Microbial ecology of the oceans

Microbial Ecology
of the Oceans


Microbial Ecology
of the Oceans
Second Edition

DAVID L. KIRCHMAN
College of Marine and Earth Studies, University of Delaware


Copyright # 2008 by John Wiley & Sons, Inc. All rights reserved.
Published by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific,
Technical, and Medical business with Blackwell Publishing.
No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by
any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted
under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright
Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400, fax 978-750-4470, or
on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the
Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, 201-7486011, fax 201-748-6008, or online at />Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in
preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or
fitness for a particular purpose. No warranty may be created or extended by sales representatives or
written sales materials. The advice and strategies contained herein may not be suitable for your situation.
You should consult with a professional where appropriate. Neither the publisher nor author shall be liable
for any loss of profit or any other commercial damages, including but not limited to special, incidental,
consequential, or other damages.
For general information on our other products and services or for technical support, please contact

our Customer Care Department within the United States at 800-762-2974, outside the United States at
317-572-3993 or fax 317-572-4002.
Wiley also publishes its books in variety of electronic formats. Some content that appears in print may
not be available in electronic format. For more information about Wiley products, visit our web site at
www.wiley.com.
Library of Congress Cataloging-in-Publication Data:
Kirchman, David L.
Microbial ecology of the oceans / [edited by] David L. Kirchman. -- 2nd ed.
p. cm.
Includes bibliographical references and index.
ISBN 978-0-470-04344-8 (pbk.)
1. Marine microbiology. 2. Marine ecology. 3. Carbon cycle
(Biogeochemistry) I. Title.
QR106.M53 2008
5790 .177--dc22
2007051389
Printed in the United States of America
10 9

8 7

6 5

4 3 2

1


CONTENTS
PREFACE

CONTRIBUTORS
1

INTRODUCTION AND OVERVIEW

xv
xvii
1

David L. Kirchman
Eukaryotic Phytoplankton and Cyanobacteria
Photoheterotrophic Bacteria
Dissolved Organic Material
Heterotrophic Bacteria
Marine Archaea
Heterotrophic Protists
Nanoflagellates (2 – 20 mm)
Microzooplanktonic Protists (20 –200 mm)
Dinoflagellates
Marine Fungi
Marine Viruses
N2 Fixers
Nitrifiers and Other Chemolithotrophs
Denitrifiers
Concluding Remarks
Summary
Acknowledgments
References

3

5
7
10
13
14
14
16
16
16
17
18
19
20
21
22
22
23

v


vi
2

CONTENTS

UNDERSTANDING ROLES OF MICROBES IN MARINE
PELAGIC FOOD WEBS: A BRIEF HISTORY

27

Evelyn Sherr and Barry Sherr

3

Introduction
Pre-1950s: The Early Years
1950 – 1974
1970s – 1980s
Improvement in Methods
Bacterial Abundance
Bacterial Activity
Marine Heterotrophic Protists
The “Microbial Loop”
1990 – Present: The Molecular Revolution
Summary
References

27
28
29
32
32
32
33
34
36
39
40
41

BACTERIAL AND ARCHAEAL COMMUNITY
STRUCTURE AND ITS PATTERNS

45

Jed A. Fuhrman and A˚ke Hagstro¨m
Introduction
Major Groups of Prokaryotes in Seawater
“Classically” Culturable Bacteria
The Roseobacter Clade of Marine Alphaproteobacteria
Gammaproteobacteria
Bacteroidetes
Cyanobacteria
“Sea Water” Culturable Bacteria
SAR11 Cluster
Not-Yet-Cultured Bacteria
Marine Gammaproteobacterial Clusters
Actinobacteria
SAR116 Cluster
SAR202
Marine Group A
Marine Group B
Betaproteobacteria
Marine Archaea
Bacterioplankton Diversity
Species Concept

45
47

49
50
51
52
52
55
55
57
57
58
59
59
59
59
59
60
63
63


CONTENTS

4

vii

Microdiversity
Components of Diversity: Richness and Evenness
Community Structure: Description and Factors
Bottom-Up Control

Sideways Control
Top-Down Control
“Kill the Winner” Hypothesis
Temporal Variation (Days to Seasonal)
Short-Term Variation
Seasonal Variation
Spatial Variation
Microscale Patterns
Global Distribution
Latitudinal Gradient and Degree of Endemism
Patchiness and Large Eddies
Summary
References

64
65
67
68
69
70
71
72
72
72
74
74
75
76
77
79

80

GENOMICS AND METAGENOMICS OF MARINE
PROKARYOTES

91

Mary Ann Moran
Introduction
The Basics of Prokaryotic Genomics
Genome Sequence and Assembly
Finding Genes
Finding Operons
Functional Annotation
Tame or Wild? Pure-Culture Genomics Versus Metagenomics
Genomics in Marine Microbial Ecology
The Ecology of Genome Composition
Reverse Biogeochemistry: Discovery of New Ecological
Processes
Environmental Reductionism: New Details About Recognized
Processes
Comparative Genomics and Metagenomics
Future Directions
Summary
Acknowledgments
References

