The Handbook
of Environmental Chemistry
Editor-in-Chief: O. Hutzinger
Volume 2 Reactions and Processes
Part N

Advisory Board:
D. Barceló · P. Fabian · H. Fiedler · H. Frank · J. P. Giesy · R. A. Hites
T. A. Kassim · M. A. K. Khalil · D. Mackay · A. H. Neilson
J. Paasivirta · H. Parlar · S. H. Safe · P. J. Wangersky

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The Handbook of Environmental Chemistry
Recently Published and Forthcoming Volumes

Environmental Specimen Banking
Volume Editors: S. A. Wise and P. P. R. Becker
Vol. 3/S, 2006
Polymers: Chances and Risks
Volume Editors: P. Eyerer, M. Weller
and C. Hübner
Vol. 3/V, 2006

Marine Organic Matter: Biomarkers,
Isotopes and DNA
Volume Editor: J. K. Volkman
Vol. 2/N, 2005
Environmental Photochemistry Part II

Volume Editors: P. Boule, D. Bahnemann
and P. Robertson
Vol. 2/M, 2005

The Rhine
Volume Editor: T. P. Knepper
Vol. 5/L, 03.2006

Air Quality in Airplane Cabins
and Similar Enclosed Spaces
Volume Editor: M. B. Hocking
Vol. 4/H, 2005

Persistent Organic Pollutants
in the Great Lakes
Volume Editor: R. A. Hites
Vol. 5/N, 2006

Environmental Effects
of Marine Finfish Aquaculture
Volume Editor: B. T. Hargrave
Vol. 5/M, 2005

Antifouling Paint Biocides
Volume Editor: I. Konstantinou
Vol. 5/O, 2006

The Mediterranean Sea
Volume Editor: A. Saliot
Vol. 5/K, 2005


Estuaries
Volume Editor: P. J. Wangersky
Vol. 5/H, 2006
The Caspian Sea
Volume Editors: A. Kostianoy and A. Kosarev
Vol. 5/P, 2005

Environmental Impact Assessment of Recycled
Wastes on Surface and Ground Waters
Engineering Modeling and Sustainability
Volume Editor: T. A. Kassim
Vol. 5/F (3 Vols.), 2005
Oxidants and Antioxidant Defense Systems
Volume Editor: T. Grune
Vol. 2/O, 2005

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Marine Organic Matter:
Biomarkers, Isotopes and DNA
Volume Editor:
John K. Volkman

With contributions by
J. Albaigés · M. A. Altabet · J. M. Bayona · E. A. Canuel
C. Corinaldesi · R. Danovaro · A. Dell’Anno · H. R. Harvey
S. W. Jeffrey · G. M. Luna · S. Schouten · B. R. T. Simoneit
J. S. Sinninghe Damsté · M. Pagani · R. D. Pancost

J. K. Volkman · S. G. Wakeham · S. W. Wright

123
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Environmental chemistry is a rather young and interdisciplinary field of science. Its aim is a complete
description of the environment and of transformations occurring on a local or global scale. Environmental chemistry also gives an account of the impact of man’s activities on the natural environment by
describing observed changes.
The Handbook of Environmental Chemistry provides the compilation of today’s knowledge. Contributions are written by leading experts with practical experience in their fields. The Handbook will grow
with the increase in our scientific understanding and should provide a valuable source not only for
scientists, but also for environmental managers and decision-makers.
The Handbook of Environmental Chemistry is published in a series of five volumes:
Volume 1: The Natural Environment and the Biogeochemical Cycles
Volume 2: Reactions and Processes
Volume 3: Anthropogenic Compounds
Volume 4: Air Pollution
Volume 5: Water Pollution
The series Volume 1 The Natural Environment and the Biogeochemical Cycles describes the natural
environment and gives an account of the global cycles for elements and classes of natural compounds.
The series Volume 2 Reactions and Processes is an account of physical transport, and chemical and
biological transformations of chemicals in the environment.
The series Volume 3 Anthropogenic Compounds describes synthetic compounds, and compound
classes as well as elements and naturally occurring chemical entities which are mobilized by man’s
activities.
The series Volume 4 Air Pollution and Volume 5 Water Pollution deal with the description of civilization’s
effects on the atmosphere and hydrosphere.
Within the individual series articles do not appear in a predetermined sequence. Instead, we invite
contributors as our knowledge matures enough to warrant a handbook article.
Suggestions for new topics from the scientific community to members of the Advisory Board or to the

Publisher are very welcome.

