November 2012

Event Date: 
Wednesday, February 27, 2013 - 14:00 - 21:00

It's that time of the year again and I'm not talking about Santa Claus. It's time for our second anniversary JAMS Presentation and Banquet. This year has been full of milestones including a microbiology display at the Australian Museum for grade school students and a trip to the Hawkesbury RIver to visit the new campus of the University of Western Sydney. JAMS also has some exciting news -- we will be incorporating next year which will make us bigger, better and official.
 
February 27th 2013 marks the second Annual JAMS Dinner at the Australian Museum with an expanded schedule, some great speakers from around the world and a poster session for PhD students. The Skeleton Gallery and over 100 skeletons -- including the horseman and the movable bicycle-riding man will play host to the banquet.
As an incentive for students to present their work, the best poster will be awarded with the Jeff Powell Perpetual Student Award.
 
The rest of the meeting is detailed below.

Event Date: 
Wednesday, November 28, 2012 - 06:00 - 06:15
Institution: 
UNSW
Title: 

Deep sequencing of secondary meta-metabolomes: A preliminary screening tool for determining natural product diversity

Abstract: 

Increasingly, natural product isolation strategies are circumventing culture-dependent methods for the isolation secondary metabolite genes directly from the environment. Many of these isolation strategies are undertaken with little knowledge of an environment's specific secondary metabolite potential. Next-generation sequencing technology was used to determine the diversity of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes within multiple environments to a depth previously not reported. A multiplexing strategy was used 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.

Event Date: 
Wednesday, November 28, 2012 - 06:15 - 06:30
Institution: 
University of Sydney
Title: 

Does Acinetobacter baumannii have an O antigen?

Abstract: 

 
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. Little is known about the virulence mechanisms, though a role for capsule has been demonstrated. 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. We 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 we propose 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.

Event Date: 
Wednesday, November 28, 2012 - 07:00 - 08:00
Institution: 
University of Sydney
Title: 

Biodegradation of dichloroethane by aerobic bacteria at the Botany Industrial Park

Abstract: 

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 our 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. We 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, we found evidence that thus-far-uncultured species of Azoarcus may play a major role in DCA bioremediation in situ in the MBR.

Event Date: 
Wednesday, February 27, 2013 - 15:15 - 15:45
Institution: 
University of Western Sydney
Title: 

Responses of soil fungi to global change: effects of elevated atmospheric CO2, temperature and drought

Abstract: 

Fungi are central to forest carbon and nutrient cycles in Australian sclerophyll forest soils, but little is known about how they will respond to future global change. Our recent research has used a combination of controlled environment glasshouse and field experimentation to investigate the interactive effects of elevated atmospheric CO2 concentration [CO2], increased temperature and drought on Australian eucalypt soil fungal biodiversity.
 
In a glasshouse experiment, seedlings of two eucalypt species (Eucalyptus saligna and E. sideroxylon) were grown in field soil for 5 months under sub-ambient (290 µl l-1), ambient (400 µl l-1) and elevated (650 µl l-1) atmospheric CO2 conditions at both ambient (26°C) and elevated temperature (30°C). Multivariate analyses conducted on molecular data generated from soil and hyphal ingrowth bags (which select for mycorrhizal fungal mycelia) showed a significant (P < 0.035) separation between fungal communities associated with the two different tree species. While there was an effect of [CO2] and temperature, the response was plant species dependent with the exception of the combined elevated [CO2] and elevated temperature treatment (650 µl l-1 CO2 and 30oC) which clustered together regardless of tree species.
 
In the field experiment, E. saligna trees were grown in 12 whole tree chambers for three years under controlled temperature conditions and exposed to either ambient (ca. 380 µl l-1) or elevated (ca. 640 µl l-1) atmospheric [CO2] and different watering regimes to simulate drought. Multivariate analyses of molecular data showed that elevated [CO2] intensified the effect of drought stress by significantly altering fungal community composition.
 
Collectively, our data demonstrate that alterations to atmospheric [CO2], temperature and drought conditions modify soil fungal communities associated with Australian eucalypts. We are currently investigating the knock-on effects of these changes for fungal driven soil processes given the potential for soil microorganisms to significantly influence the direction and magnitude of terrestrial ecosystem/atmosphere feedbacks that regulate global change.

