Person Career

Dear Australian colleagues,
Please see attached advert for the 4th New Zealand Microbial Ecology Consortium (NZMEC) meeting, to be held at the University of Auckland on 18-19thFebruary 2016.  Registration for this meeting is free, and we think you’ll agree that there is a very strong line-up of speakers.

Event Date: 
Wednesday, October 29, 2014 - 19:00 - 19:30

“On the value of reframing antibiotic resistance as a disaster risk problem”


Dr. Maurizio Labbate1,2 & A/Prof. Dale Dominey-Howes3

1School of Medical and Molecular Biosciences, University of Technology, Sydney, Australia.
2The ithree Institute, University of Technology, Sydney, Australia.
3Asia – Pacific Natural Hazards Research Group, School of Geosciences, University of Sydney, Australia.


On the 1st May 2014 the World Health Organization in its first global assessment of antimicrobial resistance reported that antibiotic resistance has now reached alarming proportions and is no longer a future problem but a contemporary reality. This comes off the back of other urgent calls from leading authorities including the Deputy Director of the Center for Disease Control (CDC) who has publicly stated that we have now reached the “end of the antibiotic era” and the UK Chief Medical Officer, Professor Dame Sally Davies who called for antibiotic resistance to be placed on the risk register above the issue of terrorism. Increasingly, the tone of the language used by these organizations and individuals is reminiscent of that used by the disaster and emergency risk management communities to describe commonly occurring disasters such as earthquakes, fires, floods and storms.

Antibiotic resistant infections are rising fast and affect millions of people globally. Antibiotic resistance has become a slow onset disaster that like climate change has struggled to elicit the sort of coordinated international response that is required to deal with the magnitude of the emergency. Anthropogenic modification of the Earth’s climate system provides the foundation for sudden onset natural disasters such as hurricanes, wildfires and storms. Likewise, increasingly widespread antibiotic resistance is laying the foundation for the future occurrence of sudden onset bacterial epidemic and pandemic disasters.

Despite the finest efforts by medical and health policy makers and communities to control the antibiotic resistance problem, the issue has reached a critical tipping point. Given the current state of the antibiotic resistance problem and the likely near future of untreatable bacterial infections, we propose an alternative and novel policy perspective. With this is mind, we propose to make antibiotic a broader issue and reframe it as a disaster risk problem and engage the expertise of emergency managers. Governments and disaster policy makers across the world use the Emergency Risk Management process in the management of and preparation for natural disasters. This process is a systematic method that through engagement with multiple stakeholders identifies, analyses, evaluates and treats risks and takes an iterative approach with well-defined activities that lead to implementation of risk-treatment strategies tailored to a specific community’s risk profile. This policy and practice framework is an excellent mechanism for reaching out to communities and communicating complex messages – an area that needs to be enhanced.

Thanks to the JAMS faithful for coming out to the Australian Museum last night. The ranks were slightly depleted given the large contingents that are at the ISME conference in Korea this week. No matter, more pizza for all. In the short presentations Robert Moran gave a great account of his work on plasmid and resistance determinants in E. coli lineages in the human gut and Igy Pang from UNSW presented his work on gene co-expression networks underlying synergistic antifungal treatments. In the long presentation by Michael Gillings from Macquarie University results were presented that send an ominous warning of how global antibiotic use is affecting evolution. Michael gave a rivetting account of how microbiology is fused with the Anthropocene. FInally a massive congratulations to JAMS co-founder Professer Ian Paulson from Macquarie University for being awarded an Australian Laureate Fellowship. Our very own home grown legend.

Event Date: 
Wednesday, May 28, 2014 - 18:15 - 18:30



In September 1999, I collected a small heath plant from a large sandstone outcrop near the Murphy’s Glen campsite in the Blue Mountains west of Sydney. This seedling had been growing in just a few centimetres of sand atop the rock. The shallowness of soil meant its root system was perpendicular to the stem, and spread out like a spider’s web from the base. Heath plants have unusual roots; they’re very fine, being only marginally thicker than a human hair. I took the plant back to the laboratories at University of Western Sydney and carefully cut these hair roots up in small pieces. I surface sterilised the pieces in bleach and placed each piece, numbered and its location in the root system recorded, onto an agar plate. From these tiny root pieces grew a host of very slow growing non-spore producing fungi. Most of these fungi were ericoid mycorrhizal (ERM) fungi – these fungi form a symbiosis with heath plants – facilitating their growth in challenging places such as acid bogs, nutrient poor sands and soils rich in metals such as cadium and zinc. Since 1999, I’ve undertaken quite a bit of work on the most abundant ERM fungus from this one seedling, and with the help of various collaborators we have observed the structures it forms in roots of heath plants, how it enhances the growth of heath seedlings and examined its carbon, nitrogen and phosphorus catabolism. It was, and still is, the most studied Australian ericoid mycorrhizal fungus. 
Upon moving to CSIRO in 2007, I left the last six cultures in the fridge in Dr. Peter McGee’s laboratory and it was here that they remained until 2013 when I retrieved them on Peter’s retirement. Just two of the last six survived the long winter. In late 2013, we had some space on an Illumina run with some other samples – and we sequenced the genome of this fungus. We’ve called it ‘Cairneyella’ after the late Professor John W. G. Cairney. There’s still much to learn about Cairneyella – and I’m seeking collaborators who’d like to share these last cultures and further the body of work on this remarkable fungus.

