Analysis of the impact of organic pollutants on marine microbial communities Elena Cerro Gálvez ADVERTIMENT La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del r e p o s i t o r i i n s t i t u c i o n a l UPCommons (http://upcommons.upc.edu/tesis) i el repositori cooperatiu TDX ( h t t p : / / w w w . t d x . c a t / ) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei UPCommons o TDX. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a UPCommons (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. 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Analysis of the impact of organic pollutants on marine microbial communities Elena Cerro Gálvez Doctoral Thesis by compendium of publications Ph.D. Program in Marine Sciences Supervised by Dra. Maria Vila Costa and Dr. Jordi Dachs Marginet Department of Environmental Chemistry (IDAEA-CSIC) Barcelona, 2019 “Educating people to understand, to love and to protect the water systems of the planet, marine and fresh water, for the well-being of future generations.” COUSTEAU, JACQUES YVES “How inappropriate to call this planet Earth when it is quite clearly Ocean.” CLARKE, ARTHUR CHARLES TABLE OF CONTENTS List of figures List of tables List of abbreviations List of publications Abstract / Resumen PART I: GENERAL INTRODUCTION General introduction 27 Organic pollutants (OPs) 27 Description and legacy 27 OPs in the ocean 30 OPs selected in this study 33 Marine microbial communities 42 Interaction between OPs and marine microorganisms 45 Thesis aims 49 A brief overview of methodology 52 Experiments and sampling sites 52 Methodological approaches 53 References 57 PART II: MAIN CHAPTERS Chapter 1 Modulation of microbial growth and enzymatic activities 73 in the marine environment due to exposure to organic contaminants of emerging concern and hydrocarbons Chapter 2 Microbial responses to perfluoroalkyl substances and 117 perfluorooctanesulfonate (PFOS) desulfurization in the Antarctic marine environment Chapter 3 Microbial responses to anthropogenic dissolved organic 153 carbon in Arctic and Antarctic coastal seawaters Chapter 4 195 Part III: EPILOGUE General discussion 239 General conclusions 245 Recommendations for future research 247 References 250 PART IV: Annex Annex I: Supporting information of chapter 1 257 Annex II: Supporting information of chapter 2 271 Annex III: Supporting information of chapter 3 297 Annex IV: Supporting information of chapter 4 331 Acknowledgements LIST OF FIGURES PART I: GENERAL INTRODUCTION Figure 1 Bioconcentration, bioaccumulation and biomagnification concepts. 28 Figure 2 Environmental transport, cycling, and fate of organic pollutants. 31 Figure 3 Heptadecane, as an example of n-alkane with 17 carbon atoms. 33 Figure 4 List of Polycyclic aromatic hydrocarbons (PAHs). 34 Figure 5 List of Organophosphate esters (OPEs). 36 Figure 6 Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA). 37 Figure 7 Overlaid chromatogram of a dissolved phase sample of the aromatic 39 fraction. Figure 8 Schematic illustration of the phylogeny of the major marine Archaea and 43 Bacteria clades. Figure 9 Some of the main approaches available to marine microbial ecologists. 44 Figure 10 Interaction between marine microbial communities and OPs. 48 Figure 11 Map of experiment locations. 52 Figure 12 Summary of techniques used in each chapter. 54 PART II: MAIN CHAPTERS Chapter 1 Figure 1 Location of the sampling stations. 87 Figure 2 Significant differences in cell abundances of heterotrophic bacteria and 91 picophytoplankton. Figure 3 Contribution of each bacterial phylogenetic group (% CARD-FISH). 94 Figure 4 Extracellular enzyme activities. 96 Chapter 2 Figure 1 Changes in microbial activities and community composition in dose- 130 response experiments. Figure 2 Variation of relative abundance of PFOS in the long-term experiment. 