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Ecology of Coastal Marine Sediments
Ecology of Coastal
Marine Sediments
Form, Function,
and Change in
the Anthropocene
Simon F. Thrush
Professor and Director, Institute of Marine Science, University of Auckland,
New Zealand
Judi E. Hewitt
Principal Scientist, National Institute of Water and Atmospheric Research, Hamilton,
and Professor, Department of Statistics, University of Auckland, New Zealand
Conrad A. Pilditch
Professor, School of Science, University of Waikato, New Zealand
Alf Norkko
Professor, Tvärminne Zoological Station, University of Helsinki, Finland and Guest
Professor, Baltic Sea Centre, Stockholm University, Sweden
1
1
Great Clarendon Street, Oxford, OX2 6DP,
United Kingdom
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and education by publishing worldwide. Oxford is a registered trade mark of
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© Simon Thrush, Judi Hewitt, Conrad Pilditch, and Alf Norkko 2021
The moral rights of the authors have been asserted
First Edition published in 2021
Impression: 1
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and you must impose this same condition on any acquirer
Published in the United States of America by Oxford University Press
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ISBN 978–0–19–880476–5 (hbk.)
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DOI: 10.1093/oso/9780198804765.001.0001
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contained in any third party website referenced in this work.
Preface
As you walk over a sandflat, swim over or watch connections between different elements of
images of the seafloor you see habitats that are cre soft-sediment ecology. Soft-sediment ecology is

ated by the activities of resident organisms—assum quintessentially an interdisciplinary science with
ing it is not too disturbed. The organisms are both habitats and ecological functions being the
involved in many interactions both with each other products of interactions between biological, chem
and with their physical and chemical environment. ical and physical processes. Thus, the capacity to
The habitats created can be diverse and heteroge connect different kinds of science is essential to
neous, they function as complex systems. Soft sedi advance our research. We hope the book provides
ments are partly fluid systems with very sharp you with a big-picture vision and inspires you
geochemical boundaries and can contain diverse to work on the necessary details and their
species with a wide range of motility at different life implications.
stages. The game rules are not necessarily the same as The principal reason we took on the job of writing
those that play out on competition-dominated this book was because as graduate students we
rocky shores or in dry terrestrial systems. The struc were all helped by John Gray’s original The Ecology
ture of these seafloor ecologies (habitat forms and of Marine Sediments published in 1981. This was the
community composition) is, itself, important but go-to book that got us started thinking about many
what the seafloor ecosystems do—their processes aspects of seafloor ecology and we continue to rec
and functioning—is profoundly important. Coastal ommend it to our students. John also was a dear
ecosystems have been critical for humanity, provid friend and inspiring colleague. We appreciated his
ing food, other resources and some of the most open mindedness, enthusiasm and striving to keep
expensive adjacent real estate. The level of human ecology real and relevant by linking theory and
impacts on these functions combined with feed application.
backs to the delivery of ecosystem services gener John prefaced his original book by emphasising
ates both intellectual challenges and a dire need to the dismal state of soft-sediment ecology with the
understand and value them. The better we under desire to move to a more experimental and
stand seafloor ecology and ecosystem function the hypothesis-testing framework. In the second edi
more robust is the advice we can offer to policy tion (2009—co-authored by Mike Elliot and finished
makers and society about the consequences of change. after John’s death), this trend was continued with
In this book we give you a chance to read about the advantage of a geographic expansion of case
some of the key elements and processes involved in studies. There is still much value in consulting these
the structure and function of soft-sediment ecosys earlier versions; we have not attempted an update,
tems. We have tried to keep the chapters short and but rather an evolution. Now, nearly 40 years since
accessible. Other authors have written books on the the publication of the first edition we can point to a
individual topics we cover in each chapter; our much more diverse and stronger science that has
efforts are not to replace these deeper dives, but continued to grow in its relevance to society and
rather to provide an overview to help you see the inform our role as stewards of marine ecosystems.