91
92
92

95
96
96
100
103
103
104
106
107
122
125
125
125


viii
5

CONTENTS

PHOTOHETEROTROPHIC MARINE PROKARYOTES

131

Oded Be´ja` and Marcelino T. Suzuki

6

Introduction
Facultative Photoheterotrophy by Unicellular Cyanobacteria

Cyanobacteria as Facultative Heterotrophs
Uptake of Urea and DMSP
Uptake of Nucleosides and Amino Acids
Field Studies Using Light and Dark Incubations
Implications of Facultative Photoheterotrophy
by Cyanobacteria
Marine AAnP Bacteria: Habitats and Diversity
Rediscovery of the Marine AAnP Bacteria
Diversity of AAnP Bacteria
Physiology of AAnP Bacteria
AAnP Bacterial Abundance and Ecological Significance
Proteorhodopsin-Containing Prokaryotes
Proteorhodopsin Genotypes and Taxonomic Distributions
Proteorhodopsin Spectral Tuning
Proteorhodopsin-Containing Prokaryotes:
Abundance and Activity
Proteorhodopsin-Containing Prokaryotes:
Ecological Significance
Summary
References

131
132
132
133
134
135

150
151

151

ECOLOGY AND DIVERSITY OF PICOEUKARYOTES

159

138
139
139
139
140
142
143
144
145
146

Alexandra Z. Worden and Fabrice Not
Introduction
Functional Roles, Classification, and Biological Traits
Photoautotrophs
Heterotrophs and Alternative Lifestyles
Environmental Diversity and Molecular Phylogenetics
Diversity of Uncultured Populations
Methodological Issues for envPCR Studies
Distribution, Abundance, and Activities
Methods for Quantifying Mixed Assemblages
Distribution, Abundance, and Activity of Mixed
Picophytoplankton Assemblages
Quantifying Specific Picoeukaryote Populations

Methodological Challenges to Quantifying Specific Populations
and Resolving Dynamics

159
162
163
170
172
174
178
179
180
182
186
190


CONTENTS

7

ix

Mortality, Contributions to Microbial Food Webs,
and Microbial Interactions
Genomic Approaches to Picoeukaryote Ecology
Integration of Picoeukaryotes to the Microbial Food
Web: Research Directions
Summary
Acknowledgments

References

194
195
196
196

ORGANIC MATTER – BACTERIA INTERACTIONS
IN SEAWATER

207

191
193

Toshi Nagata
Introduction
Organic Matter Inventory and Fluxes
DOM – Bacteria Interactions
Labile Low-Molecular Weight (LMW) DOM
Extracellular Hydrolytic Enzymes
Polymeric DOM—Protein as a Model
Refractory DOM
POM – Bacteria Interactions
POM Continuum
POM Fluxes
POM – Mineral Interactions
Bacterial Community Structure and Utilization of
Organic Matter
Future Challenges

Summary
References
8

PHYSIOLOGICAL STRUCTURE AND SINGLE-CELL
ACTIVITY IN MARINE BACTERIOPLANKTON

207
208
211
211
215
217
220
223
223
223
229
230
231
232
232

243

Paul A. del Giorgio and Josep M. Gasol
Introduction
Distribution of Physiological States in Bacterioplankton
Assemblages
The Concept of “Physiological Structure” of

Bacterioplankton Assemblages
Starvation, Dormancy, and Viability in Marine Bacterioplankton

243
245
245
246


x

CONTENTS

Describing the Physiological Structure of Bacterioplankton
Single-Cell Properties and Methodological Approaches
Operational Categories of Single-Cell Activity
Regulation of Physiological Structure of Marine
Bacterioplankton
Factors Influencing Physiological State of Bacterial
Cells in Marine Ecosystems
Factors Influencing Loss and Persistence of
Physiological Fractions
Distribution of Single-Cell Characteristics in Marine
Bacterioplankton Assemblages
Distribution of Single-Cell Activity and Physiological
States in Marine Bacterioplankton
Simultaneous Determination of Several Aspects
of Single-Cell Activity and Physiology
Patterns in Distribution of Single-Cell Activity and
Physiology Along Marine Gradients

Distribution of Activity and Growth Among
Bacterial Size Classes
Distribution of Activity Across and Within
Major Phylogenetic Groups
Dynamics of Single-Cell Activity and Physiological States
Ecological Implications of Patterns in Bacterioplankton
Single-Cell Activity
Community Versus Individual Cell Growth and
Metabolic Rates
Linking the Distribution of Single-Cell Parameters
and the Bulk Assemblage Response
Ecological Role of Different Physiological Fractions
Concluding Remarks
Summary
Acknowledgments
References
9

