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Microorganisms shape the physical, chemical and biological state of our planet by facilitating the storage, transport, and turnover of key bio-elements. While these activities are key to the production and consumption of greenhouse gases and water quality, approaches, theory and models that integrate microbial influence in the context of biogeochemical, ecosystem and climatic processes still need to be developed. Our ignorance about the microbes is even the more astonishing given their huge global biomass.
Reasons for this have been methodological limitations to study the immense diversity of complex microbial communities. However, this scenario is now dramatically changing since recent advancements in sequencing technologies and single cell approaches have revolutionized the way microorganisms can be studied.
My research focus ties in with this recent revolution by exploring the dynamics of complex microbial systems in the aquatic environments using next generation sequencing facilitated approaches such as metagenomics and metatranscriptomics. It integrates field data from study sites ranging from boreal lakes to the oligotrophic open ocean (North Pacific Subtropical gyre at Station ALOHA). To interpret and to synthesize the wide range of genomic and transcript data in an ecological context we apply systems biology approaches that have been used for cellular systems. In my research group we use the analogy that a lake, similar to a living cell, has a collective metabolism based largely on the dynamic genetic blueprint and expressed phenotypes of microorganisms that control most fluxes of energy and matter. By using a holistic approach, we hope to be able to predict ecosystem processes from the behavior of complex biological systems.
An applied aspect of my research is to screen this flood of data for enzymes that can be used in biotechnology and industrial processes. Here, we also study “odd” environments such as alkaline lakes.
We are also studying evolutionary processes that lead to genome reduction in aquatic bacteria in a population and community context. Here we are also interested in the ecological implications of genome streamlining.
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