Library of Congress Control Number: 2005930943

ISSN 1433-6839
ISBN-10 3-540-28401-X Springer Berlin Heidelberg New York
ISBN-13 978-3-540-28401-7 Springer Berlin Heidelberg New York
DOI 10.1007/b11682
This work is subject to copyright. All rights are reserved, whether the whole or part of the material
is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of
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Editor-in-Chief
Prof. em. Dr. Otto Hutzinger
Universität Bayreuth

c/o Bad Ischl Office
Grenzweg 22
5351 Aigen-Vogelhub, Austria


Volume Editor
Dr. John K. Volkman
CSIRO Marine and Atmospheric
Research Laboratories
Castray Esplanade,
7000 Hobart, Australia


Advisory Board
Prof. Dr. D. Barceló

Prof. Dr. J. P. Giesy

Dept. of Environmental Chemistry
IIQAB-CSIC
JordiGirona, 18–26
08034 Barcelona, Spain


Department of Zoology
Michigan State University
East Lansing, MI 48824-1115, USA


Prof. Dr. R. A. Hites


Prof. Dr. P. Fabian
Lehrstuhl für Bioklimatologie
und Immissionsforschung
der Universität München
Hohenbachernstraße 22
85354 Freising-Weihenstephan, Germany

Dr. H. Fiedler
Scientific Affairs Office
UNEP Chemicals
11–13, chemin des Anémones
1219 Châteleine (GE), Switzerland
hfi

Prof. Dr. H. Frank
Lehrstuhl für Umwelttechnik
und Ökotoxikologie
Universität Bayreuth
Postfach 10 12 51
95440 Bayreuth, Germany

Indiana University
School of Public
and Environmental Affairs
Bloomington, IN 47405, USA


Dr. T. A. Kassim
Department of Civil

and Environmental Engineering
College of Science and Engineering
Seattle University
901 12th Avenue
Seattle, WA 98122-1090, USA


Prof. Dr. M. A. K. Khalil
Department of Physics
Portland State University
Science Building II, Room 410
P.O. Box 751
Portland, OR 97207-0751, USA


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VI

Prof. Dr. D. Mackay

Prof. Dr. Dr. H. Parlar

Department of Chemical Engineering
and Applied Chemistry
University of Toronto
Toronto, ON, Canada M5S 1A4

Institut für Lebensmitteltechnologie

und Analytische Chemie
Technische Universität München
85350 Freising-Weihenstephan, Germany

Prof. Dr. A. H. Neilson

Prof. Dr. S. H. Safe

Swedish Environmental Research Institute
P.O. Box 21060
10031 Stockholm, Sweden


Department of Veterinary
Physiology and Pharmacology
College of Veterinary Medicine
Texas A & M University
College Station, TX 77843-4466, USA


Prof. Dr. J. Paasivirta
Department of Chemistry
University of Jyväskylä
Survontie 9
P.O. Box 35
40351 Jyväskylä, Finland

Prof. P. J. Wangersky
University of Victoria
Centre for Earth and Ocean Research

P.O. Box 1700
Victoria, BC, V8W 3P6, Canada


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Preface

Environmental Chemistry is a relatively young science. Interest in this subject,
however, is growing very rapidly and, although no agreement has been reached
as yet about the exact content and limits of this interdisciplinary discipline,
there appears to be increasing interest in seeing environmental topics which
are based on chemistry embodied in this subject. One of the first objectives
of Environmental Chemistry must be the study of the environment and of
natural chemical processes which occur in the environment. A major purpose
of this series on Environmental Chemistry, therefore, is to present a reasonably
uniform view of various aspects of the chemistry of the environment and
chemical reactions occurring in the environment.
The industrial activities of man have given a new dimension to Environmental Chemistry. We have now synthesized and described over five million
chemical compounds and chemical industry produces about hundred and fifty
million tons of synthetic chemicals annually. We ship billions of tons of oil per
year and through mining operations and other geophysical modifications, large
quantities of inorganic and organic materials are released from their natural
deposits. Cities and metropolitan areas of up to 15 million inhabitants produce
large quantities of waste in relatively small and confined areas. Much of the
chemical products and waste products of modern society are released into
the environment either during production, storage, transport, use or ultimate
disposal. These released materials participate in natural cycles and reactions
and frequently lead to interference and disturbance of natural systems.
Environmental Chemistry is concerned with reactions in the environment.

