DOCSLIB.ORG

Luo Hawii 0085A 10752.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Luo Hawii 0085A 10752.Pdf VIRAL DIVERSITY AND DYNAMICS IN THE OPEN OCEAN By Elaine Luo H. B. Sc., University of Toronto, 2014 A dissertation submitted in partial fulfillment of requirements for the degree of DOCTOR OF PHILOSOPHY in MARINE BIOLOGY at the UNIVERSITY OF HAWAI‘I AT MĀNOA May 2020 Dissertation committee: Edward DeLong, chairperson Kyle Edwards Grieg Steward Edward Ruby David Karl Keywords: marine microbiology, open ocean, bacterioplankton, bacteriophages, virioplankton, sediment trap, marine snow, metagenomics, long-read sequencing This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ ii DEDICATION To my mom, born to teenage parents in rural China during the Cultural Revolution, Who watched her younger sister die from malnutrition in her mother’s arms, Whose sunspots reflect her childhood, reading the fields and the chickens, carrying firewood to keep her three brothers warm, Who refused to apologize for birthing a daughter, when her husband and his family wanted a son, Who found creative ways to get me vaccinated while corruption lined pockets; was a life less than, in a country of a billion? Whose burn scars lay tribute to the price she paid for marriage, Who, speaking no English, determined to move to Canada, Who, with no education, learned the TOEFL and the GED, Who, as a single mom, worked full-time and put food on the table, Who, always a penny-pincher, spent $150 to frame my undergrad diploma, Whose eyes sparkle when she mentions what I am doing now, reminding me of how lucky I am to be here, inspiring me to seize the days that she never had. iii ACKNOWLEDGEMENTS First and foremost, I thank Edward DeLong for being an exemplary advisor. Throughout my PhD, his curiosity, enthusiasm, and positive attitude created a healthy environment for personal growth where I feel encouraged to try, and fail too. Witnessing Ed’s fairness, ethics, diplomacy, lab management, and open communication style taught me skills that I will continue to value beyond my PhD. I am deeply appreciative of the opportunity to learn and work in the DeLong lab. I am grateful to committee members Kyle Edwards, Grieg Steward, Edward Ruby, and David Karl for their continuous contribution and support throughout my PhD. This dissertation was enriched by their inquisitive questions and various expertise: Kyle on ecological and statistical models, Grieg on viral literature and tangential flow filtration, Ned on hypothesis generation and experimental design, and Dave on biogeochemistry and background research on Station ALOHA. I value the opportunity to interact with such an inspirational group of scientists. Thanks to all current and former DeLong lab members for creating a collaborative and exciting work environment during my time here: Frank Aylward, Dominique Boeuf, Jessica Bryant, Andrew Burger, Bethanie Edwards, John Eppley, Carla Gimpel, Andy Leu, Fuyan Li, Daniel Mende, Dan Olson, Kirsten Poff, Anna Romano, Paul Den Uyl, and Alice Vislova. In particular, I am deeply grateful to Anna for being an amazing mentor in the lab and beyond. I iv will always remember her inspiring and meticulous work ethics, and her encouragement of my personal growth exceeded any expectations of a colleague. I am grateful to Frank for being such a stellar postdoctoral mentor during our work together on Ch. II. His curiosity and openness for discussion fostered an exciting and enriching work environment. I am grateful to Jessica Bryant and Oscar Sosa for their mentorship, and I thoroughly enjoyed our interactions both in and outside the office. Special thanks to the HOT program and SCOPE-OPS team for oceanographic expeditions and sampling. Tara Clemente, Susan Curless, and Dan Sadler were exemplary Chief Scientists who insured smooth operations on the oceanographic cruises I participated in. Thanks to Ryan Tabata, Tim Burrell, and Eric Shimabukuro for collecting samples that were vital to Ch. III and showing me the ropes on cruise operations. Many thanks to Tara Clemente, Blake Watkins, Eric Grabowski for sediment trap deployment, collection, and biogeochemical analyses for samples used in Ch. IV. I would like to thank collaborators John Beaulaurier at Oxford Nanopore Technologies, as well as Ashley Coenen, Daniel Muratore, and Steven Beckett in the Joshua Weitz lab, for exciting discussions in the field of studying marine viruses. I appreciate the opportunity to interact with and learn from their diverse expertise. v I would like to thank Chris Schvarcz for mentorship on epifluorescence microscopy and tangential flow filtration. His enthusiasm and willingness to offer help is deeply appreciated. Thanks to Tina Carvalho at the UH Biological