Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand

Somboonna et al. BMC Genomics 2012, 13(Suppl 7):S29 http://www.biomedcentral.com/1471-2164/13/S7/S29 PROCEEDINGS Open Access Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand Naraporn Somboonna1*, Anunchai Assawamakin2, Alisa Wilantho2, Sithichoke Tangphatsornruang2, Sissades Tongsima2 From Asia Pacific Bioinformatics Network (APBioNet) Eleventh International Conference on Bioinformatics (InCoB2012) Bangkok, Thailand. 3-5 October 2012 Abstract Background: Tha Wang and Tham Phang coasts, though situated at similar oceanographic positions on Sichang island, Chonburi province, Thailand, are different in bay geography and amount of municipal disturbances. These affect the marine ecosystems. The study used metagenomics combined with 16S and 18S rDNA pyrosequencing to identify types and distributions of archaea, bacteria, fungi and small eukaryotes of sizes ranges 0.45 and ~30 μm. Results: Following the open bay geography and minimal municipal sewages, Tham Phang coast showed the cleaner water properties, described by color, salinity, pH, conductivity and percent dissolved oxygen. The 16S and 18S rDNA metagenomic profiles for Tha Wang and Tham Phang coasts revealed many differences, highlighting by low Lennon and Yue & Clayton theta similarity indices (66.03-73.03% for 16S rDNA profiles, 2.85-25.38% for 18S rDNA profiles). For 16S rDNA, the percent compositions of species belonging to Proteobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Verrucomicrobia, Gammatimonadetes, Tenericutes, Acidobacteria, Spirochaetes, Chlamydiae, Euryarchaeota, Nitrospirae, Planctomycetes, Thermotogae and Aquificae were higher or distinctly present in Tha Wang. In Tham Phang, except Actinobacteria, the fewer number of prokaryotic species existed. For 18S rDNA, fungi represented 74.745% of the species in Tha Wang, whereas only 6.728% in Tham Phang. Basidiomycota (71.157%) and Ascomycota (3.060%) were the major phyla in Tha Wang. Indeed, Tha Wang-to-Tham Phang percent composition ratios for fungi Basidiomycota and Chytridiomycota were 1264.701 and 25.422, respectively. In Tham Phang, Brachiopoda (lamp shells) and Mollusca (snails) accounted for 80.380% of the 18S rDNA species detected, and their proportions were approximately tenfold greater than those in Tha Wang. Overall, coastal Tham Phang comprised abundant animal species. Conclusions: Tha Wang contained numerous archaea, bacteria and fungi, many of which could synthesize useful biotechnology gas and enzymes that could also function in high-saline and high-temperature conditions. Tham Phang contained less abundant archaea, bacteria and fungi, and the majority of the extracted metagenomes belonged to animal kingdom. Many microorganisms in Tham Phang were essential for nutrient-recycling and pharmaceuticals, for instances, Streptomyces, Pennicilium and Saccharomyces. Together, the study provided metagenomic profiles of free-living prokaryotes and eukaryotes in coastal areas of Sichang island. * Correspondence: 1 Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand Full list of author information is available at the end of the article © 2012 Somboonna et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Somboonna et al. BMC Genomics 2012, 13(Suppl 7):S29 http://www.biomedcentral.com/1471-2164/13/S7/S29 Background Thailand situates around an equator, between 23.5 degree north and 23.5 degree south, causing the climate to be hot and rainy, which enhances the biodiversity of microorganisms. In addition to factors by sunlight, wind and tidal ranges, coastal niche represents areas where human disturbances are most situated, and is where land and sea meet with high influences by the bay characteristics. All these factors could affect types and distribution patterns of aquatic microorganisms and organisms [1-4]. Indeed, previous studies reported different proportions of organisms between Tha Wang and Tham Phang coasts of Sichang island, Thailand, and suggested the differences involved their differences in coastal quality (S. Piyatiratitivorakul and S. Rungsupa, personal communications). Nevertheless, no cultureindependent study for inclusive databases on free-living microorganisms had been conducted in Tha Wang and Tham Phang coasts of Sichang. Sichang island, or Koh Sichang, Chonburi province, Thailand, represents one potential place for massively diversified microbial biodiversity. Sichang island was originally a royal palace for King Rama IV-VI, and has been a gateway for local and international cargo transportation since 1800s. Nowadays, Sichang island serves as a historical sites for visitors, pier for merchants and related industries, and place for residents with assorted human-related activities, all of which affect water quality, aquatic species diversity and species richness in Sichang coastal water. The east and the west coasts of Sichang island pose the uniqueness in the bay geographies. Locating on the east named Tha Wang has comparatively close water circulation due to its closeness to two other islands, Khaam Yai and Prong islands, and the mainland of Chonburi province (Figure 1). Tha Wang is populated with residents, residential houses, piers, topioca starch agriculture, and shipping and fishing industries. In contrast, locating on the west named Tham Phang, also called collapsed cave beach, has more open water circulation (Figure 1). Tham Phang is minimally populated by islanders except occasional visitors, and has neither agriculture nor industry. Subsequently, more and increasing amount of wastes was reported in Tha Wang but Tham Phang beach. These included glass bottles, plastics, biodegradable garbage, metals and hazardous materials (S. Rungsupa, personal communication) [5]. More abundant and species-diverse of crabs were reported on Tha Wang (Shannon’s diversity index = 0.895, Margalef’s species-richness index = 4.346) than Tham Phang beaches (Shannon’s diversity index = 0.141, Margalef’s species-richness index = 0.991) because of the more deposition of organic matters from Tha Wang’s wastes that could serve as food sources for the crabs (S. Piyatiratitivorakul and S. Rungsupa, personal communications and unpublished data). Page 2 of 19 Presently, < 1% of microbiota has been discovered, primarily owning to the limited cultivation ability and limited NCBI databases [6,7]. Culture-independent approach was first proposed by Norman R. Pace and colleagues [6]. Global ocean sampling exploration (GOS) was launched in 2003 by Craig Venter to gain understanding of prokaryotic genomes and diversity for whole marine environments, including coastal water, open ocea (...truncated)