Limnologie-International Journal of Limnology (Vol. 47, No. S1, pp. S15-S33). EDP Sciences. https://doi.org/10.1051/limn/2011017
  23. Hwang, S.J., S.K. Kwun and C.G. Yoon. 2003. Water quality and limnology of Korean reservoirs. Paddy and Water Environment 1(1):43-52. https://doi.org/10.1007/s10333-003-0010-7
  24. Jung, S.W., J.H. Lee and J.S. Yu. 2003. Environmental studies of the lower part of the Han River V. Blooming characteristics of phytoplankton communities. Algae 18(4):255-262. https://doi.org/10.4490/ALGAE.2003.18.4.255
  25. Jung, S.W., O.Y. Kwon, J.H. Lee and M.S. Han. 2009. Effects of water temperature and silicate on the winter blooming diatom Stephanodiscus hantzschii (Bacillariophyceae) growing in eutrophic conditions in the lower Han River, South Korea. Journal of Freshwater Ecology 24(2):219-226. https://doi.org/10.1080/02705060.2009.9664286
  26. Jung, S.W., H. Min Joo, Y.O. Kim, J.H. Lee and M.S. Han. 2011. Effects of temperature and nutrient depletion and reintroduction on growth of Stephanodiscus hantzschii (Bacillariophyceae): implications for the blooming mechanism. Journal of Freshwater Ecology 26(1):115-121. https://doi.org/10.1080/02705060.2011.553927
  27. Jung, S.W., Y.H. Kang, S.H. Baek, D. Lim and M.S. Han. 2013. Biological control of Stephanodiscus hantzschii(Bacillariophyceae) blooms in a field mesocosm by the immobilized algicidal bacterium Pseudomonas fluorescens HYK0210-SK09. Journal of Applied Phycology 25(1):41-50. https://doi.org/10.1007/s10811-012-9836-y
  28. Ki, J.S. 2012. Hypervariable regions (V1-V9) of the dinoflagellate 18S rRNA using a large dataset for marker considerations. Journal of Applied Phycology 24(5):1035-1043. https://doi.org/10.1007/s10811-011-9730-z
  29. Kim, B., J.H. Park, G. Hwang, M.S. Jun and K. Choi. 2001. Eutrophication of reservoirs in South Korea. Limnology 2(3):223-229. https://doi.org/10.1007/s10201-001-8040-6
  30. Kiss, K.T., S.I. Genkal, L. Ector, L. Molnar, M. Duleba, P. Biro and E. Acs. 2013. Morphology, taxonomy and distribution of Stephanodiscus triporus(Bacillariophyceae) and related taxa. European Journal of Phycology 48(4):363-379. https://doi.org/10.1080/09670262.2013.843204
  31. Krienitz, L. and C. Bock. 2012. Present state of the systematics of planktonic coccoid green algae of inland waters. Hydrobiologia 698(1):295-326. https://doi.org/10.1007/s10750-012-1079-z
  32. Lee, K. and S.K. Yoon. 1996. A study on the phytoplankton in the Paldang Dam Reservoir. III. The changes of diatom community structure. Algae -Korean Phycological Society 11:277-283.
  33. Lee, S.D., S.M. Yun, P.Y. Cho, H.W. Yang and O.J. Kim. 2019. Newly Recorded Species of Diatoms in the Source of Han and Nakdong Rivers, South Korea. Phytotaxa 403(3):143-170. https://doi.org/10.11646/phytotaxa.403.3.1
  34. Li, W. and A. Godzik 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658-1659. https://doi.org/10.1093/bioinformatics/btl158
  35. Lopes, V.R., V. Ramos, A. Martins, M. Sousa, M. Welker, A. Antunes and V.M. Vasconcelos. 2012. Phylogenetic, chemical and morphological diversity of cyanobacteria from Portuguese temperate estuaries. Marine Environmental Research 73:7-16. https://doi.org/10.1016/j.marenvres.2011.10.005
  36. Malviya, S., E. Scalco, S. Audic, F. Vincent, A. Veluchamy, J. Poulain and A. Zingone. 2016. Insights into global diatom distribution and diversity in the world's ocean. Proceedings of the National Academy of Sciences 113(11):E1516-E1525. https://doi.org/10.1073/pnas.1509523113
  37. Meyer, B. and H. Hakansson. 1996. Morphological variation of Cyclotella polymorpha sp. nov. (Bacillariophyceae). Phycologia 35(1):64-69. https://doi.org/10.2216/i0031-8884-35-1-64.1
  38. Mitrovic, S.M., J.N. Hitchcock, A.W. Davie and D.A. Ryan. 2010. Growth responses of Cyclotella meneghiniana (Bacil­lariophyceae) to various temperatures. Journal of Plankton Research 32(8):1217-1221. https://doi.org/10.1093/plankt/fbq038
  39. Penna, A., S. Casabianca, A.F. Guerra, C. Vernesi and M. Scardi. 2017. Analysis of phytoplankton assemblage structure in the Mediterranean Sea based on high-throughput sequencing of partial 18S rRNA sequences. Marine Genomics 36:49-55. https://doi.org/10.1016/j.margen.2017.06.001
  40. Parsons, T.R., Y. Maita and C.M. Lalli. 1984. Amanual of chemical and biological methods for seawater analysis. Pergamon Press.