v
vi P r e fa c e
Nevertheless, we hope this edition will demon the physical and chemical conditions, these com
strate there is still a lot of research to be done in binations of species do to make these ecosystems
order to understand the distribution of soft-sediment function and respond to change. There are many
communities on the seafloor and the nature and details and we can view the ecology of these sys
consequences of change to them. For many people, tems through many lenses and much is to be learned
much of the seafloor is out of sight and out of mind, from detailed and specific studies. However, as you
making it difficult for them to understand what focus in on the details please remain mindful of the
changes over space and time are occurring, why it bigger picture. This requires innovative ways of
matters and how these changes can affect them. learning how to shift focus to recognise the value of
Although the state of soft-sediment ecology has different approaches and develop techniques to inte
improved over the last 40 years, it still takes a brave grate them. In asking questions of these ecosystems,
individual to take on the challenge of this research. from either a fundamental or a more applied per
We have a much stronger experimental basis for spective, it is critical we think about scales of space,
research now. In fact we have moved beyond study time and biological organisation and incorporate
ing simplistic cause and effect relationships into a natural history, environmental context and theory.
framework of drawing lines of evidence from mul We are increasingly aware of how humans have
tiple kinds of research conducted over different changed our seafloor ecology both locally and glo
space and time scales and into a world of context bally. Much of the growth of civilisation is linked to
dependency, interactions, networks and feedbacks. coasts and estuaries and many of our big cities are
Soft-sediment ecology has also moved to address on or near the coast (e.g. Shanghai, New York,
ecosystem function, which has led to an exciting Manila). We continue to impact these systems both
interdisciplinary science and the challenges of inte directly and indirectly over broader scales due to
grating very different scientific approaches and land–coast interactions, climate change, physical
world views. The growing societal demand on sci disturbance and loss of biodiversity. This means
ence to be relevant and connected to actions to there is a real need for solutions, for understanding
restore degraded ecosystems, assess risks and con and monitoring change in biodiversity and ecosys
serve habitats and species has meant a growing tem functions and, in many cases, for transforming
transdisciplinary and social-ecological niche for the trajectory of ecological trends from down to up.
soft-sediment ecology. There is lots to do—and a real need—from develop
It would be nice to think that the next 40 years ing methods to studying processes, interactions and
will be much more focussed on realising the deep patterns.
value of these ecosystems, moving to restore them As a point of entry this book follows the model of
and conserve them on grand scales, rather than Gray’s first edition. It is written for people starting
docu menting their decline. New techniques are out on a research career and a primer for established
coming into play ranging from molecular ecology managers. It is meant to provide a starting point for
to robotics, machine learning and ocean remote new researchers to ask innovative questions and
sensing that will provide new ways and new scales contribute to the research. We offer an overview
of practical data gathering and interpretation. But and a sense of the connections between different
you do not need expensive resources to do good fundamental concepts. Finally, let us declare our
ecology; understanding natural history, interactions bias: although we have tried to use examples from a
and generating facts about how and why these eco wide range of places, we have not delved into deep-
systems change are still vitally important to inter sea sediments, but stayed closer to the coast. There
preting data patterns—because people need to are many ‘world views’ of soft-sediment ecology
know what it all means. based on organisms (e.g. microbes, meiofauna or
Synthesis and review are important but we can macrofauna) or processes (geochemistry, biogeo
not lose sight of the need to generate primary data. chemistry, geology, physics) but this book is written
What is truly fascinating about soft sediments is not from an ecological perspective of working primar
just the diversity of species but what, together with ily with macrofauna and their interactive role in
P r e fa c e vii
ecosystem function. Traditionally there is a strong which introduce the sedimentary environment: the
North Atlantic bias in soft-sediment ecological physico-chemical environment of the sediment;
research. We have tried to find examples from fur animal, plant and sediment interactions; and the
ther afield, being conscious of the degree of human seafloor as a dynamic area resulting from natural
impact in many regions. Geographical spread of disturbances. This is followed by two practical
research is important because without generality chapters on research approaches to answering your
we can miss critical information and end up with questions. We then move on to three chapters that
disastrously biased perspectives. Throughout we focus on biodiversity and communities, followed
have tried to focus on empirical research exploring by two on ecosystem functioning. Finally we con
and testing theory and concepts. sider soft-sediment ecology and research in the
We have structured the book to cover five general Anthropocene: human impacts, climate change
areas. The scene is set by the first three chapters and restoration.