Electron Microscope Facility for guidance on transmission and scanning electron micrography. The micrographs that she helped produce look amazing. Many thanks to the C-MORE o’hana for creating such an awesome work environment in the Hale and camaraderie during oceanographic cruises. Special thanks to my undergraduate advisors James Thomson and Lauren Mullineaux for taking me under their wings. I would not have entered a research trajectory without their dedication to providing excellent undergraduate mentorship. I am deeply grateful for their commitment to offering funded undergraduate opportunities, which makes it possible for students from diverse backgrounds to pursue research. Funding for this dissertation was generously provided by the Simons Foundation (SCOPE #329108 to Edward DeLong), Gordon and Betty Moore Foundation (GBMF 3777 to Edward DeLong), and the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016 to me). vi ABSTRACT In the open oceans that cover roughly 40% of our planet, viruses influence ecosystem dynamics, microbial diversity, and biogeochemical cycling. By infecting and killing cellular hosts, viruses transform organic matter from living cells into dissolved and particulate pools that fuel organic matter recycling and export. Despite their importance, viruses in the environment remain unexplored relative to other microbes, particularly in the under-sampled open oceans that might contain large reservoirs of novel viral diversity. For example, some fundamental questions remain open in this field: how many different viral populations coexist in the open ocean, what novel genes do they encode, and how do viral diversity and virus-host interactions vary from the surface to the deep ocean, or between free-living and particle-attached habitats? To address these questions, I explored the diversity and dynamics of viruses in the open ocean, from planktonic assemblages in the upper ocean to sinking particles in the deep sea. In this body of work, I used metagenomic approaches to study viruses sampled from Station ALOHA located in the North Pacific Subtropical Gyre. From roughly 7 TB of sequencing data, I recovered over 17,000 viral population genomes, at least 9,000 of which were novel with respect to what has been studied before. I explored how viral diversity, viral reproductive strategies, and virus-host interactions varied across vertical gradients along the open ocean water column to better understand viral effects on ecosystem dynamics and biogeochemical cycling. The culmination of these projects reveals the diversity and dynamics of viruses that represent some of the most abundant yet understudied life forms in the ocean. vii TABLE OF CONTENTS Acknowledgements……………………………………………………………………iv Abstract…………………………………………………………………………………vii List of abbreviations and symbols…………………………………………………. xv Chapter 1. Background and rationale………………………………………………...1 Overview………………………………………………………………………… 1 The open oceans………………………………………………………………… 1 Station ALOHA…………………………………………………………………. 3 Importance of microbes in marine ecoystems……………………………….. 5 Importance of viruses in marine ecosystems………………………………… 7 History of marine virus research…………………………………………….. 10 Dissertation overview………………………………………………………… 13 Figures………………………………………………………………………….. 19 Figure 1.1. Station ALOHA…………………………………………... 19 Figure 1.2. Epifluorescence micrograph of SYBR gold-stained seawater samples from Station ALOHA……………….. 20 Figure 1.3. Transmission electron micrographs of putative bacteriophages at Station ALOHA……………………... 21 Figure 1.4. Some viral reproductive strategies……………………... 22 Figure 1.5. Viral reproductive strategies alternative to lysis and lysogeny…………………………………………………… 23 References……………………………………………………………………….24 Chapter 2. Bacteriophage distributions and temporal variability in the ocean’s interior…………………………………………………………………………………..32 Abstract………………………………………………………………………….32 viii Importance……………………………………………………………………... 33 Introduction……………………………………………………………………. 34 Results and discussion………………………………………………………... 37 Novel ALOHA viral genomes, genome fragments, and AMGs….. 37 Phage genotype distributions in the Station ALOHA time series depth profile…………………………………………………………… 39 Genomic trends in lytic vs. lysogenic viral life-history…………….41 Ecology of surface and mesopelagic phage………………………… 44 Conclusions……………………………………………………………………..47 Materials and methods………………………………………………………...47 Study site and sample collection……………………………………...47 Genome-centric approach Assembling ALOHA viral contigs…………………………... 48 Annotating ALOHA viral contigs…………………………… 49 Depth and temporal distributions…………………………… 49 Mapping to reference genomes……………………………….50 Detection of novel phage genes and AMGs…………………50 Gene-centric approach Phage and cell-associated gene catalogue
