Who’s doing what? A metaproteomic survey of Southern Ocean microbes near Antarctica.
The ocean around Antarctica is not just cold, it’s also dark for a large part of the winter. This means that carbon fixation by photosynthesis is inhibited during the polar winter. We used metaproteomics to reconstruct the ecology of microbes at the surface of the Southern Ocean near the Antarctic Peninsula, for both winter and summer seawater samples. Metagenomics (community genomics) tells us what kinds of genes are present. Metaproteomics goes a step further and determines which proteins (including enzymes) are actively being produced by microbes within a community. Therefore, we can use this approach to reconstruct microbial processes used for carbon fixation, nutrient acquisition, and other metabolic pathways. We found that ammonia-oxidising archaea were dominant at the Southern Ocean in winter, with the detected proteins indicating that they had a major role in ‘dark’ (light-independent) carbon fixation at the surface. In summer, by contrast, these autotrophic archaea were undetectable at the ocean surface, when photosynthesis by algae was the major route of carbon fixation. SAR11 bacteria (Pelagibacter spp.) were prevalent in both winter and summer, and detected proteins indicate that ATP-dependent uptake was important for the acquisition of nutrients by these heterotrophs, including simple organic compounds such as amino acids and taurine. Flavobacteria (especially Polaribacter) were more prevalent in summer, and the detected proteins show that these heterotrophic bacteria use exoenzymes to target complex biomolecules (polypeptides, polysaccharides) released from decaying algae. Overall, metaproteomics of the Southern Ocean surface has allowed us to identify the similarities and differences between winter and summer microbial communities, as well as which particular nutrients are being targeted by individual groups of bacteria and archaea.
Responses of soil fungi to global change: effects of elevated atmospheric CO2, temperature and drought
Fungi are central to forest carbon and nutrient cycles in Australian sclerophyll forest soils, but little is known about how they will respond to future global change. Our recent research has used a combination of controlled environment glasshouse and field experimentation to investigate the interactive effects of elevated atmospheric CO2 concentration [CO2], increased temperature and drought on Australian eucalypt soil fungal biodiversity.
In a glasshouse experiment, seedlings of two eucalypt species (Eucalyptus saligna and E. sideroxylon) were grown in field soil for 5 months under sub-ambient (290 µl l-1), ambient (400 µl l-1) and elevated (650 µl l-1) atmospheric CO2 conditions at both ambient (26°C) and elevated temperature (30°C). Multivariate analyses conducted on molecular data generated from soil and hyphal ingrowth bags (which select for mycorrhizal fungal mycelia) showed a significant (P < 0.035) separation between fungal communities associated with the two different tree species. While there was an effect of [CO2] and temperature, the response was plant species dependent with the exception of the combined elevated [CO2] and elevated temperature treatment (650 µl l-1 CO2 and 30oC) which clustered together regardless of tree species.
In the field experiment, E. saligna trees were grown in 12 whole tree chambers for three years under controlled temperature conditions and exposed to either ambient (ca. 380 µl l-1) or elevated (ca. 640 µl l-1) atmospheric [CO2] and different watering regimes to simulate drought. Multivariate analyses of molecular data showed that elevated [CO2] intensified the effect of drought stress by significantly altering fungal community composition.
Collectively, our data demonstrate that alterations to atmospheric [CO2], temperature and drought conditions modify soil fungal communities associated with Australian eucalypts. We are currently investigating the knock-on effects of these changes for fungal driven soil processes given the potential for soil microorganisms to significantly influence the direction and magnitude of terrestrial ecosystem/atmosphere feedbacks that regulate global change.
The JAMS rendezvous this October 31st took place in the fourth floor of the Museum with a magnificent view of Sydney, and began with an ad hoc presentation featuring sulphurous scents and sexy fangs. Katherina Petrou (UTS) initiated us in the science of the sulphur cycle in the oceans and how this process is dominated by the production of dimethylsulfoniopropionate (DMSP) by microalgae and its decomposition into dimethylsulphide (DMS), a strong odorous chemoattractant for a range of marine organisms. In tackling the mystery of how harmful algal blooms disappear, Katherina discovered that DMS produced by the dinoflagellate Alexandrium minutum (causative agent of toxic algal blooms) was the chemical cue for the infection of its parasitoid Parvilucifera sinerae. An elegant video illustrated how DMS at 300 nM was able to activate the parasitoid spores from a dormant state to leave the sporangium (an infected A. minutum cell) in transit to infect other cells and propagate. Activation only occurred in the range of 30 to 300 nM indicating that the effect was dependent on cell density. Thus, Katherina’s work showed that DMS plays an important role in the biological control of toxic algal blooms in the oceans. Her results contribute to the better understanding of marine chemical ecology.
Does Acinetobacter baumannii have an O antigen?
Acinetobacter baumannii is amongst the most troublesome Gram-negative pathogens worldwide, due to strains that are resistant to multiple antibiotics, disinfection and periods of desiccation. Little is known about the virulence mechanisms, though a role for capsule has been demonstrated. Previous analysis of A. baumannii genome sequences identified a region of extensive diversity presumed to be involved in the synthesis of a surface polysaccharide, variously identified as O-antigen or capsule. We used bioinformatic tools to assess whether this polysaccharide is exported as capsule, or ligated to a lipid A-core oligosaccharide moiety to become the O antigen moiety of lipopolysaccharide. A gene for O-antigen ligase was not found, and we propose that A. baumannii strains produce a capsule (and lipid A-core oligosaccharide), but no lipopolysaccharide. 9 capsule types and 3 core types were found in the 10 completed genomes and more in draft genomes. Multiple capsule types were found in members of the 2 major clonal complexes, and this variation may contribute to the success of the A. baumannii clones by factoring in the evasion of the host immune response.
Microbial methane formation and oxidation in abandoned coal mines
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.
JAMS Monthly Meeting Report 29th August 2012
Prepared by Mike Manefield
Though faced with a depleted audience owing to strong attendance of JAMS members at the 14th International Symposium on Microbial Ecology in Copenhagen, Denmark, speakers Dr Oliver Morton, Ms Jazmin Oszvar and Ms Zoe-Joy Newby gave three entertaining and informative presentations with JAMS trademark diversity of subject.
Oliver kicked off with confessions of a clinical microbiologist in his presentation entitled ‘Beware the mulch! Adaptation to its natural habitat makes Aspergillus fumigatus a formidable human pathogen’. The presentation illustrated violent interactions between germinating Aspergillus spores and human dendritic cells including a stunning transcriptomics analysis of the response of Aspergillus fumigatus to the presence of human immature dendritic cells over time.
Prepared by Valentina Wong (UNSW PhD student)
On a cold Tuesday night, Adrian Low from University of New South Wales warmed the JAMS audience with his passion on bioremediation of organochlorine contaminated groundwater. Adrian described the discovery of Australia’s first 1,2-dichloroethane (DCA) degrading consortium, AusDCA. His work in the field demonstrated the efficacy and sustainability of using organochlorine respiring bacteria to remediate organochlorine contaminants in situ. He plans to isolate the bacterial species responsible for performing this unique task.