It is about distribution and equilibria between environmental compartments.
It is about reactions, pathways, thermodynamics and kinetics. An important
purpose of this Handbook, is to aid understanding of the basic distribution
and chemical reaction processes which occur in the environment.
Laws regulating toxic substances in various countries are designed to assess
and control risk of chemicals to man and his environment. Science can contribute in two areas to this assessment; firstly in the area of toxicology and secondly in the area of chemical exposure. The available concentration (“environmental exposure concentration”) depends on the fate of chemical compounds
in the environment and thus their distribution and reaction behaviour in the
environment. One very important contribution of Environmental Chemistry to

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X

Preface

the above mentioned toxic substances laws is to develop laboratory test methods, or mathematical correlations and models that predict the environmental
fate of new chemical compounds. The third purpose of this Handbook is to help
in the basic understanding and development of such test methods and models.
The last explicit purpose of the Handbook is to present, in concise form, the
most important properties relating to environmental chemistry and hazard
assessment for the most important series of chemical compounds.
At the moment three volumes of the Handbook are planned. Volume 1 deals
with the natural environment and the biogeochemical cycles therein, including some background information such as energetics and ecology. Volume 2
is concerned with reactions and processes in the environment and deals with
physical factors such as transport and adsorption, and chemical, photochemical and biochemical reactions in the environment, as well as some aspects
of pharmacokinetics and metabolism within organisms. Volume 3 deals with
anthropogenic compounds, their chemical backgrounds, production methods
and information about their use, their environmental behaviour, analytical
methodology and some important aspects of their toxic effects. The material

for volume 1, 2 and 3 was each more than could easily be fitted into a single volume, and for this reason, as well as for the purpose of rapid publication of available manuscripts, all three volumes were divided in the parts A and B. Part A of
all three volumes is now being published and the second part of each of these
volumes should appear about six months thereafter. Publisher and editor hope
to keep materials of the volumes one to three up to date and to extend coverage
in the subject areas by publishing further parts in the future. Plans also exist for
volumes dealing with different subject matter such as analysis, chemical technology and toxicology, and readers are encouraged to offer suggestions and
advice as to future editions of “The Handbook of Environmental Chemistry”.
Most chapters in the Handbook are written to a fairly advanced level and
should be of interest to the graduate student and practising scientist. I also hope
that the subject matter treated will be of interest to people outside chemistry
and to scientists in industry as well as government and regulatory bodies. It
would be very satisfying for me to see the books used as a basis for developing
graduate courses in Environmental Chemistry.
Due to the breadth of the subject matter, it was not easy to edit this Handbook. Specialists had to be found in quite different areas of science who were
willing to contribute a chapter within the prescribed schedule. It is with great
satisfaction that I thank all 52 authors from 8 countries for their understanding
and for devoting their time to this effort. Special thanks are due to Dr. F. Boschke
of Springer for his advice and discussions throughout all stages of preparation
of the Handbook. Mrs. A. Heinrich of Springer has significantly contributed to
the technical development of the book through her conscientious and efficient
work. Finally I like to thank my family, students and colleagues for being so patient with me during several critical phases of preparation for the Handbook,
and to some colleagues and the secretaries for technical help.

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Preface

XI


I consider it a privilege to see my chosen subject grow. My interest in Environmental Chemistry dates back to my early college days in Vienna. I received
significant impulses during my postdoctoral period at the University of California and my interest slowly developed during my time with the National
Research Council of Canada, before I could devote my full time of Environmental Chemistry, here in Amsterdam. I hope this Handbook may help deepen
the interest of other scientists in this subject.
Amsterdam, May 1980

O. Hutzinger

Twenty-one years have now passed since the appearance of the first volumes
of the Handbook. Although the basic concept has remained the same changes
and adjustments were necessary.
Some years ago publishers and editors agreed to expand the Handbook by
two new open-end volume series: Air Pollution and Water Pollution. These
broad topics could not be fitted easily into the headings of the first three
volumes. All five volume series are integrated through the choice of topics and
by a system of cross referencing.
The outline of the Handbook is thus as follows:
1.
2.
3.
4.
5.

