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http://dx.doi.org/10.7850/jkso.2012.17.3.160

Molecular Monitoring of Eukaryotic Plankton Diversity at Mulgeum and Eulsukdo in the Lower Reaches of the Nakdong River  

Lee, Jee Eun (Division of Earth Environmental System, Pusan National University)
Lee, Sang-Rae (Marine Research Institute, Pusan National University)
Youn, Seok-Hyun (National Fisheries Research and Development Institute)
Chung, Sang Ok (Tidal Flat Research Institute, National Fisheries Research and Development Institute)
Lee, Jin Ae (School of Environmental Science and Engineering, Inje University)
Chung, Ik Kyo (Division of Earth Environmental System, Pusan National University)
Publication Information
The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY / v.17, no.3, 2012 , pp. 160-180 More about this Journal
Abstract
We have studied the eukaryotic plankton species diversity to compare the community structure of fresh and brackish waters in the lower reaches of the Nakdong River using metagenomic methods. We constructed 18S rDNA clone libraries of total DNAs extracted from environmental water samples collected at Mulgeum (MG100929, fresh) and Eulsukdo bridge (ES, brackish). Through the steps of colony PCR, PCR-RFLP, sequencing and similarity analysis, we discovered the diverse species composition of eukaryotic plankton. Total 338 clones (170 at MG100929 and 168 at ES) were analyzed, and then we found 74 phylotypes (49 for MG100929 and 25 for ES). From the phylogenetic analysis, we confirmed various eukaryotic plankton of broad range of taxonomic groups, including Stramenopiles, Cryptophyta, Viridiplantae, Alveolata, Rhizaria, Metazoa, and Fungi. We also found several unreported species in Korea and candidates of new taxonomic entities at levels higher than genus. Especially, the cryptic species diversity including unreported phylotypes of Pirsonia (Stramenopiles) and Perkinsea (Alveolata) suggests that the molecular monitoring method can produce new informative biological data in monitoring the changes in the Nakdong River Mouth ecosystem.
Keywords
18S rDNA; Clone library; Metagenomics; Nakdong River; Eukaryotic plankton; Cryptic species diversity;
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1 Kim, J.-H., S.M. Boo and W. Shin, 2007. Two Freshwater Cryptomonads New to Korea: Cryptomonas marssonii and C. pyrenoidifera. Algae, 22: 147-152.   과학기술학회마을   DOI   ScienceOn
2 Kim, J.S. and H.J. Jeong, 2004. Feeding by the heterotrophic dinoflageelates Gyrodinium dominans and G. spirale on the red-tide dinoflagellate Prorocentrum minimum. Mar. Ecol. Prog. Ser., 280: 85-94.   DOI
3 Kooistra, W.H.C.F., D. Sarno, S. Balzano, H. Gu, R.A. Andersen and A. Zingone, 2008. Global diversity and biogeography of Skeletonema species (Bacillariophyta). Protist, 159: 177-193.   DOI   ScienceOn
4 Lee, S.-R., J.H. Oak, I.K. Chung and J.A. Lee, 2010. Effective molecular examination of eukaryotic plankton species diversity in environmental seawater using environmental PCR, PCR-RFLP, and sequencing. J. Appl. Phycol., 22: 699-707.   DOI   ScienceOn
5 Lee, S.-R., T. Rho, J.H. Oak, J.A. Lee, T. Lee and I.K. Chung, 2012. Metagenomic examination of diversity within eukaryotic plankton from the Ulleung Basin in the East Sea of Korea. J. Plant Biol. 55: 310-315.   DOI   ScienceOn
6 Long, H. and R.A. Zufall, 2010. Diverse modes of reproduction in the marine free-living ciliate Glauconema trihymene. BMC Microbiol., 10: 108-118.   DOI   ScienceOn
7 Luo, W., C. Bock, H.R. Li, J. Padisak and L. Krienitz, 2011. Molecular and microscopic diversity of planktonic eukaryotes in the oligotrophic Lake Stechlin (Germany). Hydrobiologia, 661: 133-143.   DOI
8 McHugh, D., 2000. Molecular phylogeny of the Annelida. Can. J. Zool., 78: 1873-1884.   DOI   ScienceOn
9 Medlin, L.K., H.J. Elwood and S. Stickel and M.L. Sogin, 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71: 491-499.   DOI   ScienceOn
10 Sarno, D., W.H.C.F. Kooistra, S. Balzano, P.E. Hargraves and A. Zingone, 2007. Diversity in the genus Skeletonema (Bacillariophyceae): III. Phylogenetic position and morphological variability of Skeletonema costatum and Skeletonema grevillei, with the description of Skeletonema ardens sp. Nov., J. Phycol., 43: 156-170.   DOI   ScienceOn
11 Savin, M.C., J.L. Martin, M. LeGresley, M. Giewat and J. Rooney- Varga, 2004. Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods. Microb. Ecol., 48: 51-65.   DOI   ScienceOn
12 Seo, J.K. and I.K. Chung, 1994. The phytoplankton community structure in the Nakdong river mouth. Korean J. Limnol., 17: 227-250.   과학기술학회마을
13 Shen, X., X. Ma, J. Ren and F. Zhao, 2009. A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta. BMC Genomics, 10: 136-146.   DOI   ScienceOn
14 Stoeck, T., A. Zuendorf, H.-W. Breiner and A. Behnke, 2007. A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microb. Ecol., 53: 328-339.   DOI   ScienceOn
