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

Journal of Species Research / Journal of Species Research, (E)2713-8615
2021, v.10 no.1, pp.46-56
Buhari Lawan Muhammad
Yeon-Su Lee
JANG-SEU KI
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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
phytoplankton, Cyclotella, water quality, freshwater diatoms, metagenomics

Reference

1.

Adenan, N.S., F.M. Yusoff and M. Shariff. 2013. Effect of sal-inity and temperature on the growth of diatoms and green algae. Journal of Fisheries and Aquatic Science 8(2):397.

2.

Alverson, A.J., R.K. Jansen and E.C. Theriot. 2007. Bridging the Rubicon: phylogenetic analysis reveals repeated col-onizations of marine and fresh waters by thalassiosiroid diatoms. Molecular Phylogenetics and Evolution 45(1): 193-210.

3.

Baek, S.H., S.W. Jung and K. Shin. 2011. Effects of tempera-ture 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.

5.

Boopathi, T. and J.S. Ki. 2016. Unresolved diversity and monthly dynamics of eukaryotic phytoplankton in a tem-perate freshwater reservoir explored by pyrosequencing. Marine and Freshwater Research 67(11):1680-1691.

6.

Boopathi, T., D.G. Faria, M.D. Lee, J. Lee, M. Chang and J.S. Ki. 2015. A molecular survey of freshwater microeukar-yotes in an Arctic reservoir (Svalbard, 79 N) in summer by using next-generation sequencing. Polar Biology 38(2): 179-187.

7.

Chou, H.H. and M.H. Holmes. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17(12):1093-1104.

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.

9.

Ebenezer, V., L.K. Medlin and J.S. Ki. 2012. Molecular detec-tion, quantification, and diversity evaluation of microalgae. Marine Biotechnology 14(2):129-142.

10.

Eiler, A., F. Heinrich and S. Bertilsson. 2012. Coherent dy-namics and association networks among lake bacterio-plankton taxa. The ISME Journal 6(2):330-342.

11.

Eiler, A., S. Drakare, S. Bertilsson, J. Pernthaler, S. Peura, C. Rofner and E.S. Lindström. 2013. Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach. PLoS One 8(1):e53516.

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.

13.

Ghiglione, J.F. and A.E. Murray. 2012. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environmental Micro-biology 14(3):617-629.

14.

Graham, L.E., J.M. Graham and W.W. Lee. 2009. Algae.- Sec-ond edition, Benjamin Cummings, New York.

15.

Grigorszky, I., K. Tihamér Kiss, G. Pór, G. Dévai, A.S. Nagy, I. Somlyai and É. Ács. 2017. Temperature and growth strate-gies as the essential factors influencing the occurrence of Stephanodiscus minutulus(Kützing) Cleve and Möller and Palatinus apiculatus(Ehrenberg) Craveiro, Calado, Daugb-jerg and Moestrup. Fundamental and Applied Limnology/ Archiv für Hydrobiologie 189(2):167-175.

16.

Gugger, M., C. Lyra, P. Henriksen, A. Coute, J.F. Humbert and K. Sivonen. 2002. Phylogenetic comparison of the cyano-bacterial gen era Anabaena and Aphanizomenon. Interna-tional Journal of Systematic and Evolutionary Microbio-logy 52(5):1867-1880.

17.

Ha, K., H.W. Kim and G.J. Joo. 1998. The phytoplankton suc-cession in the lower part of hypertrophic Nakdong River (Mulgum), South Korea.- In Pytoplankton and Trophic Gradients Springer, Dordrecht(pp. 217-227).

18.

Håkansson, 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.

19.

Hammer, Ø., D.A. Harper and P.D. Ryan. 2001. PAST: Pale-ontological 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.

21.

Hilaluddin, F., F.M. Yusoff and T. Toda. 2020. Shifts in Dia-tom Dominance Associated with Seasonal Changes in an Estuarine-Mangrove Phytoplankton Community. Journal of Marine Science and Engineering 8(7):528.

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 Sci-ences.

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.

24.

Jung, S.W., J.H. Lee and J.S. Yu. 2003. Environmental studies of the lower part of the Han River V. Blooming charac-teristics of phytoplankton communities. Algae 18(4):255-262.

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.

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 mecha-nism. Journal of Freshwater Ecology 26(1):115-121.

27.

Jung, S.W., Y.H. Kang, S.H. Baek, D. Lim and M.S. Han. 2013. Biological control of Stephanodiscus hantzschii(Bacillario-phyceae) blooms in a field mesocosm by the immobilized algicidal bacterium Pseudomonas fluorescens HYK0210- SK09. Journal of Applied Phycology 25(1):41-50.

