Biology

Event Date: 
Wednesday, March 26, 2014 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Insights into the stress response of the biomining bacterium Acidithiobacillus ferrooxidans using gene expression and proteomic analysis

Abstract: 

Bioleaching is a simple and effective process used for metal extraction from low grade ores and mineral concentrates using microorganisms. The extraction of some metals such as copper from low grade ore is becoming necessary because of gradual depletion of high grade ore. The traditional methods used for extraction of copper are either Pyrometallurgy or Hydrometallurgy. However both the methods are not environmental friendly. There are many techniques proposed to extract metals but these are not practically suitable, as these requires a very high energy input as well as most of them creates environmental pollution problem, that also rises the cost of environmental protection throughout the world. Therefore, bioleaching is recognizable as the most environmentally friendly method of separating metals since it requires less energy and it reduces the amount of greenhouse gasses released to the atmosphere. Bioleaching is also a fairly simple process that does not require a lot of expertise to operate or complicated machinery.
The most commonly used bacterium in bioleaching is Acidithiobacillus ferrooxidans (former Thiobacillus ferrooxidans) and this is due to its capacity to oxidize metal sulphides. A. ferroxidans is a chemolithotrophic bacterium capable of utilizing ferrous iron or reduced sulphur compounds as the sole source of energy for its growth. It thrives optimally around pH 2.0 and 30ºC. During Bioleaching process, A. ferrooxidans is often subject to changes in the ideal growth pH and temperature, and to nutrients starvation. These changes can affect the bacterial physiology and as a consequence, the efficiency of bioleaching. Then, the stress response of this bacterium subject to heat stress and phosphate starvation has been investigated using different approaches, namely, gene expression and proteomic analysis, Fourier transform infrared spectroscopy (FT-IR), as well as morphological analysis by scanning electron microscopy (SEM).
The results showed that under the tested stress conditions A. ferrooxidans cells suffer elongation, a common stress response in bacteria. Alterations in carbohydrates, phospholipids and phosphoproteins were detected by FT-IR. By proteomic analyses (2-DE and tandem mass spectrometry), many differentially expressed protein spots were visualized and identified as proteins belonging to 11 different functional categories. Indeed, the up-regulated proteins were mainly from the protein fate category. Real time quantitative PCR was employed to analyze changes in the expression patterns of heat shock genes, as well as many other genes encoding proteins related to several functional categories in A. ferrooxidans. Cells were submitted to long-term growth and to heat shock, both at 40°C. The results evidenced that heat shock affected the expression levels of most genes while long-term growth at 40°C caused minimal changes in gene expression patterns – with exception of some iron transport related genes, which were strongly down-regulated. Further bioinformatic analysis indicated a putative transcriptional regulation, by the σ32 factor, in most heat-affected genes. These results evidence that A. ferrooxidans has an efficient range of stress-responses, which explains its ability for biotechnological purposes.
 

Event Date: 
Wednesday, January 29, 2014 - 18:00 - 18:15
Institution: 
UC Davis
Title: 

Hi-C Metagenomics: Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Abstract: 

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a synthetic metagenome sample to accurately cluster metagenome assembly contigs into a small number of groups that differentiated the genomes of each species. The Hi-C data also associated plasmids with the chromosomes of their host and with each other orders of magnitude more frequently than to other species. We further demonstrated that Hi-C data is highly informative for resolving strain-specific genes and nucleotide substitutions between two closely related E. coli strains, K12 DH10B and BL21 (DE3), indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This application of Hi-C has the potential to provide new perspective in the study of thefine-scale population structure of microbes, how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities, and the genetic architecture ofheterogeneous tumor clone populations.

Event Date: 
Wednesday, January 29, 2014 - 19:00 - 20:00
Institution: 
Royal Botanic Gardens and Domain Trust, Sydney
Title: 

Fusarium: diseases, toxins and evolution

Abstract: 

The fungal genus Fusarium contains some of the most economically and socially important species of plant pathogens affecting agriculture and horticulture.  It also contains numerous species that are important mycotoxin producers and some that are increasing in importance as pathogens of humans.  Some of these diseases, such as head blight of wheat and Fusarium wilt of bananas, are amongst the most important diseases of these hosts and have not only caused enormous losses in production around the world but have also had a huge impact on the communities that depend on these crops.  The genus is a complex, polyphyletic grouping whose taxonomy has always been controversial with species numbers ranging from over a 1000 at the beginning of the 1900s, down to 9 in the 1950s and ’60s and currently anything from nearly 100 to 500. This talk will provide an overview of Fusarium, its phylogeny and biogeography and the mechanisms involved in the evolution of pathogenicity.

