last updated 2026-03-10

Our research program integrates diverse cultivation strategies and environmental sampling with state-of-the-art analytical, molecular, and omics approaches. One of our goals is to characterize production and consumption of metabolites of interest at the cellular level and from the microbial community perspective. Additional goals include elucidating patterns of biogeography of abundant aquatic microorganisms, including micro-diversity and co-evolution of abundant lineages, and linking eco-evolutionary interaction strategies to ecosystem-level processes and biogeochemical fluxes.

Figure 1. Microorganisms are the engines that make Earth habitable. 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 the production of essential metabolites for which some other taxa are dependent (Kost et al., 2023). One of the aims of our research is to understand the microbial interaction networks in the carbon cycle through anabolic dependencies.

The pelagic zone encompasses approximately 1.3 billion km³ of aquatic habitat (Costello et al., 2010). It harbors immense biodiversity, most of it composed of uncultivated planktonic microorganisms (Del Campo et al., 2016; Menden-Deuer & Rowlett, 2014; Rodriguez-Gijon et al., 2021). Despite their microscopic size, this vast diversity is essential to planetary health (Cavicchioli et al., 2019) as it has shaped biogeochemical cycles for billions of years (Sanchez-Baracaldo et al., 2022). A defining eco-evolutionary feature of many pelagic microorganisms is genome streamlining (Giovannoni et al., 2014; Kost et al., 2023; Rodriguez-Gijon et al., 2025). Through long-term co-evolution of co-occurring microorganisms, many lineages have lost metabolic capabilities that would allow them to live independently. As a result, numerous pelagic microorganisms rely on metabolic exchanges with neighboring organisms in their community (Figure 1).

Auxotrophies, the inability to produce an essential metabolite for growth and survival (Davis & Mingioli, 1950), are widespread in aquatic microorganisms and are one of the key mechanisms underlying metabolic dependencies (Droop, 1957; Pacheco-Valenciana et al., 2025). One of the most fascinating, complex, and vital metabolites is coenzyme B₁₂ (Sultana et al., 2025; Wienhausen et al., 2024), which is essential for the survival of many microbes in the ocean but is de novo biosynthesized by only a minority of prokaryotes. Current data indicate a complex metabolic network with intermediates being exchanged.

Figure 2. Different levels of life organization for microorganisms. Modified from (Milke et al., 2026).

The widespread metabolic dependencies suggest that pelagic microorganisms are often not best understood as fully autonomous units, but as components of higher levels of biological organization, where interacting populations collectively form the functional units of ecosystems (Figure 2) (Milke et al., 2026). In aquatic systems, key ecological functions can emerge from interacting populations operating at different levels of organization. Therefore, complementary metabolisms, shared niches, and recurrent associations together shape collective properties that are not predictable from individual taxa alone. Fundamental questions remain about how the structure of these dependencies regulates ecosystem-level processes.

Although auxotrophies have been studied for over 75 years (Davis & Mingioli, 1950), we have not yet uncovered the true extent and complexity of these dependencies in nature. However, we know that over evolutionary time, such dependencies have promoted metabolic interconnections and division of labor within microbial communities (Pacheco et al., 2019; Zengler & Zaramela, 2018).

Pelagic microorganisms and their complex ecological interactions are responsible for fixing about half of the carbon dioxide on Earth (Anantharaman et al., 2016; Falkowski et al., 2008; Jardillier et al., 2010). Importantly, a long-term carbon repository (~660 Gt C) of dissolved organic matter (DOM) is present in the Oceans and consists of a complex and variable mixture of compounds that serve as substrates for heterotrophic microorganisms (Azam, 1998; Ferrer-Gonzalez et al., 2021; Patriarca et al., 2020). Aquatic microorganisms play central roles both as DOM producers (Moran et al., 2022) and consumers, connecting these dissolved substrates to larger organisms in the food web via the microbial loop (Azam, 1998; Fenchel, 2008).

Understanding the ecological and evolutionary principles that govern pelagic microbial interactions is therefore critical for improving mechanistic representations of carbon flux, for advancing predictive models of marine ecosystem function, to design biotechnological tools that are more robust and to learn the fundamental balance of how life on Earth functions so we can apply this culture into our economy and politics.

Figure 3. Integration of the research program and vision for society.
Top panels: The carbon cycle in aquatic environments linked through microbial interactions. The importance of primary producers and the flux of carbon between them and heterotrophs. Methodological innovation through the cultivation of microbial communities to observe emergent properties of microbial life. The interconnectedness of microorganisms in nature through metabolic interdependencies.
Bottom panel: A vision in which scientific knowledge generated through our research program contributes to future applications in biotechnology and to a more balanced relationship with nature, aligned with the Global Goals. Quality education serves as the foundation of a healthy democracy and a sustainable future, taking inspiration from microbial life and its ancient wisdom.

Understanding the ecological and evolutionary principles that govern pelagic microbial interactions is therefore critical for improving mechanistic representations of carbon flux, for advancing predictive models of marine ecosystem function, designing biotechnological tools that are more robust, and learning the fundamental balance through which life on Earth functions so that we can apply these principles to our culture, economy, and politics.

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