Event Date: 
Wednesday, February 27, 2013 - 15:45 - 16:15
Institution: 
King Abdullah University of Science and Technology
Title: 

Microbial Ecology of the Red Sea

Abstract: 

The Red Sea is a harsh environment characterized by high temperatures, high salinity, high solar irradiation, and strong gradients from the North to the South. It also harbors at least 25 extreme environments at its seafloor, the deep-sea brine pools. These mostly anoxic brine pools are completely saturated with salt, and are among the most hostile habitats on earth. So far, studies on the microbiology of both, the water-column of the Red Sea and the deep-sea brine pools are scarce, mostly because of logistic and political reasons. King Abdullah University of Science and Technology (KAUST) is a new, international world-class research university in the Kingdom of Saudi Arabia that realizes the value of the Red Sea for the Middle East. The Marine Microbial Microbiology Group is part of the Red Sea Research Center at KAUST. In this presentation, I will summarize our holistic approach (community analyses, metagenomes, single-cell genomes, cultures) to a better understanding of the microbial communities of the Red Sea water-column and the brine pools, with a focus on adaptations of the major players to this peculiar environment.

Event Date: 
Wednesday, February 27, 2013 - 18:00 - 18:30
Institution: 
University of Sydney
Title: 

A tale of two clones; multiple antibiotic resistance in Acinetobacter baumannii .

Abstract: 

The importance of Acinetobacter baumannii in causing nosocomial infections was only recognised in the mid 1980s, making it the least studied of the bacteria that are now resistant to most of the antibiotics that are most important for treatment of such infections. We assembled a large collection of A. baumannii isolates recovered between 1999 and 2011 at hospitals in Sydney, Canberra, Brisbane, Melbourne, Newcastle and Adelaide. All but a few of those that are resistant to multiple antibiotics belong to one of two clonal groups that have recently been found to be globally distributed. Hence, these clones, global clone 1 and 2, have been in Australia at least since the mid 1990s.
Representatives of hospitals and of groups with different carbapenem and aminoglycoside resistance patterns in our collection have been sequenced together with the GC1 and GC2 reference strains from the early 1980s. Trees based on single nucleotide polymorphisms reveal significant diversity in the Australian isolates from one clone and little in the other. Most of the genes conferring resistance to older antibiotics are in the chromosome clustered in one island in GC1 and two in GC2 isolates. However, each of these islands is continually evolving, losing and gaining resistance genes. Further variation arises from the acquisition of different plasmids carrying further resistance genes. Other major but unexpected differences arising within the clones affect the exopolysaccharides. The capsule is an important virulence determinant, and substitution of large chromosomal segments leads to many distinct loci for capsule biosynthesis in each clone.

Event Date: 
Wednesday, February 27, 2013 - 18:30 - 19:00
Institution: 
University of Queensland
Title: 

The Big Picture: lessons from a rapidly expanding genomic tree of life.

Abstract: 

Most microorganisms cannot be grown in pure culture (or at least not easily). This has been apparent for decades by comparing the number of cells seen under a microscope to the fraction of those cells that will grow into colony forming units (typically <1%). The advent of culture-independent rRNA-based molecular surveys pioneered by Norman Pace put our degree of ignorance of the microbial world into perspective: dozens of major microbial lineages have emerged over the last 20 years that lack even a single cultured representative. New approaches, such as deep metagenomics and single cell genomics, are now transforming the rRNA-based phylogenetic outlines of the tree of life into a fully fledged genome-based view of the tree. I will present a snapshot overview of the genome tree of the bacterial and archaeal domains and examples of functional insights in the context of a more complete view of microbial evolution.

JAMS REPORT
Maria-Luisa Gutierrez-Zamora

The JAMS rendezvous this October 31st took place in the fourth floor of the Museum with a magnificent view of Sydney, and began with an ad hoc presentation featuring sulphurous scents and sexy fangs. Katherina Petrou (UTS) initiated us in the science of the sulphur cycle in the oceans and how this process is dominated by the production of dimethylsulfoniopropionate (DMSP) by microalgae and its decomposition into dimethylsulphide (DMS), a strong odorous chemoattractant for a range of marine organisms. In tackling the mystery of how harmful algal blooms disappear, Katherina discovered that DMS produced by the dinoflagellate Alexandrium minutum (causative agent of toxic algal blooms) was the chemical cue for the infection of its parasitoid Parvilucifera sinerae.  An elegant video illustrated how DMS at 300 nM was able to activate the parasitoid spores from a dormant state to leave the sporangium (an infected A. minutum cell) in transit to infect other cells and propagate. Activation only occurred in the range of 30 to 300 nM indicating that the effect was dependent on cell density. Thus, Katherina’s work showed that DMS plays an important role in the biological control of toxic algal blooms in the oceans. Her results contribute to the better understanding of marine chemical ecology.