July 2015

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). 
 

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 - 19:00 - 19:45
Institution: 
University of New South Wales
Title: 

Organohalide respiration - breathing life into toxic environments

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.