UC San Diego UC San Diego Electronic Theses and Dissertations Title Bacterial Alteration and Removal of Dissolved Organic Matter in the Surface Ocean / Permalink https://escholarship.org/uc/item/4p25h3mg Author Sherwood, Byron Pedler Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Bacterial Alteration and Removal of Dissolved Organic Matter in the Surface Ocean A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Byron Pedler Sherwood Committee in charge: Professor Farooq Azam, Chair Professor Eric Allen Professor Lihini I. Aluwihare Professor Timithy Baker Professor Forest Rohwer Professor T. Frede Thingstad 2014 Copyright Byron Pedler Sherwood, 2014 All rights reserved. The Dissertation of Byron Pedler Sherwood is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2014 iii DEDICATION To my mother, thank you. iv EPIGRAPH “Aho Mitakuye Oyasin.” -Lakota Sioux v TABLE OF CONTENTS Signature Page ............................................................................................................... iii Dedication ...................................................................................................................... iv Epigraph ......................................................................................................................... v Table of Contents .......................................................................................................... vi List of Abbreviations ................................................................................................... viii List of Figures ................................................................................................................ ix List of Tables ................................................................................................................. xi Acknowledgements ..................................................................................................... xiii Vita .............................................................................................................................. xvi Abstract of the Dissertation ....................................................................................... xviii Chapter 1 Introduction: Microbial control of dissolved organic carbon in the ocean .... 1 1.1 Abstract ......................................................................................................... 2 1.2 Introduction .................................................................................................. 2 1.3 References .................................................................................................... 9 Chapter 2 Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean ...................................................................................................... 15 2.1 Abstract ....................................................................................................... 16 2.2 Significance ................................................................................................ 17 2.3 Introduction ................................................................................................ 17 2.4 Methods ...................................................................................................... 20 2.5 Results ........................................................................................................ 24 2.6 Discussion ................................................................................................... 33 2.7 Conclusion .................................................................................................. 39 2.8 Acknowledgements .................................................................................... 40 2.9 References .................................................................................................. 41 2.10 Appendix: Supporting Information .......................................................... 49 vi Chapter 3 Single strain physiology and community composition of bacteria from coastal and offshore Southern California Bight marine environments ........................ 71 3.1 Abstract ....................................................................................................... 72 3.2 Introduction ................................................................................................ 73 3.3 Methods ...................................................................................................... 74 3.4 Results ........................................................................................................ 81 3.5 Discussion ................................................................................................. 100 3.6 Acknowledgements .................................................................................. 106 3.7 References ................................................................................................ 107 Chapter 4 Physiological and genomic insights into the role of bacterial metabolism on the alteration and efficient removal of marine dissolved organic matter .................. 111 4.1 Abstract ..................................................................................................... 112 4.2 Introduction .............................................................................................. 112 4.3 Methods .................................................................................................... 114 4.4 Results ...................................................................................................... 123 4.5 Discussion ................................................................................................. 136 4.6 Acknowledgments .................................................................................... 145 4.7 References ................................................................................................ 146 vii LIST OF ABBREVIATIONS AFM atomic force microscopy AFSW autoclaved filtered seawater AltSIO Alteromonas strain SIO AMC 7-amino-4-methylcoumarin amol atto (10-18 ) mole ANOVA analysis of variance ANI average nucleotide identity CCE California current ecosystem CHN carbon, hydrogen, nitrogen 12 Ci curie (2.22 × 10 radioactive decays per minute) CO2 carbon dioxide COG cluster of orthologous groups CTD conductivity, temperature, density DAPI 4', 6-diamidino-2-phenylindole DNA deoxyribonucleic acid DOC dissolved organic carbon DOM dissolved organic matter FISH fluorescence in situ hybridization FITC fluorescein isothiocyanate FSW filtered seawater FT-ICR-MS Fourier transform, ion cyclotron resonance, mass spectrometry GF/F glass fiber filter, type F HCl hydrochloric acid KEGG Kyoto Encyclopedia of Genes and Genomes LTER Long-term ecological research MAR-FISH microautoradiography fluorescence in situ hybridization MUF 4-methyl-umbelliferone NA noble agar NPSG North Pacific subtropical gyre OD optical density OTU operational taxonomic unit PCR polymerase chain reaction PES polyethersulfone POM particulate organic matter Pg peta (1015) gram SIO Scripps Institution of Oceanography SW seawater SWC seawater community rDNA ribosomal DNA RNA ribonucleic acid rRNA ribosomal RNA TEM transmission electron microscopy XRMA X-ray microanalysis viii LIST OF FIGURES Figure 1. Bacterial growth, cell C, and DOC consumption of three treatments grown in 0.1 µm filtered coastal North Pacific seawater Bacterial growth, cell C, and DOC consumption of three treatments grown in 0.1 µm filtered coastal North Pacific seawater (A–I) ...................................................................... 26 Figure 2. Bacterial partitioning of coastal surface ocean DOC during three incubation experiments (A–C) ..................................................................................... 29 Figure 3. Long-term carbon drawdown of January 2012 incubation ........................... 30 Figure 4. Growth dynamics of Alteromonas sp. strain AltSIO cocultured with native microbial assemblages in size-fractionated coastal seawater: (A and D) <0.2 µm FSW, (B and E) < 0.8µm FSW, and (C and F) <50 µm FSW ..... 32 Figure S1. Bacterial size frequency distribution in the California Current Ecosystem 59 Figure 5. Overview of cruise CCE P0810 .................................................................... 80 Figure 6. Maximum likelihood tree of phylogentitic distribution of Scripps pier bacterial isolate 16S rRNA ......................................................................... 82 Figure 7. Scripps pier isolate growth in 0.1µm-filtered seawater. .............................. 88 Figure 8. Cluster analysis of 44 samples across CCE A-Front and adjacent flanking water masses from cruise CCE P0810. ....................................................... 93 Figure 9. Summarized results for oxidation of 95 individual substrates by AltSIO relative to phylogentically diverse bacterial strains. ................................. 86 Figure 10. Transmission electron microscopy (TEM) images of non-fixed, non- stained, air-dried Alteromonas sp. AltSIO cells grown in 0.1 µm filtered, aged seawater. ........................................................................................... 126 Figure 11.