Estimation of micro-biota in the Upo wetland using eukaryotic barcode molecular markers
0
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
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.
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.
참고문헌 (36)
- 배연재, "우포습지의 저서성 대형무척추동물 다양성과 군집 특성", 한국환경생태학회지, 18(1), pp.75~91 (2004), 한국환경생태학회
- Baek SY, "Ecological studies on the Upo wetland", 석사, pp.1988
- Barrett RDH, "Identifying spiders through DNA barcodes", Can J Zool, 83, pp.481~491 (2005)
- Behnke A, "Microeukaryote community patterns along an O2", H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway), 2006, pp.72, 3626~3636
- Creer S, "Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises", Mol Ecol, 19(1), pp.4~20 (2010)
- Díez B, "Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing", Appl Environ Microbiol, 67, pp.2932~2941 (2001)
- 도윤호, "우포늪 범람에 의한 먼지벌레류(딱정벌레목, 딱정벌레과)의 다양성과 종조성 변화", 한국하천호수학회지, 40(2), pp.346~351 (2007), 한국하천호수학회
- Erséus C, "COI variation in Scandinavian marine species of Tubificoides (Annelida: Clitellata: Tubificidae)", J Mar Biol Assoc U K, 87, pp.1121~1126 (2007)
- Fell JW, "Biodiversity of micro-eukaryotes in antarctic dry valley soils with <5% soil moisture", Soil Biol Biochem, 38, pp.3107~3119 (2006)
- Folmer O, "DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates", Mol Mar Biol Biotechnol, 3, pp.294~299 (1994)
- Harris DJ, "Can you bank on genbank", Trends Ecol Evol, 18, pp.317~319 (2003)
- Hebert PDN, "Biological identifications through DNA barcodes", Proc R Soc Lond B, 270, pp.313~321 (2003)
- Hebert PDN, "Identification of birds through DNA barcodes", PLoS Biol, 2, pp.312~ (2004)
- Huber JA, "Microbial population structures in the deep marine biosphere", Science, 318, pp.97~100 (2007)
- Jahn R, "Diatoms and DNA barcoding: A pilot study on an environmental sample. Proceedings of the 1st Central European Diatom Meeting" (2007), BGBM Press
- Jeong HJ, "Stoeckeria algicida n. gen., n. sp. (dinophyceae) from the coastal waters off southern Korea: Morphology and small subunit ribosomal DNA gene sequence", Journal of Eukaryotic Microbiology, 52(4), pp.382~390 (2005), Blackwell Publishing
- 김구연, "우포늪 물억새(Miscanthus sacchariflorus) 군락에서 생장초기에 잘라주기와 태워주기에 따른 성장변화", 한국하천호수학회지, 37(2), pp.255~262 (2004), 한국하천호수학회
- 김한순, "우포늪과 목포늪의 식물플랑크톤 군집의 계절적 변동", 생태와 환경, 34(2), pp.90~97 (2001), 한국하천호수학회
- Kress WJ, "A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region", PLoS One, 2, pp.508~ (2007)
- Lawley B, "Molecular analysis of geographic patterns of eukaryotic diversity in antarctic soils", Appl Environ Microbiol, 70, pp.5963~5972 (2004)
- Lefranc M, "Genetic diversity of small eukaryotes in lakes differing by their trophic status", Appl Environ Microbiol, 71, pp.5935~5942 (2005)
- Medinger R, "Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms", Mol Ecol, 19(1), pp.32~40 (2010)
- Nakdong River Basin Environmental Office, "A Report for Biota of Lake (Upo)" (2006), Nakdong River Basin Environmental Office
- Olsen GJ, "Microbial ecology and evolution: a ribosomal RNA approach", Annu Rev Microbiol, 40, pp.337~365 (1986)
- Potvin M, "PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries", J Eukaryot Microbiol, 56, pp.174~181 (2009)
- Quan J, "Low genetic variation of Penaeus chinensis as revealed by mitochondrial COI and 16S rRNA gene sequences", Biochem Genet, 39, pp.279~284 (2001)
- Savin MC, "Plankton diversity in the bay of fundy as measured by morphological and molecular methods", Microb Ecol, 48, pp.51~65 (2004)
- Saitou N, "The neighbor-joining method: a new method for reconstructing phylogenetic trees", Mol Biol Evol, 4, pp.406~425 (1987)
- Scicluna SM, "DNA barcoding of Blastocystis", Protist, 157, pp.77~85 (2006)
- Sogin ML, "Microbial diversity in the deep sea and the underexplored “rare biosphere”", Proc Natl Acad Sci U S A, 103, pp.12115~12120 (2006)
- Tamura K, "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0", Mol Biol Evol, 24, pp.1596~1599 (2007)
- The Entomological Society of Korea and Korean Society of Applied Entomology, "Check List of Insects from Korea" (1994), Konkuk University Press
- The Korean Society of Systematic Zoology, "List of Animals in Korea (Excluding Insects)" (1997), Academy Publishing Co
- Thompson JD, "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools", Nucleic Acids Res, 25, pp.4876~4882 (1997)
- Valentini A, "DNA barcoding for ecologists", Trends Ecol Evol, 24, pp.110~117 (2008)
- Zwolinski MD, "DNA sequencing: strategies for soil microbiology", Soil Sci Soc Am J, 71, pp.592~600 (2007)