Acknowledgements
We thank Ian Sherman for the invitation to write the and enriched our experience. This list is long but
book. He and his staff at OUP have been helpful thanks to John Gray, Paul Dayton, Bob Whitlatch,
guides and supporters on this adventure. Writing Rutger Rosenberg, Roman Zajac, Sally Woodin,
from opposite ends of the earth, we are also grateful Dave Wethey, Erik Bonsdorff, Joanna Norkko, Paul
for and acknowledge the support from The Snelgrove, Dave Schneider, Pierre Legendre, Tom
Nottbeck Foundation and Tvärminne Zoological Pearson, Ragnar Elmgren, Drew Lohrer, Vonda
Station, University of Helsinki, in giving us the Cummings, Joanne Ellis, Ivan Rodil, Anna Villnäs,
opportunity to get together to work on the book. Carolyn Lundquist, Candida Savage, Chiara
Finally, we thank Jasmine Low, who has been essen Chiantore, Riccardo Cattaneo-Vietti, Silvia de Juan,
tial in coordinating our activities in the final stages Kari Ellingsen, Doug Miller, Giovanni Coco and
of writing and has contributed some informative Karin Bryan. Thanks also to our students and post-
figures to many chapters. docs for commenting on drafts and more generally
We have been lucky enough to work with many advancing our thinking, and their good humour in
friends and colleagues that have helped, challenged the field and in joining the dots.
ix
C H A PT ER 1
The sedimentary environment
1.1 Introduction we nearly always measure but it’s not a simple

situation where physical processes drive biology
Our goal in this chapter is to introduce you to the (Snelgrove & Butman, 1995). Nevertheless, sedi-
sedimentary environment. Throughout the book ment grain size helps us characterise the near-
we are going to emphasise the importance of inter- seabed flow regime and sedimentary environment
actions between physical, chemical and biological and it is important in regulating the transfer of par
conditions. This is enormously complicated and ticles and solutes between the benthic and pelagic
complex, and this chapter sets the stage for much of realms. Grain size, and more importantly how it
this interaction by considering some fundamental affects the porosity and permeability of sediments,
geological, physical and chemical processes. profoundly influences the microbial decomposition
These processes often seem simple, ordered and of organic matter. It lays the foundation for strong
structured-until life starts to complicate the situ gradients in reactive solutes such as oxygen that
ation. We start with the grains that define sediments, influence the cycling of nutrients critical for pri-
how they are affected by hydrodynamic processes mary producers (Glud, 2008; Middleburg, 2019).
and in turn how they interact with the strong chem- For a book that focusses primarily on the ecology
ical gradients in marine sediments. This approach is of the larger sediment-dwelling fauna, this brief
simple but allows us to focus on how organic matter primer on sediment biogeochemistry, given from a
decomposition pathways vary with depth in the distinctively microbial perspective, may seem
sediment and also how this influences the cycling of unnecessary. However, we believe it provides the
nutrients that sustain primary production. In com reader with valuable context for later chapters dis-
bination, the scene set by these important physical, cussing the functional roles of sediment-dwelling
chemical and geological features influences not only fauna, and how ecological interactions influence
the evolution of seabed morphology but also a wide faunal diversity and ecosystem function.
range of ecological processes including organism
dispersal and population connectivity; primary pro-
1.2 Sediment grain size plus
duction through altered light regimes; and the
release of contaminants and nutrients. Marine sediments are often described as sand or
We want you to start thinking about the environ- mud but there is a large variation in both median
mental factors that create different seafloor habitats particle size and particle size variation. The median
and how they both set the scene for, and interact grain size is useful in characterising a habitat (e.g.
with, resident species and biological processes. We sandflat, mudflat or gravel bed), but it is usually the
focus on describing why sediment grain size is one variation in different components of the distribu-
of the first variables that researchers have used to tion of particle sizes that affects ecosystem pro-
help understand variation in the structure and cesses. As the particle size varies from fine grained
functioning of benthic ecosystems (Sanders, 1958, silts and clays (particles <63 µm diameter) to
1960). This remains a very informative variable that coarser-grained sands, dramatic shifts occur in
Ecology of Coastal Marine Sediments: Form, Function, and Change in the Anthropocene. Simon F. Thrush, Judi E. Hewitt, Conrad A. Pilditch and Alf Norkko,
Oxford University Press (2021). © Simon Thrush, Judi Hewitt, Conrad Pilditch, and Alf Norkko.
