Eukaryotic parasites of toxic and bloom-forming diatoms : molecular insights in their diversity and physiology

Despite an increasing amount of evidence acknowledges the importance of eukaryotic microbes in aquatic food webs, human / wildlife health, climate and biogeochemical cycles; their diversity is still widely underinvestigated. This statement is particularly truthful in the case of heterotrophic protists, more difficult to establish as clonal cultures in lab conditions than their phototroph counterpart. Only with the recent application of molecular ecology methods, we have started to gain deeper insights in the structure of complex microbial communities where heterotrophic protists, and especially putative parasites, resulted as an abundant and diverse component in both aquatic and terrestrial ecosystems. Diatoms, on the other hand, have long being recognised as one of the most successful group of phytoplankters and their role as main primary producers at the base of the food web in aquatic ecosystems is well-established. This thesis aims at investigating the link between heterotrophic eukaryotes and diatoms, by focussing on osmotrophic oomycete and fungi, two well-known groups of pathogens sharing similar molecular weaponries and habits despite their large evolutionary distance. By developing a method to isolate and molecularly characterise single cells (SCs) we describe nine novel oomycetes infecting bloom-forming and toxic planktonic diatoms, as well as epiphytic ones, and provide a first analysis of their distribution worldwide. Oomycete parasites infecting the toxic diatom genus Pseudo-nitzschia have been investigated in the field via DNA metabarcoding, highlighting swift parasitic outbreaks and suggesting a role in the regulation of diatom blooms. The same method resulted in the first molecular identification of a transatlantic distributed chytrid infecting the spring bloom-dominating diatom Skeletonema, advocating for a high ecological relevance for this parasite. Finally we characterised a stable cultivated pathosystem involving the freshwater diatom Asterionella formosa and a chytrid parasite, and started investigating the physiology of this interaction by means of RNA sequencing and transmission electron microscopy (TEM). Overall this thesis highlights an unsuspected cryptic diversity hidden within morphologically similar parasites of diatoms underpinning a high complexity of interactions, which cannot be appreciated but by integrating microscopy observation, SC molecular analysis and investigation of cultivated pathosystems.