Integrating high-throughput genomic analyses with experimental strategies to understand parasitic interactions in the aquatic food web

Freshwater lakes provide many indispensable ecosystem services most importantly via supplying drinking water, global climate regulation, and offering recreational services. Many of these services are directly affected by diversity and function of microorganisms that inhabit these ecosystems. Microbes play a significant role in lake’s primary production and cycling of nutrients. They fulfil these roles via their extensive metabolic capabilities and by developing complex trophic interactions known as the aquatic food web.

Lake ecosystems and their microbial communities are vulnerable to perturbances caused by land use change, accelerating climate change and other anthropo-pressures. For example eutrophication or increased nutrient availability, is a growing threat for lakes and water resources. This can cause excessive primary production via phytoplankton. Phytoplankton are microscopic plant-like microorganisms that perform primary production by converting atmospheric carbon dioxide (CO2) into organic carbon. This can lead to mass development of toxin producing microorganisms known as “harmful algal blooms” and consequently affect the whole microbial community of the lake.

Undoubtedly understanding the diversity and interactions of lake microorganisms is vital for ensuring the sustainability of ecosystem services provided by lakes. This is particularly important in the Anthropocene era, which is associated with rapid changes in environmental state and ecological stability.

In my research, I study different microbial groups including bacteria, phytoplankton, fungi, and viruses in lake ecosystem. I study their diversity, dynamics and most importantly focus on their interactions. In my lecture, I will provide an overview of my research using high throughput sequencing methods in the context of our current knowledge of lake’s bacterial and viral composition. Growing majority of aquatic microbes in the lab using routine cultivations efforts remains a bottleneck in our research field. However, recent advances in high throughput sequencing approaches (such as metagenomics and single cell genomics) allow us to bypass this limitation by directly analyzing the genomic content of these microbes that has been extracted from environmental samples. In my lecture, I will highlight how applying these methods we have made remarkable advances in our understanding of the diversity, and dynamics of different lake microorganisms.

Despite these advances, we are still far from fully comprehending their interactions with other members of the aquatic food web. In a natural ecosystem, all microbes evolve in the context of their interactions with other groups in their habitat. For example phytoplankton get infected by parasites such as viruses and chytrid fungi. Virus- or chytrid-mediated infections can cause the collapse of phytoplankton blooms in a matter of days and are known to prevent bloom formation by exerting control on phytoplankton population sizes. Viruses exert control on Lake’s bacterial populations as well. In my research, I specifically focus on the effect of these parasitic interactions on the host population to reveal the functional basis of these interactions.

I develop cultivated model systems for bacterial and phytoplankton hosts and their parasites. These model systems enable me to study how these hosts respond to infection, how these parasitic infections affect host’s metabolism, and what are the potential defense mechanisms evolved against infection. To disentangle the functional traits responsible for these interactions, I use genomic and metagenomic methods. The knowledge derived from these studies lay the foundation for using these parasites as biocontrol agents to modulate the population dynamics of their respective hosts in case of undesirable perturbations and to ensure ecosystem sustainability.