The Natural Environment and the Biochemical Cycles,
Reaction and Processes,
Anthropogenic Compounds,
Air Pollution,
Water Pollution.

Rapid developments in Environmental Chemistry and the increasing breadth

of the subject matter covered made it necessary to establish volume-editors.
Each subject is now supervised by specialists in their respective fields.
A recent development is the accessibility of all new volumes of the Handbook
from 1990 onwards, available via the Springer Homepage springeronline.com
or springerlink.com.
During the last 5 to 10 years there was a growing tendency to include subject
matters of societal relevance into a broad view of Environmental Chemistry.
Topics include LCA (Life Cycle Analysis), Environmental Management, Sustainable Development and others. Whilst these topics are of great importance
for the development and acceptance of Environmental Chemistry Publishers
and Editors have decided to keep the Handbook essentially a source of information on “hard sciences”.
With books in press and in preparation we have now well over 40 volumes
available. Authors, volume-editors and editor-in-chief are rewarded by the
broad acceptance of the “Handbook” in the scientific community.
Bayreuth, July 2001

Otto Hutzinger

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Contents

Sources and Cycling of Organic Matter
in the Marine Water Column
H. R. Harvey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1


Lipid Markers for Marine Organic Matter
J. K. Volkman . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

27

Pigment Markers for Phytoplankton Production
S. W. Wright · S. W. Jeffrey . . . . . . . . . . . . . . . . . . . . . . . . .

71

Molecular Tools for the Analysis of DNA in Marine Environments
R. Danovaro · C. Corinaldesi · G. M. Luna · A. Dell’Anno . . . . . . . . . 105
Biological Markers for Anoxia
in the Photic Zone of the Water Column
J. S. Sinninghe Damsté · S. Schouten . . . . . . . . . . . . . . . . . . . . 127
Atmospheric Transport
of Terrestrial Organic Matter to the Sea
B. R. T. Simoneit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Controls on the Carbon Isotopic Compositions
of Lipids in Marine Environments
R. D. Pancost · M. Pagani . . . . . . . . . . . . . . . . . . . . . . . . . . 209
Isotopic Tracers of the Marine Nitrogen Cycle: Present and Past
M. A. Altabet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251

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XIV


Contents

Degradation and Preservation
of Organic Matter in Marine Sediments
S. G. Wakeham · E. A. Canuel . . . . . . . . . . . . . . . . . . . . . . . . 295
Sources and Fate of Organic Contaminants in the Marine Environment
J. M. Bayona · J. Albaigés . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371

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Foreword

The oceans play a vital role in moderating the Earth’s climate and in providing food for the Earth’s human inhabitants and yet many of the processes of
carbon and nutrient cycling are still not well understood. Modern advances
in molecular biology are revealing a myriad of uncultured organisms in marine ecosystems, many having unknown ecology and function. These organisms have a rich variety of unusual genes and biochemistries which produce
a diverse array of organic compounds ranging from colourful carotenoids and
chlorophylls to lipids with structures ranging from the simple to the complex.
This book brings together 10 chapters on the use of lipid biomarkers, pigments, isotopes and molecular biology to ascertain the sources and fate of
organic matter (both natural and pollutant) in the sea and underlying sediments. The authors are expert in their field and they have been able to bring
their broader knowledge of marine processes to provide both an overview of
the state-of-the-art and knowledge gaps with sufficient detail to satisfy the
needs of specialists and non-specialists alike. All are very busy researchers at
the leading edge of their science and I am grateful that they were able to find
the time to write these reviews.
A characteristic feature of today’s marine science is the need for multidisciplinary approaches. Thus the skills and knowledge of the chemist, biologist,
physical oceanographer and modeller are needed to unravel the interactions
between organisms in marine food-webs and the cycling of the major elements. A multi-marker approach is also desirable – an approach that makes
use of biomarkers, isotopes and DNA which might be thought of as the ultimate biomarker. Advances in methodology have played a major role with

a range of highly sensitive “hyphenated techniques” now available including
gas chromatography and high performance liquid chromatography linked to
mass spectrometry systems (GC-MS and HPLC-MS) for compound identification. Continuous flow GC-irm-MS systems can now provide stable isotope
values for compounds separated by GC. Methods are also now available to
measure the 14 C-content of individual compounds and thus estimate their age
which has revealed that some of the more refractory compounds in the sea
may have been synthesized many hundreds (or in some cases thousands) of
years previously.

