last updated 2023-09-05

The pelagic zone occupies approximately 1.3 billion km³ (1). Moreover, these aquatic environments hold a large biodiversity, most of it in the form of uncultivated planktonic microorganisms (2-5). This vast pelagic microbial biodiversity is essential to planetary health (6). They have heavily influenced biogeochemical cycles for at least a billion years (7). Moreover, their long-term co-evolutionary history has led, in many cases, to reduced genome size (3) which leaves pelagic microorganisms depending on interactions with other organisms. This makes the study of their ecology relevant to update fluxes in biogeochemical cycles (8), to update climate models (6), to design biotechnological tools that are more robust (9) among others. Our research plans and vision include four main topics:

1. Topic one: Interactions and dependencies on the pelagic microbial world

Aquatic microorganisms and their complex ecological interactions (Figure 1) are responsible for fixing about half of the carbon dioxide on Earth (10-12). Among microbial interactions, auxotrophies are important and yet key questions about them remain unanswered. Auxotrophy is defined as the inability to produce an essential metabolite (13). As environmental microorganisms evolved auxotrophies, they also developed dependencies and division of labor (14, 15). This untapped ecological knowledge has significant potential applications in biotechnology.

Figure 1. In this simplified scheme, different taxa are represented with different colors and are responsible for the transformation of carbon. Moreover, these different taxa interact through production of essential metabolites for which some other taxa are auxotrophic. One of the aims of my research is to understand the microbial interaction networks in the carbon cycle through auxotrophies and essential metabolites.

Microorganisms offer a number of advantages for testing social evolution theory (16). Our research topic tackles the question of how pelagic microorganisms interact as communities directly in their natural environment. Investigating the microbial interactions on naturally occurring microbial assemblages is of great importance to understand ecosystem functioning and to be able to use the principles in future biotechnological designs. Part of our reserach integrates innovative approaches (17): (i) a holistic exploration such as full community analysis of environmental samples, (ii) a reductionist approach, such as a physiological experiments in pure cultures, and finally (iii) model communities in culture or natural cohorts of microorganisms as an intermediate approach bridging holistic and reductionist approaches. In our research group, we will validate the patterns observed in nature through full community metagenomic studies, by doing fitness test in model communities and synthetic communities

2. Topic two: Patterns of biogeography of abundant aquatic microorganisms, including micro-diversity and co-evolution of abundant lineages.

Through the analysis of large metagenomic datasets in time-series or multi-geographic characteristics, we aim to answer questions regarding ecology and evolution across time and space.

3. Topic three: Key microbial players in the carbon and nitrogen cycle of aquatic environments.

In an era of increasing anthropogenic greenhouse gas emissions, decreasing food security and increasing need for clean energy sources, understanding the carbon cycle is crucial and relevant (Figure 2). Aquatic microorganisms are one of the largest contributors to carbon and nitrogen fixation in the atmosphere (20, 28, 29). However, the biogeochemical cycles have been severely affected by a new agent for change: humans. It is time for humans to seek and understand the balance that microorganisms brought to Earth and to take a hold of their rich biodiversity to build a sustainable green bioeconomy (30, 31).

Figure 2. Integration of all research topics and vision. Carbon cycle in aquatic environments linked through microbial interactions. The importance of primary producers and the flux of carbon between them and the heterotrophs. The vision of the scientific knowledge gained through the difference scientific topics, leading to applied research in the future in biotechnology. The Global goals reached through the research.

4. Topic four: Learn the fundamentals of microbial ecology and evolution that can lead to the improvement of biotechnological tools

One ambition long term is that all the ecological concepts and the cultures of cyanobacteria obtained in the research topics 1 and 3 will eventually lead to the development of better biotechnological tools (9). I strongly believe that our oceans and our lakes hold wisdom in their pelagic microorganisms that we can harvest to build a bioeconomy that is sustainable

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