Another great JAMS evening at the Australian Museum. Nicolas Barraud from UNSW kicked off with a biotechnology story about the use of nitric oxide in biofilm control. John-Sebastien Eden from Eddie Holmes group at USyd gave us the low down on norovirus evolution using the Sydney 2012 strain (the chunder from downunder) as a case study. Somehow our two 15 min presentations consumed an hour so starting back late after the break JAMS co-founder Prof Andrew Holmes gave an excellent presentation on what shapes microbial communities in the the gut. Despite the late start Andy had the audience glued to their seats with a showcase of technology used to unravel human-gut microbiome interactions.

Mike Manefield
JAMS this week was a real blast with an excellent presentation by Prof Rainer Meckenstock, director of the Helmholtz Institute for Groundwater Ecology. Rainer's presentation took the fed and watered JAMS audience through a tour de force of anaerobic polyaromatic hydrocarbon degradation from hard core biochemistry to field studies revealing what limits the clean up of hydrocrabons in polluted groundwater resources (the biggest freshwater resource on Earth). Tim Lachnit gave a revealing presentation on disease in seaweed (Ecklonia) driven not by bacteria but by viral infection. Ali Khameneh gave another great short talk on evolutionary responses of Burkholderia cepacia to environmental and host conditions. Ian Paulsen advertised the Synthetic Biology and Bio-engineering Workshop (see attached) - registration closes 1st Oct 2013. The audience was on fire with probing questioning of speakers giving all plenty to think about and pushing the quality of science in our community to further heights.

Event Date: 
Wednesday, September 25, 2013 - 07:00 - 08:00
Helmholtz Centre for Groundwater Ecology, Munich, Germany

Limiting factors for anaerobic aromatic hydrocarbon degradation in contaminated aquifers and oil reservoirs



  • Rainer Meckenstock studied biology at University of Konstanz, Germany 1985-1990. He finished with a thesis in the group of Prof. Winfried Boss on microbial sugar transport systems (molecular microbiology). He did his PhD at the Swiss Federal Institute of Technology (ETH) in Zürich, Switzerland, with a thesis on biochemistry of light-harvesting complexes of phototrophic bacteria (1990-1993) in the Institute of Molecular Biology and Biophysics with Prof. Zuber. During his post-doc at the Swiss Federal Institute of Environmental Science andTechnology (EAWAG) in the group of Dr. van der Meer in Dübendorf, Switzerland, he developed molecular methods to monitor trichlorobenzene-degrading microorganisms and their degradation activities in the environment (PCR, RT/PCR, in situ hybridisation) (1993-1995). He changed to the investigation of anaerobic degradation of aromatic hydrocarbons in the Microbial Ecology Group of Prof. Bernhard Schink, University of Konstanz, Germany, in 1996. Here, he isolated novel anaerobic BTEX and PAH-degrading organisms and studied the degradation pathways. A new method to study microbial activities in the environment with analysis of stable isotope fractionation was developed. Since 2000 he changed to the Center of Applied Geosciences at the University of Tübingen, Germany, and set up a Geomicrobiology group within the Chair of Environmental Mineralogy (Prof. Stefan Haderlein). Research topics were the anaerobic degradation of mono- and polycyclic aromatic hydrocarbons (BTEX, PAH), isotope fractionation as a means to monitor biodegradation in contaminated groundwaters, limitations of natural attentuation, and the reduction of iron minerals as electron acceptor. Since July 2003, he became the director of the Institute of Hydrology at GSF which changed its name to Institute of Groundwater Ecology at the beginning of 2004. In 2007 he was appointed as a full professor for Groundwater Ecology at the Life Science Center (WZW) of the Technical University of Munich.

Ani Penesyan
On the last Wednesday of spring we were spoiled with the room on the top floor of the Australian Museum and magnificent views of Sydney, yes, once again! Joining us were not only our regular JAMS crowd, but also visitors from Europe (yes, that is really cold in Europe during this time of the year!)

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