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XVI

Foreword

My intention as editor has been to include detailed information of practical
use to new researchers. I hope that the book can provide a roadmap for the
analysis of the different organic compounds found in the sea, atmosphere and
sediments. In addition, detailed information is provided on the fundamental
concepts underlying the use of isotopes, lipids and pigments for studying
organic matter cycling. The book opens with a broad overview of the carbon
cycle in the sea followed by chapters on lipid, pigment and DNA biomarkers
for studying its sources and sinks. Much of this organic matter is remineralised
(i.e. becomes food for consumers), but a small proportion sinks to the depths
and an even smaller proportion becomes incorporated into the sedimentary
record either as the original biochemicals or as diagenetically altered forms.
Distributions of biomarkers in sediments can provide a great deal of information about the type of environment present at the time of deposition.
Specific environmental types can be recognized such as the example discussed
here of photic zone anoxia. Biomarkers are used by petroleum companies to

identify the likely sources for petroleum based on the fingerprint of molecules
preserved in the oil. These same molecules can be used to identify pollution of
the oceans together with the many hundreds of manufactured compounds that
are unfortunately found throughout the marine realm. Biomarker distributions
can be used to decipher the many environmental changes that have occurred
in the Earth’s past. Such information can greatly assist our understanding of
the effects of climate change, so it is vital to ascertain how the organic matter
preserved in sediments relates to water column processes.
I hope that you find this book interesting, useful and enjoyable.
Hobart, Tasmania, June 2005

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John K. Volkman


Hdb Env Chem Vol. 2, Part N (2006): 1–25
DOI 10.1007/698_2_001
© Springer-Verlag Berlin Heidelberg 2005
Published online: 6 October 2005

Sources and Cycling of Organic Matter
in the Marine Water Column
H. Rodger Harvey
University of Maryland Center for Environmental Science, Chesapeake Biological
Laboratory, PO Box 38, Solomons, MD 20688, USA

1

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .


1

2

Global Reservoirs of Organic Carbon . . . . . . . . . . . . . . . . . . . . .

3

3

Defining the Compartments – The Size Continuum . . . . . . . . . . . . .

4

4

The Flux of Organic Carbon in the Ocean . . . . . . . . . . . . . . . . . .

5

5

The Importance of DOM . . . . . . . . . . . . . . . . . . . . . . . . . . . .

8

6

Kinetics of Organic Matter Recycling . . . . . . . . . . . . . . . . . . . . .


10

7

Organic Matter Composition During Decay . . . . . . . . . . . . . . . . .

12

8

Pathways for Preservation . . . . . . . . . . . . . . . . . . . . . . . . . . .

16

9

The Role of Microbes in Organic Matter Cycling . . . . . . . . . . . . . . .

18

10

Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

20

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

21


Abstract The organic carbon cycle operates on multiple time scales with a only small
fraction of the global reservoir actively exchanged. For the marine system, the sources
are principally recently synthesized material from autotrophic production which annually contribute 44–50 Pg/year of new organic carbon. This is supplemented by terrestrial
carbon arriving from rivers, erosion and the atmosphere which contribute to the complex mixture present on oceanic waters. The focus of this review is to highlight the major
sources or organic carbon and describe how the interaction of biological, chemical and
physical processes provides an efficient mechanism for its eventual recycling.
Keywords Carbon reservoirs · Diagenesis · DOM · Global carbon cycle · Microbial loop ·
Particles · POC

1
Introduction
The cycling of organic carbon in the marine environment is a key process in
the global carbon cycle. Marine systems are roughly equal to the terrestrial

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2

H.R. Harvey

system as a source of new organic carbon to the biosphere, contributing an estimated 44–50 Pg/year of new production [1]. Over 80% of this amount is in
the open ocean [2]. Yet only a small fraction (< 1%) of this material escapes
recycling in the water column or active sediments to be ultimately buried
and preserved in the sedimentary record [3, 4]. The interaction of biological,
chemical and physical processes in oceanic systems thus provides an efficient
mechanism for the production of new organic carbon as well as its eventual
recycling as part of the global carbon cycle.
The sources of organic matter in the oceans are myriad, and dependent

upon the intensity of the autochthonous signal and the proximity and magnitude of inputs from rivers, coastal erosion, and the atmosphere (Fig. 1).
Although organic carbon is ultimately a product of biological synthesis, its
sources are often viewed as a dichotomy between terrestrial inputs of particles and dissolved fractions, and primary production by phytoplankton in
the water column. Primary production by algae is the larger of these two
sources to the marine system, but terrestrial material eroded from rivers has
received heightened interest in recent years as a recorder of changing coastal
systems and increased sea level. The balance between these two end members
is highly variable in differing ocean regions, ranging from systems such as the
Arctic which receive large freshwater and erosional inputs [5] to the pelagic

