Chemistry

Event Date: 
Thursday, October 9, 2014 - 16:00 - 17:00

Dear All,

 

You are invited to the Sydney Next Generation Sequencing Special Interest Group Meeting,  which will be held at the University of Technology, Sydney.

 

Further details are below:

 

Speakers: 

Event Date: 
Wednesday, July 30, 2014 - 18:15 - 18:30
Institution: 
Macquarie University
Title: 

Effect of Low Temperature on Tropical and Temperate Isolates of Marine Synechococcus.

Abstract: 

An abundant and globally occurring marine picocyanobacterium, the genus Synechococcus is an important player in oceanic primary production and global carbon cycling. In the complex marine environment, this widespread organism has evolved to successfully colonize and inhabit different environmental niches. Their biogeographic distribution suggests that Synechococcus ecotypes exhibit thermal niche preferences. Temperature is a key environmental variable and the elucidation of the temperature stress acclimation in members of this genus can shed light on the molecular mechanisms involved in their adaptive capability. The growth of four representative Synechococcus isolates of various ecotypes from tropical and temperate regions were monitored under various temperature conditions. This revealed drastic differences in growth rates in correlation with their thermal niche preferences. The temperate strains CC9311 and BL107 displayed higher growth rates at lower temperatures while tropical strains WH8102 and WH8109 grew better at higher temperatures. In order to further elucidate their thermal niche preference, the molecular factors influencing the temperature-related growth patterns were explored through global proteomic analysis of WH8102 and BL107. Whole cell lysates of the strains grown at different temperature conditions were fractionated using 1D SDS-PAGE and analysed using label-free quantitative proteomics. Protein identifications provided 27% and 40% coverage of the whole genome for WH8102 and BL107, respectively. Quantitation of protein expression revealed 22% and 20% of the identified proteins were differentially expressed in WH8102 and BL107, respectively. The results were further investigated using qRT-PCR and PAM fluorometry. Differential expression revealed that low temperature appeared to have a significant effect on the photosynthetic machinery. The light harvesting components, phycobilisomes exhibited a reduced expression which could be the result of protein degradation due to photo-oxidative damage and/or as a mechanism to restore the energy balance disturbed as a consequence of low temperature. The lowered phycobilisome expression is found to be a common low temperature-related response between the tropical and temperate isolates. Within the photosynthetic reaction centres, differences in the expression of some core proteins were observed between the two isolates. The expression of core proteins could correlate with the efficiency of repair mechanisms involved in the replacement of photo-damaged core proteins. This differential expression sheds light on the underlying factors which potentially influence the differences in the thermal ranges of tropical and temperate isolates.

Event Date: 
Wednesday, June 25, 2014 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Nitric oxide treatment for the control of reverse osmosis membrane biofouling

Abstract: 

Biofouling remains a key challenge for membrane based water treatment systems.  This study investigated the dispersal potential of the nitric oxide (NO) donor compound, PROLI NONOate, on single species biofilms formed by bacteria isolated from industrial membrane bioreactor and reverse osmosis (RO) membranes, as well as on mixed species biofilms.  The potential of PROLI NONOate to control RO membrane biofouling was also examined.  Confocal microscopy revealed that different bacteria responded differently to PROLI NONOate exposure.  However, the addition of NO induced dispersal in all but two of the bacteria tested and successfully reduced mixed species biofilms.  The addition of 40 µM PROLI NONOate at 24 h intervals to a laboratory-scale RO system led to a 92% reduction in the rate of biofouling (pressure rise over a given period) by a bacterial community cultured from an industrial RO membrane.  Confocal microscopy and EPS extraction revealed that PROLI NONOate treatment led to a 48% reduction in polysaccharides, a 66% reduction in proteins and a 29% reduction in microbial cells compared to the untreated control.  A reduction in biofilm surface coverage (59% vs. 98%, treated vs. control) and average thickness (20 µm vs. 26 µm, treated vs. control) was also observed.  The addition of PROLI NONOate led to a 22% increase in the time required for the RO module to reach its maximum TMP, further indicating that NO treatment delayed fouling.  Pyrosequencing analysis revealed that the NO treatment did not significantly alter the microbial community composition of the membrane biofilm.  These results present strong evidence for the application of PROLI NONOate for prevention of RO biofouling in an industrial setting.

