Marine sponges acquire nutrients by filtering and eating bacteria from the seawater, but they also at the same time harbour a remarkable diversity of bacterial symbionts that don’t get digested. ...
Room 350, Biological Sciences D26
UNSW, Kensington 2052
RESEARCH ACTIVITIES AND BIOGRAPHY
My research focuses on the interaction of bacteria with their environment and aims to understand the function of the enormous diversity of bacteria in natural systems. My students, co-workers and I explore the microbial world, for example by high-throughput DNA sequencing and use bioinformatics to make predictions about functional and ecological properties of bacterial communities. Ultimately, we perform directed molecular experiments to support our predictions and establish a clear link between function and diversity. Current project include:
1. Bacteria-sponge symbiosis
Marine sponges acquire nutrients by filtering and eating bacteria from the seawater, but they also at the same time harbour a remarkable diversity of bacterial symbionts that don’t get digested. We have recently discovered that the genomes of bacterial sponge symbionts carry a large number of proteins that are similar to eukaryotic proteins controlling phagocytosis and cytoskeletal formation (Fan et al. PNAS USA 2012, Nguyen et al. Molecular Ecology 2013). We hypothesise that symbionts use these protein to “manipulate” the sponge and will test this with a range of phylogenetic and molecular approaches. The outcome of this project will provide important information on the evolution of microbe-host interactions.
2. Effect of charcoal on microbial processes in agricultural soil
Charcoal is an emerging supplement to agricultural soil and several studies have shown its benefits in terms of plant yield and greenhouse gas emission. How charcoal excerts its positive effect is largely unknown, but there is evidence that it changes the composition and function of the soil's microbial communities (Nielsen et al. Agriculture, Ecosystems & Environment 2014). In this project we will use high-throughput sequecing to characterise the diversity of soil micoorgansims and high-resolution analytical technique to define their interactions with charcoal particles. Outcome of the project will help to develop charcoal as new tool for sustainable and improved agriculture.
3. Genomics of evolving, bacterial populations
Microbial genomes exhibit a high degree of plasticity (or variability) and any given microbial population (defined as a collection of closely-related individuals) is far more heterogenous in its genetic composition than previously assumed. High-throughput genome sequencing of entire populations now allows for a comprehensive observation of genome evolution on a molecular level. This approach is being employed to the model organism Pseudomonas aeruginosa to understand its adaptation and evolution to conditions of environmental and medical relevance (McElroy PNAS USA 2041). This project also develops novel bioinformatics tool to process large volumes of next-generation sequencing data.
4. Functional diversity and redundancy of marine communities
Microbial diversity in the marine environment is enormous and often 1000s of different species are found in a single habitat. We have recently postulated that much of the diversity encountered is due to chance (“lottery hypothesis”) and that bacterial communities are assembled from “guilds” of functional equivalent organisms (Burke et al. PNAS USA 2011). Through high-throughput sequencing we have provided evidence for this hypothesis and we are currently exploring, which functions define particular communities in specific habitats. This project will provide an important conceptual advancement in the field of microbial ecology as it aims to define the assembly of microbial communities by functional properties rather than by the species.
5. Antibiotics and resistance in the marine environment
Given the large diversity of microorganisms in the marine environment, it is likely that the harbour novel antibiotics as well as resistance against existing antibiotics. We explore this by high-throughput screening and functional analysis of microbial communities. This research is particular important in the light of “superbugs” that are resistant to most existing antibiotics and that cause substantial problems in the health system. This work is being done in close collaboration with Dr. Suhelen Egan.
I hold a Masters degree from the Rheinische Friedrich Wilhelms University in Bonn, Germany (1996) and obtained a PhD from University of New South Wales (2001). From 2001-2004 I worked as a Senior Scientist at the biotech company Nucleics Pty Ltd. In 2004 I returned to academia as Senior Research Associate within the Centre for Marine Bio-Innovation (CMB) at UNSW and received a fellowship from the American Australian Association in 2005. I went on to become a Senior Research Fellow after being awarded a fellowship from the Australian Research Council (2006-2009). In December 2009, I took on Senior Lecturer position at the School of Biotechnology and Biomolecular Sciences at UNSW and was appointed an Associate Professor in 2013.
I have published over 80 peer-reviewed scientific articles including 2 books and have been awarded three patents related to my commercial work in field of DNA amplification, sequencing and protein purification. I have mentored (or currently supervise) 7 PostDocs, 17 PhD, 3 Masters and 12 Honours students. I have attracted over $7 million in research funding, including grant from Australian Research Council (ARC), the Gordon and Betty Moore Foundation, the Australian Cystic Fibrosis Research Trust and the Hermon Slade Foundation.
I regularly review grants for the ARC (Discovery, Linkage and Federation Fellowship schemes) and for the US National Science Foundation. I am an Associated editor for the “Journal of Aquatic Microbiology” and Founding Editorial Member of the journal “Microbial Bioinformatics and Experimentation” and a regular ad hoc reviewer for the journals Science, Molecular Microbiology, ISME Journal, Environmental Microbiology, Applied and Environmental Microbiology, Extremophiles, Aquatic Microbial Ecology, PLOS One, Aquatic Microbial Ecology to name a few.
I was selected to be the representative for the NSW branch of the Australian Society of Microbiology (ASM) at the annual Science meets Parliament program (2008). I am also the current Chair for of Special Interest Group "Microbial Informatics" of the ASM and a member of the ASM’s National Scientific Advisory Committee. In 2010 I joint the Executive Team of the Centre for Marine Bio-Innovation.