February 2016

Event Date: 
Wednesday, March 16, 2016 - 15:00 - 15:30
Institution: 
Australian Centre for Ecogenomics, University of Queensland
Title: 

Whoever smelt it, dealt it: a metagenomic view of the seedy underworld of microbial methane cycling

Abstract: 

Over the last decade, metagenomics has changed the face of microbial ecology. Metagenomics bypasses traditional culture-dependent approaches and holds the promise of genome-level insights into the mostly uncharted microbial world. However, for most environments it was not possible to obtain genomes from these data because the complexity of the microbial communities under consideration and limited throughput of the sequencing technology precluded assembly. The primary way to extract biologically meaningful information from these largely unassembled datasets was to use “gene-centric” approaches that explored the distribution and abundance of genes and gene families between different environments. However, recent advances in high-throughput sequencing and development of new tools for analyzing metagenomic data are driving the evolution of this field.
 
Anaerobic archaea are major contributors to global methane cycling. Methanogenic archaea are estimated to produce one billion tons of methane per year with an equal amount estimated to be oxidized by archaeal methanotrophs. All previously described archaeal methane metabolizing microorganisms belong to the phylum Euryarchaeota and share a core set of bidirectional enzymes responsible for their respective metabolisms. This restricted phylogenetic distribution has led to the hypothesis that archaeal methane metabolism originated within the Euryarchaeota, although an origin outside this phylum has also been proposed. My research team is applying metagenomic techniques to recover a large number of archaeal genomes from many previously uncultivated archaeal lineages and from increasingly complex environments. This has greatly expanded our understanding of the metabolic capabilities of these lineages and changing our understanding of the diversity and evolution of microorganisms involved in methane cycling.
 
Biography
Associate Professor Gene Tyson is a microbial ecologist whose research applies culture-independent molecular approaches to understand the structure and function of microbial communities in the environment. During Gene’s dissertation research (University of California, Berkeley) he was the lead author on one of the first studies to use metagenomics. In this work he investigated the metabolic potential and population diversity of microbial communities involved in acid mine drainage (AMD) generation, and demonstrated, for the first time, that metagenomic data could be used to reconstruct near complete genomes directly from environmental samples.
Associate Professor Tyson’s group at the University of Queensland, is now using the metagenomic and metatranscriptomic approaches he helped pioneer, to investigate microbial communities in a wide range of different communities in both engineered systems and natural environments. His group is continuing to develop new ways to analyze omic data by leading efforts in error correction for high-throughput sequencing platforms, single cell sequencing and deep spatio-temporal metagenomics

Event Date: 
Wednesday, March 16, 2016 - 15:30 - 16:00
Institution: 
Nordic Centre for Earth Evolution, University of Southern Denmark
Title: 

Electric interspecies cooperations

Abstract: 

The electroactive properties of microorganisms are poorly understood, like the ability of certain bacteria to donate electrons to electrodes (electrogens) or to retrieve electrons from electrodes (electrotrophs). Recently, we have learned that certain electrogenic and electrotrophic microogranisms establish an unusual type of microbial interactions via direct electric contact. During direct interspecies electron transfer (DIET) an electrogenic Geobacter, utilizes ethanol only in the presence of cytochrome-containing methanogens (Methanosarcinales), but not with non- cytochrome containing methanogens. The interaction between Geobacter and Methanosarcinales relies on an extracellular network of pili and cytochromes. The same extracellular network of pili and cytochromes was many times implicated in interactions between Geobacter and solid electron acceptors such as electrodes or iron oxides.
On the other hand, the natural manifestation of DIET associations remains mysterious. One case, of a DIET driven process, is the treatment of brewery waste in 24 UASB reactors in the United States. Geobacter and Methanosaeta essentially dominated the granules in these UASB reactors. However DIET syntrophy is not a common trait in UASB reactor granules worldwide. Moreover, we still do not know what other environments are accommodating DIET, rather than H2/formate-transfer. Thus, we recently started investigating if DIET could drive methanogenesis in natural systems, and discovered supporting evidence for DIET driven methanogenesis in iron rich aquatic sediments. More importantly, we are now investigating what drives direct electron uptake in methanogens, which is of significance for future’s biorefineries, recycling of materials and storage of excess renewable electricity. 

 
Biography
I’m a recently appointed Assistant Prof. at the University of Southern Denmark. In my research group we are searching for solutions to harness microbial metabolism in order to produce fossil fuel free renewable resources and control harmful microbial processes.