HETEROTROPHIC BACTERIAL RESPIRATION

250
250
259
260
261
263
265
265
270
271

273
274
276
279
280
282
283
284
285
285
285
299

Carol Robinson
Introduction
Measurement of Bacterial Respiration and Production
Routine Measurement Techniques for Bacterial
Respiration and Their Limitations
Routine Measurement Techniques for Bacterial
Production and Their Limitations

299
301
301
304


CONTENTS

Magnitude and Variability of Bacterial Respiration

Temporal Variability
Spatial Variability
Relationship Between Bacterial Respiration and
Environmental and Ecological Factors
Bacterial Respiration as a Proportion of Community Respiration
Predicting Bacterial Respiration
Comparison Between Measurements and Predictions
of Bacterial Respiration
Magnitude of Bacterial Respiration in Relation to
Primary Production
Bacterial Respiration in a Changing Environment
Summary
Acknowledgments
References

10 RESOURCE CONTROL OF BACTERIAL DYNAMICS
IN THE SEA

xi
304
308
309
311
315
317
319
321
324
326
327

327

335

Matthew J. Church
Introduction
Growth in the Sea
Growth and Nutrient Uptake Kinetics
Approaches to Understanding Resource Control of Growth
Comparative Approaches
Experimental Approaches for Defining Limitation of
Bacterial Growth
Limitation by Dissolved Organic Matter
Bacterial Growth on Bulk DOM Pools
Limitation by Specific DOM Compounds
Limitation by Inorganic Nutrients
Nitrogen
Phosphorus
Trace Nutrients
Temperature– DOM Interactions
Light
Resource Control of Specific Bacterial Populations in the Sea
Summary
Acknowledgments
References

335
336
339
343

343
349
351
353
354
361
361
364
365
366
368
369
371
371
371


xii

CONTENTS

11 PROTISTAN GRAZING ON MARINE BACTERIOPLANKTON

383

Klaus Ju¨rgens and Ramon Massana
Introduction
New Insights into Phylogenetic Organization
Functional Size Classes of Protists
Natural Assemblages of Marine Heterotrophic Nanoflagellates

Functional Ecology of Bacterivorous Flagellates
Living in a Dilute Environment
Using Culture Experiments to Infer the
Ecological Role of HNF
Impact of Protistan Bacterivory on Marine Bacterioplankton
Search for the Perfect Method to Quantify Protistan Bacterivory
Rates of Protistan Bacterivory in the Sea
Balance of Bacterial Production and Protistan Grazing
Bottom-Up Versus Top-Down Control of Bacteria
and Bacterivorous Protists
Ecological Functions of Bacterial Grazers
Grazing as a Shaping Force of Bacterial Assemblages
Bacterial Cell Size Determines Vulnerability
Towards Grazers
Other Antipredator Traits of Prokaryotes
Grazing-Mediated Changes in Bacterial
Community Composition
Molecular Tools for Protistan Ecology
Culturing Bias and Molecular Approaches
Global Distribution and Diversity of Marine Protists
Linking Diversity and Function for Uncultured
Heterotrophic Flagellates
Summary
Acknowledgments
References

12 MARINE VIRUSES: COMMUNITY DYNAMICS,
DIVERSITY AND IMPACT ON
MICROBIAL PROCESSES

383
386
390
391
394
394
397
401
401
403
404
405
406
408
408
411
413
414
414
420
422
423
424
424

443

Mya Breitbart, Mathias Middelboe, and Forest Rohwer
Introduction
Viruses and the Marine Microbial Food Web

Direct Counts and Viral Numbers

443
444
444


CONTENTS

Viral Production and Decay Rates
Viral Decay and Rates of Production in Pelagic Systems
Measurements of Viral Production in Marine Sediments
General Rates of Viral Production
Role of Viruses in Biogeochemical Cycling
Impact of Viruses on Bacterial Diversity and
Community Dynamics
Marine Viral Diversity
Methods for Examining Marine Viral Diversity
Culture-Based Studies of Viral Diversity
The Need for Culture-Independent Methods
Culture-Independent Studies of Viral Diversity
Using Transmission Electron Microscopy
Whole-Genome Profiling of Viral Communities
Based on Genome Size
Studies of Viral Diversity Using Signature Genes
Metagenomic Studies of Viral Diversity
A Vision for the Future
Summary
References
13 MOLECULAR ECOLOGICAL ASPECTS OF NITROGEN

FIXATION IN THE MARINE ENVIRONMENT

xiii
447
447
449
449
450
452
457
457
458
459
460
461
461
462
466
467
468

481

Jonathan P. Zehr and Hans W. Paerl
Introduction
Chemistry, Biochemistry, and Genetics of N2 Fixation
Genetics and Enzymology
Evolution of N2 Fixation
Phylogeny of Nitrogenase
Genomics of N2 Fixation

