[논문]Archaeal Diversity in Tidal Flat Sediment as Revealed by 16S rDNA Analysis

Kim Bong Soo; Oh Huyn Myung; Kan Ho Jeong; Chun Jong Sik

Archaeal Diversity in Tidal Flat Sediment as Revealed by 16S rDNA Analysis 원문보기

The journal of microbiology, v.43 no.2, 2005년, pp.144 - 151

Kim Bong Soo (School of Biological Sciences, Seoul National University) , Oh Huyn Myung (School of Biological Sciences, Seoul National University) , Kan Ho Jeong (Department of Environmental Science and Engineering, School of Engineering, Ewha Womans University) , Chun Jong Sik (School of Biological Sciences, Seoul National University)

Abstract ▼ AI-Helper

During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota ($53.9\%$) and Euryarchaeota ($46.1\%$) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities ($83.25 - 100\%$) to sequences..from other environments in the public database than did those ($75.22 - 98.46\%$) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.

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문제 정의

This observation led to our increased interest in the community structure of Archaea in tidal flat. The objective of this study is to investigate the community structure and phylogenetic diversity of Archaea in tidal flat sediment of Ganghwa Island. This information may help to establish a framework for future study regarding the ecology of microorganisms in tidal flat sediments.

제안 방법

The 16S rDNA sequences determined in this study expand our current knowledge regarding the archaeal community in tidal flat sediment, and provide a framework for fiiture molecular ecological studies, using relatively high-throughput techniques, such as denaturing gradient gel electrophoresis. In addition, biogeochemical measurements will constitute a critical next step in the correlation of the distribution of novel Archaea with their potential activity and ecological roles in tidal flat sediments.

대상 데이터

Getbol sediment soils were obtained at a site in Dongmak (37°35.319N, 126°27.245'E), on Ganghwa Island. Section from depths of 5 cm, was subsampled and stored in polypropylene bags.
12 clones of this study were redundant, and so were not submitted to the GenBank database. The sequences determined in this study were submitted to the GenBank database, and are designated by the accession numbers AY396615-AY396704.
Archaeal 16S rDNA clones were characterized by partial sequencing (the average length of the sequence was 640 bases) and phylogenetic analysis. There were 105 total 이ones. Using the RDP' CHECK_CHIMERA program, 3 clones were determined to be probable chimeric amplicons, and these were omitted from the final analysis.
Clone BS1-1-64 was found to be similar to the thermophilic acetoclastic methanogen, Methanosarcina thermophila (GenBank # M59140), but represented a deep branch within the Methanosarcinales cluster, which was clustered with the O₂₃F7 clone from the Monterey Formation reservoir (Orphan et al, , 2000). Two clones (BS1-1-47, -99) were determined to be closely related to the SYA 2000-35 clone obtained from Lake Soyang in South Korea (83.69 and 96.3% similarity, GenBank # AF291787). The uncultured euryarchaeal clone sequences obtained from the getbol were found to be relatively similar to one another, and were clustered with the sequences obtained from other marine sediments, lakes, gas hydrates, and gold mine waters.

데이터처리

gov/BLAST/), constituted a guide for the determination of which 16S rRNA sequences should be used in the sequence alignments. The calculation of sequence similarity and the phylogenetic tree inference were carried out using thejPHYDIT program (available at http://chunlab.snu.ac.kr/jphydit/). Similarity matrices were constructed via pairwise analysis, and evolutionary distance matrices were generated according to the method described by Jukes and Cantor (Jukes and Cantor, 1969).

성능/효과

Using the RDP' CHECK_CHIMERA program, 3 clones were determined to be probable chimeric amplicons, and these were omitted from the final analysis. All clones were determined to belong to the phyla Crenar- chaeota and Euryarchaeota, whereas none of clones were found to be members of either Korarchaeota or Nanoar- chaeota.
37%, with the BBA6 clone from the NW Atlantic Ocean Buzzards Bay sediments (GenBank # AF004345). Nine clones (BSl-1-1, -16, -34, -50, -68, -70, -72, -75 and 83) were determined to form a monophyletic clade, and were also determined to be distantly related to other archaeal sequences, both cultured and uncultured. Archaea that belong to this crenarchaeotal clade may be widely spread throughout anoxic sediments, marine benthic sediments, and deep-sea hydrothermal vents.
Clone BS1-1-52 was only distantly related to the other sequences, and represented a deep branch. The highest similarity value of this clone was 89.37%, with the BBA6 clone from the NW Atlantic Ocean Buzzards Bay sediments (GenBank # AF004345). Nine clones (BSl-1-1, -16, -34, -50, -68, -70, -72, -75 and 83) were determined to form a monophyletic clade, and were also determined to be distantly related to other archaeal sequences, both cultured and uncultured.

후속연구

The objective of this study is to investigate the community structure and phylogenetic diversity of Archaea in tidal flat sediment of Ganghwa Island. This information may help to establish a framework for future study regarding the ecology of microorganisms in tidal flat sediments.

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