Load more

Recommended publications
  • Oceans of Archaea Abundant Oceanic Crenarchaeota Appear to Derive from Thermophilic Ancestors That Invaded Low-Temperature Marine Environments
    Oceans of Archaea Abundant oceanic Crenarchaeota appear to derive from thermophilic ancestors that invaded low-temperature marine environments Edward F. DeLong arth’s microbiota is remarkably per- karyotes), Archaea, and Bacteria. Although al- vasive, thriving at extremely high ternative taxonomic schemes have been recently temperature, low and high pH, high proposed, whole-genome and other analyses E salinity, and low water availability. tend to support Woese’s three-domain concept. One lineage of microbial life in par- Well-known and cultivated archaea generally ticular, the Archaea, is especially adept at ex- fall into several major phenotypic groupings: ploiting environmental extremes. Despite their these include extreme halophiles, methanogens, success in these challenging habitats, the Ar- and extreme thermophiles and thermoacido- chaea may now also be viewed as a philes. Early on, extremely halo- cosmopolitan lot. These microbes philic archaea (haloarchaea) were exist in a wide variety of terres- first noticed as bright-red colonies trial, freshwater, and marine habi- Archaea exist in growing on salted fish or hides. tats, sometimes in very high abun- a wide variety For many years, halophilic isolates dance. The oceanic Marine Group of terrestrial, from salterns, salt deposits, and I Crenarchaeota, for example, ri- freshwater, and landlocked seas provided excellent val total bacterial biomass in wa- marine habitats, model systems for studying adap- ters below 100 m. These wide- tations to high salinity. It was only spread Archaea appear to derive sometimes in much later, however, that it was from thermophilic ancestors that very high realized that these salt-loving invaded diverse low-temperature abundance “bacteria” are actually members environments.
    [Show full text]
  • Link to the Report
    DISCLAIMER This report was prepared as an account of a workshop sponsored by the U.S. Department of Energy. Neither the United States Government nor any agency thereof, nor any of their employees or officers, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of document authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. Copyrights to portions of this report (including graphics) are reserved by original copyright holders or their assignees, and are used by the Government’s license and by permission. Requests to use any images must be made to the provider identified in the image credits. On the cover: Argonne National Laboratory’s IBM Blue Gene/P supercomputer Inset visualization of ALG13 courtesy of David Baker, University of Washington AUTHORS AND CONTRIBUTORS Sponsors and representatives Susan Gregurick, DOE/Office of Biological and Environmental Science Daniel Drell, DOE/Office of Biological and Environmental Science Christine Chalk, DOE/Office of Advanced Scientific
    [Show full text]
  • Profile of Edward Delong Paul Gabrielsen Enzymes Among Four Genera of Marine Bac- Science Writer Teria and Infer Evolutionary Relationships
    PROFILE PROFILE Profile of Edward DeLong Paul Gabrielsen enzymes among four genera of marine bac- Science Writer teria and infer evolutionary relationships. “That’s where the inkling started that I Every year, gray whales travel up and down Finding Himself could combine my interests in biology and my passion for the ocean,” DeLong says. “I the Pacific coast, migrating between the Born in 1958, the third of six children, hadn’t even realized up until that point that Bering Sea and Baja California. In the mid- DeLong grew up in Sonoma, California on an research was an option.” The findings were 1970s, Northern California amateur skin “overdose of Jacques Cousteau,” he says. As diver Edward DeLong tried to swim out to published in the Archives of Microbiology a teenager, he encountered sea lions and sea with DeLong as first author (1). meet them. With his sights set on some of otters on skin diving expeditions with friends, ’ the ocean s largest creatures, DeLong was and attempted to reach gray whales. “We Setting His Compass oblivious to the microecosystem swirling never actually met them face to face,” he says. DeLong arrived at the Scripps Institution of around him in the cool water. Instead, his DeLong’s father, a high school English Oceanography in 1982 to begin graduate fascination for the vast and mysterious ocean teacher, encouraged his children in academ- school. Under biophysicist Art Yayanos, impelled him to reach for the huge, shadowy ics, but 18-year-old DeLong did not feel DeLong studied pressure-adapted micro- whales in the distance.
