Congratulations to Emily Chase (MEB) who defended her thesis on Wednesday, December 15, 2021
On the following subject: "PHYCOVIR: diversity and impact of viruses on intensive culture of microalgae in open environment".
Thesis supervisor: Guillaume Blanc, Research Director
Co-supervisor: Christelle Desnues, Research Director
Abstract:
In order to better understand the diversity and role of phytoplankton viruses, this thesis work was devoted to the study of an industrial scale microalgae culture system, called an intensified culture lagoon (HRAP for "high rate algal pond" in English), located in Palavas-les-Flots, France. The objective 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 hypothesized that microalgal viruses could coexist with microalgae in the HRAP, and therefore affect the culture - to the point of causing or contributing to microalgal death. This study represents the first attempt to explore viral diversity in a HRAP, along with collecting data of potential hosts through 18S metabarcoding. The study targets all viral compartments through sequencing of RNA and DNA viromes, as well as potential giant virus populations (Nucleocytoviricota). Bioinformatics analysis of the sequences identified viruses present in the HRAP, and their population dynamics were monitored by (RT)-qPCR on a series of water samples collected over two years of culture. The viromes were used to identify putative microalgal viruses, in other words, potential infectious agents that can influence the HRAP culture and directly contribute to or cause microalgal death. These include key players such as the Marnaviridae family (Order Picornavirales; RNA viruses), NCDLVs from the Phycodnaviridae and Mimiviridae families, a member of the Lavidaviridae family (i.e., a virophage), and "polinton-like viruses" (PLVs), all of which have known associations with microalgae. A thorough exploration of these key players, the putative new HRAP viruses, is performed 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, particularly putative microalgal viruses, in the context of industrial scale culture and maintenance. The last chapter of the thesis describes a bioinformatic study of the genomic sequences of unicellular green algae of the genus Tetraselmis which allowed the identification and characterization of integrated viral forms (i.e., viral DNA inserted into the algal chromosomes) related to the Tsv-N1 virus, to the PLVs identified in HRAP, and to the giant TetV-1 virus. This analysis extends our knowledge on the diversity of Tetraselmis viruses and the complexity of biological and evolutionary interactions between these partners.