2017 Doctorado en Oceanografía Mireia Mestre Mireia Spatial and temporal patterns of marine prokaryotic diversity along the particulate matter continuum Mireia Mestre Martín Barcelona, 2017 Spatial and temporal patternsdiversity of marine prokaryotic along the particulate matter continuum UNIVERSIDAD DE LAS PALMAS DE GRAN CANARIA Facultad de Ciencias del Mar ANEXO I Dª MARÍA ISABEL PADILLA LEÓN, SECRETARIA DE LA FACULTAD DE CIENCIAS DEL MAR, ÓRGANO RESPONSABLE DEL PROGRAMA DE DOCTORADO EN OCEANOGRAFÍA, DE LA UNIVERSIDAD DE LAS PALMAS DE GRAN CANARIA. CERTIFICA Que el Consejo de Doctores del Programa de Doctorado en Oceanografía, en su sesión de fecha 25 de mayo de 2017, tomó el acuerdo de dar el consentimiento para su tramitación, a la tesis doctoral titulada: “Spatial and temporal patterns of marine prokaryotic diversity along the particulate matter continuum ”, presentada por la doctoranda: Dª Mireia Mestre Martín y dirigida por los Doctores: D. Josep M. Gasol i Piqué y Dª M. Montserrat Sala. Asimismo, se acordó el informar favorablemente la solicitud para optar a la Mención Internacional del Título de Doctora, por cumplir los requisitos reglamentarios. Y para que así conste, a efectos de lo previsto en el Artº 6 del Reglamento para la elaboración, tribunal defensa y evaluación de tesis doctorales de la Universidad de Las Palmas de Gran Canaria, firmo el presente en Las Palmas de Gran Canaria, a veinticinco de mayo de dos mil diecisiete . PÁGINA 1 / 1 ID. DOCUMENTO TkzrZnXBDItJmglkpmkRng$$ FIRMADO POR FECHA FIRMA ID. FIRMA 43646105V ISABEL PADILLA LEÓN 24/05/2017 MTIyMzI3 13:49:34 Documento firmado digitalmente. Para verificar la validez de la firma copie el ID del documento y acceda a / Digitally signed document. To verify the validity of the signature copy the document ID and access to https://sede.ulpgc.es/VerificadorFirmas/ulpgc/VerificacionAction.action Anexo II UNIVERSIDAD DE LAS PALMAS DE GRAN CANARIA Departamento/Instituto/Facultad______________________________________ Programa de doctorado____________________________________________ Título de la Tesis Tesis Doctoral presentada por D/Dª___________________________________ Dirigida por el Dr/a. D/Dª. __________________________________________ Codirigida por el Dr/a. D/Dª. ________________________________________ El/la Director/a, El/la Codirector/a El/la Doctorando/a, (firma) (firma) (firma) Las Palmas de Gran Canaria, a _____ de_________________ de 20__ A tothom Contents SUMMARY / RESUM / RESUMEN 15 GENERAL INTRODUCTION 21 AIMS OF THE THESIS 43 CHAPTER1. Patterns of bacterial diversity in the marine planktonic particulate matter continuum 49 CHAPTER 2. Seasonality and dynamics of bacterial community structure along the pelagic particulate matter continuum in a temperate oligotrophic coastal site 85 CHAPTER 3. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum 123 CHAPTER 4. Vertical connectivity in the ocean microbiome: Sinking particles as dispersal vectors 157 GENERAL DISCUSSION AND FUTURE PERSPECTIVES 195 GENERAL CONCLUSIONS 221 SUMMARY IN SPANISH / RESUMEN EN CASTELLANO 225 ACKNOWLEDGEMENTS 235 Contents (extended version) Page SUMMARY .................................................................................................................. 15 Resum ...................................................................................................................................... 16 Resumen ........................................................................................................ ..........................1 7 GENERAL INTRODUCTION ................................................................................... 21 1 Why studing diversity? .......................................................................................................2 1 2 Measuring diversity ............................................................................................................2 2 3 Diversity of prokaryotes in the ocean ................................................................................ 23 4 Particles in the ocean ..........................................................................................................2 4 5 Prokaryotic lifestyles: free-living and attached ................................................................ 24 6 How separation of gree-living and attached prokaryotes is commonly done? .............. 26 7 Sampling proposal .............................................................................................................3 0 8 References ...........................................................................................................................3 2 AIMS OF THE THESIS .............................................................................................. 43 CHAPTER 1. Patterns of bacterial diversity in the marine planktonic particulate matter continuum ......................................................................................................... 49 1.1 INTRODUCTION ............................................................................................................5 0 1.2 MATERIALS AND METHODS .................................................................................... 52 1.2.1 Study area, sampling and basic parameters 1.2.2 DNA extraction, sequencing and sequences processing 1.2.3 Data analysis 1.3 RESULTS .........................................................................................................................5 5 1.4 DISCUSSION ...................................................................................................................6 2 1.5 Acknowledgements ..........................................................................................................6 8 1.6 References .........................................................................................................................6 9 1.7 Supplementary Material.................................................................................................. 75 1.7.1 Supplementary Methods 1.7.2 Supplementary Figures 1.7.3 Supplementary Tables CHAPTER 2. Seasonality and dynamics of bacterial community structure along the pelagic particulate matter continuum in a temperate oligotrophic coastal site 85 2.1 INTRODUCTION ............................................................................................................ 87 2.2 MATERIALS AND METHODS .................................................................................... 89 2.2.1 Study area, sampling and basic parameters 2.2.2 DNA extraction, sequencing and sequences processing 2.2.3 Characterization of the microbial community 2.3 RESULTS .................................................................................................................... ..... 93 2.3.1 Seasonality of the bacterial communities 2.3.2 Diversity changes along 2.3.3 Temporal variability of the preference for a given size class of the dominant taxonomic groups 2.4 DISCUSSION .................................................................................................................1 00 2.4.1 Dynamics of bacterial community composition in the various size fractions 2.4.2 Some bacterial taxonomic groups seasonally mantained the preference for particular size fractions, while others did not 2.5 CONCLUSIONS ............................................................................................................1 05 2.6 Acknowledgements ........................................................................................................1 05 2.7 References ....................................................................................................................... 106 2.8 Supplementary Material................................................................................................ 111 2.8.1 Supplementary Figures 2.8.2 Supplementary Tables CHAPTER 3. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum .................................................................. 123 3.1 INTRODUCTION ..........................................................................................................1 24 3.2 MATERIALS AND METHODS ................................................................................. 126 3.2.1 Sampling and basic parameters 3.2.2 DNA extraction, sequencing and sequences processing 3.2.3 Data analysis 3.3 RESULTS ....................................................................................................................... 129 3.3.1 Environmental setting 3.3.2 Spatial variability of prokaryotic communities 3.3.3 Variability of diversity with depth 3.3.4 Bacterial vs . archaeal vertical variability 3.3.5 Vertical variability of most abundant taxonomic groups 3.4 DISCUSSION .................................................................................................................1 37 3.4.1 Depth is a stronger driver of prokaryotic community structure than station or size- fraction 3.4.2 Communities along the particulate size continuum become more similar with depth 3.4.3 High variability in alpha-, beta- and gamma diversity in the vicinity of the DCM 3.4.4 Bacteria and archaea exhibit opposite patterns of richness along the particulate size continuum and with depth 3.4.5 Most prokaryotic groups maintain their preferences for certain size-fractions through depth 3.4.6 Environmental filtering and/or distinct ecotypes may explain the lack of conserved patterns of