Event Date: 
Wednesday, November 27, 2013 - 18:15 - 18:30
Institution: 
School of Civil and Environmental Engineering, UNSW
Title: 

Metal(loid) bioaccessibility dictates microbial community composition in acid sulfate soil horizons and sulfidic drain sediments

Abstract: 

 
Microbial community compositions were determined for three soil horizons and drain sediments within an anthropogenically-disturbed coastal acid sulfate landscape using 16S rRNA gene tagged 454 pyrosequencing.  Diversity analyses were problematic due to the high microbiological heterogeneity between each geochemical replicate.  Taxonomic analyses combined with measurements of metal(loid) bioaccessibility identified significant correlations to genera (5 % phylogenetic distance) abundances. A number of correlations between genera abundance and bioaccessible Al, Cr, Co, Cu, Mn, Ni, Zn, and As concentrations were observed, indicating that metal(loid) tolerance influences microbial community compositions in these types of landscapes.  Of note, Mn was highly bioaccessible (≤ 24 % total soil Mn); and Mn bioaccessibility positively correlated to Acidobacterium abundance, but negatively correlated to Holophaga abundance and two unidentified archaeal genera belonging to Crenarchaeota were also correlated to bioaccessible Mn concentrations, suggesting these genera can exploit Mn redox chemistry. 

Event Date: 
Wednesday, September 25, 2013 - 07:00 - 08:00
Institution: 
Helmholtz Centre for Groundwater Ecology, Munich, Germany
Title: 

Limiting factors for anaerobic aromatic hydrocarbon degradation in contaminated aquifers and oil reservoirs

Abstract: 

 
Biography

  • Rainer Meckenstock studied biology at University of Konstanz, Germany 1985-1990. He finished with a thesis in the group of Prof. Winfried Boss on microbial sugar transport systems (molecular microbiology). He did his PhD at the Swiss Federal Institute of Technology (ETH) in Zürich, Switzerland, with a thesis on biochemistry of light-harvesting complexes of phototrophic bacteria (1990-1993) in the Institute of Molecular Biology and Biophysics with Prof. Zuber. During his post-doc at the Swiss Federal Institute of Environmental Science andTechnology (EAWAG) in the group of Dr. van der Meer in Dübendorf, Switzerland, he developed molecular methods to monitor trichlorobenzene-degrading microorganisms and their degradation activities in the environment (PCR, RT/PCR, in situ hybridisation) (1993-1995). He changed to the investigation of anaerobic degradation of aromatic hydrocarbons in the Microbial Ecology Group of Prof. Bernhard Schink, University of Konstanz, Germany, in 1996. Here, he isolated novel anaerobic BTEX and PAH-degrading organisms and studied the degradation pathways. A new method to study microbial activities in the environment with analysis of stable isotope fractionation was developed. Since 2000 he changed to the Center of Applied Geosciences at the University of Tübingen, Germany, and set up a Geomicrobiology group within the Chair of Environmental Mineralogy (Prof. Stefan Haderlein). Research topics were the anaerobic degradation of mono- and polycyclic aromatic hydrocarbons (BTEX, PAH), isotope fractionation as a means to monitor biodegradation in contaminated groundwaters, limitations of natural attentuation, and the reduction of iron minerals as electron acceptor. Since July 2003, he became the director of the Institute of Hydrology at GSF which changed its name to Institute of Groundwater Ecology at the beginning of 2004. In 2007 he was appointed as a full professor for Groundwater Ecology at the Life Science Center (WZW) of the Technical University of Munich.
Event Date: 
Wednesday, June 26, 2013 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Towards a hexachlorobenzene bioreactor

Abstract: 

Hexachlorobenzene (HCB) is highly persistent environmental pollutant due to its chemical stability. It has been used in the production of rubber, as wood preserving agent and as pesticide and it is considered a possible human carcinogen.  HCB is particularly relevant in Australia, since it holds the largest HCB stockpile in the world (Botany Bay Industrial Park, NSW). So far only physic-chemical technologies have been applied for the destruction of HCB; however, these methods do not ensure full destruction and may lead to the generation of more harmful compounds, such as dioxins.  On the other hand, it is well known that obligate anaerobic bacteria are able to reductively dechlorinate HCB to less chlorinated congeners.  Therefore, a biological approach seems to be a more suitable and environmental friendly solution.

In this study we present a microbial community, taken from a site contaminated with chlorinated solvents, capable of reductively dechlorinating HCB and 1,2,4,5- Tetrachlorobenzene (TeCB). Cultures were established using acetate and H2 or lactate as carbon source and electron donor, respectively. 1,3- and 1,4- dichlorobenzenes were the main breakdown products in the cultures supplied  with 1, 2, 4, 5- TeCB, monochlorobenzene was also observed in a lower extent. Cultures with HCB only showed  1, 3, 5-Trichlorobenzene as breakdown product. Quantitative PCR, targeting Dehalococcoides´ 16S (a well-known dechlorinating bacterium) showed high abundance of this species in the cultures. 

