24-25 February 2014
The Australian Museum
Microbiology is undergoing a revolution bought about by advances in next-generation DNA sequencing technology. Researchers are now required to understand an array of bioinformatics principles and tools to interpret the vast amounts of data being generated. Presented by leading Australian researchers, TOAST is a 2-day event aimed at postgraduate students and early career postdocs providing in-depth tutorials encompassing concepts and software available to molecular microbiologists and microbial ecologists including:
Deep sequencing of secondary meta-metabolomes: A preliminary screening tool for determining natural product diversity
Increasingly, natural product isolation strategies are circumventing culture-dependent methods for the isolation secondary metabolite genes directly from the environment. Many of these isolation strategies are undertaken with little knowledge of an environment's specific secondary metabolite potential. Next-generation sequencing technology was used to determine the diversity of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes within multiple environments to a depth previously not reported. A multiplexing strategy was used to amplify thousands of ketosynthase and amino acid condensation domain sequences from over thirty different environments. Sequences were differentiated according to function and taxonomic origin, as well as their distribution within distinct environments. Similar patterns of NRPS and PKS occurrence were observed between functionally similar but geographically distinct environments. Furthermore, increases in microbial diversity between environments did not influence the occurrence of these genes. It is expected that this approach will be applied to any environment enabling for the tailoring of culture-dependent and culture-independent strategies for the isolation of novel natural products.
Metagenomic insights into microbial community control: From the global to the microscale.
The recent application of next-generation DNA sequencing tools has provided a wealth of new information about the diversity of microbial life, however the ecological factors which determine spatial patterns in prokaryotic gene abundance remain elusive. Using metagenomics and high-throughput sequencing of taxonomic marker genes, we have demonstrated shifts in microbial taxonomy and function along a salinity and nutrient gradient in the Coorong lagoon, South Australia. Functionally, genes showing the greatest response to physiochemical variability are related to salinity tolerance and photosynthesis. Taxonomically, Cyanobacteria and Archaea showed the greatest shifts in abundance along the gradient. Despite this variability however, the overall signature of metagenomic profiles remained remarkably conserved between sampling sites, and when compared to metagenomes from diverse habitats clustered with diverse sediment and soil habitats, regardless of salinity. This data indicates that the substrate type of the sample, fluid or porous, is a fundamental determinant of patterns in microbial community function globally, regardless of local chemical conditions. Whilst microbial community structure is determined on varying global and local scales, as demonstrated by the above data, the behaviour of microorganisms is determined on the microscale, with individual cells responding to gradients in specific nutrients in a patchy ecosystem. Using novel in situ sampling devices, and next-generation DNA sequencing techniques, our future work will focus on describing the microscale interactions between cells and nutrients in the ocean and how this relationship relates to ocean scale biogeochemical processes within the Carbon, Nitrogen and Sulfur cycles.