Macquarie University

 
Beneath Australia’s large, dry Nullarbor desert lies an extensive underwater cave system, where microbial communities known as ‘slime curtains’ exist in complete darkness. In the absence of photosynthesis and other nutrient inputs from above, these microbial cave communities may derive their energy from the oxidation of inorganic compounds, such as ammonia, sulfate, nitrate and nitrite, which are relatively abundant in cave waters. We have carried out metagenomic sequencing to explore the diversity and metabolic potential of Nullarbor ‘cave slime’ from Weebubbie cave. Of particular interest was the finding that the dominant organism in this community was an archaea related to Nitrosopumilus maritimus. N. maritimus derives energy by oxidising ammonia to nitrite via the enzyme ammonia monooxygenase and is capable of growing at the very low concentrations of ammonia found in the open ocean. Putative ammonia monooxygenase encoding genes were recovered from this environment using metagenomic sequencing and PCR.  Other genes involved in biological nitrogen cycling, including archaeal nitrite oxidoreductase were also observed in the metagenome. 16S ribosomal RNA surveys conducted to compare multiple bacterial communities from two cave systems, Warbla and Weebubbie, indicate that communities from different caves are distinct and harbor a wide range of microorganisms. We are presently carrying out Scanning Electron Microscopy and Fluorescence In Situ Hybridization to gain further insight into the structure of this unusual microbial slime community. 

DMSP (dimethylsulfoniopropionate) is a key organic compound in the sulfur cycle with ~10^9 tons of this anti-stress compatible solute being made each year by marine phytoplankton, macro-algae and some salt marsh plants. The DMSP that is liberated is catabolised in a series of different microbial reactions that comprise a massive set of biotransformations in the global sulfur cycle. Some of the reaction products, such as DMS (dimethylsulfide), have major environmental consequences in their own right, from climate regulation to animal behaviour. Our work investigates microbial populations that cycle DMSP and DMS in coastal intertidal sediments. Combining geochemical and molecular biological approaches, such as stable isotope probing (SIP) and targeted high throughput sequencing, we are identifying the main microbial players that catabolise DMSP and DMS in oxic and anoxic parts of intertidal sediments alongside the key genes and cognate biochemical pathways that contribute to the turnover of these influential molecules. Early work led to the observation of a vertical microbial population structure within the salt marsh sediment, partially linked to the sulfur cycle biochemistry of this ecosystem. SIP experiments are allowing the characterisation of active microbial processing of DMSP and DMS compounds by separate new bacterial groups, closely associated to salt marsh plants and within the oxic sediment layer. This work is filling in major gaps in our knowledge of the global organic S cycle and the role of microbial populations in major environmental biochemical processes.

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).