28.

Ki, J.S. 2012. Hypervariable regions (V1-V9) of the dinofla-gellate 18S rRNA using a large dataset for marker consi-derations. Journal of Applied Phycology 24(5):1035-1043.

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.

30.

Kiss, K.T., S.I. Genkal, L. Ector, L. Molnár, M. Duleba, P. Bíró and É. Ács. 2013. Morphology, taxonomy and distri-bution of Stephanodiscus triporus(Bacillariophyceae) and related taxa. European Journal of Phycology 48(4):363-379.

31.

Krienitz, L. and C. Bock. 2012. Present state of the systematics of planktonic coccoid green algae of inland waters. Hydro-biologia 698(1):295-326.

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.

34.

Li, W. and A. Godzik 2006. Cd-hit: a fast program for clus-tering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658-1659.

35.

Lopes, V.R., V. Ramos, A. Martins, M. Sousa, M. Welker, A. Antunes and V.M. Vasconcelos. 2012. Phylogenetic, chem-ical and morphological diversity of cyanobacteria from Portuguese temperate estuaries. Marine Environmental Research 73:7-16.

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.

37.

Meyer, B. and H. Håkansson. 1996. Morphological variation of Cyclotella polymorpha sp. nov. (Bacillariophyceae). Phycologia 35(1):64-69.

38.

Mitrovic, S.M., J.N. Hitchcock, A.W. Davie and D.A. Ryan. 2010. Growth responses of Cyclotella meneghiniana (Bacil­-lariophyceae) to various temperatures. Journal of Plankton Research 32(8):1217-1221.

39.

Penna, A., S. Casabianca, A.F. Guerra, C. Vernesi and M. Scardi. 2017. Analysis of phytoplankton assemblage struc-ture in the Mediterranean Sea based on high-throughput sequencing of partial 18S rRNA sequences. Marine Geno-mics 36:49-55.

40.

Parsons, T.R., Y. Maita and C.M. Lalli. 1984. Amanual of che-mical and biological methods for seawater analysis. Perga-mon Press.

41.

Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza and F.O. Glöckner. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41(D1):D590-D596.

42.

Reynolds, C.S. 2006. The ecology of phytoplankton. - Cam-bridge University Press.

43.

Round, F.E., R.M. Crawford and D.G. Mann. 2007. Diatoms: biology and morphology of the genera. Cambridge univer-sity press.

44.

Rumyantseva, A., S. Henson, A. Martin, A.F. Thompson, G.M. Damerell, J. Kaiser and K.J. Heywood. 2019. Phytoplank-ton spring bloom initiation: The impact of atmospheric forcing and light in the temperate North Atlantic Ocean. Progress in Oceanography 178:102202.

45.

Saros, J.E. and N.J. Anderson. 2015. The ecology of the plank-tonic diatom Cyclotella and its implications for global environmental change studies. Biological Reviews 90(2): 522-541.

46.

Sathyendranath, S., R. Ji and H.I. Browman. 2015. Revisiting Sverdrup’s critical depth hypothesis. ICES Journal of Mar-ine Science 72(6):1892-1896.

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 multi-technique approach for the quantification of Microcystis aeruginosa FACHB-905 biomass during high algae-laden periods. Environmental Technology 33(15):1773-1779.

50.

Wang, C., S. Lek, Z. Lai and L. Tudesque. 2017. Morphology of Aulacoseira filaments as indicator of the aquatic environ-ment in a large subtropical river: The Pearl River, China. Ecological Indicators 81:325-332.

51.

Wehr, J.D. and J.P. Descy. 1998. Use of phytoplankton in large river management. Journal of Phycology 34(5):741-749.

52.

Wolanski, E. and M. Elliott. 2016. Estuarine ecological struc-ture 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 env-ironment. PLoS One 9:e106510.

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 com-munities and changes in water quality along the lower Han River, South Korea. Journal of Freshwater Ecology 29(3): 363-375.

55.

Zapomělová, E., J.P. Jezberová, D. Hrouzek, Hisem, K. Ře-háková and J. Komárková. 2009. Polyphasic characteri-zation of three strains of Anabaena reniformis and Apha-nizomenon aphanizomenoides (cyanobacteria) and their reclassification to Sphaerospermum gen. nov. (incl. Ana-baena kisseleviana) 1. Journal of Phycology 45(6):1363-1373.

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