Abundance and diversity of marine microbial eukaryotes

Abstract

Microeukaryotes are important ecological players in any kind of ecosystem, most notably in the ocean, and it is therefore essential to collect information about their abundance and diversity. To achieve this general goal this thesis was structured in two parts. The first part represents an effort to define our “diversity unit” from studies based on the well-known cloning and Sanger sequencing approach. Basically, we wanted to establish a solid baseline for the second part of the thesis. We started with data from one cruise (Chapter 1) and then continued with the analysis of the complete dataset of 18S rDNA sequences available at that time (Chapter 2). From this analysis we found that the V4 region of the 18S rDNA was a good proxy of the variability of the entire gene. We also determined that the maximal genetic distance for sequences belonging to a same class was 0.25. Once defined this framework, it was used in the second part of the thesis for studying deep ocean microeukaryotes. Thanks to the Malaspina 2010 expedition, we had a comprehensive set of deep samples with associated abiotic and biotic parameters from all over the world. We found that the microeukaryotes abundance averaged 54 cells mL-1 in the mesopelagic layer and 14 cells mL-1 in the bathypelagic layer, and its variability was explained by depth, prokaryotes abundance and oxygen concentration (Chapter 3). Finally, the diversity of deep microeukaryotes was determined by pyrosequencing and metagenomic tags (Chapter 4). The bathypelagic community was mainly composed by Collodaria, Chrysophyceae, MALV-II and Basidiomycota. However, the relative abundance of these classes varies a lot among samples. The variability in community composition between samples was well explained by the water mass they belong and by the abundance ratio between prokaryotes and microeukaryotes