Fig. 1 The global organic carbon cycle. The major reservoirs (1015 G C) are shown as
boxes with arrows depicting fluxes (1015 G C year–1 ) of the cycle

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Sources and Cycling of Organic Matter in the Marine Water Column

3

Pacific, which is dominated by marine-derived material. Atmospheric input
is a quantitatively minor fraction from the perspective of total organic input,
but has indirect importance for transport of essential trace metals needed for
phytoplankton growth [6, 7]. Atmospheric transport may also be of unique
consequence, since the organic materials deposited range from soil-derived
particles to highly labile dissolved forms of local and remote origins [8, 9].
The intention of this review is not to provide a comprehensive discussion
of the processes that alter the organic matter signature, but instead focus on
the major sources and how biological processing in the marine water column
alters the amount and composition of organic matter in marine systems. Recent reviews of the literature which detail processes and organic character are

emphasized. The active carbon cycle is a dynamic environment where single measures of organic carbon content integrate complex mixtures; mixtures
that arise from the combined effects of multiple sources and varied reactivity.

2
Global Reservoirs of Organic Carbon
An examination of organic matter cycling in marine systems must begin with
the realization that the vast majority of organic carbon does not actively
participate in the global carbon cycle, but is retained as finely distributed
material in sedimentary rocks (Table 1). Fossil fuel combustion has returned
a measurable, albeit minor, fraction of this material back to the active carbon cycle in recent years [10, 11], largely as CO2 . Of the global total, only
about 0.1% of the organic reservoir actually cycles through the active pool.
Within this active cycle, soils which represent the largest pool, with decreasing amounts of organic matter contained in land biota, dissolved organic
matter in seawater, and surficial marine sediments. The smallest fraction
includes marine biota and particulate pools, encompassing highly variable

Table 1 Major reservoirs of organic carbon on Earth
Reservoir

Size (Pg C)

References

Kerogen and fossil fuels
Soil
Land biota
Ocean DOC
Marine surface sediments
Marine biota

15 000 000

1550
950
680
150
3

Berner, 1989 (3) [115]
Lal, 2003 [116]
Olson et al., 1985 [117]
Hansell and Carlson, 1998 [118]
Emerson and Hedges, 1988 [119]
Siegenthaler and Sarmiento, 1993 [120]

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4

H.R. Harvey

mixtures ranging from recently synthesized material as intact living cells to
heavily degraded detrital substances with little resemblance to their original
precursor. Although the particulate organic carbon (POC) reservoir is small,
it undergoes rapid exchange and plays a central role in both amount and
composition of organic mater which reaches underlying sediments. Over long
time scales, the small fraction of organic matter remaining after extensive
exposure to degradative processes is transferred to the geological reservoir.
A complication in describing each organic reservoir is that they comprise
complex fractions having multiple origins and different turnover times. A recent example is black carbon, which represents a refractory and chemically
complex product of incomplete combustion. It includes both ancient fossil

fuels and modern biomass, including vegetation burns and forest fires. Operationally defined, the presence of black carbon in particles from the atmosphere,
ice, rivers, soils and marine sediments suggests that this material is ubiquitous
in the environment [12–14]. Black carbon accumulates in sediments and thus
appears refractory, comprising 10–50% of sedimentary organic carbon [15]
and having much older ages than other organic fractions [16]. Recent evidence
suggests that black carbon also comprises a significant fraction of marine DOM
in coastal zones [17]. The widespread presence of this organic component suggests that it represents an important fraction of the ocean’s carbon cycle, yet its
poorly defined structure and multiple origins complicates interpretation of its
cycling and transfer from the active carbon cycle.