DOI: 10.1093/oso/9780198804765.003.0001
4 E C O L O G Y O F C O A S TA L M A R I N E S E D I M E N T S
densities and types of fauna found inhabiting the Table 1.1 Wentworth description of sediments based on particle
sediment and how they interact to influence ecosys- diameter size and the phi scale
tem function. The range of particle sizes that com-
Grain size (mm) Phi (Ø) scale Sediment type
prise the sediment regulates the abilities of animals
to construct burrows, how easily sediments are >4 <−2 Pebbles–boulders Gravel
transported by waves and currents and the 2 −1 Granule
exchange of solutes across the sediment–water 1 0 Very coarse sand Sand
interface. Shifts in benthic diversity and ecosystem
0.5 1 Coarse sand
function often cor rel
ate well with grain size
0.25 2 Medium sand
although the form of these relationships can vary
depending on the range of sediment grain sizes 0.125 3 Fine sand
included in the study. At the extremes, the finest- 0.0625 4 Very fine sand
grained mudflats and the coarsest beach sands, the 0.031 >4–8 Silt Mud
diversity will be low but important changes occur <0.0039 >8–10 Clay
across a range of muddy sands to medium sand
habitats (e.g. Douglas et al., 2018; Pratt et al., 2014).
In coastal habitats grain size varies across mul convenience these size classes are often transformed
tiple spatial scales as a function of sediment supply to the arithmetic phi (Ø) scale which is defined as the
from land and the near-bed hydrodynamic forces –log2 of the particle size in mm, so that a unit change
which transport and sort sediments. These pro- in Ø represents a factor of two change in grain size.
cesses can be in play on a regular basis associated Unless the system is high energy, such as a beach
with tidal flows or wave action, but extreme events, face exposed to waves, or extremely low energy,
such as storms, can set up sediment sources and accumulating fine silts/clays, most coastal sedi
physical structures, such as sand waves, that may ments represent a mixture of size classes reflecting
structure habitats for longer periods (Green & the complex interactions between supply, physical
Coco, 2014; Hall, 1994; Traykovski et al., 1999). As transport and ecology. Thus, it is important to con-
we will see in Chapter 2 the activities of benthic sider not only a median grain size but also a sorting
organisms are also an important driver of grain size index. This index describes the distribution of par
distribution. On the continental shelf, distribution ticles in a sample. Although there are a number of
reflects bathymetry where finer grains accumulate ways to measure sorting, the recommended index is
in deeper waters and coarser grains persist in an the Inclusive Graphic Standard Deviation.
absence of fine sediment sources and/or persistent Whereas the median grain size and a sorting
winnowing by near-bed flows. Within estuaries, coefficient are sterile numbers, a critical element,
variations in grain size are correlated with different depending on your questions, is either the percent-
habitats where muds accumulate in some areas and age of fine particles or the percentage of coarse
coarser sands in others. These basic physical set- particles. In a sedimentary matrix these two per-
tings (sediment supply and hydrodynamics) are centages fundamentally change the sediment’s
further modified by the presence or activities of properties. Thus, we frequently characterise sedi-
organisms (e.g. seagrass meadows and mangrove ment based on amount of mud (or particles <63 µm
forests may trap fine particles). A detailed review of in the silt/clay fraction) according to Folk’s (1954)
the particle grain size analysis methods for marine terminology, which provides a more informative
sediments can be found in Kenny and Sotheran summary of the grain size distribution and physical
(2013). properties (Figure 1.1).
Size classes used for characterising the sediment Grain size and sorting alone are not the only sedi
ary environment follow the sedimentary geology ment characteristics useful to measure (Box 1.1). The
Wentworth scale, which is a geometric scale that other key measures are the sediment porosity and
covers 32 mm, 16 mm, 8 mm, 4 mm and so on permeability. Porosity (Ø) is a measure of the void
down to 0.0039 mm (Table 1.1; Leeder, 1982). For space between grains (VP) but is presented as a ratio
T H E S E D I M E N TA RY E N V I R O N M E N T 5
GRAVEL
M Mud
G sM Sandy mud
80 (g)M Slightly gravelly mud
(g)sM Slightly gravelly sandy mud
EL gM Gravelly mud
ca RAV
mG msG sG S Sand
tt EG
le)
mS Muddy sand
(no TAG
(g)S Slightly gravelly sand

os
(g)mS Slightly gravelly muddy sand

EN
30
RC
gmS Gravelly muddy sand

PE
gS Gravel sand
gM gmS gS
G Gravel
5 mG Muddy gravel
msG Muddy sandy gravel
(g)M (g)sM (g)mS (g)S sG Sandy gravel
1
M sM mS S
1:9 1:1 9:1

MUD SAND
SAND:MUD RATIO
(not to scale)
Figure 1.1 Simplified Folk classification system for sediments with mixed particle size ranges. From Figure 1, Long (2006).
in terms of the bulk volume of the sediment (VT; i.e.

