Browsing by Author "Schroeder, Declan"

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    Marine algal virus communities along Southern African coasts
    (2015) Morrissey, Kathryn Lee; Rybicki, Edward P; Pfaff, Maya; Schroeder, Declan
    Southern Africa is home to highly diverse marine environments along its coasts. The main reason for the contrasting environments is the two major boundary currents, the Benguela and Agulhas currents, and their interaction around the tip of South Africa. Algal blooms are known to proliferate predominantly off the nutrient - rich west coast, however, sporadic inshore upwelling on the east coast can also illicit these events. In addition, solar salt - pans located on the coast that draw their water from the bay area are affected by bloom events. Algal viruses play a key role in regulating phytoplankton communities and modulate the dynamics of these bloom events. Identifying the viruses associated with algal blooms is the first step in determining the role they play in the bloom dynamics. Here I chose to focus on phycodnaviruses, known agents of bloom termination. Samples were taken from two specific algal blooms that occurred in 2013 in different bioregions namely Elands Bay (west coast) and Algoa Bay (east coast). Additionally the Cerebos solar salt pans located along the west coast were selected as sample sites to investigate viral composition. DNA polymerase (pol) gene fragments were amplified from environmental samples using algal - virus specific PCR primers AVS1 and POL. Amplified fragments were then sequenced. Viral sequences were identified and mapped to existing virus families. Amplicon specific primers were designed for select dominant virus group identified for both bloom events. These were used to screen across all samples to determine viral prevalence. Phylogenetic analysis of viral sequences revealed new clades of Phycodnaviridae in the Elands Bay and Algoa Bay regions. A bloom terminating virus, EB1, is proposed for the Elands Bay bloom event. The Cerebos salt pans showed the greatest diversity of all samples analysed and novel halophilic algal viruses were identified in regions with the highest salinity.
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    Microbial biodiversity in the southern Indian Ocean and Southern Ocean
    (2017) Flaviani, Flavia; Rybicki, Edward P; Schroeder, Declan; Pfaff, Maya C
    The multi-phylotype and ecologically important community of microbes in aquatic environments ranges from the numerically dominant viruses to the diverse climate-change regulating phytoplankton. Recent advances in next generation sequencing are starting to reveal the true diversity and biological complexity of this previously invisible component of Earth's hydrosphere. An increased awareness of this microbiome's importance has led to the rise of microbial studies with marine environmental samples being collected and sequenced daily around the globe. Despite the rapid advancement in knowledge of marine microbial diversity, technical difficulties have constrained the ability to perform basin wide physical and chemical oceanographic assessments in tandem with microbiological screening with the majority of studies only looking at a single component of the microbial community. In this study the full microbial diversity, from viruses to protists, was characterised within the southern Indian Ocean and the Southern Ocean from a small volume of seawater collected using the same CTD equipment used by oceanographers. Throughout this study it will be demonstrated how this small volume is sufficient to describe the core microbial taxa in the marine environment. The application of a bespoke bioinformatics pipeline, integrated with sequencing replication, improved the description of the dominant core microbiome whilst removing OTUs present due to PCR and sequencing artefacts thereby improving the accurate description of rare phylotypes. Analyses confirmed the dominance of Cyanobacteria, Alphaproteobacteria and Gammaproteobacteria in the pelagic prokaryotic microbiome, while the Stramenopiles-Alveolata-Rhizaria (SAR) cluster dominates the eukaryotic microbiome. A decrease in the SAR community will be reported for the Southern Ocean with a concomitant increase in the haptophyte community. Whilst the virome confirmed the dominance of tailed phages and giant viruses across all stations, there was a significant variation caudoviruses and Nucleocytoplasmic Large DNA viruses (NCLDV) across defined biogeographical boundaries. The described method will allow the characterisation of the microbial biodiversity as well as future integration with oceanographic data with a much reduced sampling effort. The characterisation of the whole microbial community from a single water sample will improve the understanding of microbial interactions and represent a step towards in the inclusion of viruses into biogeochemical models.