JAMS November 2012 Report

JAMS REPORT
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!)
 

After a usual start with few getting-together drinks, the first speaker of the night, Jason Woodhouse, from the University of New South Wales, presented his work on deep sequencing of secondary meta-metabolomes as a preliminary screening tool for determining natural product diversity in environmentl samples.  In his work he used next-generation sequencing to determine the diversity of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes within multiple environments to a depth previously not reported.  By using multiplexing he was able to amplify thousands of ketosynthase and amino acid condensation domain sequences from over thirty different environments. Sequences were differentiated according to function and taxonomic origin, as well as their distribution within distinct environments. Similar patterns of NRPS and PKS occurrence were observed between functionally similar but geographically distinct environments. Furthermore, increases in microbial diversity between environments did not influence the occurrence of these genes. It is expected that this approach will be applied to any environment enabling for the tailoring of culture-dependent and culture-independent strategies for the isolation of novel natural products.
 
The second speaker, Johanna Kenyon from the University of Sydney, steered us away from the environmental microbiology more towards medical microbiology talking about the a human opportunistic pathogen Acinetobacter baumannii ; this certainly also showcases the wide range of topics covered during JAMS meetings! Acinetobacter baumannii is amongst the most troublesome Gram-negative pathogens worldwide, due to strains that are resistant to multiple antibiotics, disinfection and periods of desiccation. Nevertheless, little is known about the virulence mechanisms, though a role for capsule has been demonstrated.  The fundamental question Johanna was trying to find an answer to was whether Acinetobacter baumannii has an O antigen. Previous analysis of A. baumannii genome sequences identified a region of extensive diversity presumed to be involved in the synthesis of a surface polysaccharide, variously identified as O-antigen or capsule. Johanna used bioinformatic tools to assess whether this polysaccharide is exported as capsule, or ligated to a lipid A-core oligosaccharide moiety to become the O antigen moiety of lipopolysaccharide. A gene for O-antigen ligase was not found, and she proposes that A. baumannii strains produce a capsule (and lipid A-core oligosaccharide), but no lipopolysaccharide.  9 capsule types and 3 core types were found in the 10 completed genomes and more in draft genomes. Multiple capsule types were found in members of the 2 major clonal complexes, and this variation may contribute to the success of the A. baumannii clones by factoring in the evasion of the host immune response.
 
After the first two talks it was a traditional pizza time! Pizza was great, as usual, apparently the only flaw that pizza place has is the lack of delivery service which is compensated by our own volunteers, who are always happy to do the job as they might as well be the most highly anticipated people after the first two talks are concluded! Sometimes you can be given a choice between delivering the pizza or preparing the JAMS report which I am not going to talk about (now I can say I have done both!).
 
After all the pizza was consumed, accompanied by few drinks and insightful scientific discussions, the seminar resumed with the main speaker, Nick Coleman from the University of Sydney, taking the central stage.
 
Nick presented his group’s work on biodegradation of dichloroethane by aerobic bacteria at the Botany Industrial Park The chlorinated hydrocarbon 1,2-dichloroethane (DCA) is a common pollutant of groundwater, and poses both human and environmental health risks. The Botany Industrial Park in south Sydney is heavily contaminated with DCA and other organochlorines. The main user of the site (Orica Ltd) operates a large groundwater treatment plant (GTP) on site to contain and remediate the DCA-contaminated groundwater. At present, remediation is done by air-stripping and thermal oxidation, but this is very costly and energy-intensive. Orica is interested in alternative technologies for treating the groundwater, including bioremediation. In 2010, a pilot scale membrane bioreactor (MBR) was set up to treat a fraction of the groundwater. The aims of the study were to identify DCA-degrading bacteria and genes in the GTP and on the site at large, define the community structure and ecological successions occurring in the MBR, develop a qPCR for catabolic genes in the DCA biodegradation pathway, and field-test this qPCR assay in the MBR and in a survey of groundwater in monitoring wells on the site. The have discovered that DCA-degrading bacteria using a hydrolytic pathway (dhlA/dhlB genes) were widespread and diverse at this site, and that the dhlA gene was carried on a catabolic plasmid. The community in the MBR was dominated by alpha- and beta-proteobacteria, and was highly dynamic, changing dramatically in composition as the percentage of raw groundwater in the feed was increased. By combining dhlA qPCR and 16S pyrosequencing data, they found evidence that thus-far-uncultured species of Azoarcus may play a major role in DCA bioremediation in situ in the MBR.
 
JAMS November meeting concluded with a preview of the upcoming 2nd anniversary JAMS Presentation and Banquet to be held on Wednesday, February 27, 2013! See you all there and Happy Birthday to JAMS (which, to be precise, actually started in November 2010!)