Ø = VP/VT) with values ranging from 0 to 1. It can Box 1.1 Sediments can also be defined as
be easily measured gravimetrically (see Kenny & cohesive or non-cohesive
Sotheran, 2013). The relationship between grain
size distribution and porosity is somewhat counter- In non-cohesive sediments the individual grains can be
intuitive; a sandy sediment will have a greater eroded whereas cohesive sediments stick together and do
not behave as separate particles. This is a property deter-
porosity than a silty sand because the silt particles
mined largely by the silt/clay fraction. Non-cohesive sedi
clog the interstitial voids, but then as the silt/clay
ments are generally sands with a low silt/clay content
content increases so does the porosity as the water (< ~10%) and are characterised by a high permeability.
content increases (e.g. Kamann et al., 2007). However, as the silt/clay content increases, filling the void
Permeability (K; m2) is an indication of how easily spaces and ultimately binding the sediment together, due
water can move through the pore spaces and can be to electromagnetic forces, it creates a cohesive sediment
measured as the rate at which water under a con- with low permeability. The distinction between these two
stant head of pressure passes through a sediment sediment types is an important one because it helps
core of known diameter and length (Klute & define the erosive behaviour when subjected to increas-
Dirksen, 1986). Porosity and permeability are not ing currents. It also regulates the non-biologically medi-
necessarily correlated because permeability is a ated transport of solutes (such as oxygen and nutrients)
across the sediment–water interface. In cohesive sedi
function of the size of the pore spaces and their
ments the process is slow and dominated by molecular
interconnectivity. Muddy sediments can have a
diffusion where solutes must follow a twisted path
high porosity (water content) but, due to the very through the sediment matrix, whereas in permeable sedi
small pore spaces and lack of connectivity, have a ments near-bed flows and pressure variations can induce
low permeability. Sandy sediment on the other much more rapid exchanges of solutes (see section 1.4).
hand can have a high porosity and permeability.
In many coastal settings sediment grain size is interactions. The forces generating flows on the
not uniform. Whether these sediment mixtures coastal seabed vary widely in their spatial and tem
behave cohesively or non-cohesively depends on poral scales and include tides, waves, upwelling,
many factors including the fraction of fines; com- storms and coastal currents. The importance of
paction and the size ratio of the small and large flow interactions with microbes, larger plants and
fractions; and, of course, ecological processes (see, animals will be covered in Chapter 2, here we will
e.g. Bartzke et al., 2013; Le Hir et al., 2007; Jacobs give a general overview of near-bed flows and
et al., 2011; Staudt et al., 2017 and references therein; their consequences for particle and solute fluxes.
Box 1). The important thing is that relatively small -see Nowell and Jumars (1984), Jumars (1993) and
amounts of fine sediments added to the surface of Boudreau and Jorgensen (2001) for an in-depth
sands can cause a shift between these two behav- introduction to the physics and consequences of
iours—a small amount of silt and clay can make a benthic processes.
big difference! If we measure grain size of the near- Whether flow is likely to be turbulent or laminar
surface sediments (0–2 cm) we may see this effect, can be assessed by calculating the Reynolds num-
but if we take deeper cores to assess the average ber (Re), a dimensionless number (i.e. it has no units
grain size of the sediments we may dilute the effects so is independent of the scale of observation). It
of these surficial deposits. This is important because compares the factors responsible for generating tur-
in many coastal areas fine sediment addition has bulence (fluid speed and an appropriate length
changed or is changing grain size distribution (see scale that the fluid is interacting with) to those that
Chapter 11). dampen it out (viscosity of the fluid). Estimating
The larger plants and animals can radically the Re for a given situation gives a first-order
change the physical characteristics of sediments, approximation as to how quickly mixing will occur
for example, by creating faecal pellets that bind and can also give an indication of the boundary
small particles into larger ones or selecting certain layer characteristics (Box 1.2).
