JAMS Goes West report

Report by Jeff Powell

On 12 April, the 'cowboys' at the Hawkesbury Institute for the Environment played host to the 'aliens' from the Sydney region for JAMS Goes West. The mood was both enthusiastic and informative and approximately 30 people participated. The morning consisted of five short talks by representatives of five Sydney-based institutions.

Ian Anderson (UWS) started things off with descriptions of the research strengths in the HIE, including those related to microbiology (plant-microbe symbioses, mycorrhizas, microbial community ecology, carbon cycling). He followed that up with information on the various analytical and experimental facilities available on the UWS campus in Richmond (the next-generation sequencing facility, EucFACE woodland elevated CO2 experiment, whole tree chambers, automated tree-scale rainout shelters, and flux tower).

Justin Seymour (UTS) talked about two research groups: the Aquatic Microbiology group within the Climate Change Cluster (focusing on the interactions among microbial communities, climate, and oceanography) and the ithree Institute (focusing largely on infectious diseases). He also highlighted the Microbial Imaging Facility, including an overview of the available equipment (various infrastructure for cell separation and imaging) and software for image analysis.

Mike Manefield (UNSW) talked about microbiological research happening in his group, largely linked to environmental remediation applications, and elsewhere in the University, including the mathematical modeling of evolutionary processes in bacteria. Mark finished by talking about the Mark Wainwright Analytical Centre, a series of facilities devoted to imaging and chemical analyses and organised into a (mostly) single unit.

David Midgely and Nai Tran-Dinh (CSIRO) talked about the environmental microbiology and microbial ecology happening in their divisions; I won't provide the names of divisions, as these will have probably changed by the time this summary has been posted. The work was specifically focused on the microbiology of coal seam gas and around food and nutrition. CSIRO has additional strengths in mathematics and bioinformatics support and it was expressed that there are some good people with nice ideas that would be interested in collaborations.

Michael Kertesz (USyd) gave an overview of microbiology at the University of Sydney, covering two Faculties and several Departments. Research in the Faculty of Agriculture and Environment focuses on biological nitrogen fixation, rhizosphere microbiology, sulfur cycling, microbial ecology as well as some peripheral avenues (soil science, precision agriculture, and systems biology). Additional staff in the Department of Biological Sciences (Faculty of Sciences) work on mycorrhizal associations, bacterial symbioses, and amphibian pathogenesis. Across these research groups there are a number of analytical facilities for sequencing and genomics, DNA community fingerprinting, and chemical analyses.

After lunch, Brajesh Singh led the group on a tour of some of the major experimental facilities on the UWS campus. First, David Ellsworth gave a tour of the EucFACE experiment: an ecosystem-level study of a native woodland exposed to anticipated future levels of atmospheric carbon dioxide. Discussion focused on current plans for microbiological research in the system, which is currently mainly focused on microbial communities and nutrient cycling in soil. It also touched on opportunities for external researchers to piggyback on this sampling and on identifying areas of research that are not being covered; if interested in learning more, contact Brajesh Singh (b.singh@uws.edu.au) or Jeff Powell (jeff.powell@uws.edu.au). Then, Burhan Amiji gave an overview of the research happening in the rainout shelters (into which trees are planted and rainfall manipulated over multi-year timescales) and whole tree chambers (in which trees are grown, up to heights of 10m, under manipulated temperature and CO2 concentrations).

Finally, Federico Lauro led a discussion on a number of topics related to overcoming many limitations facing microbiologists in Sydney, including the cost of doing research in Australia and the low visibility of our research in the public sphere. These were summarised and circulated by Fede the day after the meeting but are included again below:

  • A number of one-to-one collaborations were discussed. It is important to note that if you have experiments that you would like to conduct at HIE, there are small pots of money accessible for these collaborations to occur. For more info contact Brajesh Singh (b.singh@uws.edu.au)
  • It is preposterous that most of us are forced to outsource sequencing to China and the USA when next-gen sequencing machines are lying unused in our labs. For starters, Brajesh Singh said he would look into getting a good deal for 16S amplicon sequencing at UWS. We would all contribute to the initial purchase of barcoded multiplex primers and then get rates comparable to Texas R&T or China's BGI with the added bonus of saving on shipping and carbon footprint and being able to harass the technician over the phone when something goes wrong.
  • Many of us are faced with computational bottlenecks when it comes to analysing large datasets. David Midgley and Nai Tran-Dinh said they would look into the possibility of utilising the bioinformatics team (programmers and statisticians) and computing resources available at CSIRO on a collaborative basis.
  • A number of students were very enthusiastic about a multi-institution training course in environmental-micro/microbial-ecology at a graduate level taught by JAMS academics. However significant issues were raised on how to get money to run the course. Any ideas are welcome.
  • There is the potential to partner with the Australian museum for a microbiology display. I will give them a call next week but if you would like to be on the organising committee (or just have some good ideas on how to make microbiology accessible to the general public) just drop me an email.
  • Issues were raised about making JAMS a corporation sometime in the near future. While I dread the idea of more paperwork, this will probably be an unfortunate side-effect of the benefits we enjoying. If you feel strongly in favour or against such a transition please drop me an email.

There was also some discussion around getting ready for potential LIEF funding applications, specifically for a NanoSIMS or TOF-SIMS for high-resolution analysis of surfaces (contact Federico Lauro) and a GC/C/IRMS for stable isotope probing applications (contact Brajesh Singh). David Midgely expressed that he thought CSIRO might have the latter (although it may just be a GC-IRMS) and would look into it.

Finally, with a reminder that the next meeting would take place Tuesday 24 April, due to ANZAC day falling on the regular date, the meeting concluded. Thanks to all the speakers, the guides, and to Fede and Braj for organising the event.