A metagenomic analysis of the epiphytic bacterial community from the green macroalga Ulva australis

Abstract

In the marine environment, the surface of macroalgae are colonised by complex microbial communities, which are known to interact with their hosts in a variety of ways. Despite the importance of macroalgae to coastal ecosystems, comprehensive assessments of algal associated bacterial communities are rare. This thesis describes a metagenomic analysis of the epiphytic microbial community of the green macroalga, Ulva australis. A DNA extraction method was developed, which was selective for and representative of the bacterial community from the algal surface. Samples of U. australis, and for comparison, seawater, were collected with spatial and temporal replication, and analysed by the creation of large 16S rRNA gene clone libraries, metagenomic sequencing, and the creation and functional screening of large insert fosmid libraries. 16S rRNA gene analysis revealed that the U. australis bacterial community was almost completely distinct from the planktonic seawater community, but also highly variable between algal samples, at the level of species. The analysis of metagenomic sequencing data revealed that the seawater and algal communities were also functionally distinct. In addition, despite the high level of species variability, a core set of functions were identified which were consistently detected in U. australis samples, and are indicative of a host and surface associated lifestyle. The observations of taxonomic distinctness from seawater, species level variability, and the presence of a consistent set of functional genes relevant to the algal surface environment, has been framed in terms of a competitive lottery model for colonisation of the U. australis surface. The remainder of this thesis describes the construction and functional screening of large insert (40kb) fosmid metagenomic libraries, of the algal associated community, for both antibacterial activity, and the induction of LuxR/I type quorum sensing systems. Two antibacterial and four quorum sensing inducing clones were detected, sequenced and partially chacterised, using subcloning, transposon mutagenesis, and chemical extraction and analysis. Metagenomic analysis has provided an overview of this complex host associated microbial community, in terms of both community membership and function.