grain sizes to build tubes (see Chapter 2). This led to In coastal environments the thickness and struc-
consideration about how we should actually define ture of the benthic boundary layer (BBL) are highly
grain size, but measuring the size of the physical dynamic, due to spatial and temporal variations in
particles (involving removal of organic matter and flow speed and bottom roughness. Under slow,
disaggregation) gives us more consistent and com- steady currents the BBL thickness may be tens of cm
parable data. Nevertheless, it is im portant to but under high flows it may only extend a few cm
remember that realised grain size distributions, above the seabed. Furthermore, as flow speed and/
porosity and permeability may be quite different or bottom roughness increases, the viscous and dif-
than those predicted from inorganic particle size fusive layers may disappear altogether and the
analysis. logarithmic turbulent layer penetrates all the way
to the bed.
1.3 Flow, waves and the benthic The steepness of the velocity gradient in the BBL
determines the force exerted at the seabed which
boundary layer
influences particle deposition and resuspension.
The characteristics of the near-bed flow play a key This force is represented by the bed shear stress (τ;
role in regulating solute and particle fluxes to and N m−2 s−1) and it is probably the single most import
from the water column and thus the degree of con- ant parameter to know when thinking about flow–
nectivity between the benthic and pelagic environ- sea bed interactions. It is commonly estimated from
ments. The interaction between flow, the sediment vertical profiles of time-averaged velocity or meas-
and organisms inhabiting the seafloor influences urements of turbulence in the BBL (e.g. Kim et al.,
feeding rates of benthic organisms, supply of 2000) and is often reported as shear velocity
organic matter, resuspension potential of sediments (u* = t / r where ρ is the fluid density). The reason
and thus disturbance regime, recruitment and the for this conversion is that the shear stress is
strength of biotic interactions such as adult–juvenile expressed in units of velocity and therefore can be
Box 1.2 The benthic boundary layer
A fundamental characteristic of the flow close to the seabed seabed influence on flow speed. In this layer, vertical mixing
is the presence of a benthic boundary layer (BBL) and the is rapid because of turbulence (high-frequency irregular
flow characteristics of this layer are worth describing motions—eddies—of water parcels) that pervades the fluid
because this is where interactions between the sediments undergoing shear at the bed. As we move closer to the sea-
and water column actually happen. If we assume a constant bed, the frictional effects of the sediment begin to exert a
current velocity then as we approach the seabed the fric- greater impact on the fluid and the turbulence is dampened.
tional effects of the sediment extract momentum and the This is called the viscous sublayer and vertical mixing in this
flow velocity begins to slow down until at the seabed (with layer is a combination of much slower molecular diffusion
stationary sediment) it approaches zero (Figure 1.2). and smaller-scale turbulence and as a consequence is much
This reduction in flow changes the characteristics of the slower. Finally, right close to the bed we have the diffusive
fluid environment and the BBL can be divided up into differ- sublayer which is where the frictional effects have damp-
ent sections based on these. The outer logarithmic layer is ened out all the turbulence and viscous effects (stickiness
characterised by a log decline in the mean flow velocity between fluid layers) dominate. This means flow tends to
toward the bed. Nominally the top of this layer is at 99% of follow streamlines, turbulence is absent and vertical trans-
the freestream flow speed and represents the extent of the port of solutes is dominated by molecular diffusion.
Outer layer
Height Above the Bed
Logarithmic layer
Fully turbulent, rapid & intense mixing
Viscous layer
Weak turbulence, vertical mixing = molecular diffusion
0 Diffusive sub-layer
No turbulence, mixing by molecular diffusion
0 Mean Velocity
Figure 1.2 Different layers and flow characteristics of the benthic boundary layer.
used to estimate a Reynolds roughness number A key modifier of BBL dynamics in coastal set-
(Re*) which characterises the nature of the flow at tings is the presence of short-period (1–5 s) wind-
the seabed. When calculating Re* the appropriate driven waves and longer-period (10–50 s) swell
length scale will be the feature that dominates the waves on exposed coasts. When the wave orbitals
seabed roughness at the scale of interest, most com- penetrate to the bed (a function of the water depth,
monly median grain diameter but it can also be rip- wave height and frequency), they add a periodic
ples or biogenic structure protruding off the seabed oscillation of flow acceleration and deceleration in
(for plants and fauna; see Chapter 2). When Re* < 3.5 the BBL created by the mean current. These oscilla-
the BBL will be hydraulically smooth with viscous tions generate additional shear in the BBL and as a
and diffusive sublayers, but at values >100 the flow consequence wave–current boundary layers are vir-
is hydraulically rough and turbulent with no sub- tually always hydraulically rough. The detailed
layers. The nice thing about Re* (and other dimen- physics of the wave–current boundary layer are
sionless numbers) is that it highlights how different complicated but it is worthwhile noting their
combinations of bed roughness and u can generate importance for ecological processes. The additional
similar BBL conditions. shear generated by waves is often needed to initiate
sediment resuspension and the associated transport/ they can be carried along with the currents.
