Metagenomes and genomes of the mediterranean sea pelagic microbiota
- Autores: José Manuel Haro Moreno
- Directores de la Tesis: Francisco Rodríguez Valera (dir. tes.), Mario López-Pérez (codir. tes.)
- Lectura: En la Universidad Miguel Hernández de Elche ( España ) en 2019
- Idioma: español
- Tribunal Calificador de la Tesis: Gerhard J. Herndl (presid.), Josefa Antón Botella (secret.), Silvia G. Acinas (voc.), Michael Sacher (voc.), Eva Sintes Elvelin (voc.)
- Programa de doctorado: Programa de Doctorado en Biología Molecular y Celular por la Universidad Miguel Hernández de Elche
- Materias:
- Enlaces
- Tesis en acceso abierto en: RediUMH
- Resumen
The application of genomic tools, commonly known as metagenomics, has represented a revolution in the dawn of the XXI century Microbiology. It allows to directly study microbial assemblages in their habitat, without the isolation and culture of each one of the species present in the sample. Moreover, thanks to the widely used high-throughput sequencing, the assembly of multiple genomes obtained from metagenomes (“MAGs”) have been achieved. The assembly of these MAGs allows a precise assignment of their phylogeny, distribution and, also, their ecology and metabolism. During the development of this Thesis, high-throughput sequencing has been used to study the prokaryotic community present in the off-shore water column of the Mediterranean Sea. The water column is thermally stratified during summer. However, during winter, the water column is mixed, triggering the upwelling of nutrients from mesopelagic waters. Six metagenomic samples were taken from the uppermost 100 m of the stratified (summer) water column at intervals of 15 m deep. Also, two more samples were taken during winter for comparison. By genome recruitment of the novel assembled MAGs and some reference microbes, results showed a marked distribution of microorganisms through the stratified water column. These microbes seemed to be found in layers of no more of 30-m. After comparing the two seasons, results showed a persistent prokaryotic community, although some microbes were to the season-associated, appearing only during summer or winter. Also, the analysis of rhodopsins indicated a sharp gradient of the copy number of this gene, being present in more than half of the prokaryotes in surface waters. From the pool of assembled contigs, a few fragments were detected with genes matching the genome of Ca. Nitrosopumilus, a marine archaeon belonging to the phylum Thaumarchaeota. Besides, in these contigs some common viral genes of the order Caudovirales were detected. Therefore, the second work included in this Thesis is the discovery of the first putative viruses capable of infecting this archaeal group. Lastly, in this Thesis is also included the discovery of eight novel MAGs of marine group III Euryarchaeota (MG-III), six of them collected from the photic zone, and two more from samples collected in the aphotic zone. Due to the fact that there are no cultured representatives of this group, the study of their genomes allowed to obtain information about their phylogeny and abundance in the ocean, indicating that they are ubiquitously distributed but in low numbers. Besides, from their genome, traits about their heterotrophic metabolism were attained.