133 Figure 3 Changes in microbial community activities and composition between 135 controls and PFAA amendments in long-term experiment. Figure 4 Contribution of each taxonomical group to the total number of transcripts 136 in controls and PFAAs amendments after 24 h and 6 days. Figure 5 Total number of significantly enriched and depleted transcripts detected 139 by edgeR (FDR < 0.05). Figure 6 Relative abundance of transcripts of Sulfur metabolism. 140 Figure 7 Suggested pathways of bacterial PFOS desulfurization. 141 Chapter 3 Figure 1 Enrichment factor of growth rate of prokaryotic community microcosms 167 amended with different ADOC fractions. Figure 2 Abundance of the taxa that increased by 10-fold or were absent in 172 controls. Figure 3 Contribution of genes and transcripts differently present in ADOC 175 treatments versus controls to the total number of genes harboured or expressed by each taxa. Figure 4 Heatmap of changes in gene expression. 176 Figure 5 Schematics of the strategies to cope with hydrophobic ADOC. 181 Chapter 4 Figure 1 Location of the sampling site of the seawater used for the experiments. 208 Figure 2 Relative abundance of transposases. 213 Figure 3 Heatmap of changes between controls and ADOC amendments. 214 Figure 4 Taxonomical affiliation of metagenomes, 24 h after treatment. 218 Figure 5 Summary of up- and down-regulated transcripts detected by edgeR 221 (FDR < 0.05). Figure 6 Summary of Spearman correlations between transposases and 222 significant up- and down-regulated genes. Figure 7 Abundances in the taxa that increased by 10-fold or were absent in 223 controls after 24 h of incubation. Part III: EPILOGUE Figure 1 Interaction between OP and marine bacteria 240 PART IV: Annex Annex I: Supporting information of chapter 1 Figure S1 Concentration of alkanes, PAHs and OPEs in the initial surface waters. 264 Figure S2 Mean cell abundances of heterotrophic bacteria and picophytoplankton 265 in the controls quantified by flow cytometry. Figure S3 Bacterial community composition of initial surface waters quantified by 265 CARD-FISH. Figure S4 Cell-specific EEA in the initial time point for each sampling site. 266 Figure S5 PCA of standardized biological descriptors at the initial time. 266 Figure S6 Pearson’s correlations between microbial growth rates. 267 Annex II: Supporting information of chapter 2 Figure S1 NMDS plot showing the similarities of sample 16S rDNA composition 290 Figure S2 Relative abundance of each taxonomic affiliation by 16S rDNA. 290 Figure S3 Absolute and relative abundance of each taxonomical group in 291 metatranscriptomic profiles Figure S4 Relative abundance of general SEED categories in the 292 metatranscriptomes. Figure S5 Heatmap of changes in sulfur metabolism transcritps. 292 Annex III: Supporting information of chapter 3 Figure S1 Relative abundance of major taxonomic groups in metaG and metaT. 318 Figure S2 Comparison between relative abundance of metaG and CARD-FISH. 319 Figure S3 Taxonomical affiliation of Antarctic and Arctic metaG. 319 Figure S4 Up- and down-regulated gene expression after 0.5 and 24 h. 320 Figure S5 Heatmap of changes in gene expression. 321 Figure S6 Scheme of the main degradation routes of PAHs. 322 Figure S7 Transcript abundances of methylotrophic groups in Arctic experiment. 322 Figure S8 Taxonomical affiliation of Type I phosphodiesterase and Alk_ 323 phosphatase Pfam domains in Arctic experiment. Figure S9 Relative abundances of LPS in metaG and metaT of Arctic experiment. 323 Figure S10 Location of the sampling sites. 324 Annex IV: Supporting information of chapter 4 Figure S1 Growth rates of prokaryotic community amended with different ADOC 336 concentrations after 4, 24 and 48 h. Figure S2 Bacterial production of bacterial community. 337 Figure S3 Percentage of actively-respiring bacteria in the dose-response 338 experiment. Figure S4 Pearson’s correlations between microbial growth rates added 339 concentrations of pollutants.