15 Swofford, D.L., 2001. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland.
16 Unrein, F., I. Izaguirre, R. Massana, V. Balague and J.M. Gasol, 2005. Nanoplankton assemblages in maritime Antarctic lakes: characterization and molecular fingerprinting comparison. Aquat. Microb. Ecol., 40: 269-282.   DOI   ScienceOn
17 Yang J.R. and M. Dickman, 1993. Diatoms as indicators of lake trophic status in Central Ontario, Canada. Diatom Res., 8: 179-193.   DOI
18 Moon-van der Staay, S.Y., R. De Wachter and D. Vaulot, 2001. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature, 409: 607-610.   DOI   ScienceOn
19 Medlin, L.K. and K. Töbe, 2011. Molecular techniques to estimate biodiversity with case studies from the marine phytoplankton. In Sofo A (ed) Biodiversity, Croatia, InTech, pp 118-138.
20 Monchy, S., G. Sanciu, M. Jobard, S. Rasconi, M. Gerphagnon, M. Chabé, A. Cian, D. Meloni, N. Niquil, U. Christaki, E. Viscogliosi and T. Sime-Ngando, 2011. Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/ sequencing and SSU tag pyrosequencing. Environ. Microbiol., 13: 1433-1453.   DOI   ScienceOn
21 Not, F., R. Gausling, F. Azam, J.F. Heidelberg and A.Z. Worden, 2007. Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environ. Microbiol. 9: 1233-1252.   DOI   ScienceOn
22 Park, S.-J., B.-J. Park, V.H. Pham, D.-N. Yoon, S.-K. Kim and S.-K. Rhee, 2008. Microeukaryotic diversity in marine environments, and analysis of surface layer sediments from the East Sea. J. Microbiol., 46: 244-249.   과학기술학회마을   DOI   ScienceOn
23 Potter, D., T.C. Lajeunesse, G.W. Saunders and R.A. Anderson, 1997. Convergent evolution masks extensive biodiversity among marine coccoid picoplankton. Biodvers. Conserv., 6: 99-107.   DOI   ScienceOn
24 Richards, T.A., A.A. Vepritskiy, D.E. Gouliamova and S.A. Nierzwicki-Bauer, 2005. The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ. Microbiol., 7: 1413-1425.   DOI   ScienceOn
25 Romari, K. and D. Vaulot, 2004. Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol. Oceanogr., 49: 784-798.   DOI
26 박재림, 하 경, 손연주, 주기재, 2001. 낙동강 중, 하류에서 식물 플랑크톤과 세균의 계절적 동태. 한국환경과학회지, 10: 529-267.
27 김보경, 이상래, 이진애, 정익교, 2010. 분자 모니터링을 이용한 서낙동강과 남해 연안 플랑크톤 군집 분석. 한국해양학회지 바다, 15: 25-36 (=Kim et al. (2010) in Tables 2 and 3).   과학기술학회마을
28 문은영, 김영옥, 김백호, 공동수, 한명수, 2004. 팔당호 섬모충 플랑크톤 분류 및 생태학적 연구. 한국육수학회지, 37: 149-179.
29 문창호, 최혜지, 1991. 낙동강 하구 환경특성 및 식물플랑크톤의 군집구조에 관한 연구. 한국해양학회지, 26: 144-154.   과학기술학회마을
30 박태규, 김성연, 2010. 선박평형 수 내 유해 와편모조류(Dinophyceae)의 분자생물학적 검출. 한국해양학회지 바다, 15: 36-40.   과학기술학회마을
31 신만균, 최기룡, 1996. 울산공단 주변의 토양오염에 따른 원생동물의 분포. 한국환경과학회지, 5: 187-194.   과학기술학회마을
32 윤지미, 이지은, 이상래, 노태근, 이진애, 정익교, 이동섭, 2012. 부산 연안역의 진핵플랑크톤 종다양성에 대한 메타게놈 분석 연구. 한국해양학회지 바다 17: 59-75.   과학기술학회마을
33 임병진, 김범철, 유광일, 유재근, 1997. 낙동강에서 남조류 대발 생시 동물플랑크톤 군집의 변화. 한국육수학회지, 30: 337-346.
