Methane

Event Date: 
Wednesday, June 24, 2015 - 18:00 - 18:45
Institution: 
University of Western Australia
Title: 

Microbial life in Movile Cave – an unusual cave ecosystem

Abstract: 

Movile Cave (Mangalia, Romania) is a unique cave ecosystem sustained by in situ chemoautotrophic primary production, analogous to deep-sea hydrothermal vents. The cave has been cut-off from the surface for the past 5.5 million years with the primary energy source coming mainly from hydrogen sulfide and methane released from the thermal fluids. Invertebrates, many of which are endemic to Movile Cave, are isotopically lighter in both carbon and nitrogen than surface organisms, indicating that chemoautotrophic primary production, primarily driven by methane and sulfur oxidizing microorganisms, occurs in the cave. In this talk, I will present our recent work on the microbiology of the Movile Cave ecosystem, with particular emphasis on functional diversity of Bacteria involved in aerobic one-carbon (methane and methylated amine) metabolism. Insights from metagenomic and genomic sequence analyses of the microbial community and isolates, respectively, will be discussed in detail.

Event Date: 
Wednesday, February 25, 2015 - 15:00 - 15:30
Institution: 
University of East Anglia
Title: 

Bacterial metabolism of isoprene

Abstract: 

Isoprene (methyl isobutene), is a climate-active volatile organic compound that is released into the atmosphere in similar quantities to that of methane, making it one of the most abundant trace volatiles. Large amounts of isoprene are produced by trees but also substantial amounts are released by microorganisms. The consequences on climate are complex. Isoprene can indirectly act as a global warming gas but in the marine environment it is also thought to promote aerosol formation, thus promoting cooling through increased cloud formation. We have been studying bacteria that grow on isoprene. These aerobic bacteria appear to be widespread in the terrestrial and marine environment. Rhodococcus AD45, our model organism, oxidizes isoprene using a soluble diiron centre monooxygenase which is similar to soluble methane monooxygenase. The physiology, biochemistry and molecular biology of Rhodococcus AD45 will be described, together with genome analysis, transcriptome analysis and regulatory mechanisms of isoprene degradation by bacteria. The ecology of isoprene degraders in both the terrestrial and marine environment will be described, together with DNA-Stable Isotope Probing experiments which have enabled us to identify active isoprene degraders in the environment.

Event Date: 
Wednesday, September 26, 2012 - 19:00 - 20:00
Institution: 
University of New South Wales
Title: 

Microbial methane formation and oxidation in abandoned coal mines

Abstract: 

 
Worldwide, mine gas is being used increasingly for heat and power production. About 7% of the annual methane emissions originate from coal mining. In abandoned coal mines, stable carbon and hydrogen isotopic signatures of methane indicate a mixed thermogenic and biogenic origin. The thermogenic methane is a reminder of geological processes, but its biogenic formation is still going on. Besides hard coal, possible sources for methane are large amounts of mine timber left behind after the end of mining.
Methanogenic archaea are responsible for the production of substantial amounts of methane. Mine timber and hard coal showed an in situ production of methane with isotopic signatures similar to those of the methane in the mine atmosphere. Long-term incubations of coal and timber as sole carbon sources formed methane over a period of 9 months. We directly unraveled the active methanogens mediating the methane release as well as the active bacteria potentially involved in the trophic network. Furthermore, we proved the presence of an active methanotrophic community. Directed by the methane production and oxidation, respectively, samples for DNA stable-isotope probing (SIP) coupled to subsequent quantitative PCR and DGGE analyses were taken from long term incubations over 6 months. The stable-isotope-labeled precursors of methane, [13C]acetate and H2-13CO2, and 13CH4 were fed to liquid cultures from hard coal and mine timber. Predominantly acetoclastic methanogenesis was stimulated in enrichments containing acetate and H2+CO2. The H2+CO2 was mainly used by acetogens similar to Pelobacter acetylenicus and Clostridium species forming acetate as intermediate and providing it to the methanogens. Active methanogens, closely affiliated to Methanosarcina barkeri, utilized the readily available acetate rather than the thermodynamical more favourable hydrogen. Furthermore, the activity of a distinct methane-oxidizing community is predominated of a member belonging to the type I methanotrophs similar to Methylobacter marinus that assimilated 13CH4 nearly exclusively. Thus, active methanotrophic bacteria are associated with the methanogenic microbial community that is highly adapted to the low H2 conditions found in the coal mines with acetate as the main precursor of the biogenic methane.

Event Date: 
Wednesday, August 29, 2012 - 18:15 - 18:30
Institution: 
University of Sydney
Title: 

What is the substrate of the sMMO-like genes of Mycobacterium strain NBB4?

