Microbial species. How to define them, and what lies beyond?

Most research questions in Ecology require the identification of discrete biological units, which are then studied to determine how they interact between themselves and with the environment. Regardless of how these units are defined, it is imperative that they are ecologically meaningful, i.e., that they group together organisms that play an equivalent role in the ecosystem. Finding the right resolution at which to analyse biological diversity thus becomes an overarching question in ecological science: if groups are made too broad then they risk confounding organisms with different ecological roles, but if they are too narrow they risk separating equivalent organisms into different units.

In plant and animal ecology studies, species have long been used as the basic units of diversity, but translating this practice to the realm of microorganisms has proven difficult. Species have been traditionally defined based on the ability of organisms to interbreed and produce viable offspring, but this definition can not be readily applied to microorganisms: on one hand, they are capable of asexual reproduction, and on the other hand they are capable of exchanging genes via horizontal gene transfer, even across large phylogenetic distances. This problematic has been compounded by methodological challenges that, until very recently, precluded a comprehensive characterization of the microbial tree of life.

So how to define eco-evolutionary units in microorganisms? Do entities resembling plant and animal species also exist in microorganisms? What is the right level of phylogenetic resolution at which to study microbial ecosystems? Over the last decades, our ability to measure microbial diversity has increased exponentially, and at every step these advances have confirmed that discrete biological units do in fact exist for microorganisms. But we are still not sure about their nature or how they originate. Furthermore, recent studies have shown that what seemed to be coherent species were in fact hiding a staggering amount of functional diversity. Crucially, this can mean that individuals that in principle belong to the same species could be playing different roles in the ecosystem, challenging the notion that species are the ultimate conceivable unit in microbial ecology.

In this talk I will review the different methods and definitions historically used to characterize microbial diversity, and introduce the state-of-the-art and future perspectives in microbial ecology, including my own research plans to assess the potential consequences of intra-species diversification in freshwater ecosystems at a global scale.