3
Defining the Compartments – The Size Continuum
The physical size (or more appropriately the density) of the organic fraction
is an important control over where recycling occurs. Given the operational
definitions inherent in the collection of samples prior to analysis of organic
matter composition, the size distribution from dissolved molecules to large
particles is an important influence over the fraction which is sampled and
subsequently measured. The distribution of organic matter in the ocean is
continuous yet variable, with the overall total abundance decreasing as size
increases (Fig. 2). Although particles represent a quantitatively small fraction
of the total organic carbon present in marine waters, they have historically
attracted much attention, largely due to the ability of oceanographers and
geochemists to collect them in traps or filter material from seawater in adequate amounts for chemical characterization.
Traditional collections have used filters having a variety of pore sizes or
mesh supports, generally from 0.2 to 1.0 µm which operationally define the
particulate fraction before analysis. Particles for organic analysis are often
collected on glass fiber filters (e.g. GF/F nominally 0.7 µm pore size) which
can be made organic-free through combustion. Depending on the definition

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Sources and Cycling of Organic Matter in the Marine Water Column

5

Fig. 2 The log abundance of particles versus log diameter in aquatic environments
together with major components and collection ranges. Ranges among varying compartments are shown as well as arrows of major inorganic and soot components. The vertical
shading shows the major cutoff for commonly used glass fiber filters (GF/F)

of what constitutes a particulate fraction [18], such filters might be considered either quantitative or highly selective (Fig. 2). Comparative measures of
the organic composition of differing size fractions have shown important differences suggesting that the context of collection is required to fully interpret
the organic signatures observed.

4
The Flux of Organic Carbon in the Ocean
The movement of organic carbon between compartments and its eventual
recycling to inorganic phases are illustrated in Fig. 1 and summarized in
Table 2. In the ocean the autotrophic production by phytoplankton represents the major source of organic carbon [19], supplemented by terrestrial
material supplied by rivers. Most particulate forms of terrestrial matter, however, are rapidly deposited in coastal shelf and slope environments [20], with
the general character of particles as seen in molecular biomarkers and isotopic values shifting to one where marine phytoplankton in surface waters

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6

H.R. Harvey

Table 2 Fluxes of organic carbon in the global carbon cycle

Type

Flux
References
(Pg C year–1 )

Terrestrial primary
42–68
Production
Marine primary
44–50
Production
Riverine DOC discharge 0.25–0.36
Riverine POC discharge
Burial in marine
Sediments
Kerogen weathering
Eolian input

Potter et al., 2003 [119]; Schimel et al., 2001 [120]

0.15
0.098

Behrenfeld and Falkowski, 1997 [121]; Antoine
et al., 1996 [122]; Longhurst et al., 1995 [27]
Hedges et al., 1997 [124];
Aitkenhead and McDowell, 2000 [125]
Hedges et al., 1997 [126]
Schlunz and Schneider, 2000 [36]


0.1
0.1

Berner, 1989 [3]
Romankevich, 1984 [127]

dominate the organic carbon signal. Although autotrophic production occurs
in the lighted surface waters, sinking provides the major pathway for transport of particulate organic carbon (POC) from surface waters to the ocean
depths and sediments. Estimates of the transfer of material and losses during sinking have often relied on data from particle (i.e. sediment) traps [21]
which have shown that larger particle settling accounts for the majority of the
flux, but also show an exponential decrease of surface productivity flux with
depth [22, 23]. Such estimates come with the realization that the efficiency
of such traps are affected by particle sinking rates, hydrodynamics at the
opening, trap design and the nature of the particles themselves [24, 25]. All
suggest, however, that in oxic waters most (> 80%) of the particulate organic
material originating in surface waters is recycled at depths < 1000 m.
To understand the movement of POC, an extensive comparison of organic
carbon flux estimates was conducted by Lampitt and Antia [26], who examined a total of 68 data years of trap deployments to provide a global picture
of carbon flux to the deep (> 2000 m) ocean and its seasonal variability. Calculations included estimates of total annual primary production derived from
long-term satellite observations at the same sites [27]. The annual range was
large, with organic carbon flux varying by a factor of 375 when extreme values
seen in high latitude environments are included (Table 3). Excluding high latitudes where episodic primary production is common and variable; however,
a much narrower range was evident, with organic carbon flux varying by
a factor of 11. The estimated range was similar to that estimated for primary
production (factor of 5) for the same stations. In comparing the relationship
between primary production and flux, they also found organic carbon reaching deep waters to comprise from 0.4 to 2.7% of annual primary production

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Sources and Cycling of Organic Matter in the Marine Water Column

