JAMS June 2012 meeting report by Sabrina Beckmann

Cold, pitch dark and walls dripping with slime. Sasha Tetu from Macquarie University kicked off the JAMS meeting yesterday evening by taken us along on an exploration into the underwater cave system just beneath Australia’s Nullarbor desert. The picturesque scenery of these caves did not bare the impression of life at first glance. Surprisingly a broad range of cave dwelling bacteria and archaea was revealed thriving in this extreme environment  lacking photosynthesis and input of nutrients from above. Those microbes oxidise inorganic compounds supplied by the cave water to maintain their energy. Amidst novel chemolithotrophic community, an dominant archaeon related to Nitrosopumilus maritimus, the „Ammonium-oxidizing dwarf from the ocean“ turned out to be the „Giant in the caves“. This organism derives energy from very low concentrations of ammonium by oxidizing it to nitrite via the ammonia monooxygenase. Genes involved in the biological nitrogen cycle were recovered using metagenomic sequencing. In the future, Sasha and her slime team will unravel more secrets about those distinct microbial communities living in the darkness of the caves.
Vice versa Loic Nazaries from the University of Western Sydney accomplished his research mission „Larger the Better“ based on a robust design method. Loic applied the Taguchi concepts to develop a procedure for the optimization of PCR for targeting functional genes. Originally, Genichi Taguchi developed statistical methods to improve the quality of manufactured goods long before his methods made their way into the field of engineering and eventually into the life of molecular biologists. Those methods use orthogonal arrays to organise the control parameters and factors affecting a process as well as the levels at which they should vary. An advantage is to test only a few combinations to identify the optimum condition of several factors and therefore decrease the total number of experiments. Loic succesfully optimised the PCR conditions in a quick and efficient way for targeting pmoA genes of methanotrophic bacteria. Honestly, who wouldn’t prefer running 18 experiments instead of 729 in order to solve a problem?
After enjoying pizza and beer in an exciting talkative atmosphere, Michael A. Kertesz from the University of Sydney plowed our minds with all the phenomena harvested from managing the rhizosphere as a factory where microbes work. If the factory is set up properly (sulfur is available) microbes volunteer to work. Besides the supplementation of sulfur via inorganic fertilizer, the conversion of soil organosulfur to bioavailable sulfur for plants is of significant relevance for high-yielding crop plants. Over 95% of sulfur is organically bound. In order to gain more insights into the microbial sulfur-turmover processes, Michael investigated genes and enzymes involved in the mobilization of organically-bound sulfur, specifically the regulation of sulfatase (atsA) and sulfonatase (asfA) genes. Functional TRFLP analysis was used to reveal the diversity of those genes. Differences in sulfatase communities and activity were associated with land use and soil type. Furthermore, two species, Variovorax and Polaromonas, dominated the sulfonatase community in both, in wheat and sulfate- limited Agrostis rhizospheres. Both genera appear to be key players in the sulfonate transformation in the rhizosphere of various environments. „Increasing our understanding of the rhizosphere microbes that catalyse soil organosulfur turnover, will allow us to develop management practices to maximize soil sulfur availability, and minimize the costs associated with fertilization (M. Kertesz)“.
Now go and discover new scientific horizons – not always an easy chore -  and come back to JAMS on Tuesday 31st July (not Wednesday this time around) where science, wisdom, pizza, and explorations meet.