Ecology of Marine Diatoms through Omics: From Community Structure to Single Species Investigation

Campese, Lucia (2022). Ecology of Marine Diatoms through Omics: From Community Structure to Single Species Investigation. PhD thesis The Open University.

DOI: https://doi.org/10.21954/ou.ro.00015203

Abstract

Diatoms are a major component of marine phytoplankton and play a key role in global elemental cycles and marine food webs. Their ecological success relies to their underlying genetic and functional diversity, both at community and single species levels; despite their importance, diatoms’ biology and ecology is far from being completely understood, given the scarcity of global-scale observations and the large number of uncultured species. The general aim of my thesis was to explore diatom global-scale diversity from community to species level by applying and developing different methodological frameworks. This study was mainly based on metabarcoding, metagenomic and metatranscriptomic data sets provided by Tara Oceans and Tara Oceans Polar Circle expeditions. I first described diatom communities from a statistical perspective to provide a general overview of the macroecological structure of different types of High Throughput Sequencing data. I further investigated diatom diversity across the currents that bring waters from the North Atlantic to the Arctic Ocean; I here characterized taxonomic composition of communities, along with the description of the main environmental features that shape diatom assemblages. Moreover, I described how the expression of functional genes involved in iron uptake, transport and varied across the sampling sites. I then moved to a lower taxonomic rank and focused on a single genus, i.e., Pseudo-nitzschia, one of the most abundant and ubiquitous diatom genera that includes toxigenic species responsible of harmful blooms. I described Pseudo-nitzschia biogeography at global scale at high taxonomical resolution and explored its ecology through links to abiotic and biotic factors, with a particular focus on the interactions with bacteria. Finally, I performed a functional analysis of a set of genes whose expression in diatoms is strongly up-regulated during sexual reproduction; by integrating a phylogeny-based approach, I tested the role of these genes as potential molecular markers to detect sexual reproduction events in diatom natural populations.

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