The deep sea sediment molecular repository: metagenetic study of past, recent and present micro-eukaryotic communities by ultra-deep sequencing of RNA, DNA and ancient DNA.

Deep sea sediments represent the largest and most mysterious ecosystem on Earth, concealing the real extent of micro-eukaryotic diversity from taxonomists but also from next-generation molecular biologists. Micro-eukaryotic nucleic acids arising both from autochthonous, thriving species as well as from the remains of dead, pelagic organisms accumulate at extremely high concentration in the sediments. During the thesis I will make use of ultra-deep sequencing technologies to characterize the present, recent and past micro-eukaryotic diversities looking both to RNA and DNA contents of the sea floor, paying special attention to biological factors skewing biodiversity estimates. Among the numerous biases impairing environmental metagenetic data is the inevitable occurrence of extracellular DNA, found in extremely high density in abyssal sediments. For a proper representation of thriving species RNA should overcome this hurdle. In fact, this hurdle turns to an advantage due to the high preservation potential of DNA molecules in the environment, allowing the retrieval of ancient sedimentary DNA corresponding to the extracellular DNA fraction that survived total degradation. Thus, my main interest is to improve paleoenvironmental reconstructions of past oceans and climate using molecular tools and along with the study of recent successions (inferred from the comparison of RNA and DNA versions), to predict significant changes that may occur nowadays. Environmental barcoding approaches involving targeted enrichment methods, ultra-deep sequencing and identification of modern deep sea sediment RNA and DNA as well as highly degraded ancient DNA in down core sediments will be applied to SSU rRNA gene sequences of micro-eukaryotic taxa, with a special emphasis on Foraminifera.