Open Access Research article

Structural and functional diversity of free-living microorganisms in reef surface, Kra island, Thailand

Naraporn Somboonna1*, Alisa Wilantho2, Anunchai Assawamakin3, Somchai Monanunsap4, Duangjai Sangsrakru2, Sithichoke Tangphatsornruang2 and Sissades Tongsima2*

Author Affiliations

1 Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

2 Genome Institute, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum thani 12120, Thailand

3 Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand

4 Department of Marine and Coastal Resources, Ministry of Natural Resources and Environment, Bangkok 10400, Thailand

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BMC Genomics 2014, 15:607  doi:10.1186/1471-2164-15-607

Published: 18 July 2014

Abstract

Background

Coral reefs worldwide are being harmed through anthropogenic activities. Some coral reefs in Thailand remain well-preserved, including the shallow coral reefs along Kra island, Nakhon Si Thammarat province. Interestingly, the microbial community in this environment remains unknown. The present study identified biodiversity of prokaryotes and eukaryotes of 0.22-30 μm in sizes and their metabolic potentials in this coral reef surface in summer and winter seasons, using 16S and 18S rRNA genes pyrosequencing.

Results

The marine microbial profiles in summer and winter seasons comprised mainly of bacteria, in phylum, particular the Proteobacteria. Yet, different bacterial and eukaryotic structures existed between summer and winter seasons, supported by low Lennon and Yue & Clayton theta similarity indices (8.48-10.43% for 16S rRNA, 0.32-7.81% for 18S rRNA ). The topmost prokaryotic phylum for the summer was Proteobacteria (99.68%), while for the winter Proteobacteria (62.49%) and Bacteroidetes (35.88%) were the most prevalent. Uncultured bacteria in phyla Cyanobacteria, Planctomycetes, SAR406 and SBR1093 were absent in the summer. For eukaryotic profiles, species belonging to animals predominated in the summer, correlating with high animal activities in the summer, whereas dormancy and sporulation predominated in the winter. For the winter, eukaryotic plant species predominated and several diverse species were detected. Moreover, comparison of our prokaryotic databases in summer and winter of Kra reef surface against worldwide marine culture-independent prokaryotic databases indicated our databases to most resemblance those of coastal Sichang island, Chonburi province, Thailand, and the 3 tropical GOS sites close to Galapagos island (GS039, GS040 and GS045), in orderly.

Conclusions

The study investigated and obtained culture-independent databases for marine prokaryotes and eukaryotes in summer and winter seasons of Kra reef surface. The data helped understand seasonal dynamics of microbial structures and metabolic potentials of this tropical ecosystem, supporting the knowledge of the world marine microbial biodiversity.

Keywords:
Biodiversity; Prokaryote; Eukaryote; 16S ribosomal RNA; 18S ribosomal RNA; Reef surface; Pyrosequencing