Microbial Ecology of the Oceans

Josep M. Gasol, David L. Kirchman, David L. Kirchman, Josep M. Gasol

• Publisher: Wiley-Blackwell
• Year: 2018
• ISBN:
  9781119107200
• Edition: 1
• Topic: Sciences biologiques
• Subtopic: Microbiologie

The newly revised and updated third edition of the bestselling book on microbial ecology in the oceans

The third edition of Microbial Ecology of the Oceans features new topics, as well as different approaches to subjects dealt with in previous editions. The book starts out with a general introduction to the changes in the field, as well as looking at the prospects for the coming years. Chapters cover ecology, diversity, and function of microbes, and of microbial genes in the ocean. The biology and ecology of some model organisms, and how we can model the whole of the marine microbes, are dealt with, and some of the trophic roles that have changed in the last years are discussed. Finally, the role of microbes in the oceanic P cycle are presented.

Microbial Ecology of the Oceans, Third Edition offers chapters on The Evolution of Microbial Ecology of the Ocean; Marine Microbial Diversity as Seen by High Throughput Sequencing; Ecological Significance of Microbial Trophic Mixing in the Oligotrophic Ocean; Metatranscritomics and Metaproteomics; Advances in Microbial Ecology from Model Marine Bacteria; Marine Microbes and Nonliving Organic Matter; Microbial Ecology and Biogeochemistry of Oxygen-Deficient Water Columns; The Ocean's Microscale; Ecological Genomics of Marine Viruses; Microbial Physiological Ecology of The Marine Phosphorus Cycle; Phytoplankton Functional Types; and more.

• A new and updated edition of a key book in aquatic microbial ecology
• Includes widely used methodological approaches
• Fully describes the structure of the microbial ecosystem, discussing in particular the sources of carbon for microbial growth
• Offers theoretical interpretations of subtropical plankton biogeography

Microbial Ecology of the Oceans is an ideal text for advanced undergraduates, beginning graduate students, and colleagues from other fields wishing to learn about microbes and the processes they mediate in marine systems.

1
INTRODUCTION: THE EVOLUTION OF MICROBIAL ECOLOGY OF THE OCEAN

JOSEP M. GASOL

Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain

DAVID L. KIRCHMAN

School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA

1.1 INTRODUCTION

Microbes are everywhere in large numbers. They were on Earth ca. 4 billion years ago, and they will be on Earth long after multicellular eukaryotes go extinct. In some environments they are the only living beings around because they can thrive in hot and cold environments; they develop inside rocks and can tolerate toxins and ultraviolet (UV) radiation. Covering 3.6 × 10¹¹ km² (71% of the Earth surface) and reaching a depth of 3.7 km on average, the marine habitat is likely the largest ecosystem on Earth. It is where all life started. Today, the ocean habitat is teeming with morphologically, genetically, and functionally diverse microbes. Half of the primary production in the planet occurs in the ocean (Field et al. 1998), 90% of which is done by microorganisms (Duarte and Cebrián 1996). They are also responsible for most of the ocean respiration and are crucial in most, if not all, key transformations in the cycles of nitrogen, phosphorus, sulfur, iron, and other metals.

All these topics and more are part of “microbial ecology of the ocean.” The field has maintained momentum since publication of the first edition of this book in 2000 (Kirchman 2000), and arguably its importance has even increased. There is a journal, Aquatic Microbial Ecology, specifically devoted to the field (also including other aquatic environtments), and leading general journals such as Nature and Science have devoted mini‐reviews and special issues to it (Rees 2005; DeLong 2007; Ash et al. 2008; Lupp 2009; Bork et al. 2015), as have more specialized journals in oceanography and microbiology (Nature Reviews Microbiology, 2007, volume 5; Oceanography 2007, volume 20, issue 2). In addition, funding initiatives supported by public (e.g., the US Joint Genome Institute) and private sources (such as the Gordon & Betty Moore Foundation with its Marine Microbiology Initiative, the Agouron Institute, and the Simons Foundation) have sponsored research in marine microbial ecology. A specific Gordon Research Conference on marine microbes has been running since 2004, again reflecting the current dynamism of the field. It has even been the subject of a cultural anthropology book, which analyzes knowledge and practitioners of microbial oceanography (nearly synonymous with marine microbial ecology) in the context of global culture. It claims that microbes in “alien oceans” have come to be an excellent viewpoint for thinking about humans (Helmrich 2009).

One could also claim that marine microbial ecology is a large fraction of general microbial ecology. For example, about 30% of the habitat‐specific papers published in the ISME Journal during 2015 were partially or totally marine, here including sediments, estuaries, and high‐salinity systems. Also microbial research is a large part of marine sciences; about one‐third of the papers in Annual Review of Marine Sciences between 2009 and 2015 are about microbes.

