Journal of Ecology and Environment

The Ecological Society of Korea (한국생태학회)
권호 표지
DOI QR코드

DOI QR Code

Estimation of micro-biota in the Upo wetland using eukaryotic barcode molecular markers

  • Park, Hyun-Chul (National Institute of Biological Resources, Environmental Research Complex) ;
  • Bae, Chang-Hwan (National Institute of Biological Resources, Environmental Research Complex) ;
  • Jun, Ju-Min (National Institute of Biological Resources, Environmental Research Complex) ;
  • Kwak, Myoung-Hai (National Institute of Biological Resources, Environmental Research Complex)
  • Received : 2011.04.28
  • Accepted : 2011.07.10
  • Published : 2011.09.01
Download PDF
⟨ Previous Next ⟩

Abstract

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

Keywords

References

  1. Bae YJ, Jo SI, Hoang, DH, Lee HG, Na KB. 2004. Biodiversity and community composition of benthic macroinvertebrates from Upo wetlands in Korea. Korean J Environ Ecol 18: 75-91.
  2. Baek SY. 1988. Ecological studies on the Upo wetland. MS Thesis. Chung-Ang University, Seoul, Korea.
  3. Barrett RDH, Hebert PDN. 2005. Identifying spiders through DNA barcodes. Can J Zool 83: 481-491. https://doi.org/10.1139/z05-024
  4. Behnke A, Bunge J, Barger K, Breiner HW, Alla V, Stoeck T. 2006. Microeukaryote community patterns along an $O_2/H_2S $gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Appl Environ Microbiol 72: 3626-3636. https://doi.org/10.1128/AEM.72.5.3626-3636.2006
  5. Creer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, Power DM, Packer M, Carvalho GR, Blaxter ML, Lambshead PJD, Thomas WK. 2010. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol 19(Suppl 1): 4-20. https://doi.org/10.1111/j.1365-294X.2009.04473.x
  6. Diez B, Pedros-Alio C, Massana R. 2001. Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 67: 2932-2941. https://doi.org/10.1128/AEM.67.7.2932-2941.2001
  7. Do Y, Jang MH, Kim DK, Joo GJ. 2007. Change of carabid beetle (Coleoptera, Carabidae) diversity and species composition after flooding events in Woopo wetlands. Korean J Limnol 40: 346-351.
  8. Erseus C, Kvist S. 2007. COI variation in Scandinavian marine species of Tubificoides (Annelida: Clitellata: Tubificidae). J Mar Biol Assoc U K 87: 1121-1126.
  9. Fell JW, Scorzetti G, Connell L, Craig S. 2006. Biodiversity of micro-eukaryotes in antarctic dry valley soils with <5% soil moisture. Soil Biol Biochem 38: 3107-3119. https://doi.org/10.1016/j.soilbio.2006.01.014
  10. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3: 294-299.
  11. Harris DJ. 2003. Can you bank on genbank? Trends Ecol Evol 18: 317-319. https://doi.org/10.1016/S0169-5347(03)00150-2
  12. Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc R Soc Lond B 270: 313-321. https://doi.org/10.1098/rspb.2002.2218
  13. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PLoS Biol 2: e312. https://doi.org/10.1371/journal.pbio.0020312
  14. Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML. 2007. Microbial population structures in the deep marine biosphere. Science 318: 97-100. https://doi.org/10.1126/science.1146689
  15. Jahn R, Zetzsche H, Reinhardt R, Gemeinholzer B. 2007. Diatoms and DNA barcoding: A pilot study on an environmental sample. Proceedings of the 1st Central European Diatom Meeting. 2007 Mar 23-25, Berlin-Dahlem. BGBM Press, Berlin.
  16. Jeong HJ, Kim JS, Park JY, Kim JH, Kim S, Lee I, Lee SH, Ha JH, Yih WH. 2005. Stoeckeria algicida n. gen., n. sp. (Dinophyceae) from the coastal waters off southern Korea: morphology and small subunit ribosomal DNA gene sequence. J Eukaryot Microbiol 52: 382-390. https://doi.org/10.1111/j.1550-7408.2005.00051.x
  17. Kim GY, Lee CW, Joo GJ. 2004. The evaluation of early growth pattern of miscanthus sacchariflorus after cutting and burning in the Woopo wetland. Korean J Limnol 37: 255-262.
  18. Kim HS. 2001. Seasonal changes of phytoplankton community in the Woopo and Mokpo swamp. Korean J Limnol 34: 90-97.
  19. Kress WJ, Erickson DL. 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One 2: e508. https://doi.org/10.1371/journal.pone.0000508
  20. Lawley B, Ripley S, Bridge P, Convey P. 2004. Molecular analysis of geographic patterns of eukaryotic diversity in antarctic soils. Appl Environ Microbiol 70: 5963-5972. https://doi.org/10.1128/AEM.70.10.5963-5972.2004
  21. Lefranc M, Thenot A, Lepere C, Debroas D. 2005. Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 71: 5935-5942. https://doi.org/10.1128/AEM.71.10.5935-5942.2005
  22. Medinger R, Nolte V, Pandey RV, Jost S, Ottenwalder B, Schlotterer C, Boenigk J. 2010. Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol 19(Suppl 1): 32-40. https://doi.org/10.1111/j.1365-294X.2009.04478.x
  23. Nakdong River Basin Environmental Office. 2006. A Report for Biota of Lake (Upo). Nakdong River Basin Environmental Office, Changwon. (in Korean)
  24. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40: 337-365.
  25. Potvin M, Lovejoy C. 2009. PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries. J Eukaryot Microbiol 56: 174-181. https://doi.org/10.1111/j.1550-7408.2008.00386.x
  26. Quan J, Lü XM, Zhuang Z, Dai J, Deng J, Zhang YP. 2001. Low genetic variation of Penaeus chinensis as revealed by mitochondrial COI and 16S rRNA gene sequences. Biochem Genet 39: 279-284. https://doi.org/10.1023/A:1010234816514
  27. Savin MC, Martin JL, LeGresley M, Giewat M, Ronney-Varga J. 2004. Plankton diversity in the bay of fundy as measured by morphological and molecular methods. Microb Ecol 48: 51-65. https://doi.org/10.1007/s00248-003-1033-8
  28. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
  29. Scicluna SM, Tawari B, Clark CG. 2006. DNA barcoding of Blastocystis. Protist 157: 77-85. https://doi.org/10.1016/j.protis.2005.12.001
  30. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120. https://doi.org/10.1073/pnas.0605127103
  31. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599. https://doi.org/10.1093/molbev/msm092
  32. The Entomological Society of Korea and Korean Society of Applied Entomology. 1994. Check List of Insects from Korea. Konkuk University Press, Seoul.
  33. The Korean Society of Systematic Zoology. 1997. List of Animals in Korea (Excluding Insects). Academy Publishing Co., Seoul.
  34. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882. https://doi.org/10.1093/nar/25.24.4876
  35. Valentini A, Pompanon F, Taberlet P. 2008. DNA barcoding for ecologists. Trends Ecol Evol 24: 110-117.
  36. Zwolinski MD. 2007. DNA sequencing: strategies for soil microbiology. Soil Sci Soc Am J 71: 592-600. https://doi.org/10.2136/sssaj2006.0125