Metabolic interactions between algae and bacteria in changing conditions
Résumé
Brown algae form key marine ecosystems and live in tight relationships with microbes essential to their growth and development. Environmental changes can cause imbalances in these biological systems, leading to shifts in bacterial communities and sometimes giving rise to pathogenic interactions. Hence, considering both the algae and their microbiome (i.e. the holobiont) is essential to better understand their reactions to environmental challenges. In this memoir, I will outline the research I have conducted over the past nine years to explore this topic and highlight some of my ideas and challenges for the future. I will first touch on my work establishing the small filamentous brown alga Ectocarpus and in particular, a freshwater strain of the species Ectocarpus subulatus that we have shown to depend on a specific microbiome for freshwater tolerance, as a model system for algal-bacterial interactions. This includes the coordination of the sequencing and annotation of the E. subulatus genome, the characterization of its microbiome both in the field and in laboratory samples, and the establishment of a collection of cultivated bacteria representative of its microbiome now comprising ca. 400 strains from nearly 100 different species or genera, many of which have been genome-sequenced. Using multi-omics analyses we have furthermore put forward new hypotheses on the role of bacteria during the algal stress response, notably, the continued provision of bacterial services, most importantly vitamin K production, and the induction of quorum sensing pathways (potentially indicative of a change in the bacterial lifestyle towards dysbiosis). To identify key services provided to the algae by bacteria without strong a priori assumptions, we have, in collaboration with Anne Siegel’s team from the IRISA Rennes, turned to metabolic complementarity as a predictor for potential mutualistic exchanges. The underlying idea is that beneficial metabolic exchanges between symbionts most likely occur where metabolic functions have been lost by one of the symbiotic partners, or vice versa functions may be lost once they have been replaced by external sources. Such points of intersection can be identified in silico using genome-scale metabolic networks. We have recently been able to prove the utility of this concept to predict beneficial metabolic interactions as well as the metabolic capacities of simplified holobiont systems in vitro, i.e. the algal host in co-culture with selected bacterial strains. Parallel to this work on Ectocarpus, we are starting to expand our research to the economically and ecologically more relevant kelp species Saccharina latissima. In this context, we have recently characterized the microbiome associated with both healthy and diseased S. latissima from different seasons and regions and generated a large collection of cultivated Saccharina-derived bacterial strains. These form a solid basis for both more targeted work with this model, such as more detailed studies on the role of Quorum Sensing (QS) in governing algal-bacterial interactions. Most recently we also commenced work on the S. latissima virome. The most important challenges in my future research will be, on one hand, to improve the reproducibility of experiments and thus to better control model systems, and the possible use of reverse genetics to gain precise functional insights into specific interactions. In parallel, I intend to expand our view of brown algal holobionts beyond bacteria and lately viruses to include fungi. Lastly, I hope to link work carried out in the laboratory to its potential applications, e.g. by assessing the impact of the microbiome on the defense-stimulating effect of Ascophyllum nodosum extracts in terrestrial plants.
Origine : Fichiers produits par l'(les) auteur(s)
Licence : CC BY NC - Paternité - Pas d'utilisation commerciale
Licence : CC BY NC - Paternité - Pas d'utilisation commerciale