Diversity of N2-Fixing Microorganisms
Regulation in Diazotrophs
Methods for Assessing Diazotroph Diversity,
Gene Expression, and N2 Fixation Activity
Ecophysiological Aspects of N2 Fixation
Ecology of Diazotrophs in the Open Ocean
Estuarine and Coastal Waters
Benthic Habitats, Including Microbial Mats and Reefs
Deep Water and Hydrothermal Vents
Summary
Acknowledgments
References

481
482
483
485
487
487
489
489
490
494
499
505
506
507
508
509
509

xiv

CONTENTS

14 NITROGEN CYCLING IN SEDIMENTS

527

Bo Thamdrup and Tage Dalsgaard
Introduction
Inputs
Transformations
Microbes and Microbial Processes
Processes Involving Mn and Fe
Nitrogen Budgets
Benthic Budgets
Oceanic Budgets
Summary
References
INDEX

527
531
532
532
548
550
550

552
554
555
569


PREFACE
It has been nearly 10 years since work started on the first edition of this book. Ten years
is a long time for just about any field of science, but especially for a fast-moving one
such as marine microbial ecology. Here, finally, is the second edition.
This book is more than just a revision of the first edition which was published back
in 2000. Some chapters from that edition are not repeated here, because work in those
areas has slowed and the basic principles covered before have not changed. However,
those topics and principles remain as important and as valid today as 10 years ago,
and readers should hang onto the 2000 book (or get it if they do not have it
already); much of it is still relevant. Other chapters of this book have titles similar
to those in the first edition, but even in these cases, the chapters have been substantially rewritten, often by authors who have different perspectives on the topics
covered previously. Finally, several chapters discuss microbes and biogeochemical
processes that we were just beginning to learn about 10 years ago, and still others
that we did not even know existed back then.
What remains the same is the intended audience: advanced undergraduates, beginning graduate students, and colleagues from other fields wishing to learn about
microbes and the processes they mediate in marine systems. This book, aided by
the first edition, is meant to be as close to a textbook as a multi-authored book can be.
I wish to thank several people who helped to get this book published. First and
most importantly, I thank the chapter authors for agreeing to work on this project
and also for looking over another chapter (or two) in the book. Each chapter was
reviewed by another chapter author and an outsider not connected to the book. I
especially want to thank Jens Boenigk, Hugh Ducklow, Pete Conway, Stefan
Hulth, Rick Keil, Karin Lochte, Alison Murray, Jack Middelburg, Jarone Pinhassi,
Thomas Reinthaler, Janice Thompson, Daniel Vaulot, Tracy Villareal, and Peter

Williams. The anonymous reviewers (and those I’ve forgotten to mention by
name—sorry) also deserve thanks. I greatly appreciated Dave Karl’s support
during a critical junction of this project, and I acknowledge the help of Karen

xv


xvi

PREFACE

Chambers, Thom Moore, and others at Wiley. Finally, I thank the readers of the first
edition of this book. This second edition would not have come about if not for your
positive comments and feedback.
DAVID KIRCHMAN
Lewes, Delaware


CONTRIBUTORS
ODED BE´JA` Faculty of Biology, Technion– Israel Institute of Technology,
Haifa, Israel []
MYA BREITBART College of Marine Science, University of South Florida,
St. Petersburg, FL 33701, U.S.A. []
MATTHEW J. CHURCH Department of Oceanography, University of Hawaii,
Honolulu, HI 96822, U.S.A. []
TAGE DALSGAARD National Environmental Research Institute, University of Aarhus,
DK-8600 Silkeborg, Denmark []
JED A. FUHRMAN Department of Biological Sciences, University of Southern
California, Los Angeles, CA 90089, U.S.A. []
JOSEP M. GASOL Institut de Cie`ncies del Mar, CMIMA (CSIC), Passeig Marı´tim de la

Barceloneta 37– 49, 08003 Barcelona, Catalunya, Spain []
PAUL A. DEL GIORGIO De´partement des Sciences Biologiques, Universite´ du Que´bec
a` Montre´al, CP 8888, succ. Centre Ville, Montre´al, Que´bec, Canada H3C 3P8
[]
˚ KE HAGSTRO¨M
A

Kalmar University, Sweden []

KLAUS JU¨RGENS Leibniz Institute for Baltic Sea Research, 18119 Rostock, Germany
[]
DAVID L. KIRCHMAN College of Marine and Earth Studies, University of Delaware,
Lewes, DE 19958, U.S.A. []
RAMON MASSANA Institut de Cie`ncies del Mar, CMIMA (CSIC), Passeig
Marı´tim de la Barceloneta 37 – 49, 08003 Barcelona, Catalunya, Spain
[]
MATHIAS MIDDELBOE Marine Biological Laboratory, University of Copenhagen,
DK-3000 Helsingør, Denmark []
xvii


xviii

CONTRIBUTORS

MARY ANN MORAN Department of Marine Sciences, University of Georgia, Athens,
GA 30602-3636, U.S.A. []
TOSHI NAGATA Ocean Research Institute, The University of Tokyo, Tokyo, Japan
[]
FABRICE NOT Evolution du Plancton et PaleOceans Laboratory, CNRS, Universite´

