University of New South Wales

Professor Jill Banfield presents a public lecture entitled 'Metagenomic views of the microbial biosphere within us and in the world below us'.
9th July 2012, 6 pm for a 6:30 pm start
Tyree Room Scientia Building, University of New South Wales (Map ref G19)
Light capapes and refrshments will be served
RSVP essential: rsvp@science.unsw.edu.au or phone 93857919
 

Event Date: 
Wednesday, May 30, 2012 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Deep sequencing of evolving populations in bacterial biofilms

Abstract: 

 

Bacterial communities growing as biofilms are subject to a distinct lifecyle, featuring initial surface attachment, microcolony formation and dispersal of cells. Bacterial biofilms are sometimes characterised by high levels of heritable phenotypic variants, presumably resulting from genetic diversification during the biofilm lifecyle. As biofilms are a favoured lifestyle of many environmental and pathogenic bacteria, identifying the evolutionary processes responsible for this diversification has important implications, both for our understanding of ecological processes, such as niche adaptation, and to clinically relevant questions, such as the evolution of antibiotic resistance.
I've used longitudinal genome-wide deep sequencing to reveal the underlying genetic structure of bacterial populations growing as biofilms, for the model organisms Phaeobacter gallaeciensis 2.10 (an abundant marine bacterium) and Pseudomonas aeruginosa 18A (a clinical Cystic Fibrosis isolate). Biofilms were grown under defined laboratory conditions known to generate reproducible phenotypic diversification. Samples from different stages of biofilm development were then sequenced to very high coverage (>800x). By accounting for sequencing errors using a matched-sample approach, variants with population frequencies as low as 0.5% could be accurately identified.
In general, the extent and nature of genetic variation was comparable for biofilms of both model organisms, being driven by selection for a small number of non-synonymous variants within key genes involved in biofilm- and competition-related pathways. These results also demonstrate that genome-wide deep sequencing can rapidly, accurately and comprehensively describe genetic variation within evolving populations.

 

Last week’s ABC Science Show had a large chunk on microbial ecology, with interviews with Janet Jansson, Jack Gilbert, and Tiffany Nelson from UNSW at the AAAS meeting.
Here’s a link to the podcast

Event Date: 
Wednesday, February 29, 2012 - 14:30 - 21:00

You are invited to our inaugural anniversary half-day meeting at the Australian Museum, set for February 29th. Please sign-up to this event if you wish to attend or email us if need be.

Registration costs have been reduced to $35 for students and $75 for everyone else, thanks to the generous sponsorships of POCD Scientific, BD, The School of Molecular Bioscience (U. Sydney), The School of Biotechnology and Biomolecular Sciences (UNSW), The School of Medicine (UWS), The Biomolecular Frontiers Research Centre (Macquarie U.), The Environmental Microbiology Initiative (UNSW), The C3 and I3 Institutes (UTS).

There is an expanded schedule with some great speakers from out of town and a poster session for PhD students. As an incentive for students to present their work, the best poster will be awarded with the inaugural EMI Best Poster Award.

If you intend to present your work, please provide a poster title during registration.

The schedule of the meeting is as follows:

2.30 - 3.00pm Poster setup.
3.00 - 3.15pm Welcomes, introductions and acknowledgements.

Event Date: 
Wednesday, January 25, 2012 - 18:15 - 18:30
Institution: 
UNSW
Title: 

The impact of petroleum hydrocarbons on microbial diversity in a sub-Antarctic soil; a proxy for soil health

Abstract: 

Anthropogenic sources of contamination remain a legacy throughout the Antarctic Region, with the majority of contamination occurring alongside concentrated human activities at research stations. At Macquarie Island, an Australian Sub-Antarctic territory we have been investigating the impact of petroleum hydrocarbon contamination in the form of Special Antarctic Blend (SAB) diesel fuel on the microbial ecology of sub-Antarctic soils. Whilst bioremediation strategies are currently underway on the Island, there is a lack of petroleum hydrocarbon contamination guidelines specific to Antarctic or sub-Antarctic regions. Additionally, there is insufficient site-specific toxicity data available for remediation end points to be established. Therefore, we have assessed the bacterial and fungal response to increasing concentrations of SAB diesel fuel through a combination of novel culturing methods, flow cytometric analysis of cell numbers and massively paralley pyrosequencing targeting the 16S and ITS genes. Results of this investigation will provide the scientific basis for understanding how much fuel is too much and how clean is clean enough?

