Microbiology

Event Date: 
Wednesday, October 28, 2015 - 18:15 - 18:30
Institution: 
UTS
Title: 

Heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation

Abstract: 

Australia’s tropical waters represent predicted “hotspots” for nitrogen (N2) fixation based on empirical and modelled data. However, the identity, activity and ecology of N2 fixing bacteria (diazotrophs) within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size fractionated N2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (∂-proteobacteria and gamma-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N2 fixation rates ranged from < 1 to 91 nmol L-1 d-1, and size fractionation indicated that unicellular organisms dominated N2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than spring. Relative abundances of UCYN-A1 and gamma-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia’s tropical waters are indeed hotspots for N2 fixation, and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.

Event Date: 
Wednesday, October 28, 2015 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Key to living in the extreme desert soils of eastern Antarctica: a chemolithotrophic lifestyle

Abstract: 

Mitchell Peninsula is located at the south of the Windmill Islands, Eastern Antarctica. It is described as a nutrient poor, extreme polar desert and limited knowledge on the microbial diversity of  the soils in this area exists. We examined the microbial taxonomic composition and metabolic potential of Mitchell Peninsula soils  using 16S metagenomics and shotgun metagenomics. We found the site to be a potential biodiversity hotspot, containing a high abundance of Candidate Phyla WPS2 and AD3. Subsequently, differential binning was used to recover 23 draft genomes, including 3 genomes from WPS-2 and two from AD3.  Further analysis of the metagenome revealed a novel Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene to be abundant in the bacterial community, despite a lack of evidence for photosynthesis related genes. We believe that unlike many other Antarctic regions, chemolithautrophic carbon fixation via CBB cycle is the dominant carbon fixation pathway, hence this pathway is providing the key to survival is this very dry, hostile environment. 



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, September 30, 2015 - 18:00 - 18:15
Institution: 
Macquarie University
Title: 

Aquifer microbial community assembly: do neutral processes dominate?

Abstract: 

Community assembly processes can be condensed into four categories: dispersal, selection, drift and speciation. We tested aquifer communities (of Archaea, Bacteria, Fungi, and Eukarya generally) for evidence that dispersal limitation and environmental selection play a role in determining community biodiversity and composition. We found only weak evidence for these processes at a regional scale of up to 250 km and spanning several significant dispersal barriers. I discuss the possibility that neutral (i.e. non-deterministic, non-selective) processes dominate in groundwater ecosystems, and the spatial scaling of these processes.

 

Event Date: 
Wednesday, September 30, 2015 - 19:00 - 19:45
Institution: 
University of Southern California
Title: 

Microbial evolutionary surprises in the future ocean:  Long-term adaptation of marine nitrogen-fixing cyanobacteria to high CO2

Abstract: 

The globally-distributed marine cyanobacterium Trichodesmium plays a key role in ocean biogeochemical cycles, as it is a major source of newly fixed atmospheric nitrogen to marine food webs.  Trichodesmium N2 fixation rates have been shown to increase under expected future high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity, but its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. My lab has been carrying out a nearly decade-long experimental evolution study with Trichodesmium growing under selection by projected future elevated CO2 levels.  Unexpectedly, selection under high CO2 results in large increases in nitrogen fixation and growth rates that appear to be irreversible, even after adapted cell lines are moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained even after returning to the ancestral environment. These constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, up-regulation of cellular energetic pathways, elevated expression of non-coding intergenic DNA, and increased activity of a potentially regulatory DNA methyltransferase enzyme. Ongoing work in my lab is examining the consequences of multiple nutrient limitation interactions (iron and phosphorus) for the physiology, biochemistry and genetics of Trichodesmium adapted to growing in a more nutrient-limited, acidified future ocean environment.  
 

Event Date: 
Wednesday, August 26, 2015 - 19:00 - 19:45
Institution: 
CSIRO
Title: 

The evolution of mutualistic trait variation in rhizobial symbionts across genetic and geographic scales

Abstract: 

Interactions between plants and nitrogen-fixing rhizobial bacteria are characterized by high genetic diversity for traits important to the outcome of the interaction at the population and species level. However, the selective processes underpinning the generation and maintenance of genetic and phenotypic variation in such interactions are not well understood. I will present an overview of data gathered from a series of experiments using interactions between Acacia spp. and their associated rhizobia, and that address questions regarding the ecological and evolutionary drivers of trait variation across different scales.  Specifically, I will discuss how 1) phylogenetic constraint; 2) within-species local adaptation; 3) nutrient availability; and 4) partner diversity and identity, influence patterns of specialization and community structure in legume-rhizobial mutualistic interactions. Our results suggest that both host-bacterial and bacterial-bacterial interactions are important for understanding evolutionary and ecological dynamics and highlight the importance of designing experiments that span different genetic and geographic scales.