Paris 06, UMR7144, Station Biologique de Roscoff, 29682, Roscoff, Cedex
BP 74, France []
HANS W. PAERL Institute of Marine Sciences, University of North Carolina at
Chapel Hill, Morehead City, NC 28557, U.S.A. []
CAROL ROBINSON School of Environmental Sciences, University of East Anglia,
Norwich NR4 7TJ, U.K. []
FOREST ROHWER Department of Biology, San Diego State University, San Diego,
CA 92182, U.S.A. []
EVELYN SHERR College of Oceanic and Atmospheric Sciences, Oregon State
University, Corvallis, OR 97331-5503, U.S.A. []
BARRY SHERR College of Oceanic and Atmospheric Sciences, Oregon State
University, Corvallis, OR 97331-5503, U.S.A. []
MARCELINO T. SUZUKI Chesapeake Biological Laboratory, University of
Maryland, Center for Environmental Science, Solomons, MD 20688, U.S.A.
[]
BO THAMDRUP Institute of Biology, University of Southern Denmark, DK-5230
Odense M, Denmark []
ALEXANDRA Z. WORDEN Monterey Bay Aquarium Research Institute, Moss
Landing, CA 95039, U.S.A. []
JONATHAN P. ZEHR Ocean Sciences Department, University of California, Santa
Cruz, CA 95064, U.S.A. []


1
INTRODUCTION AND OVERVIEW
DAVID L. KIRCHMAN
College of Marine and Earth Studies, University of Delaware, Lewes, DE 19958, U.S.A.

Marine microbes are capable of flourishing in all oceanic habitats, from several
kilometers below the seafloor to the top millimeter of the ocean surface. They

thrive in environmental conditions where other organisms cannot, ranging from
supercooled brine channels of Arctic ice floes to near-boiling waters of hydrothermal
vents. Consequently, marine microbes are the most numerous group of organisms on
the planet. In addition to being abundant, the many different types of marine
microbes carry out many different types of metabolism. As a consequence of this
diversity, marine microbes are involved in virtually all geochemical reactions occurring in the oceans.
Many of these microbes, the ecological interactions among them, and the biogeochemical processes they mediate are the topics covered by this book.
What is marine microbial ecology? A complicated answer is given in the first
edition of this book (Kirchman and Williams 2000). A simple answer is that it
is the study of the ecology of microbes in marine systems. “Microbes” includes
all organisms smaller than about 100 mm, which can be seen only with a
microscope. These organisms include bacteria, archaea, and protists (single-celled
eukaryotes). Chapter 12 examines the ecological roles of viruses and phages,
things that arguably are not living and thus are not microbes. Colleagues outside
the field sometimes assume that “microbe” and “microorganisms” refer only to bacteria, even just heterotrophic bacteria. Certainly these microbes are quite abundant
and ecologically important in the oceans, and readers will see several chapters

Microbial Ecology of the Oceans, Second Edition. Edited by David L. Kirchman
Copyright # 2008 John Wiley & Sons, Inc.

1


2

INTRODUCTION AND OVERVIEW

about them. But there is more to microbial ecology than just the study of
heterotrophic bacteria.
The purpose of this chapter is to provide an overview of the book and of some

important marine microbes and the parts of biogeochemical processes they
mediate. The summary by Sherr and Sherr (2000) remains relevant today, and
you are urged to read it. This chapter will take a complementary approach. In fact,
much of the entire first edition of this book remains relevant today, and readers are
urged to look it over. Table 1.1 summarizes some of the functional groups of
microbes discussed here and in the book as a whole.

TABLE 1.1 Functional Groups of Microbes in the Oceans Discussed in this Book
Discussed in
Chapters

Functional Group

Function

Type of Microbe

Primary producers

Fix CO2 to produce organic
material using light energy
Use organic material, aided by
light energy
Mineralize and oxidize
dissolved organic matter
(DOM) to produce biomass
and inorganic byproducts
Control prey populations and
release dissolved material
Control prey populations,

release dissolved material,
and mediate genetic
exchange
Reduce N2 to ammonium

Eukaryotes and
cyanobacteria
Cyanobacteria and
other bacteriaa
Bacteria and
archaea

2, 3, 5, 6, 13,
14
3, 5, 10

Eukaryotes

2, 6, 8, 11

Not applicable

3, 8, 12

Cyanobacteriab

3, 13, 14

Oxidization of ammonium to
nitrate

Release of N2 or N2O during
oxidation of ammonium or
reduction of nitrate

Bacteria and
archaea
Bacteria and
archaea

3, 4, 14

Photoheterotrophs
Heterotrophic
prokaryotes

Grazers
Viruses

N2 fixers
(diazotrophs)
Nitrifiers
Denitrifiersc

2–5, 7–11,
13, 14

14

a
Many protists are mixotrophs (see Chapters 6 and 11) and some eukaryotic phytoplankton are capable of

using DOM, but heterotrophic bacteria and archaea usually dominate DOM fluxes.
b
Some heterotrophic bacteria and archaea are capable of fixing N2, but cyanobacteria dominate N2, fixation
in the oceans.
c
The term “denitrification” is often reserved for the production of N2 or N2O by dissimilatory nitrate
reduction. Here the anammox reaction (oxidation of ammonium) is included because it too results in the
loss of N as N2 gas from the system. See Chapter 14 for more on these definitions.


