Diatom viruses and their role in organic matter cycling in the coastal seas

Viruses are important elements of marine pelagic ecosystems. They actively participate in marine microbial communities by infecting bacteria, archaea, and phytoplankton. The most important effect of viral infection of phytoplankton is the so-called 'viral shunt', in which particulate organic matter in the form of living cells and cell debris is converted to the dissolved form providing a substrate for heterotrophic prokaryotes. This has profound implications for the biological carbon pump (BCP) that are not easily understood. By returning organic material that has accumulated in primary producers to its dissolved form, the transport of carbon through the trophic chain is disrupted while allowing continued growth of phytoplankton in the photic zone. Most of the marine viruses studied are prokaryotic. Viruses that infect eukaryotic phytoplankton are much less well known. Diatom viruses, one of the most abundant and diverse phytoplankton groups responsible for 40% of the world's primary production, were first described only in 2004. To date, about 20 different diatom viruses infecting 7 different genera have been described and characterized. They are all small, about 30nm in size, and harbor either ssRNA or ssDNA genomes. The impact of viral infections on diatom populations can be significant, rivaling that of zooplankton grazing in terms of biomass loss. However, the lack of data and research prevents the integration of viral lysis into studies of phytoplankton community structure and function and the subsequent construction of robust carbon and production models. Thus, there is an urgent need to expand the known universe of diatom viruses, especially for the most important taxa. Diatoms of the genus Pseudo-nitzschia are globally distributed, bloom-forming, and can cause food safety and ecosystem health disruptions through production of the neurotoxin domoic acid. Viruses infecting these diatoms were previously suspected from cross-infection studies with mixed viral communities isolated from natural samples and from a preliminary study I conducted in which transmission electron microscopy (TEM) detected strong evidence for the presence of viruses in a culture of Pseudo-nitzschia calliantha. The overall goal of the proposed research is to develop study systems and protocols for the study of diatom viruses that will open a new level of understanding of plankton ecology, organic matter turnover, diatom life cycles, and infection mechanisms. Specific objectives include: 1. to expand the study of a propagating Pseudo-nitzschia virus host system with native Pseudo-nitzschia cultures of different species and strains from the Gulf of Trieste. 2. characterization of the virus using TEM and state-of-the-art genomic tools, including assembly of the viral genome from shotgun sequencing of culture viromes and mining of existing transcriptomic libraries for viral clues. 3. determining functional features of the virus, such as virus-host growth dynamics, viral titers and burst sizes, and defining host ranges for different strains and species. 4. developing a qPCR assay to track the virus in the environment and in cultures. This information will be used at the end of the project and in subsequent work to integrate into models of ecosystem functioning and organic matter turnover where the viral component is largely absent. The proposer of this research project has demonstrated experience in the molecular study of phytoplankton and, in particular, Pseudo-nitzschia diatoms. Prior work on diatom viruses has given him an understanding of the methodological and theoretical requirements to carry out the proposed activities. He has strong institutional, infrastructural and scientific support from the Marine Biological Station Piran and the Department of Biotechnology and Systems Biology of the National Institute of Biology and the Royal Netherlands Institute for Sea Research.