Archaeal community structure in the tropical coastal waters of Peninsular Malaysia

Abstract

In this study, we used a direct cloning method to explore the archaeal diversity at four locations along the Straits of Malacca. Four 16S rDNA clone libraries were constructed with archaeal specific primers (Arc21F and Arc958R) and, in total, 1,074 randomly selected clones were screened by PCR-restriction fragment length polymorphism analysis using three different restriction enzymes (RsaI, CfoI and DdeI). Good’s coverage suggested that >85 % of archaeal sequence types were obtained in our libraries. The majority of the sequences from Port Dickson and Sungai Muar were affiliated to Euryarchaeota, whereas Port Klang and Kuala Selangor clone libraries were dominated by Thaumarchaeota sequences. Phylogenetic analysis of 16S rDNA sequences showed high archaeal diversity, with a Shannon index ranging from 2.16 to 3.24. Using weighted, non-normalized principal coordinate analysis, the archaeal communities of the four sites were clearly separated from each other. We also showed via canonical correspondence analysis that the distribution of archaeal operational taxonomic units could be related to environmental variables (salinity and chlorophyll a).