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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, August 26, 2015 - 18:00 - 18:15
Institution: 
Institut de Ciencies del Mar
Title: 

Seasonal diversity patterns of marine picoeukaryotes from a Mediterranean coastal site

Abstract: 

Picoeukaryotes are the most abundant eukaryotes in the sea and are  
recognized as fundamental components of marine ecosystems,  
contributing to phytoplankton biomass, primary production and food web  
interactions. The study of their diversity requires molecular surveys,  
which have been lately expanding with the emergence of High Throughput  
Sequencing (HTS). Hitherto, many studies have focused in describing  
the diversity present in different sites but not along time. In this  
work we performed a time series study in order to find out the  
seasonal patterns in the diversity of picoeukaryotes. We analyzed a  
sample dataset taken monthly during 4 years in a Northwestern  
Mediterranean coastal site and processed by HTS of the 18S rDNA. Our  
results showed that only 1% of the OTUs were present in all samples. A  
few taxonomic groups were the most abundant in the community yearlong,  
while different groups were the most diverse. Interestingly, we found  
that the OTUs presenting the highest number of reads generally did not  
show a seasonal pattern, whereas some less abundant OTUs might exhibit  
a very marked temporal distribution.

Dear Australian colleagues,
 
Please see attached advert for the 4th New Zealand Microbial Ecology Consortium (NZMEC) meeting, to be held at the University of Auckland on 18-19thFebruary 2016.  Registration for this meeting is free, and we think you’ll agree that there is a very strong line-up of speakers.
 

Event Date: 
Wednesday, July 29, 2015 - 19:00 - 19:45
Institution: 
University of New South Wales
Title: 

Organohalide respiration - breathing life into toxic environments

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.

Event Date: 
Wednesday, July 29, 2015 - 18:00 - 18:15
Institution: 
University of New South Wales
Title: 

Host-virus Interactions in a Frigid, Hypersaline Antarctic Lake Revealed by Metaproteomics

Abstract: 

Deep Lake is a marine derived, hypersaline system in Antarctica that remains perennially ice-free with water temperatures dropping to -20°C. These harsh environmental conditions have led to a low complexity microbial community, completely dominated by members of the haloarchaea, including four isolated species (tADL, DL31, Hrr. lacusprofundi and DL1) that account for ~72% of the lakes cellular population. Genomic sequencing and analysis of the four isolated species combined with metagenomics have revealed an unprecedented level of inter-genera exchange of long (up to 35 kb) stretches of identical DNA. However, despite the rampant, promiscuous exchange of DNA, distinct haloarchaeal lineages appear to prevail in the lake by virtue of their unique capacities for niche adaptation (1, 2). With no apparent metazoan grazers present in the lake, viruses are hypothesised to play a dominant role in shaping the microbial community of Deep Lake. In this present study we applied metaproteomics for the first time on a hypersaline environment and combined it with in-depth genomic and metagenomic analysis of Deep Lake CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) and BREX (Bacteriophage Exclusion) (3) systems to elucidate host-virus interactions.
Shotgun metaproteomics was performed on Deep Lake biomass from 5 distinct depths, captured by sequential filtration through 3 µm, 0.8 µm and 0.1 µm filters during the Antarctic summer of 2008/2009. All identified proteins were manually annotated and grouped into taxonomic and functional categories. We characterized CRISPR systems of the four genomes and the Deep Lake metagenome and used CRISPR spacer and repeat sequences to identify sources of invading DNA.
The Deep Lake metaproteome comprised around 1100 detected proteins. A striking feature was the identification of multiple, highly abundant cell surface proteins with a high degree of sequence variation compared to the genomes of the isolate species (“variants”). E.g. we identified 6 distinct proteins all matching the main S-layer component of tADL. Furthermore we detected variants for archaella (archaeal flagella), pili and other cell surface proteins. Multiple viral proteins were detected with sequence similarity to other, mainly haloarchaeal viruses. Functional CRISPR loci could be identified in the genomes of all four isolated species and CRISPR-associated (Cas) proteins were detected for two of them. CRISPR spacers could be linked to different sources of invading DNA, with most, but not all spacers targeting viruses. We detected one BREX protein (PglX) for Hrr. lacusprofundi. Some detected proteins, including cell surface proteins, were encoded on metagenome contigs together with putative viral genes.
The detection of multiple protein variants for cell surface structures like S-layer and archaella is indicative of phylotypes that are present in the lake. Introducing variation in cell surface structures likely provides the haloarchaeal populations with a way of evading viral infection. Consistent with this is the presence of a diverse viral population in Deep Lake. We detected proteins from at least eight distinct haloarchaeal viruses (eight major capsid proteins), with some proteins confirming active viral life cycles (e.g. prohead protease). Furthermore, the CRISPR spacer analysis revealed that some viruses infect multiple species (broad host range). In addition to the acquired cell surface variation, haloarchaeal host cells have employed active CRISPR and BREX systems as defense against viral infection.                             The presence of cell surface genes on metagenomic contigs together with putative viral genes, and the high degree of sequence variation observed in many cell surface proteins, suggests that viruses are involved in the acquisition, mutation and distribution of cell surface variants within the haloarchaeal populations. Overall, we were able to identify and describe a complex network of virus-host interactions, revealing a pivotal role of viruses in shaping the microbial community in Deep Lake (4). 
 

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