EUKARYOTIC PHYTOPLANKTON AND CYANOBACTERIA

3

EUKARYOTIC PHYTOPLANKTON AND CYANOBACTERIA
A starting point for the carbon cycle is carbon fixation or the transformation of CO2 to
a “fixed,” nongaseous form—organic carbon (Fig. 1.1). Unlike terrestrial ecosystems,
carbon fixation in marine systems is nearly exclusively by free-floating microbial
“plants.” The exceptions include a few near-shore environments such as salt
marshes and mangrove stands where higher-plant production dominates, and in
some shallow marine environments where much of the primary production can be
by benthic algae (Behringer and Butler 2006; Gattuso et al. 2006; Segal et al.
2006). Aquatic ecologists use the term “phytoplankton” (or algae) rather than
“plants,” but in fact there are some important similarities between plants on land
and phytoplankton in lakes and the oceans. (Algae are found in terrestrial environments, but here I use “land plants” to mean larger, higher plants, which dominate
terrestrial primary production.) Both land plants and phytoplankton are autotrophs
(CO2 is their carbon source) and are the main primary producers in their respective
ecosystems, using the same mechanism for fixing CO2, the Calvin – Benson –
Bassham cycle. Both have chlorophyll a in reaction centers where light energy is converted to chemical energy. However, unlike land plants, in marine phytoplankton the
main pigments absorbing light energy, “the light-harvesting pigments,” are not chlorophylls. An example of these other pigments include the carotenoids, one being

fucoxanthin, which is abundant in diatoms. For this reason, many phytoplankton
are not green, because their dominant light-harvesting pigments absorb light with
wavelengths (color) that differ from that absorbed by land plants.
The most important difference, however, between land plants and phytoplankton
is the most obvious one: land plants, such as California coastal redwoods and giant
sequoias that tower 100 m above the ground, are among the largest creatures on the

Figure 1.1 The role of microbes in the oceanic carbon cycle. The numbers in parentheses are
standing stocks of carbon with units of pgC (1 pgC ¼ 1015 gC). The other numbers are rates
with units of pgC per year. The numbers are from Hedges and Oades (1997) and from estimates
of the average fraction of primary production routed through dissolved organic carbon (DOC)
to bacteria (Chapter 9), assuming a growth efficiency of 15 percent.


4

INTRODUCTION AND OVERVIEW

planet, while phytoplankton are among the smallest, some as tiny as a micrometer or
less (1026 m). This difference in size has many implications for how marine and
indeed all aquatic ecosystems are structured. By “structured,” I mean the size and
number of organisms, biochemical composition, phylogenetic diversity, growth
rates and net changes in population sizes, and trophic interactions (who is eating
whom). Size matters for many of the processes discussed in this book.
Another huge difference between terrestrial plants and phytoplankton is that the
latter includes cyanobacteria, in addition to eukaryotic algae. Cyanobacteria are discussed in Chapters 3 and 5. Especially in the nutrient-poor, oligotrophic oceans,
cyanobacteria can account for a high fraction (nearly 90 percent) of primary production and of total phytoplankton biomass. Estimates for cyanobacteria may
decrease as we learn more about small eukaryotic phytoplankton (see Chapter 6),
but cyanobacteria will undoubtedly remain important in the oceans. Two groups of
cyanobacteria are especially large contributors to primary production and phytoplankton biomass: Synechococcus and Prochlorococcus (Table 1.2). The cells in

both cyanobacterial groups are small (1 mm in diameter or less), smaller than eukaryotic phytoplankton. Phylogenetically, cyanobacteria are bacteria; they lack a nucleus,
and their cell wall and membranes are like those of Gram-negative bacteria (Hoiczyk
and Hansel 2000). Functionally, however, both Synechococcus and Prochlorococcus
are members of the phytoplankton community because they are mainly photoautotrophic and use light energy to fix CO2 by similar mechanisms (e.g., both have the
Calvin – Benson cycle) as found in eukaryotic phytoplankton.
Cyanobacteria and Blue – Green Algae
The old term for cyanobacteria is “blue – green algae,” which hints at the main
pigments of some of these microbes. The green is due to chlorophyll a, while
the blueish tinge comes from phycocyanin. When isolated from other pigments,
the striking blue color of phycocyanin emerges. Marine Synechococcus, one
of the main cyanobacteria found in the ocean, has phycocyanin, but this
microbe in pure cultures is blood-red due to phycoerythrin.
TABLE 1.2 Comparison of the Two Major Coccoid Cyanobacterial Genera
Found in the Oceans
Property