    [Show full text]
  • MMI Evaluation Summary Report June 2013
    SUMMARY1 OF AAAS 2012 EVALUATION OF THE GORDON AND BETTY MOORE FOUNDATION’S MARINE MICROBIOLOGY INITIATIVE, PHASE 1 (2004–2010) BACKGROUND Oceans account for ~70% of Earth’s surface. Primary productivity, many chemical cycles, and food webs depend on the ocean’s microorganisms, which also convert carbon, nitrogen, sulfur, and trace minerals like iron from inorganic to biologically usable forms. We know that these important marine systems and processes Box 1. Marine microbial ecology defined have been experiencing unprecedented stress due to Marine microbial ecology is the study of increased nutrient run-off, overfishing, and pervasive and the single-celled organisms (bacteria, significant changes in ocean chemistry and temperature archaea, and eukaryotes) and viruses that live in the ocean and their interactions driven by increased emissions of greenhouse gases, yet our with each other and the environment specific knowledge is limited. Despite the fact that research around them. These microorganisms and in this field began more than 75 years ago, as recently as viruses are the ocean’s smallest and most the early 2000s, even the most basic ecological questions— abundant creatures, and they drive many Which organisms are present? What do they do? How do of the chemical reactions that comprise they interact?—remained unanswered due primarily to the Earth’s marine biogeochemical cycles. major obstacles such as: • An inability to grow most microbes in culture in tandem with limited morphological characteristics capable of differentiating species, creating a major taxonomic impediment resulting in treatment of broad groups of microbes as “black boxes” with little knowledge of the role of each species.
    [Show full text]
  • Reviewer Biographies
    Biosciences Area Review 2015 Lawrence Berkeley National Laboratory Reviewer Biographies Janet Braam, Ph.D., Rice University Janet Braam has a diverse scientific background, being involved in research that spans from translation medical research to basic plant cell biology. She received her PhD in Molecular Virology and Biology from the Sloan-Kettering Division of the Cornell Graduate School of Medical Sciences, elucidating the roles of influenza viral polymerase subunits. She then joined Stanford University School of Medicine as an NSF postdoctoral fellow in plant biology. Dr. Braam’s research at Stanford led to the discovery that plants turn on genes in response to touch and shed light on the importance of calcium signal transduction in mechanical perturbation responses in plants. In 1990, Dr. Braam joined the faculty at Rice University and rose through the ranks. She has had continual federal grant support and served on diverse grant and advisory panels Dr. Braam’s research contributions include uncovering roles of calcium-binding and cell wall proteins in plant responses to environmental stress, and elucidating aspects of nitric oxide signaling, autophagy regulation, and jasmonate dependent defense. Most recently, her research focus also includes the role of the circadian clock in plant defense, the complex regulation of chlorophyll biogenesis, phytohormone regulation, and autophagy control. Her discoveries in basic plant biology have potential translational application in drug discovery, crop nutrient enhancement, and nanomaterial toxicity analysis in plants. Charles Craik, Ph.D., University of California, San Francisco Charles S. Craik is a Professor in the Department of Pharmaceutical Chemistry at the University of California at San Francisco.
