On the following subject: "PHYCOVIR: diversity and impact of viruses on the intensive cultivation of microalgae in an open environment".
Thesis supervisor: Guillaume Blanc, Research Director
Co-director: Christelle Desnues, Research Director
Summary:
In order to gain a better understanding of the diversity and role of phytoplankton viruses, this thesis was devoted to the study of an industrial-scale microalgae culture system, known as a high rate algal pond (HRAP), located in Palavas-les-Flots, France. The aim of the study was to examine culture accidents (i.e. episodes of mass mortality of microalgae) occurring in the HRAP, the cause of which is unknown. We hypothesised that microalgal viruses could co-exist with the microalgae in the HRAP, and therefore affect the culture - to the point of causing or contributing to the death of the microalgae. This study represents the first attempt to explore viral diversity in a HRAP, at the same time as collecting data on potential hosts using 18S metabarcoding. The study targets all viral compartments through the sequencing of RNA and DNA viromes, as well as potential populations of giant viruses (Nucleocytoviricota). Bioinformatics analysis of the sequences was used to identify viruses present in the HRAP, and their population dynamics were monitored using the (RT)-qPCR method on a series of water samples taken over two years of cultivation. The viromes were used to identify putative microalgae viruses, in other words, potential infectious agents that can influence HRAP culture and contribute to or directly cause the death of microalgae. These include key players such as the Marnaviridae family (Order Picornavirales; RNA viruses), NCDLVs from the Phycodnaviridae family and the Mimiviridae family, a member of the Lavidaviridae family (i.e. a virophage), and 'polinton-like viruses' (PLVs), all of which have known associations with microalgae. An in-depth exploration of these key players, the putative new HRAP viruses, is carried out and host inferences are made using 18S metabarcoding data, coupled with dynamic data from our (RT)-qPCR approach. The results are a comprehensive look at HRAP viruses, in particular putative microalgal viruses, in the context of industrial-scale culture and maintenance. The final chapter of the thesis describes a bioinformatic study of the genomic sequences of unicellular green algae of the genus Tetraselmis, which enabled us to identify and characterise integrated viral forms (i.e. viral DNA inserted into the algal chromosomes) related to the Tsv-N1 virus, the PLVs identified in HRAP, and the giant TetV-1 virus. This analysis extends our knowledge of the diversity of Tetraselmis viruses and the complexity of the biological and evolutionary interactions between these partners.