Synechococcus

Prochlorococcus

Size (diameter)
Chlorophyll a
Chlorophyll b
Phycobilinsa
Distributionb
N2 fixation

0.9 mm
Yes
No

Yes
Cosmopolitan
Some species

0.7 mm
Yes, but modified
Yes, but modified
Variable
Oceanic gyres
No

a

Phycobilins are the major light-harvesting pigments in cyanobacteria.
Neither group of cyanobacteria is found in cold, high-latitude oceans. Synechococcus can be abundant in
coastal waters, unlike Prochlorococcus.

b


PHOTOHETEROTROPHIC BACTERIA

5

Microbiologists knew about cyanobacteria for over a century, but the high
abundances of oceanic Synechococcus and Prochlorococcus were discovered only
around 1977 and 1986, respectively (Chisholm et al. 1988; Waterbury et al. 1979).
Since then, we have learned much about these organisms. In contrast to most
other marine bacteria, marine cyanobacteria have convenient markers, their
pigments, for studying them. These unique pigments make it possible to examine

Prochlorococcus by flow cytometry and Synechococcus by microscopy as well as
by flow cytometry (see Chapter 6 for a description of flow cytometry). Again
unlike many other marine bacteria, ecologically relevant representatives from the
two cyanobacterial groups can be isolated and grown alone in pure culture in the laboratory. Consequently, we have learned much about the physiology and biochemistry
of these microbes, and the genomes of several of them have been completely
sequenced (Dufresne et al. 2003; Palenik et al. 2007; Rocap et al. 2003).
The eukaryotic members of the phytoplankton community are also important in
many oceanic waters. The large species (10 – 100 mm, which is large in the microbial
world) are relatively easy to identify because they have distinctive shapes and sizes,
in addition to their distinctive light-harvesting pigments. Large phytoplankton, such
as diatoms and coccolithophorids, have been studied for years, and are well known
for their importance in coastal waters, especially in spring when they form dense
blooms. But often, much smaller eukaryotic phytoplankton species are much more
abundant and dominate phytoplankton biomass, along with the cyanobacteria.
These small eukaryotes are only slightly larger than bacteria and are members of
the “picoplankton” community, which includes all microbes 2 mm or less in size
(see Chapter 2). Unlike large phytoplankton, the picophytoplankton are hard to
identify by traditional methods, because of their size and lack of distinguishing features. In Chapter 6, Worden and Not discuss these important microbes and the use of
molecular tools and other methods for examining them.

PHOTOHETEROTROPHIC BACTERIA
All microbes, not just eukaryotic phytoplankton and cyanobacteria, are affected by
light directly or indirectly in the surface layer of the oceans (Moran and Zepp
2000). An example of an indirect effect is the photochemical modification of dissolved organic matter (DOM) used by heterotrophic bacteria. The direct effects
include the damage of microbial DNA by short-wavelength light, especially in the
ultraviolet region (200 – 400 nm). These types of light effects are well known.
Less well known is the use of light by phototrophic bacteria to drive adenosine
triphosphate (ATP) synthesis while also obtaining energy from other sources, most
prominently the oxidation of organic material (Table 1.3). Chapter 5 discusses
photoheterotrophic bacteria in the oceans, including cyanobacteria, proteorhodopsinbearing bacteria and aerobic anoxygenic phototrophic bacteria (AAP bacteria, or

AAnP in Chapter 5). Except for cyanobacteria, these bacteria are not autotrophic
and do not contribute to primary production. We think that they can synthesis
ATP via both phototrophic and heterotrophic mechanisms, hence making them


6

INTRODUCTION AND OVERVIEW

TABLE 1.3 Phototrophic Microbes in the Oceans
Microbial Group
Eukaryotic phytoplankton
Cyanobacteria
AAP bacteriab
Several

Pigment in Energy Productiona

CO2 Fixation?

Chlorophyll a
Chlorophyll a
Bacteriochlorophyll a
Proteorhodopsin

Yes
Yes
No
No

a
The pigment most directly involved in ATP production. Chlorophyll a and bacteriochlorophyll a are the
main pigments in the reaction centers in the respective microbes. Other pigments, called “accessory
pigments,” such as fucoxanthin for eukaryotic diatoms and phycoerythrin for Synechococcus, often
absorb more light energy than the energy-production pigment.
b
Aerobic anoxygenic phototrophic bacteria. The abbreviation “AAnP” is used in Chapter 5 and by some
authors of studies published in the primary literature.