34 정영호, 노경희, 이옥민, 1987. 식물플랑크톤에 의한 낙동강 하구와 하구언수역의 환경관리시안. 환경생물학회지, 5: 51-60.
35 정익교, 강영작, 권오섭, 서정관, 2000. 낙동강 하구 해역 식물플랑크톤의 군집 동태. Algae, 15: 99-110.
36 최철만, 김진호, 김원일, 이종식, 정구복, 이정택, 문성기, 2007. 낙동강하류의 식물플랑크톤상과 군집구조. 한국환경농학회지, 26: 159-170.   과학기술학회마을   DOI   ScienceOn
37 Behnke, A., K.J. Barger, J. Bunge and T. Stoeck, 2010. Spatio-temporal variations in protistan communities along and $O_{2}/H_{2}S$ gradient in the anoxic Frmvaren Fjord (Norway). FEMS Microbiol. Ecol., 72: 89-102.   DOI   ScienceOn
38 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. Mol. Phylogenet. Evol., 45: 193-210.   DOI   ScienceOn
39 Andersen, R.A., Y.V. Peer, D. Potter, J.P. Sexton, M. Kawachi and T. LaJeunesse, 1999. Phylogenetic Analysis of the SSU rRNA from Members of the Chrysophyceae. Protist, 150: 71-84.   DOI   ScienceOn
40 Anderson, D.M., D.M. Kulis, G.J. Doucette, J.C. Gallagher and E. Balech, 1994. Biogeography of toxic dinoflagellates in the genus Alexandrium from the northeastern United States and Canada. Mar. Biol., 120: 467-478.   DOI   ScienceOn
41 Chen, M., F. Chen, Y. Yu, J. Ji and F. Kong, 2008. Genetic diversity of eukaryotic microorganisms in lake Taihu, a large shallow subtropical lake in China. Microb. Ecol., 56: 572-583.   DOI
42 DeLong, E.F., 2007. Microbial domains in the Ocean: A lesson from the Archaea. Oceanography, 20: 124-129.
43 DeLong, E.F., 2009. The microbial ocean from genomes to biomes. Nature, 459: 200-206.   DOI   ScienceOn
44 Geist, J., 2011. Intergrative freshwater ecology and biodiversity conservation. Ecol. Indic., 11: 1507-1516.   DOI   ScienceOn
45 Guillou, L., M. Viprey, A. Chambouvet, R.M. Welsh, A.R. Kirkham, R. Massana, D.J. Scanlan and A.Z. Worden, 2008. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ. Microbiol., 10: 3349-3365.   DOI   ScienceOn
46 Jeanmougin, F., J.D. Thompson, M. Gouy, D.G. Higgins and T.J. Gibson, 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci., 23: 403-405.   DOI   ScienceOn
47 Handelsman, J., 2004. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev., 68: 669-685.   DOI   ScienceOn
48 Hoef-Emden, K., B. Marin and M. Melkonian, 2002. Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity. J. Mol. Evol., 55: 161-179.   DOI
49 Hays, G.C., A.J. Richardson and C. Robinson, 2005. Climate change and marine plankton. Trends Ecol. Evol., 20: 337-344.   DOI   ScienceOn
50 Jo, O.J., Y.U. Kim and M.K. Shin, 2005. Redescription of three newly recorded Gastrostyla ciliates (Ciliophora: Spirotrichea: Stichotrichida) with morphological variations from Korea. Korean J. Syst. Zool., 21: 45-56.   과학기술학회마을
51 Joo, S.B., S.-R. Lee and S.K. Park, 2010. Monitoring of phytoplankton community structure using terminal restriction fragment length polymorphism (T-RFLP). J. Microbiol. Methods, 81: 61-68.   DOI   ScienceOn
52 Jurgens, K. and E. Jeppesen, 2000. The impact of metazooplankton on the structure of the microbial food web in a shallow, hypertrophic lake. J. Plankton Res., 22: 1047-1070.   DOI   ScienceOn
53 Keckeis, S., C. Baranyi, T. Hein, C. Holarek, P. Riedler and F. Schiemer, 2003. The significance of zooplankton grazing in a floodplain system of the River Danube. J. Plankton Res., 25: 243-253.   DOI   ScienceOn
54 Kim, H.-W., K.-H. Chang and G.-J. Joo, 2005. Characteristics and Inter-annual variability of zooplankton dynamics in the middle part of the river (Nakdong River). Kor. J. Limnol., 38: 412-419.