    [Show full text]
  • CURRICULUM VITAE DANIEL JAMES REPETA Senior Scientist
    CURRICULUM VITAE DANIEL JAMES REPETA Senior Scientist Department of Marine Chemistry & Geochemistry Woods Hole Oceanographic Institution Woods Hole, MA 02543 Tel.: (508) 289-2635 Fax: (508) 457-2075 (Watson Lab) E-Mail: [email protected] (internet) Education: B.S., Chemistry, University of Rhode Island, September 1977 Ph.D., Chemical Oceanography, Massachusetts Institute of Technology/Woods Hole Oceanographic Institution, September 1982 Professional Experience: NIH Postdoctoral Research Fellow, Columbia University, 1983 NATO Postdoctoral Fellow, Institute du Chimie, Universite Louis Pasteur, Strasbourg, France, 1984 Assistant Scientist, Department of Chemistry, Woods Hole Oceanographic Institution, 1985 to 1989. Associate Scientist, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 1989 to 1998 Senior Scientist, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 1998-present Chair, Department of Marine Chemistry and Geochemistry, 2010 Awards and Fellowships: WHOI Vetleson Award, 2004 Stanley W. Watson Chair in Oceanography, 2000 National Institutes of Health, National Research Service Award, 1983-1984 NSF/NATO Postdoctoral Fellowship Award, 1982 Paul Fye Award for Best Student Paper, MIT/WHOI Joint Program, 1982 Phi Beta Kappa, Graduated Highest Distinction, University of Rhode Island, 1977 Analytical Chemistry Award, URI Chapter of the American Chemical Society, 1976 Research Interests: Cycling of organic matter in seawater and sediments. Chemistry and biochemistry
    [Show full text]
  • Virginia Rich [email protected] 393 Broadway #20 • Cambridge, MA 02139 • 617-694-5087
    V. Rich, p. 1 Virginia Rich [email protected] 393 Broadway #20 • Cambridge, MA 02139 • 617-694-5087 RESEARCH INTERESTS I am interested in understanding the dynamic link between microbial community ecology and global biogeochemistry. In my thesis work I am applying a novel microarray platform to track the changes in marine microbial communities across environmental gradients, in concert with metagenomics analyses, and have previously examined changes in terrestrial methane-oxidizing microbial communities under simulated global change conditions. My goal is to continue to map these complex interactions, since we remain far from understanding their baseline conditions. In addition, I’d like to incorporate a personal or collaborative emphasis on modelling, prediction and potential remediation opportunities. EDUCATION Massachusetts Institute of Technology, Joint Program with the Woods Hole Institute of Oceanography Ph.D. candidate, expected completion date March 2008 Co-advisors: Ed DeLong, MIT, and George Somero, Stanford Committee members: Martin Polz, MIT, Sonya Dyhrman, WHOI University of California at Berkeley B.A. Molecular and Cell Biology, emphasis Genetics B.A. Integrative Biology PUBLICATIONS Rich, V, DeLong EF. A “genome proxy” oligonucleotide microarray for marine microbial ecology. Manuscript in preparation. Preston, CM, Suzuki M, Rich V, Heidelberg J, Chavez F, DeLong EF. Detection and distribution of two novel form II RuBisCos in the Monterey Bay. Manuscript in preparation. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 311:496-503. Horz, H-P, Rich V, Avrahami S, and Bohannan BJ.
