Interactions between marine picoeukaryotes and their viruses one cell at a time = Interacciones entre picoeucariotas marinos y sus virus célula a célula

Abstract

Marine viruses are key components of marine microbial communities, as they influence the cellular abundances and the community structure of microbes, participate in their genetic exchange, and intervene in the ocean biogeochemical cycles. Most studies dealing with the role of viruses in the marine environment have been done from a bulk community point of view, but going from the bulk community perspective to specific virus─host relationships is essential in order to understand the role of viruses in shaping a determined host community, in modifying host genomes, and ultimately in the release of organic compounds from the lysed cells. For this reason, in this thesis we implemented and applied different methodologies that are able to detect, visualize and quantify virus─host interactions in marine eukaryotes at the single cell level. We focused on picoeukaryotes (cells <3 µm) because they play crucial roles in marine food webs and biogeochemical cycles, and virus─host interactions in natural populations of these minute eukaryotes are largely unknown.

In the first chapter we combined previously developed techniques, used to assess prokaryotic host─phage interactions, to implement VirusFISH for detecting specific virus─host dynamics, using as a model system the photosynthetic picoeukaryote Ostreoccocus tauri and its virus OtV5. With the VirusFISH technique, we could also monitor the infection, as well as quantify the free viruses produced during the lysis of the host in a non-axenic culture, which allowed the calculation of the burst size. This study set the ground for the application of the VirusFISH technique to natural samples.

In the second chapter of this thesis, we applied VirusFISH to seawater samples from the Bay of Biscay (Cantabrian Sea) to study the dynamics of viral infection in natural populations of Ostreococcus along a seasonal cycle. We were able to quantify the percentage of cells infected over time, and compared these results with the transcriptional viral and host activities derived from metatranscriptomic data. This constitutes the first study where a specific viral─host interaction has been visualized and monitored over time in a natural system.

Picoeukaryotes in the ocean are prevalently uncultured, and thus, in the third chapter of this thesis we went an step further to unveil novel viral─host relationships in eukaryotic uncultured hosts. For this purpose, we mined single amplified genomes (SAGs) of picoeukaryotes obtained during the Tara Oceans expedition for viral signatures. We found that almost 60% of the cells analyzed presented an associated virus with narrow host specificity. Some of the viral sequences were widely distributed and some geographically constrained, and they were preferentially found at the deep chlorophyll maximum. Moreover, we found a mavirus virophage potentially integrated in four SAGs of two different lineages, suggesting the presence of virophages is more common than previously thought.

In summary, in this thesis we have implemented and used techniques that allow us to detect and monitor specific virus─host interactions, which is one of the major challenges in marine viral ecology. On the one hand, VirusFISH arises as a powerful technique that can be easily adapted to any host─virus system that has been genome-sequenced. On the other hand, the results obtained with the single cell genomics offer the opportunity to formulate hypothesis based on detected viral─host interactions in uncultured prevalent marine picoeukaryotes, which can be later tested using experimental approaches.

Se han realizado muchos estudios sobre el rol de los virus en ambientes marinos desde el punto de vista de comunidad global, pero es esencial que vayamos hacía una visión más específica de relación virus─hospedador. Por ello, en esta tesis implementamos y aplicamos diferentes metodologías para estudiar interacciones virus─hospedador, centrándonos en picoeucariotas marinos ya que se conoce muy poco de ellos en poblaciones naturales.

En el primer capítulo implementamos la técnica VirusFISH, permitiendo detectar dinámicas específicas virus─hospedador eucarióticos, usando como modelo Ostreococcus tauri y su virus OtV5. VirusFISH permitió monitorizar la infección, cuantificar en un cultivo no axénico los virus libres producidos durante la lisis y calcular el tamaño de explosión. Este estudio estableció la base para la aplicación de VirusFISH en muestras naturales.

En el segundo capítulo aplicamos VirusFISH en muestras de agua natural para estudiar las dinámicas de infección en Ostreococcus. Cuantificamos el porcentaje de células infectadas durante un ciclo estacional y lo comparamos con las actividades transcripcionales de virus y Ostreococcus spp. Este constituye el primer estudio donde se visualiza y monitoriza una interacción específica virus─hospedador en el tiempo en un sistema natural.

En el tercer capítulo descubrimos nuevas relaciones virus─hospedador en células no cultivadas, analizando genomas amplificados individuales de picoeucariotas, encontrando que la mayoría de las células presentaron al menos un virus. Estas secuencias víricas se encontraron preferentemente en el máximo profundo de clorofila, algunas de ellas ampliamente distribuidas por los océanos y otras constreñidas geográficamente. Además, encontramos un virofago mavirus potencialmente integrado en dos linajes distintos, sugiriendo que los virofagos son más comunes de lo que se pensaba.

En resumen, hemos implementado y usado técnicas que nos han permitido detectar y monitorizar interacciones específicas virus─hospedador, uno de los mayores retos en la ecología microbiana marina. Por un lado, VirusFISH surge como una técnica potente que puede ser fácilmente adaptada a cualquier sistema virus─hospedador del cual tengamos el genoma secuenciado. Por otro lado, los resultados obtenidos con la genómica de célula individual muestran la oportunidad de formular hipótesis basadas en interacciones virus─hospedador detectadas en picoeucariotas marinos no cultivados, que pueden ser posteriormente testadas mediante aproximaciones experimentales.