photoheterotrophic, but little else is known about them. We probably know more about
the diversity of genes encoding proteorhodopsin and of the diagnostic gene ( pufM ) for
AAP bacteria than we do about their ecophysiology and biogeochemical roles in the
oceans. For instance, the number and diversity of proteorhodopsin genes in the
oceans suggest that bacteria bearing them are abundant, but how proteorhodopsin
benefits these bacteria is not entirely clear; light has no effect on the growth of
Pelagibacter ubique, a cultured marine bacterium from the SAR11 clade with proteorhodopsin (Giovannoni et al. 2005), whereas light does stimulate the growth of another
marine heterotrophic bacterium in pure culture experiments (Gomez-Consarnau et al.
2007). One hypothesis is that photoheterotrophic bacteria should be most abundant in
oligotrophic oceans, where light energy can augment that gained from heterotrophy
and the oxidation of organic material. However, AAP bacteria can be quite abundant
in eutrophic estuaries and coastal waters (Cottrell et al. 2006; Schwalbach and
Fuhrman 2005; Sieracki et al. 2006; Waidner and Kirchman 2007). We know little
about even basic parameters of photoheterotrophic bacteria.
One measure of the importance of photoheterotrophic microbes is the effect of
light on bacterial production, as measured by leucine incorporation. This effect
varies among environments (Pakulski et al. 2007). In some cases, visible light can
inhibit leucine incorporation, whereas in other systems, it stimulates incorporation
rates. One factor hypothesized to explain this variable effect is the abundance of
Prochlorococcus (Church et al. 2004). The role of Prochlorococcus in DOM
fluxes has been demonstrated by flow cytometric studies of methionine assimilation

(Zubkov et al. 2003; Zubkov and Tarran 2005). More recent flow cytometric studies
confirmed that Prochlorococcus was responsible over 75 percent of light-stimulated
leucine incorporation in the North Atlantic Ocean, but Synechococcus and probably
other bacterial groups also accounted for substantial light-dependent leucine incorporation (Michelou et al. 2007). While per cell rates can be quite high for
Prochlorococcus and Synechococcus, their abundance is not as high as other
microbial groups, such as heterotrophic bacteria and photoheterotrophic
bacteria other than cyanobacteria. Consequently, heterotrophic bacteria and photoheterotrophic bacteria other than cyanobacteria account for most of leucine incorporation in the oceans regardless of light intensities.


DISSOLVED ORGANIC MATERIAL

7

Chapter 5 calls cyanobacteria “operational heterotrophs” because they appear to
use relatively few organic compounds in experiments with laboratory cultures.
However, we really do not know which DOM compounds are used by cyanobacteria
in the oceans. These microbes are probably mainly photoautotrophic, but they could
still contribute substantially to the uptake of some DOM components.

DISSOLVED ORGANIC MATERIAL
This chapter is focused on organisms and viruses, but DOM is the “800-pound
gorilla” in the ocean, making it hard to ignore: it is the largest pool of organic
carbon in the ocean and one of the largest in the biosphere. Concentrations of
DOM are not measured directly, but rather the key components are examined,
given here in decreasing concentration and order of our understanding: dissolved
organic carbon (DOC), dissolved organic nitrogen (DON), and dissolved organic
phosphorus (DOP). The amount of C in the DOC pool is nearly equivalent to
the carbon in atmospheric CO2 (Hedges and Oades 1997), but concentrations of
individual DOM components are very low, often nanomolar (1029 mol/L). The
book edited by D. Hansell and C. Carlson provides an excellent overview of DOM

in the oceans (Hansell and Carlson 2002) and another book discusses DOM –
microbe interactions in several aquatic environments (Findlay and Sinsabaugh
2003). Chapter 7 also discusses DOM extensively.
The large size of the DOC pool is perhaps the most obvious reason why it is
included in oceanic carbon budgets and climate change models, but the flux
through this pool is also quite large and in many ways is a more important parameter.
By “flux,” I mean the rate (usually expressed as mgC/m2/d or mmol-C/m2/d) at
which DOM components are produced or utilized. Chapter 7 discusses what we
know about the fluxes of different components of the DOM pool. In spite of most
oceanic DOC being old and refractory, the rest of the DOC pool is sufficiently
labile (used readily by bacteria) that overall DOC fluxes are usually equivalent to
about 50 percent of primary production, and in some marine systems, the fraction is
even higher (Chapter 9). Some DOM comes directly from phytoplankton, for
example via release of small compounds or the sloughing off of large polymers associated with the outside of phytoplankton cells. However, most of the DOM appears to be
produced by grazers (Nagata 2000), but every organism (and virus) in the ocean
contributes to the production of DOM. Organic carbon from terrestrial sources can
be a substantial fraction of total DOM in lakes and estuaries (Cauwet 2002).
The high fluxes of DOM help explain many features of biological communities in
marine water columns. One important feature is the retention of material in the surface
layer of the oceans. Because most of the DOC used by bacteria is respired and
because of the small size of microbes, as much as 90 percent of primary production
is mineralized by grazers and heterotrophic bacteria in the upper surface layer of the
open oceans and only 10 percent or less sinks out to deeper waters. These percentages
vary greatly, especially in coastal waters where less primary production is mineralized
in the surface layer and more is exported to deep waters or horizontally to less