    [Show full text]
  • International Census of Marine Microbes 1St Annual Meeting June
    International Census of Marine Microbes 1st Annual Meeting June 12th-15th, 2006 NH Leeuwenhorst Noordwijkerhout, The Netherlands Meeting Organizers Principal Investigators Mitchell L. Sogin Marine Biological Laboratory (MBL) Jan W. de Leeuw The Royal Netherlands Institute for Sea Research (NIOZ) Secretariat Linda Amaral-Zettler (MBL) Scientific Organizing Committee Gerhard Herndl (NIOZ) David J. Patterson (MBL) Stefan Schouten (NIOZ) Lucas Stal (NIOO) Staff Coordinator Trish Halpin (MBL) 1 Table of contents: Programme, logistics and hotel information 3 Programme 4 List of Participants 11 Research Summaries 19 ICoMM Science Plan 62 Working Group Reports 77 Technology WG 78 Benthic Systems WG 92 Open Ocean and Coastal Systems WG 105 Informatics and Data Management WG 128 2 Programme and Logistics 3 International Census of Marine Microbes 1st Annual Meeting Agenda June 12th-15th, 2006 NH Leeuwenhorst Noordwijkerhout, The Netherlands Monday, June 12th, 2006 All day Arrival at NH Leeuwenhorst, Noordwijkerhout 1700: ICoMM Scientific Organizing Committee (SOC) Meeting 1700-1900: Poster Set-up 1900-2100: Icebreaker party/reception with drinks and food. Tuesday, June 13th, 2006 0830: Welcome, logistics, purpose of the meeting (Baross, Sogin, de Leeuw, Amaral Zettler) 0900: Sogin/de Leeuw: Meeting the ICoMM Challenge, Unfathomable microbial diversity in the deep sea: an unexplored “rare biosphere” 1000: Coffee Break 1030 Carles Pedrós-Alió: Marine microbial diversity: can it be determined? (30 minutes) 1100: Slava Epstein: Rarefaction (30 minutes)
    [Show full text]
  • Press Release Wednesday July 2, 2008
    Press Release Wednesday July 2, 2008 New Pathway for Methane Production in the Oceans Honolulu, HI – A new pathway for methane production has been uncovered in the oceans, and this has a significant potential impact for the study of greenhouse gas production on our planet. The article, released in the prestigious journal Nature Geoscience, reveals that aerobic decomposition of an organic, phosphorus-containing compound, methylphosphonate, may be responsible for the supersaturation of methane in ocean surface waters. Methane is a more potent greenhouse gas than CO2 on a per weight basis. Although the volume of methane in the atmosphere is considerably less than CO2, methane is much more efficient at trapping the long wavelength radiation that keeps our planet habitable but is also responsible for enhanced greenhouse warming. Today, between 20- 30% of the total radiative forcing of the atmosphere is due to methane. Terrestrial sources of methane production are well known and studied (including extraction from natural gas deposits and fermentation of organic matter), but those known sources did not account for the levels of methane observed in the atmosphere. David Karl, an Oceanographer in the School of Ocean and Earth Science and Technology at the University of Hawaii at Manoa and lead author of this paper, was interested in this “methane enigma” and why the surface ocean was loaded with methane, over and above levels found in the atmosphere. When looking at the literature, Karl found a possible solution to the A conceptual view of the role of sunlight in enigma, in the compound methylphosphonates, a very unusual organic producing methylphosphonate through food‐web compound only discovered in the 1960s.