Event Date: 
Wednesday, August 26, 2015 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Effects of temporal pH shifts on ammonia oxidiser community structure and function

Abstract: 

Soil nitrification, the oxidation of ammonia to nitrate, is and driven by bacterial and archaeal autotrophic ammonia oxidisers (AOB and AOA) that carry out the first, rate limiting, step of oxidising ammonia to nitrite.  Previous work has suggested that adaptation and selection in AOA and AOB communities is, to some extent, pH driven.  Acidophilic, acido-neutral, and alkalinophilic groups have been identified by environmental surveys of amoA genes.  These studies of the role of pH in determining ammonia oxidiser community structure and activity have largely relied on spatial pH gradients.  In many managed soil systems (e.g., agricultural systems) edaphic factors (e.g., pH, N concentrations) vary widely temporally and the implications of short term temporal shifts in factors thought to govern oxidiser community structure, and therefore our ability to manipulate edaphic factors to direct community structure, are not well understood.   We investigated the roles of pH in driving nitrifier activity (potential) and community structure over a crop growing season (6 sampling points) in agricultural soils by comparing unamended soils with soils amended with lime to create a temporal pH gradient.  Liming induced a rapid and sustained change in the pH of surface soils (0-10cm), with pH in these soils increasing from 4.8 to 6.5, while in subsurface soils pH increased to a lesser degree after liming (4.3 – 4.5).  After liming, potential nitrification rates increased significantly throughout the production season in both surface and subsurface soils.   TRFLP analysis of total bacterial and archaeal communities showed significant partitioning of the broader communities with soil depth, pH treatment and time, suggesting that microbial communities respond rapidly to changes and that temporal variation in community structure is an important, if often overlooked, factor in assessing microbial diversity patterns. These changes were greater for bacterial, than archaeal, communities. We then utilised amoA gene microarrays to investigate specific AOA and AOB community responses to temporally induced pH changes.  Despite significant changes to ammonia oxidiser function, we saw only very weak changes in community structure of AOA and AOB, suggesting that over shorter temporal periods soil communities are resilient to environmental change and that niche partitioning of ammonia oxidiser communities is likely to be spatially, rather than temporally, governed.

Event Date: 
Wednesday, July 29, 2015 - 18:15 - 18:30
Institution: 
Australian Institute of Marine Sciences
Title: 

Coral Reefs Go Viral: Unveiling the viruses associated with corals in a changing climate.

Abstract: 

Viruses are the most common biological agents in the global oceans, with numbers typically averaging ten billion per litre. The ability of viruses to infect all organisms indicates they most likely play a central role in marine ecosystems and have important consequences for the entire marine food web. Marine viruses influence many biogeochemical and ecological processes, including energy and nutrient cycling, host distribution and abundance, and horizontal gene transfer events. Research into viruses associated with coral reefs is a newly emerging field. Corals form an obligate symbiotic relationship with the dinoflagellate genus Symbiodinium, upon which the coral relies heavily for nutrition and calcification. Disruption of this symbiosis can lead to loss of the symbiotic algae from their host, resulting in coral bleaching and, if the symbiosis cannot re-establish, death of the coral colony. While a number of factors, including elevated reactive oxygen species production by Symbiodinium have been linked to coral bleaching, viral infection has not been methodically examined as a possible cause. Viruses that potentially target the algal symbiont, Symbiodinium sp., have been reported previously; therefore, we examined whether Symbiodinium in culture is host to a virus that switches to a lytic infection under stress, such as UV exposure or elevated temperature. Analysis of algal cultures, using techniques including flow cytometry and transmission electron microscopy, revealed prevalent viral activity, regardless of experimental conditions. This talk will present recent results and results allow for the development of molecular diagnostic probes for rapid detection of viruses in field samples, and will help monitor and assess the role of viruses in coral bleaching and holobiont functioning.

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