dispersal of organic matter, sediment porewater Naturally, as grain size increases the shear stress
nutrients and organisms. As the waves are primar- required to erode non-cohesive sediment also
ily generated by passing weather systems this intro- increases, a simple product of the fact that larger
duces a stochastic element into the frequency and particles are heavier and more difficult to move.
intensity of sediment transport (see Hall, 1994 for The behavioural response of cohesive sediments to
an ecologically focussed review). increasing shear stress is different and they behave
more like a bed of jelly than individual particles. As
the erosion threshold (the point at which the applied
1.4 Consequences of the BBL on shear stress causes the sediment bed to release par
ticles) is exceeded, sediment is ejected (often as
bio-physical processes
aggregates) directly into the water column (i.e. there
The propensity of a sediment to be mobilised is a is no bedload transport). Also, somewhat counter-
function of the sediment grain size (and sorting), intuitively, the force required to erode a cohesive
seabed roughness and the force exerted on it by the bed increases with decreasing grain size because of
BBL. Figure 1.3 shows a simplified relationship increasing inter-particle electromagnetic forces and
between beds of uniform grain size and the flow decreasing bed roughness which reduces the force
velocity required to erode them. There are funda- that can be exerted on particles.
mental differences in the response of non-cohesive Much of our understanding of sediment resus-
and cohesive sediments to increasing bed shear pension and critical erosion thresholds is based on
stress. Non-cohesive sandy sediment erosion ini- laboratory studies of single grain sizes. In the real
tially starts as bedload with grains bouncing along world, coastal sediments are often comprised of
the sediment surface (taking microbes and animals mixed assemblages of fine and coarse grains which
with them). As the force increases there is enough alters the cohesive properties, and the ability of
energy to move particles into suspension and then water to penetrate the seabed, altering the erosion
Clay Silt Sand Pebble

1,000
Erosion
EROSION AND TRANSPORT
curve
AD
100 LO Deposition
ED
Flow velocity (cm/s)
N DB curve
R TA
PO
NS
TRA
10
TRANSPORT
IN SUSPENSION
DEPOSITION
1
0.1
0.001 0.01 0.1 1 10 100
Grain size (mm)
Figure 1.3 Annotated Hjulström curve showing transport properties as a function of grain size (see Hjulström, 1935).
dynamics. For example, Bartzke et al. (2013) showed water column. The magnitude of this exchange is
that even small amounts of silt added to a sandy a function of the sediment permeability and the
sediment (a few percent by weight, and well below flows/topography generating the pressure gradient
the amount needed to cause cohesion) filled the (Huettel & Webster, 2001), but in terms of solute
void spaces between sand grains and substantially exchange it is many times more efficient than
increased the flow speed needed to mobilise the molecular diffusion. Advective porewater exchange
bed. Superimposed on this is the capability of ben- also introduces organic matter (Figure 1.4) into the
thic organisms to alter the erosion properties of sediment simultaneously with oxygen where it
sediments (see Chapter 2). This means it is very undergoes rapid decomposition by microbes. As a
difficult to predict erosion thresholds for coastal result, nutrients are released back to the water col-
sediments based only on the physical grain size umn. Santos et al. (2012) have estimated that the
distribution. process of advective porewater exchange in perme-
At flows below the erosion threshold, the BBL can able coastal sediments results in the entire volume
still play a crucial role in regulating solute and par- of the ocean being filtered every 3000 years. It is this
ticle fluxes across the sediment–water interface. In process combined with high rates of primary pro-
permeable sediments (i.e. K > ~ 10−12 m2) pressure duction which contributes to the importance of
differentials generated by passing waves and/or coastal sediments in global biogeochemical cycles.