Abstract: 

Monooxygenase (MO) enzymes are important for biogeochemistry, biocatalysis and bioremediation. In microbes, MOs are best known as the catalysts for methane oxidation, which is a process of immense importance for the global carbon cycle and for influencing climate change. Mycobacterium strain NBB4, an ethene-oxidising isolate from estuarine sediment, contains a diverse array of MO genes, including homologs of the particulate and soluble methane MOs (pMMO/sMMO), cytochrome p450's, and an ethene MO. We have previously shown that NBB4 can biodegrade several chlorinated pollutants, and that the pMMO homolog is actually an ethane/propane/butane MO. The function of the sMMO homolog in NBB4 (genes designated smoXYBCZ) is currently unknown. This gene cluster has only low identity to sMMO, and methane is not a substrate for growth of NBB4. The aim of this Honours project is to identify the substrate of this novel MO via knockout and heterologous expression experiments. Our hypothesis is that smoXYBCZ acts in the second step of the butane oxidation pathway to convert butanol to butanediol.

Event Date: 
Wednesday, June 27, 2012 - 18:15 - 18:30
Institution: 
University of Western Sydney
Title: 

The Taguchi methods, or how to quickly and efficiently optimise PCR conditions.

Abstract: 

Originally, the Taguchi methods were formulated for the optimisation of industrial processes, where several factors (3 to 50) of complex multifactorial experiments were tested at different levels (Taguchi, 1986). The Taguchi methods use orthogonal arrays to organise the ‘control’ parameters/factors affecting a process and the levels at which they should vary. A particular algorithm (quadratic loss function) is then applied in order to predict the optimum conditions of a process, whilst accounting for performance variations due to ‘noise’ factors beyond the control of the design. In a normal factorial strategy, every parameter should be individually tested at several levels, thus becoming extremely time-consuming, labour-intensive and expensive. The Taguchi methodology allows for testing only a few combinations, therefore dramatically decreasing the total number of experiments and simultaneously identifying the optimum condition of several factors.
Because some functional genes are present only in small fractions of microbial communities, and only few copies can be present in each genome, their detection by classical PCR methods can be challenging. Optimisation of the experimental conditions of a PCR includes the different components of the reaction mix (concentrations of salt, primers, enzyme, DNA template, etc.) as well as the cycling features (time and temperature of the denaturation, annealing and extension steps, number of cycles, etc.). We used this approach for the optimisation of the detection by PCR of functional genes of non-cultivable microorganisms present in environmental samples. In particular, we tested the different parameters involved in a (touchdown/nested) PCR and estimated the optimum settings for the detection of the functional gene pmoA, coding for the putative active site of the particulate methane monooxygenase, involved in the oxidation of methane by methanotrophic bacteria. The application of the Taguchi method allowed the suppression of a nesting step and thus a significant reduction in the amplification time, as well as reagent cost.
 

Event Date: 
Wednesday, February 29, 2012 - 18:30 - 19:00
Institution: 
CSIRO Livestock Industries, St. Lucia, Australia
Title: 

Differences downunder: macropodids, methane and metagenomics.

Abstract: 

The agricultural sector accounts for a large amount of Australia’s greenhouse gas emissions, and strategies that reduce the production and (or) release of methane from ruminant livestock has resurfaced as a viable research topic. While there has been a relatively intense focus on better understanding how rumen microbiology, nutrition and (or) animal genetics might be targeted and productively altered to reduce these emissions; less attention has been directed towards the comparative study of those native Australian herbivores thought to produce small amounts of methane during feed digestion. These animals include the Australian macropodids (kangaroos and wallabies), which have evolved to retain a foregut microbiota that effectively converts plant biomass into nutrients for the host animal; and appears to do so with much less methane emitted. Our research group in Brisbane has used metagenomics approaches with a view to characterize the foregut microbiota of the Tammar wallaby (Macropus eugenii). There is a reduced number of methanogenic archaea resident in the macropodid foregut compared to ruminants, but the species present appear to have some unique attributes relative to their counterparts from other environments. We have also used a combination of metagenomic data and cultivation-based methods to identify and isolate several “new” bacteria that support feed digestion and fermentation schemes consistent with a low methane emitting phenotype. The structure-function relationships inherent to these interesting gut microbiomes warrant further investigation.

Event Date: 
Wednesday, June 29, 2011 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Metabolic methanisation of chloroform by a three component microbial community.

Abstract: 

Chloroform is a highly toxic organochlorine found in subsurface environments due to its poor handling and disposal techniques by industry. Bioremediation of organochlorine polluted environments is a well established technique that utilises dehalogenating bacteria to reductively dechlorinate organochlorines to their hydrocarbon counterpart. One drawback of bioremediation is that chloroform is inhibitory to this microbial process. A key to the advancement of the bioremediation industry is the discovery of dahalogenating bacteria capable of complete chloroform metabolism.

Here we report for the first time a microbial population capable of rapid metabolic transformation of chloroform at high concentrations (~50 ppm) to methane. Cultures were established with sediment sampled 4.5 m below ground surface from an aquifer polluted for over 40 years with a mixture of organochlorine compounds. A combination of functional data, pyrosequencing, quantitative PCR and the application of labelled substrates were used to elucidate the participating microbial community members. Members of the Dehalobacter genus were found to first dehalo-respire chloroform to dichloromethane which was then fermented to formate and acetate. A hydrogenotrophic syntroph (i.e. a methanogen) was then required to drive this process forward to methane.

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