    [Show full text]
  • Virginia Rich • [email protected]
    V. Rich, p. 1 Virginia Rich • [email protected] Postdoctoral Researcher • University of Arizona • Ecology and Evolutionary Biology Department • Tucson, AZ 85721 • 617-694-5087 RESEARCH INTERESTS I am interested in understanding the dynamic link between microbial communities and global biogeochemistry. My postdoctoral and longer-term research goal is to map complex microbial-ecosystem interactions, and to work with collaborators to incorporate this knowledge into predictive modelling frameworks to allow for practical applications as well as comprehensive ecosystem studies. EDUCATION Massachusetts Institute of Technology, Joint Program with the Woods Hole Institute of Oceanography Ph.D. September 2008 Co-advisors: Ed DeLong, MIT, and George Somero, Stanford Thesis: “Development of a "Genome-Proxy" Microarray for Profiling Marine Microbial Communities, and its Application to a Time Series in Monterey Bay, California”. I developed a novel microarray platform to track the changes in marine microbial communities and applied it across environmental gradients, in concert with metagenomic analyses. University of California at Berkeley B.A. Molecular and Cell Biology, emphasis Genetics B.A. Integrative Biology, graduated 1998 PUBLICATIONS Rich, V, K. Konstantinidis, DeLong EF. Design and testing of “genome proxy” microarrays to profile marine microbial communities. Environmental Microbiology, 10: 506-521. Preston, CM, Suzuki M, Rich V, Heidelberg J, Chavez F, DeLong EF. Detection and distribution of two novel form II RuBisCos in the Monterey Bay. Manuscript in preparation. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. 2006. Community genomics among stratified microbial assemblages in the ocean's interior.
    [Show full text]
  • The Prokaryotes
    The Prokaryotes Eugene Rosenberg (Editor-in-Chief) Edward F. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Applied Bacteriology and Biotechnology Fourth Edition With 132 Figures and 63 Tables Editor-in-Chief Eugene Rosenberg Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv, Israel Editors Edward F. DeLong Fabiano Thompson Department of Biological Engineering Laboratory of Microbiology, Institute of Biology, Center for Massachusetts Institute of Technology Health Sciences Cambridge, MA, USA Federal University of Rio de Janeiro (UFRJ) Ilha do Funda˜o, Rio de Janeiro, Brazil Stephen Lory Department of Microbiology and Immunology Harvard Medical School Boston, MA, USA Erko Stackebrandt Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ISBN 978-3-642-31330-1 ISBN 978-3-642-31331-8 (eBook) ISBN 978-3-642-31332-5 (print and electronic bundle) DOI 10.1007/978-3-642-31331-8 Springer Heidelberg New York Dordrecht London Library of Congress Control Number: 2012955035 3rd edition: © Springer Science+Business Media, LLC 2006 4th edition: © Springer-Verlag Berlin Heidelberg 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work.
    [Show full text]
  • Agouron07 Sym3 Flyer Draft2.Indd
    C•MORE-Agouron Summer Symposia A symposium series on microbial oceanography presented at the University of Hawai‘i linking genomes to biomes Biodiversity, speciation, and the “-omics” of marine microorganisms Moderated by Michael Rappé Symposium 3: Friday, July 27, 2007 8:30 am to 5 pm • East-West Center Asia Room Visit cmore.soest.hawaii.edu/agouron2007/agouron_syllabus.htm for details Within the last 20 years, our perspective on the evolution- However, the extent that this diversity matters to questions ary and physiological diversity of marine microbes has of microbial speciation and biogeochemical and energy been vastly enhanced by the widespread application of cycling in the world’s oceans is not yet clear. molecular biology techniques. The interrogation of both Speakers for this Symposium represent some of the world’s isolated microorganisms and entire microbial communities leading experts on the application of molecular method- via single gene, whole genome, messenger RNA, and pro- ology in investigations of marine microbial diversity, and tein methodology is now fairly routine. In general, these the application of this knowledge to questions of biodiver- studies reveal an astounding level of genetic diversity with- sity, microbial speciation, and biogeochemical cycling in the marine microbial plankton, which is often inferred in the oceans. Please join us for what promises to be an to indicate high diversity in physiology and metabolism. engaging and lively discussion of this important topic. Invited Speakers: Carlos Pedrós-Alió • Instituto de Ciències del Mar in Barcelona Alexandra Worden • University of Miami Saul Kravitz • The Center for the Advancement of Genomics, J. Craig Venter Institute Paul Gilna • Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Janelle Thompson • Massachusetts Institute of Technology Gabrielle Rocap • University of Washington Edward DeLong • Massachusetts Institute of Technology Lunch will be provided, reception to follow.
    [Show full text]