Previously, I worked as a postdoc on direct interspecies interactions at the University of Massachusetts Amherst, and biorecovery of rare metals from waste at the University of Aarhus. I did my PhD at the Max Planck Institute for Marine Microbiology in Bremen, Germany – studying anaerobic biodegradation of hydrocarbons. Part of my PhD was dedicated to syntrophic interactions - topic which I’m still exploring today. 

 

Event Date: 
Wednesday, March 16, 2016 - 16:00 - 16:30
Institution: 
School of Chemistry and Molecular Biosciences, University of Queensland
Title: 

Molecular characterisation of a globally disseminated multidrug resistant E. coli clone

Abstract: 

Many multidrug resistant (MDR) bacterial strains are now
recognized as belonging to clones that originate in a specific locale,
country or even globally. Escherichia coli sequence type 131 (ST131) is
one such recently emerged and globally disseminated MDR pandemic clone
responsible for community and hospital acquired urinary tract and
bloodstream infections. E. coli ST131 was identified in 2008 as a major
clone linked to the spread of the CTX-M-15 extended-spectrum β-lactamase
(ESBL)-resistance. Since then, E. coli ST131 has also been strongly
associated with fluoroquinolone resistance, as well as co-resistance to
aminoglycosides and trimethoprim-sulfamethoxazole. In
this seminar, I will discuss our recent work on the molecular
characterisation of E. coli ST131, including the use of genome sequencing
to demonstrate its rapid and recent global dispersal and the development
of a high-throughput transposon mutagenesis system in combination with
transposon directed insertion-site sequencing (TraDIS) to define different
virulence properties.
 
Biography
Professor Mark Schembri is an NHMRC Senior Research Fellow in
the School of Chemistry and Molecular Biosciences at the University of
Queensland. He is also Deputy Director of the Australian Infectious
Diseases Research Centre. His specialist interest is in the area of
uropathogenic E. coli, with a focus on the global epidemiology of
multidrug resistant clones and the molecular genetics of virulence factors
associated with infection of the urinary tract. Professor Schembri has
published >160 papers and his research has been cited >6000 times.
 

Event Date: 
Wednesday, March 16, 2016 - 16:30 - 17:00
Institution: 
Microbial Oceanography, University of Technology Sydney
Title: 

Molecular mechanisms of resistance of opportunistic pathogens to predation by heterotrophic protists

Abstract: 

Protozoan predation is one of the main biological factors constraining bacterial growth in aquatic environments, and the long history of coevolution of predator and prey has led to a wide range of defensive mechanisms that protect the bacteria from predation.  These mechanisms may also function as virulence factors in infection of animal and human hosts, thus leading to a pathogenic lifestyle.
This talk will give two examples of the molecular mechanisms regulating the resistance of Vibrio cholerae to predation.  These studies support the Coincidental Evolution hypothesis that states that factors expressed by pathogenic bacteria that are responsible for virulence, may have evolved for some purpose other than virulence to the host, i.e. virulence is a result of selection acting on the pathogen in a different environmental niche.  We are currently trying to understand how predation pressure affects the evolution and expression of factors related to virulence.  Understanding bacteria-protozoa interactions has wide implications for our understanding of microbial responses involved in formation of multicellular bacterial consortia, biofilm persistence in the environment and the host, and the evolution of defence mechanisms of sessile microorganisms.

Event Date: 
Wednesday, March 16, 2016 - 17:00 - 17:30
Institution: 
Microbial Oceanography, University of California Santa Cruz
Title: 

Unusual marine nitrogen-fixing symbiosis: implications for evolution and global nitrogen fixation

Abstract: 

 
Biography
Dr. Zehr is a Professor of Ocean Sciences at the University of California, Santa Cruz. He received his B.S in Biology from Western Washington University in 1981 and his Ph.D in Ecology from the University of California, Davis, in 1985. Dr. Zehr did postdoctoral work in nitrogen cycling at the State University of New York, Stony Brook and Brookhaven National Laboratory, and in molecular biology at New England Biolabs, Inc. in Beverly, Massachusetts. He joined the faculty of Biology at Rensselaer Polytechnic Institute in 1992. In 1999, Dr. Zehr began his current position as Professor of Ocean Sciences at the University of California. He was elected Fellow of the Academy of Microbiology in 2009. His research has focused on nitrogen cycling by aquatic microorganisms, although he has publications spanning topics in microbial diversity in freshwater and hypersaline systems, organic matter metabolism, selenium metabolism in estuarine sediments, and nitrogen metabolism in oligotrophic oceans. His major focus is oceanic nitrogen fixation. Dr. Zehr is the Editor-in-Chief for “Frontiers in Aquatic Microbiogy”.