Event Date: 
Wednesday, May 29, 2013 - 19:00 - 19:45
Institution: 
CSIRO
Title: 

Sediment Biobarriers for Chlorinated Aliphatic Hydrocarbons in Groundwater Reaching Surface Water

Abstract: 

 
This study explored the potential of eutrophic river sediments to attenuate the infiltration of chlorinated aliphatic hydrocarbon (CAH)-polluted groundwater discharging into the Zenne River near Brussels, Belgium. Active biotic reductive dechlorination of CAHs in the riverbed was suggested by a high dechlorination activity in batch- and column biodegradation tests performed with sediment samples, and by the detection of dechlorination products in sediment pore water. Halorespiring Dehalococcoides spp. were present in large numbers in the riverbed as shown by quantification of their 16S rRNA and reductive dehalogenase genes. By using DGGE-fingerprint analysis of relevant nucleic acid markers, it was shown that the Zenne River sediments were inhabited by a metabolically diverse bacterial community. A large diversity of sulfate-reducing bacteria, Geobacteraceae and methanogens, which potentially compete with halorespiring bacteria for electron resources, was identified. The high organic carbon level in the top of the riverbed, originating from organic matter deposition from the eutrophic surface water, resulted in a homogeneous microbial community structure that differed from the microbial community structure of the sediment underneath this layer. Monitoring of CAH concentrations and stable isotope ratios of the CAHs (δ13C) and the water (δ2H and δ18O), allowed to identify different biotic and abiotic CAH attenuation processes and to delineate their spatial distribution in the riverbed. Reductive dechlorination of the CAHs was the most widespread attenuation process, followed by dilution by unpolluted groundwater discharge and by surface water-mixing. During a 21-month period, the extent of reductive dechlorination ranged from 27 to 89% and differed spatially but was remarkably stable over time, whereas the extent of abiotic CAH attenuation ranged from 6 to 94%, showed large temporal variations, and was often the main process contributing to the reduction of CAH discharge into the river. Although CAHs were never detected in the surface water, CAHs were not completely removed from the discharging groundwater at specific locations in the riverbed with high groundwater influx rates. Therefore, it was concluded that an increase in the extent of biotransformation in the riverbed is needed for acceptance of the Zenne biobarrier as a viable remedial option for attenuation of discharging CAH-polluted groundwater.

Event Date: 
Wednesday, April 24, 2013 - 18:15 - 18:30
Institution: 
University of Western Sydney
Title: 

Comparative Analysis Of Saxitoxin-Producing And Non-Toxic Ecotypes Of Anabaena circinalis

Abstract: 

During bloom events, freshwater cyanobacteria often produce a variety of harmful toxins with devastating health, environmental and economic consequences. The paralytic shellfish toxins are a large group of neurotoxic alkaloids including saxitoxin (STX), which is the most potent identified to date. In Australia, STX production is strain dependent within the cyanobacterium Anabaena circinalis. The following study utilised two strains of cyanobacteria, A. circinalis AWQC131C (131C) and A. circinalis AWQC310F (310F), as model organisms; 131C is a saxitoxin-producer whilst 310F serves as a non-toxic control. We aimed to characterise 131C and 310F at the genomic and proteomic levels using genome sequencing and isobaric tags for relative and absolute quantitation (iTRAQ), respectively, in order to identify key differences in not only their secondary but, primary metabolic pathways.
 
Draft genome sequencing of 131C and 310F revealed a genome length of 4.4 Mbp and a GC content of 37%, and the number of encoded genes was predicted to be 4447 and 4443 for 131C and 310F, respectively. A scan of each genome revealed a total of 740 unique coding regions within 131C, and 651 within 310F. Interestingly, the proteomic profile of 131C was significantly different from 310F. Using iTRAQ, we found that under standard laboratory conditions, 131C was highly abundant in photosynthetic and metabolic proteins compared to the non-toxic control.  This suggests a high C:N ratio and intracellular 2-oxoglutarate concentration and may be a novel site for posttranslational regulation of STX. Overall, 131C is potentially a high energy ecotype likely to inhabit the water surface. Conversely, 310F was more abundant in molecular chaperones and proteins that neutralise reactive oxygen species, indicating activation of cellular stress response. Therefore, 310F seems to be experiencing cellular stress under laboratory conditions and in the environment, may inhabit low-light areas below the water surface.
 
In conclusion, this study has provided an insight into fundamental differences between the toxic 131C and non-toxic 310F strains of A. circinalis. These findings will provide a platform for future experiments and hopefully pave the way to identify the cellular function of STX.

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