Event Date: 
Wednesday, February 26, 2014 - 15:45 - 16:15
Institution: 
University of Perugia, Italy
Title: 

The intricate cross-talk of the microbiome in Resistance and Tolerance to pathogens

Abstract: 

The diverse microbial population characterizing the human host represents the result of different complex scenarios impacting the human microbiome assembly. The variety of the microbial species involved plays an important role on the human health by affecting the tissue differentiation, the modulation of the immune system as well as the general response against infectious pathogens, which has been recently revised and divided into two different strategies named Resistance and Tolerance. Resistance being the strategy where the host protects himself by reducing the pathogen load whereby the Tolerance being the opposite strategy, which consists in tolerating the pathogen to avoid tissue damage due to the occurrence of subsequent inflammatory pathologies. The host microbiome seems to play a crucial role in determining which strategy the host will exploit to avoid infection. We recently found that highly adaptive lactobacilli, switching from sugar to Tryptophan (Trp) as an energy source  are expanded and produce an aryl hydrocarbon receptor (AhR) ligand—indole-3-aldehyde—that contributes to AhR-dependent IL-22 transcription, which then trigger the release of antimicrobial peptides by the gut epithelium. Importantly, innate lymphocytes IL-22 producers were already described as a typical innate Resistance strategy to protect the host from intragastrical Candida albicans infections in mice. Thus, the resulting IL-22-dependent balanced mucosal response allows for survival of mixed microbial communities yet provides colonization resistance to the fungus Candida albicans. Therefore, the microbiota-AhR axis might represent an important strategy pursued by co-evolutive commensalism for fine-tuning host mucosal reactivity contingent on Trp catabolism.

Event Date: 
Wednesday, February 26, 2014 - 15:15 - 15:45
Institution: 
Singapore Centre on Environmental Life Sciences Engineering
Title: 

Dissecting Structure-Function Relationships In Complex Microbial Communities Using Perturbation Transcriptomics

Abstract: 

Application of ‘omics technologies, including high-throughput nucleic acid sequencing and advanced mass spectrometry, show huge potential to increase our understanding of bioprocesses occurring in both natural and engineering microbial ecosystems. Field studies of such systems are inherently complicated, while laboratory reactor models involve extensive community modifications following inoculation and may not accurately reflect the biology of the source community. Here we develop a complementary approach to dissecting structure-function relationships of complex microbial communities, by applying experimental perturbations to freshly sourced, intact communities in a controlled fashion. In an investigation examining nitrogen transformation in wastewater treatment, we use metatranscriptomics in a time series design (n=20 samples) to study changes associated with onset of oxygenation. This stimulus switches the community between de-nitrification and nitrification phases of the nitrogen cycle, thus modeling a key aspect of wastewater process control. This model permits identification of functional genes, in both known and previously unknown taxa, and represents a readily adaptable model studying structure-function relationships in microbial communities. If time permits, I will discuss how this perturbation metatranscriptomics approach has implications for improving our ability to perform metagenome assembly.

Event Date: 
Monday, February 24, 2014 - 09:30 - Tuesday, February 25, 2014 - 17:00

 

Registration Closed

24-25 February 2014
The Australian Museum

Microbiology is undergoing a revolution bought about by advances in next-generation DNA sequencing technology.  Researchers are now required to understand an array of bioinformatics principles and tools to interpret the vast amounts of data being generated. Presented by leading Australian researchers, TOAST is a 2-day event aimed at postgraduate students and early career postdocs providing in-depth tutorials encompassing concepts and software available to molecular microbiologists and microbial ecologists including:

Another great JAMS evening at the Australian Museum. Nicolas Barraud from UNSW kicked off with a biotechnology story about the use of nitric oxide in biofilm control. John-Sebastien Eden from Eddie Holmes group at USyd gave us the low down on norovirus evolution using the Sydney 2012 strain (the chunder from downunder) as a case study. Somehow our two 15 min presentations consumed an hour so starting back late after the break JAMS co-founder Prof Andrew Holmes gave an excellent presentation on what shapes microbial communities in the the gut. Despite the late start Andy had the audience glued to their seats with a showcase of technology used to unravel human-gut microbiome interactions.

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. 

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