Environmental microbiology



The Centre for Systems Genomics is holding a 1-day symposium on metagenomics and microbiome research, Tuesday November 17 at Bio21. 

Interested in presenting? Register now! and complete the abstract section.

This free event will feature talks on a range of microbiome-related topics including new computational and lab methods, covering a range of application areas including the human microbiome in health and disease, environmental metagenomics, ecology, agriculture and ancient DNA.

Event Date: 
Wednesday, February 25, 2015 - 17:30 - 18:00
Institution: 
University of Melbourne
Title: 

Genomic epidemiology of antibiotic resistant bacteria

Abstract: 

Microbial populations contribute to human disease in a variety of ways, both as agents of infection and as healthy components of the microbiome. Genomic approaches can offer deep insights into this hidden microbial world, including revealing the composition of microbial communities, tracking the movement of individual organisms, and illuminating evolutionary changes. Here I will present recent work applying genomic epidemiology to investigate the emergence and spread of antibiotic resistance in a range of important pathogens, including typhoid, dysentery and the emerging hospital superbug Klebsiella.

Event Date: 
Wednesday, February 25, 2015 - 17:00 - 17:30
Institution: 
University of Southern Maine
Title: 

Prochlorococcus: the “invisible forest” in the ocean’s Outback.

Abstract: 

The smallest, most abundant phototroph in the world, Prochlorococcus, dominates the base of the food web in the “Outback” of the world’s oceans, the nutrient-depleted ocean gyres. This unicellular, marine cyanobacterium, unknown only 30 years ago, is an oligotrophic specialist with a streamlined genome and reduced cellular requirement for the limited resources available in this environment. Based on physiological and molecular analyses of isolated strains from different oceans and depths, two broad groupings of Prochlorococcus were characterized: high- and low-light adapted “ecotypes”. Within these broad groupings are many subclades, some of which have been shown to dominate under certain temperature and light conditions. Through additional culture-based studies, my lab has been exploring nutrient physiology and other physiological characteristics that may contribute to the ecology and evolution of other Prochlorococcus subgroups. Some subgroups have the capacity to utilize nitrate, which was not the case for the initial isolates of Prochlorococcus, and others differ in their pigmentation. We have also found that Prochlorococcus regulates its uptake velocity and specific affinity for inorganic and organic phosphorus under P stress conditions. Examining the physiology, ecology and genomics of Prochlorococcus isolates and natural populations is providing insights into how these tiny photosynthesizing cells create a stable, yet invisible forest in the deserts of the world’s oceans.

Event Date: 
Wednesday, June 25, 2014 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Biomes of Australian Soil Environments (BASE)

Abstract: 

The Biomes of Australian Soil Environments (BASE) is a soil microbial diversity database faciliatated by Bioplatforms Australia and currently involving 14 Australian agencies. The BASE project is collecting biodiversity data from Australian soils in the form of amplicon sequences and amplication free metagenomic sequences. Sequence data is accompanied by rich contextual data describing soil physical and chemical attributes, land use, overlying vegetation and climate. All information collected is made publicly available via the BASE database. Thus far BASE has collected approximately 900 samples, with data from over 400 of these being currently available. I will briefly introduce the BASE project and its newly deployed database by describing the sampling and sequencing protocols and demonstrating the databases search capabilities.

Event Date: 
Wednesday, March 26, 2014 - 18:15 - 18:30
Institution: 
Radboud University Nijmegen, Netherlands
Title: 

The gut microbiome of phytopathogenic root fly larvae: insights into the detoxification of plant secondary metabolites by insect-associated microbes

Abstract: 

Plants of the genus Brassica produce various toxic compounds such as isothiocyanates in response to herbivore damage. Despite their toxicity, some insects can cope well with these compounds. One example is the larva of the cabbage root fly (Delia radicum) which is a serious agricultural pest. The mechanism by which these root feeding insects detoxify isothiocyanates is not explored. Our hypothesis is that microorganisms residing in the gut contain enzymes that break down the isothiocyanates and are thus crucial for survival of the root fly larvae. We substantiated this hypothesis by metagenome studies of the microbial gut community. Combined with functional screens of isolated gut microbes these analyses indicated that indeed the gut microbiota plays a vital role in the breakdown of isothiocyanates. Some genes encoding proteins that are involved in this process have already been identified. Ongoing genome and transcriptome studies of isolated gut microbes will enable us to find new candidate genes encoding proteins used for isothiocyanate breakdown that will subsequently be functionally characterized. This will lead to an in-depth understanding of the role of microbes in the plant secondary metabolite – insect interaction.

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, 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:

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