  41. Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza and F.O. Glockner. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41(D1):D590-D596. https://doi.org/10.1093/nar/gks1219
  42. Reynolds, C.S. 2006. The ecology of phytoplankton. - Cambridge University Press.
  43. Round, F.E., R.M. Crawford and D.G. Mann. 2007. Diatoms: biology and morphology of the genera. Cambridge university press.
  44. Rumyantseva, A., S. Henson, A. Martin, A.F. Thompson, G.M. Damerell, J. Kaiser and K.J. Heywood. 2019. Phytoplankton spring bloom initiation: The impact of atmospheric forcing and light in the temperate North Atlantic Ocean. Progress in Oceanography 178:102202. https://doi.org/10.1016/j.pocean.2019.102202
  45. Saros, J.E. and N.J. Anderson. 2015. The ecology of the planktonic diatom Cyclotella and its implications for global environmental change studies. Biological Reviews 90(2):522-541. https://doi.org/10.1111/brv.12120
  46. Sathyendranath, S., R. Ji and H.I. Browman. 2015. Revisiting Sverdrup's critical depth hypothesis. ICES Journal of Marine Science 72(6):1892-1896. https://doi.org/10.1093/icesjms/fsv110
  47. Spaulding, S. and M. Edlund. 2008. Aulacoseira. In Diatoms of North America. https://diatoms.org/genera/aulacoseira.
  48. Spaulding, S.A., I.W. Bishop, M.B. Edlund, S. Lee, P. Furey, E. Jovanovska and M. Potapova. 2019. What are diatoms? In diatoms of North America. https://diatoms.org/what-are-diatoms.
  49. Sun, F., H.Y. Pei, W.R. Hu and M.M. Song. 2012. A multitechnique approach for the quantification of Microcystis aeruginosa FACHB-905 biomass during high algae-laden periods. Environmental Technology 33(15):1773-1779. https://doi.org/10.1080/09593330.2011.644868
  50. Wang, C., S. Lek, Z. Lai and L. Tudesque. 2017. Morphology of Aulacoseira filaments as indicator of the aquatic environment in a large subtropical river: The Pearl River, China. Ecological Indicators 81:325-332. https://doi.org/10.1016/j.ecolind.2017.06.020
  51. Wehr, J.D. and J.P. Descy. 1998. Use of phytoplankton in large river management. Journal of Phycology 34(5):741-749. https://doi.org/10.1046/j.1529-8817.1998.340741.x
  52. Wolanski, E. and M. Elliott. 2016. Estuarine ecological structure and functioning. Second Edition. (Elsevier) pp. 157-193.
  53. Xiao, X., H. Sogge, K. Lagesen, A. Tooming-Klunderud, K.S. Jakobsen and T. Rohrlack. 2014. Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment. PLoS One 9:e106510. https://doi.org/10.1371/journal.pone.0106510
  54. Yun, S.M., H.M. Joo, S.W. Jung, C.H. Choi, J.S. Ki and J.H. Lee. 2014. The relationship between epilithic diatom communities and changes in water quality along the lower Han River, South Korea. Journal of Freshwater Ecology 29(3):363-375. https://doi.org/10.1080/02705060.2014.902778
  55. Zapomelova, E., J.P. Jezberova, D. Hrouzek, Hisem, K. Rehakova and J. Komarkova. 2009. Polyphasic characterization of three strains of Anabaena reniformis and Aphanizomenon aphanizomenoides (cyanobacteria) and their reclassification to Sphaerospermum gen. nov. (incl. Anabaena kisseleviana) 1. Journal of Phycology 45(6):1363-1373. https://doi.org/10.1111/j.1529-8817.2009.00758.x