The 16s rRNA gene is used as a tool for phylogenetic and ecological research on various microbes. This MPhil research is focused on the application and optimization of 16S rRNA gene in modern microbial research. In the first part, based on 16S rRNA gene pyro-sequencing, a study focused on the Thuwal cold seep microbial structure changes was conducted. This study compared the difference of microbial community in this cold seep between 2011 and 2013. The results showed that Marine Group I (MGI) Thaumarchaeota increased significantly in 2013, coped with a significant decrease in salinity. This results indicated a possible driving force for cold seep microbial community changing, which is the physicochemical change of cold seep influx. In the second part, the focus is identifying optimal v...[ Read more ]

The 16s rRNA gene is used as a tool for phylogenetic and ecological research on various microbes. This MPhil research is focused on the application and optimization of 16S rRNA gene in modern microbial research. In the first part, based on 16S rRNA gene pyro-sequencing, a study focused on the Thuwal cold seep microbial structure changes was conducted. This study compared the difference of microbial community in this cold seep between 2011 and 2013. The results showed that Marine Group I (MGI) Thaumarchaeota increased significantly in 2013, coped with a significant decrease in salinity. This results indicated a possible driving force for cold seep microbial community changing, which is the physicochemical change of cold seep influx. In the second part, the focus is identifying optimal variable regions for studying bacterial taxonomy via geodesic distance algorithm. Geodesic distance is a method designed to quantitatively compare the difference between different phylogenetic trees. Combined with Agglomerative Hierarchical Clustering (AHC) analysis, the results showed that fourth variable region (V4) was the optimal single region for phylogenetic study on Bacteria and V4-V5-V6 were overall the best combination for Bacterial phylogenetic study. Optimal primer pairs were also suggested according to the results. Collectively, this MPhil research utilized 16S rRNA gene pyrosequencing to compare the temporal difference in microbial community of a cold seep ecosystem and identified the optimal regions for bacterial taxonomic study with a in silico method.