The role of microdiversity in aquatic systems

• Autores: Natalia García García
• Directores de la Tesis: Javier Tamames de la Huerta (dir. tes.), Fernando Puente Sánchez (dir. tes.)
• Lectura: En la Universidad Autónoma de Madrid ( España ) en 2023
• Idioma: inglés
• Número de páginas: 231
• Títulos paralelos:
  • El papel de la microdiversidad en ambientes acuáticos
• Tribunal Calificador de la Tesis: Jaime Huerta Cepas (presid.), Alberto Rastrojo Lastras (secret.), Anna Julia Székely (voc.)
• Programa de doctorado: Programa de Doctorado en Microbiología por la Universidad Autónoma de Madrid
• Materias:
  • Matemáticas
  • Física
  • Química
• Enlaces
  • Tesis en acceso abierto en: Biblos-e Archivo
• Resumen

  • The world in which we live would not exist without the microorganisms. In spite oftheir importance in quantity and in a lot of the processes that control the differentplanet ecosystems, we still ignore a lot about them. This is due to the fact thatduring many years, only microorganisms that could be isolated were studied. Newadvances in sequencing methods, as well as in the analysis methodologies, haveraised new questions such as the role of the microdiversity in the preservation ofspecies and their respective microbial communities. Although their relevance hasbeen clearly proved in health disciplines, there are still some questions regarding therole that microdiversity plays in environmental microbial communities. The objective of this dissertation is to throw some light to 1) the characterizationand quantification of the intra-species diversity and 2) the understanding of theirpatterns in two different aquatic environments (freshwaters and solar salterns). Todo that, we have used data from the 16S rRNA gene in the case of freshwaters andmetagenomic data from a solar crystallizer in the saltern. In the first place, we distinguished the different variants within each species ofthe 16S rRNA gene in the freshwater microbial communities using ASVs (AmpliconSequence Variants), which would correspond with the level of microdiversity. Theabundance profile of these variants across the years for the most abundant speciescorrelated well with the variations in environmental factors such as water temperature and dissolved oxygen due mainly to the water column mixings. We calledecotypes to those variants within the same species that are adapted to specific environmental parameters. Likewise, we also observed that species with a higher levelof microdiversity were more persistent and less variable than those with a low microdiversity. Next, we analyzed a time series of samples collected in a crystallizer of a solarsaltern to, using metagenomics, analyze the microdiversity of the most abundantspecies. The lower species diversity of this environment in comparison with othermore complex environments like freshwaters, improved the retrieval of the speciespangenomes. To examine the microdiversity in the most abundant species of thecrystallizer, we used the FST (Fixation Index) to measure the variation in the SNPs(Single Nucleotide Polymorphisms) between pair of samples. We observed that, likein freshwaters, the difference in microdiversity is higher within samples collected inopposite seasons in comparison with those collected in the same season in spite ofsampling one year later, which led us to think in a seasonality in microdiversity. Finally, as a result of this work, two different bioinformatic tools have also beendeveloped. Despite the fact that they have different purposes and are intended fordifferent users profiles, they share that they are user-friendly for the less specializedusers and they include recent advances in the Microbial Ecology area, like the analysis of metagenomes and of microdiversity. On the one hand, M&Ms is a tool aimedto simulate 16S rRNA metagenomic data taking into account the intra-species diversity like in real microbial communities and SQMtools aims to facilitate the analysisand visualization of metagenomic data