RESEARCH

Diversity, ecology and biogeography of aquatic microorganisms

My research focuses on understanding the links between the diversity and function of microorganisms (mainly bacteria) in aquatic ecosystems, as well as the factors controlling such links. Bacteria are present in all types of ecosystems, and in spite of their very small size, their activity influences biogeochemical processes of global importance. Although the study of microbial ecology goes back several decades, it was not until the appearance of high-throughput sequencing techniques when the revolution in the field of microbial ecology took place, enabling a very deep taxonomic characterization of microbial communities. Still, however, our ability to understand or predict the responses of microbial communities to changes in environmental conditions remains limited. This is partly because shifts in taxonomic composition do not always translate into changes in community function (and therefore, changes in processes at the ecosystem level). In addition, due to their small cell size and their capacity to persist under unfavorable conditions much longer than other organisms, bacteria can potentially be dispersed anywhere, making the study of their distribution challenging. There is thus the need to deepen our understanding of the factors that condition microbial distribution, diversity and functioning in natural ecosystems.
During my research career I have tried to answer questions related to this issue using different approaches and techniques, combining experimental and field surveys, and working in ecosystems as different as soils, rivers, lakes, estuaries, groundwater, and the ocean.
Below I enumerate some of the research lines that I am following now:

Following bacteria from soils to lakes: Biogeography and functioning along the terrestrial-aquatic continuum

Microbial biogeography aims at understanding the factors that explain the distribution of microbial species in nature. Traditionally, most studies on microbial biogeography have been restricted to individual types of ecosystems (e.g., only soils, only lakes, only streams, only the ocean), but there are recent evidences showing that the terrestrial runoff can transport a vast amount of soil bacteria to rivers and lakes. Most of them cannot survive in the aquatic environment and gradually disappear, but some are able to persist in soils and grow when inoculated in the water. We have recently shown that boreal lakes and rivers are largely dominated by bacterial taxa that come from soils, meaning that we cannot understand changes in the species composition of communities without considering such linkages between ecosystems and the different dispersal routes of microbes. I am interested in understanding how this connectivity and dispersal between local assemblages shapes local microbial communities and how it can influence links between microbial diversity and community functioning.

The biogeography of marine bacteria and their connectivity across the ocean

Compared to freshwaters, identifying dispersal barriers and dispersal routes of microbes in the ocean is more challenging. We have tried to do so by exploring the distribution patterns of individual bacterial taxa, as well as changes in their abundances over space. We have shown that marine bacterial communities are composed of taxa showing largely different spatial patterns, and that shifts in environmental conditions promotes changes in the relative contribution of rare and abundant taxa across communities. In addition, we have recently discovered that sinking particles transport microorganisms from surface waters to the deep ocean, down to 4000 m. This implies that marine microbial communities are largely connected by this vertical dispersal of taxa, and thus that we cannot understand the biogeography of deep-sea bacteria without considering variations in the bacterial communities colonizing particles in surface marine waters.

Microbial ecology and dispersal across the groundwater-marine interface

Groundwater discharge into the ocean is a hydrologic pathway that is receiving increasing attention because it can transport a much larger amount of nutrients and material to coastal waters than previously thought. However, the biological responses of coastal microbial communities to these freshwater inputs are largely unknown, and so are the microbial species inhabiting these underground ecosystems. Combining field surveys with experimental approaches, we are trying to assess the effect of groundwater discharge on marine bacterioplankton communities from the coastal ocean. In addition, we want to detect the presence of groundwater taxa in the coastal ocean as a way to trace groundwater discharge events, pollution episodes, etc. Given the magnitude of the groundwater flow into many coastal areas, it is essential to consider it as a potentially relevant source of microbial diversity.

Rarity, seed banks and ultramicrobacteria

The capacity of bacteria to persist inactive or dormant (i.e., in a reversible state of low metabolic activity) for longer times than other microorganisms explains why microbial dispersal is such an important issue. Dormant bacteria do not grow, so they become rare and can persist inactive until a more suitable environment is found, like for example when transported from soils to water, or during long-range airborne transport of marine bacteria over the ocean. Thus, the dispersal of allochthonous bacteria from other systems can represent sources of viable diversity for local communities. I am interested in understanding how dispersal can shape the rare biosphere of bacterial communities, as well as to which extent dispersed bacteria can represent a seed bank for microbial assemblages. Finally, I am studying the diversity and ecology of ultramicrobacteria, tiny bacteria that scape most current sampling strategies. Some of these bacteria are bacteria that miniaturize in response to a stressful situation but that can grow again upon changes in conditions, and thus they also represent a reservoir of potentially ‘reactivable’ diversity.