Metagenomic exploration of natural product biosynthesis in marine microbial communities

Marine environments are home to a staggering diversity of microbial life, the majority of which has yet to be cultivated in a laboratory setting. These microbes are the base of the food chain that supports marine life and key drivers of the planets biogeochemical cycles. Marine microbes also produce biologically active natural products, yet surprisingly little is known about the diversity and ecological roles of microbial natural products in marine ecosystems. Beyond their possible ecological roles, natural products from marine microbes are of immense interest as a source of new drug leads. The aim of this thesis was to develop experimental and bioinformatic approaches for the metagenomic exploration of marine microbes. Initial work was conducted on planktonic marine microbes and sea ice microbes with the goal of developing a robust method for constructing large insert (30-45 kb) metagenomic libraries from these challenging low-biomass samples. A series of optimisation experiments were conducted to this end, with some success, however this goal proved intractable given the sample availability and time frame of this thesis. Instead, direct shotgun sequencing, metagenome binning and biosynthetic pathway analysis was used to examine the microbiomes of six Tongan marine sponges. This collection included a sample of the marine sponge Cacospongia mycofijiensis, which contained high levels of the cytotoxic polyketides (-)-zampanolide, latrunculin A and laulimalide A. A large insert (30-45 kb) metagenomic library was ultimately constructed from this sponge sample. The newly sequenced Tongan sponge metagenomes were also compared to a collection of marine sponge metagenomes from New Zealand as well as publicly available metagenomes obtained from Mediterranean marine sponges. In addition to developing robust and cost effective experimental and bioinformatic techniques for marine sponge microbiome analysis, key findings from this work were: (1) Host taxonomy and large-scale oceanographic location both appear to be important drivers of microbial community composition (2) Tongan marine sponge microbiomes are more similar to Mediterranean sponge microbiomes than New Zealand marine sponge microbiomes (3) Tongan marine sponge microbiomes are rich in natural product biosynthesis, particularly in ribosomally synthesized and post-translationally modified peptides with potential antimicrobial activity that may play an important defensive role in the context of this symbiosis.