7

Table 3 Particle flux and composition compiled from 68 data years of deep (> 1000 m)
trap deployments in all major ocean basins by Lampitt and Anita (1997) [26]. Maximum
and minimum flux in all ocean basin are shown. Columns include all except polar stations
which show large variability. Rates in g m–2 year–1
All ocean basins collected
Max
Min
Median+SD
Dry weight
Organic carbon
Corg 2000
Inorganic carbon
Opaline silica

147.88
5.24
5.94
3.64
8.92

0.259
0.014
0.007
0.001
0.10


22.3 ± 22.0
1.00 ± 0.94
1.37 ± 1.27
1.40 ± 0.90
1.60 ± 2.02

Sites excluding polar oceans
Max
Min
Median+SD
66.26
3.07
4.24
3.64
8.92

7.77
0.26
0.38
0.60
0.37

22.89 ± 13.66
1.02 ± 0.74
1.50 ± 1.08
1.68 ± 0.83
1.91 ± 1.94

(Fig. 3). This suggests that for many ocean basins where primary production

is not episodic (i.e. polar oceans) that there is a large scale balance in the fraction of new primary production which is exported from upper ocean waters
over annual cycles despite known seasonal variability [28, 29]. Recent models
of particulate flux have explored the complex interactions which occur during sedimentation [30, 31] and suggested that mesozooplankton are more
important in decreasing particle fluxes than macrozooplankton, particularly
in midwater zones where much POC is remineralized. In the context of organic matter cycling, it reinforces the long held belief that the vast majority
of organic matter produced in oceanic surface waters as particles are recycled
during descent, never to be incorporated into oceanic sediments.

Fig. 3 Relationship between annual primary production and flux of organic carbon at
2000 m depth in the oceans. The line represents hyperbolic tangent fit with polar environments (open circles) excluded. Redrawn from Lampitt and Antia (1997) [26] with
modifications. BS represents sites in the Bering Sea excluded from the line fit

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8

H.R. Harvey

Recent estimates and modeling have shown that at least part of the variability observed in the flux of organic carbon might also be due to the fraction
of mineral ballast associated with sinking particles [32]. The presence of
mineral matrices affects the time particles spent in the water column, with organic materials associated with denser minerals having more rapid transit to
the ocean floor. In addition, mineral matrices have been suggested to provide
direct physical protection of organic material through either adsorptive processes or perhaps as binding agents [33, 34], thus influencing the amount and
composition of organic matter that survives descent and is incorporated into
sediments.
Among the varied sources of organic carbon to marine systems, terrestrial
organic matter is an important component, yet its fate in the ocean is not
clear [35]. Much arrives through river transport, with estimates of the flux of
organic carbon to the sea ranging from 0.25–0.36 Pg C year for dissolved OC

and less for particles (Table 1). The range encompasses much variability, due
in part to the lack in uniformity in the estimates themselves. Some of the issues which affect the accuracy of estimates have been discussed by Schlünz
and Schneider (2000) [36] in their compilation of published estimates of terrestrial transport by rivers. They noted a lack of uniformity in approaches
and assumptions, particularly for flux estimates where data may not include
seasonal trends in discharge or measures of both particulate and dissolved
components. This appears particularly true for Asian rivers, which account
for 40% of the total annual sediment discharge but are poorly documented.
Despite these gaps, it is apparent that terrestrial organic matter represents
a large source of reduced organic carbon to marine systems which principally
arrives in dissolved form. Much of this terrestrial export by rivers appears
to be derived from soils [37] and includes the highly degraded remnants of
vascular plants which have been used to provide a detailed suite of molecular structures as tracers of their input (Ittekot, this volume). The primary
drainage sources which account for terrestrial discharge are varied, but the
majority has been estimated to be from forested catchments, with decreasing
contributions from other forests, cultivated lands, wetlands, grasslands, tundra and deserts. Eolian input of terrestrial carbon to the ocean surface has
been difficult to quantify, partly due to the highly variable and complex wind
patterns. Estimates for total carbon range as high as 0.1 pg C year [38] and is
particularly important for terrestrial input to open ocean areas [39, 40].

5
The Importance of DOM
Although the dissolved organic phases of carbon which pass through various filters (Fig. 2) have been long studied (see [41]), intense interest did not
developed until the late 1980s. In several papers describing new approaches

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