PhD Oral Exam - Thomas Grevesse, Biology

When studying for a doctoral degree (PhD), candidates submit a thesis that provides a critical review of the current state of knowledge of the thesis subject as well as the student’s own contributions to the subject. The distinguishing criterion of doctoral graduate research is a significant and original contribution to knowledge.

Once accepted, the candidate presents the thesis orally. This oral exam is open to the public.

Abstract

The world’s oceans are of utmost importance for us humans: they are a source of food and half the oxygen we breathe, they act as climate regulators, trade routes, tourism attraction, and harbor an incredible diversity of life. The Arctic Ocean represents a particular ocean, with acute variations of temperatures, ice and solar radiation regimes throughout the year, as well as a strong terrestrial signature imparted by its immense watershed. But the oceans are now under threat from a changing climate. The polar oceans are especially susceptible to these changes with already dramatic visible consequences. The most visible consequence in the Arctic Ocean is a continuous loss of sea ice that decreases the albedo effect and its protection against heat, leading to an increased vicious circle of ice melt and temperature increase. The escalating loss of sea ice already has dramatic consequences of the diversity of species depending on it for survival. The loss of sea ice also exposes the surface water to extended periods of solar radiation, triggering phytoplankton blooms earlier in the year and overall increasing the Arctic Ocean primary productivity. The Arctic Ocean is also freshening due to the increased freshwater input from its warming watershed, with perturbations of the water column stratification. In addition, this increased freshwater input consequently carries growing amounts of nutrients and organic matter from terrestrial sources to the Arctic Ocean. The thawing of permafrost and the carbon stores it releases further contributes to the load of terrestrial organic matter to the Arctic Ocean. All these perturbations profoundly modify the sources and dynamics of organic and inorganic matter in the Arctic Ocean. However, the fate of the inorganic and organic matter and their impact on the Arctic Ocean geochemical cycles are not well understood. Given that microbial life is at the base of cycling this organic and inorganic matter, it plays pivotal roles by controlling biogeochemical cycles and forming the base of the food web. Specifically, the diversity of metabolic processes carried on by microbes determines how they interact with and shape their environment. Despite the importance of understanding microbial metabolism in a rapidly changing Arctic Ocean, our knowledge on the microbial processes that distinguish the Arctic Ocean from the rest of the global oceans is still very fragmented.

In this thesis, I undertook to address the lack of knowledge about the metabolism of the Arctic Ocean microbiomes by elucidating the biogeography and phylogenetic distribution across bacteria of metabolic processes of importance in the Arctic Ocean, and how they are linked to the changing geochemical cycles. I first discovered that metabolic pathways for the degradation of aromatic compounds were enriched and expressed in the Arctic Ocean compared to the rest of the global ocean, in particular in the subsurface waters characterized by the maximum of fluorescent dissolved organic matter. The diversity of aromatic compounds degraded by these microbial pathways reflected the ability of microbial communities to degrade the disproportionately high amount of terrestrial organic matter discharged to the Arctic Ocean. In addition, I showed that the presence of numerous aromatic compound degradation genes in Arctic Ocean genomes may reflect an adaptation to use the vast amount of terrestrial organic matter. These results show that the microbiomes of the Arctic Ocean are equipped to process terrestrial organic matter and that the taxa most involved may gain importance with the climate change-induced ever-increasing loads of terrestrial organic matter.

I then found that the metabolic pathways involved in the storage of neutral lipids was also enriched in the Arctic Ocean microbial communities. I highlighted the importance of picoeukaryotes in the storage of neutral lipids and discovered an unexpected phylogenetic diversity of prokaryotes able to store neutral lipids in the Arctic Ocean. I postulated that the storage of neutral lipid may be an important strategy to survive the Arctic Ocean winter, but also an important growth resource for heterotrophic microbes.

Finally, I undertook a global ocean study to unravel the metabolic genes and pathways favored by the microbiomes of the Arctic Ocean. I confirmed the importance of aromatic compound degradation and neutral lipid metabolism. But I also uncovered a myriad of other metabolic processed favored by the microbiomes of the Arctic Ocean compared to other oceanic zones. In particular, I discovered the prevalence of genes and pathways involved in the metabolism of glycans that might be involved in cold adaptation mechanisms within the photic zone. Importantly, I highlighted correspondences between the genes and pathways favored by the Arctic Ocean microbiomes and the composition and transformations of dissolved organic matter. Specifically, I found an enrichment in transformations involving sugars moieties in the photic zone and a strong aromaticity signature in the dissolved organic matter of the fluorescent dissolved organic matter maximum.

This thesis represents the first work to explore the metabolism of the Arctic Ocean microbiomes in such a comprehensive fashion. Not only does this thesis systematically uncovers a multitude of metabolic processes of importance for the Arctic Ocean microbiomes but also brings new discoveries on their biogeography, ecological context and phylogenetic diversity across prokaryotes and picoeukaryotes. Moreover, the thesis highlights the importance of these processes by linking them to the composition and transformation of dissolved organic matter, and hence biogeochemical cycles. As such, this thesis will serve as a base to guide experimental and field work that will quantify the role of microbiomes in the biogeochemical cycles of the Arctic. This will have important implications to understand and quantify how climate change perturb Arctic Ocean ecosystems.