Event Date: 
Wednesday, November 30, 2011 - 19:15 - 20:00
Institution: 
UNSW
Title: 

Rocking the cradle of life: Functional complexity of modern stromatolites.

Abstract: 
One of the major challenges in science is to identify modern living systems that present unique opportunities to address fundamental questions in diverse fields ranging from microbiology, geology, evolution, chemical biology, functional genomics, and biotechnology. The living stromatolites of Shark Bay on the western coast of Australia represent such a system. The overarching aim of our research program is to comprehensively characterise the functional complexity of modern stromatolites, in particular the diversity, biogeochemistry, and key interactions of the microorganisms forming the Shark Bay stromatolites. Understanding modern stromatolite systems is of fundamental significance to shed light on the evolution of early microbial life and the impacts of these ecosystems on both past and present global nutrient cycling.

Shark Bay is notable for its living marine stromatolites, and is listed as a World Heritage Site. In addition to their established evolutionary significance, these stromatolites, located in a hypersaline environment, are an ideal biological system for studying survival strategies of microorganisms to a range of stresses and their metabolic cooperation with other microorganisms. To further our understanding of these geobiological structures, detailed analyses of associated microbial communities and their functional characteristics are crucial.

This presentation will summarise the platform of our work over the last several years, focusing on recent discoveries and how these have led to new research directions employing a range of cutting edge technologies. This includes a comprehensive study elucidating major microbial populations, novel organism characterisation, signature lipid profiles, adaptive mechanisms of novel stromatolite isolates, creating a detailed biogeochemical profile of living stromatolites, whole genome analyses, and mechanisms of communication in these systems.

Finally, from an educational perspective, an interactive virtual field trip is being developed that will be an invaluable tool for both future research and conservation. Through the application of a rational and integrated approach, this research has provided valuable insights into these evolutionally significant biological systems. We now know who the key microbial players are, and can use this knowledge to examine specific functional characteristics to take the research to the next level, utilising the new suite of techniques now revolutionising the field of environmental microbiology.

  1. Allen MA, et al. (2010) Lipid biomarkers in Hamelin Pool microbial mats and stromatolites. Org Geochem 41, 1207-1218.
  2. Leuko S, et al. (2011) Molecular assessment of UVC radiation-induced DNA damage repair in the stromatolitic halophilic archaeon, Halococcus hamelinensis. J Photochem Photobiol B: Biology 102, 140–145.
  3. Goh F, et al. (2011) Osmoadaptive strategies of the archaeon Halococcus hamelinensis isolated from a hypersaline stromatolite environment. Astrobiology 11, 529-536.
Event Date: 
Wednesday, April 27, 2011 - 19:15 - 20:00
Institution: 
UNSW
Title: 

Protozoan grazing as a driving force in the evolution of pathogenicity in bacteria.

Event Date: 
Wednesday, April 27, 2011 - 18:15 - 18:30
Institution: 
UNSW
Title: 

The first chlorophyll to be discovered in 60 years: chlorophyll F.

Abstract: 

This remarkable compound, found in stromatolite-inhabiting cyanobacteria from Shark Bay, Western Australia, can absorb light further in the red region of the electromagnetic spectrum than any of the other known chlorophylls.
This work was a truly collaborative effort between Sydney-based (University of New South Wales, the University of Sydney and Macquarie University) and international researchers (University of Munich).

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