A microbial perspective of coral from the Great Barrier Reef
Coral reefs are fundamental in providing ecological, social and economical benefits to local communities, governments and nations. In Australia, the Great Barrier Reef is an iconic symbol in our national psyche, representing approximately 17% of the global tropical coral reef area with an estimated economic value at greater than AUD$5 billion per year. Coral reefs are constructed through the close association between reef building corals and their symbiotic dinoflagellate microalgae (Symbiodinium). However just as in other animal systems, corals are now thought of as a holobiont, forming additional close and intricate associations with a range of other microbial organisms such as bacteria, archaeae, fungi and viruses. Over the last decade a greater understanding has been obtained in how corals shape and structure their microbial partners, providing important functional roles in maintaining overall coral fitness. The cycling of nitrogen and sulfur compounds within the holobiont are increasingly being recognised as driving many of these coral microbial associations and have important consequences for coral health and the subsequent resilience of coral reefs. For example, nitrogen fixing bacteria (diazotrophs) within the Rhizobia group, which accomplish nitrogen fixation after establishing symbiosis in the roots of host plants, also appear common and specific to corals. These associations are established at the earliest larval life stages and maintained as the coral grows in mature colonies. Using fluorescence in situ hybridization (FISH) and nanoscale secondary ion mass spectrometry (NanoSIMS) the uptake of diazotrophic bacteria and passage of nitrogen into coral larvae can be observed, providing evidence that diazotrophs can provide an additional nitrogen source to the animal. Reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP), a molecule central in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide (DMS). Recent work has shown that the coral animal itself can produce DMSP, hence overturning the paradigm that photosynthetic organisms are the sole biological source of this compound. DMSP represents a rich nutrient source for bacteria with diversity surveys highlighting an extensive overlap between bacterial species associated with corals and species implicated in the degradation of dimethylsulfoniopropionate (DMSP). Again using FISH and NanoSIMS approaches, this close interaction between corals, their Symbiodinium partners and associated bacteria can be visualised. Interestingly, through the metabolism of DMSP, a Pseudovibrio sp. commonly associated with corals produced tropodithietic acid (TDA), a sulfur-containing antimicrobial which is suspected to act in protecting corals from invasive microbial species. Anthropogenic stresses such as increased sea surface temperatures, nutrient input and sedimentation can shift these coral-microbiota associations, thereby contributing to reduced coral fitness. For example, production of TDA by the coral associated Pseudovibrio sp.was significantly reduced at higher temperatures potentially reducing the protective effect the compound can provide the coral holobiont. Temperature stress also causes shifts in coral associated microbial communities, with a metagenomic approach demonstrating a shift in the microbial community away from autotrophy and an increase in virulence associated genes. Coral diseases are on the rise with disease outbreaks contributing to significant loss of both key reef organisms and coral cover. Recent assessments have documented sharp declines in coral reefs globally, therefore an understanding of the microbial factors that underlie coral health and fitness are paramount.
Fusarium: diseases, toxins and evolution
The fungal genus Fusarium contains some of the most economically and socially important species of plant pathogens affecting agriculture and horticulture. It also contains numerous species that are important mycotoxin producers and some that are increasing in importance as pathogens of humans. Some of these diseases, such as head blight of wheat and Fusarium wilt of bananas, are amongst the most important diseases of these hosts and have not only caused enormous losses in production around the world but have also had a huge impact on the communities that depend on these crops. The genus is a complex, polyphyletic grouping whose taxonomy has always been controversial with species numbers ranging from over a 1000 at the beginning of the 1900s, down to 9 in the 1950s and ’60s and currently anything from nearly 100 to 500. This talk will provide an overview of Fusarium, its phylogeny and biogeography and the mechanisms involved in the evolution of pathogenicity.
Hi-C Metagenomics: Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a synthetic metagenome sample to accurately cluster metagenome assembly contigs into a small number of groups that differentiated the genomes of each species. The Hi-C data also associated plasmids with the chromosomes of their host and with each other orders of magnitude more frequently than to other species. We further demonstrated that Hi-C data is highly informative for resolving strain-specific genes and nucleotide substitutions between two closely related E. coli strains, K12 DH10B and BL21 (DE3), indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This application of Hi-C has the potential to provide new perspective in the study of thefine-scale population structure of microbes, how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities, and the genetic architecture ofheterogeneous tumor clone populations.
Indirect electron transfer in microbial fuel cells: Role of electron shuttles
The energy conversion can be realized using microbial fuel cells (MFCs) in which electrons extracted from organics are transferred to a solid electrode by electrogenic microorganisms. To make use of electrons donated by bacteria far away from the electrode, external electron transfer mediators were added to MFCs to enable the shuttles of electrons, causing a significant improvement of electron transfer efficiency and thus an increased power performance. Quinones and iron oxides are two types of electron shuttles that have been extensively studied in MFCs recently. Researchers have also employed different electrochemical approaches to explore the extracellular electron transfer mechanisms from cell to electrode mediated by these two electron shuttles. This presentation will mainly provide information about the different electron transfer mechanisms of quinones and iron oxides.