Marine microbial ecology is one of the most dynamic scientific fields because it is at the crossroads of many disciplines such as oceanography, biogeochemistry, microbiology (including protistology and virology), physiology, evolution, and genomics. Being at a crossroad implies that a current practitioner of the field should have working and conceptual knowledge in all these fields, in addition to practical skills in bioinformatics and statistics (and microscopy). All these fields have advanced greatly in the last few years as have the temporal and spatial scales the researchers study. Microbial ecologists now consider spatial scales ranging from the global ocean, the ocean basins, or a particular ecosystem to the interactions at the microscale or even inside a cell, as is apparent in the different chapters of this book. The temporal scales are also diverse, from the hourly or the diel changes in activity, to the seasonal or interannual scale, including the effects of long‐term global change on the dynamics, activity, and diversity of microbes, or even the short‐ or long‐term evolution of marine microbes. The focus of interest also varies. Although the organisms tend to occupy the central point, some studies are more centered on the communities (so‐called “microbiomes”), whereas others focus on the environment (how the communities are structured in or within environments, rooted in “hard” ecology). Still other studies tend to skip the cellular level (or the species level) and focus on the gene level. This variety of approaches, this diversity of focuses, is what constitutes the field of marine microbial ecology. For this reason the field has been christened with the motto “from genomes to biomes” (Karl 2007; DeLong 2009) to reflect the wide range of scales and methodological approaches currently used (Fig. 1.1).

Fig. 1.1 The subject of marine microbial ecology. Organisms and communities are studied in the framework set by oceanography, while genes and organisms determine the biogeochemical effect of microbial communities. Genes and organisms also determine the physiological response to the environment. In addition, genes and organisms evolve with time, and communities and their biogeochemical effects are subject to ecosystem dynamics, most notably those forced by global change.

Modified after DeLong (2009).

This introduction tries to put this book in the context of what has happened in the field in recent years. We evaluate the current state of the field and highlight some approaches or questions that are at its center and end with some predictions of what issues or approaches will dominate in the coming years.

1.2 A BRIEF HISTORY OF MARINE MICROBIAL ECOLOGY

The following historical account highlights some major developments in marine microbial ecology and discusses changes in our ideas about the role of microbes in the biology and ecology of the oceans. The account also discusses the ways in which microbial ecologists have practiced their science over the years (Table 1.1). What follows is focused on carbon (C), nitrogen (N), and phosphorus (P) biogeochemistry and is strongly planktocentric.

TABLE 1.1 History of marine microbial ecology, focusing on the water column

Year	Concept	Key References	Cits.
1959	Early direct count method reveals much larger numbers of bacteria than indicated by traditional plate counts, later termed the “Great Plate Anomaly.”	Jannasch and Jones (1959)	262
1966–1970	Incorporation of organic matter in the oceans occurs mostly in the bacterial‐size fractions	Williams (1970)	166
1974–1977	More bacteria in the ocean than previously thought	Hobbie et al. (1977)	3856
1978	More active bacteria than suggested by the difference between total plate counts	Meyer‐Reil (1978)	169
1979	Large numbers of cyanobacteria (Synechococcus) in the ocean	Waterbury et al. (1979) Johnson and Sieburth (1979)	600 430
1980	Bacterial growth and biomass production is substantial	Hagström et al. (1979) Fuhrman and Azam (1980)	345 769
1981	Large fraction of respiration in the oceans is by bacteria	Williams (1981)	117
1982	Bacteria are actively predated particularly by heterotrophic nanoflagellates	Johnson and Sieburth (1982) Fenchel (1982)	216 491
1982	Dilution approach for estimating phytoplankton growth and grazing	Landr...

Table of contents

• COVER
• TITLE PAGE
• TABLE OF CONTENTS
• PREFACE
• CONTRIBUTORS
• 1 INTRODUCTION
• 2 MARINE MICROBIAL DIVERSITY AS SEEN BY HIGH‐THROUGHPUT SEQUENCING
• 3 ECOLOGICAL SIGNIFICANCE OF MICROBIAL TROPHIC MIXING IN THE OLIGOTROPHIC OCEAN
• 4 METATRANSCRIPTOMICS AND METAPROTEOMICS
• 5 ADVANCES IN MICROBIAL ECOLOGY FROM MODEL MARINE BACTERIA
• 6 AN INSEPARABLE LIAISON
• 7 MICROBIAL ECOLOGY AND BIOGEOCHEMISTRY OF OXYGEN‐DEFICIENT WATER COLUMNS
• 8 THE OCEAN’S MICROSCALE
• 9 ECOLOGICAL GENOMICS OF MARINE VIRUSES
• 10 MICROBIAL PHYSIOLOGICAL ECOLOGY OF THE MARINE PHOSPHORUS CYCLE
• 11 PHYTOPLANKTON FUNCTIONAL TYPES
• 12 THEORETICAL INTERPRETATIONS OF SUBTROPICAL PLANKTON BIOGEOGRAPHY
• INDEX
• END USER LICENSE AGREEMENT