flow over topography such as ripples induce The sediment surface is a region of strong and
regions of high and low pressure in the sediment, active vertical gradients in reactive solutes such as
which drives a porewater exchange between the oxygen (see section 1.5). In non-permeable cohe-
sediment (to depths of several cm) and the overlying sive sediments (i.e. K < ~ 10−12 m2) where molecular
chl a μg cm–3
(a) 2
1.5
0 1.2
0.9
Height above/below minimum bed elevation (cm)
–2
0.6
–4 0.3
0.0
(b) 2
0
–2
–4
(c) 4 (d) 4 (e)
2 2
0 0
–2 –2
–4 –4
30 50 70 90 110 130 150 170 190 210 4 8 12 16 4 8 12 16

Distance from start of working section (cm) Distance across water tunnel (cm)
Figure 1.4 Diatom biomass measured by chlorophyll a accumulations with increasing bed geometry (a–c). (d) and (e) show a cross section
through a large ripple trough and crest respectively. From Figure 1, Pilditch and Miller (2006). Reprinted from Continental Shelf Research, 26 (15),
Pilditch C A, and Miller D C, Phytoplankton Deposition to Permeable Sediments under Oscillatory Flow: Effects of Ripple Geometry and
Resuspension, 1806–1825., © 2006 reused with permission from Elsevier.
iffusion physically dominates solute exchange,

d that act like parachutes lifting it off the sediment
BBL dynamics can still influence solute concentra- surface, allowing dispersal over large scales
tion gradients. The demand for oxygen in marine (100s–1000s of m). Many benthic species exhibit this
sediments is high due to aerobic bacterial activity post-settlement dispersal, and what is clear from
and the oxidation of reduced solutes moving up field studies is that the diversity and magnitude of
from deeper in the sediments. This demand creates dispersers are functions of the near-bed hydro
an oxygen gradient not only in the sediment but dynamics (e.g. Lundquist et al., 2006; Valanko et al.,
one that can extend into the sublayers of the BBL. 2010; see Pilditch et al., 2015 for a review). There is
The oxygen gradient in the near-bed water is known still much to be done to understand how temporal
as the diffusion boundary layer (DBL) and its thick- and spatial variability in the interacting factors
ness (typically <1 mm) is regulated by a combin regulating dispersal (sediment properties, behav-
ation of the sediment oxygen demand, concentration iour, species interactions and hydrodynamics)
in the overlying water column and the BBL dynam- influence dispersal but such studies are critical to
ics. Because the DBL is governed in part by the sedi understanding the dynamics of benthic populations
ment oxygen demand, its thickness may not and communities (Pilditch et al., 2015).
correspond directly to the diffusive and viscous
sublayers of the BBL. Under slow flow, this concen-
tration gradient can extend beyond the diffusion
1.5 Organic matter
sublayer of the BBL. Under fast, turbulent flows the
DBL may disappear altogether. The presence or The quality and quantity of the organic matter
absence of the DBL will influence oxygen availabil- arriving at the sediment surface are critical environ-
ity in surface sediments with implications for aer mental variables, providing fuel directly for meta-
obic bacterial activity (see Glud, 2008 for an in-depth zoans or indirectly by fuelling microbes for
discussion). decomposition that then become food for others. In
Near-bed flows also play a critical role in the dis- general, the organic content of sediments increases
persal of benthic invertebrates and, as such, an with decreasing grain size because the lower flows
important role in recovery from disturbances and allow the accumulation of low-density particles but
meta-community dynamics (Chapter 3). Although also the increased surface area promotes high bac
dispersal is discussed in many places within the terial biomass.
book, related to aspects of recovery, design and In coastal environments, organic matter has
biotic interactions, here we briefly describe it from a numerous sources: primary production in the water
flow perspective. Traditionally, the pelagic larval column, detritus from macrophytes such as kelp,
phase was considered most important for dispersal seagrass and mangroves as well as inputs from ter-
as this was a period that they could potentially be restrial ecosystems. In many benthic ecosystems,
moved long distances by currents. However, storms organic matter fuels secondary production. Except
may move organisms around passively and it is not in the most turbid regions, the production of the
uncommon to see benthic animals washed up on microphytobenthos at the sediment–water interface
beaches. Under more typical conditions behaviour is the major source of organic material (Cahoon,
can influence the effect of waves and currents, e.g. 2002; Hope et al., 2020; Miller et al., 1996).
crawling onto the sediment surface can increase the The input of organic matter is the base of the food
chances of hitching a ride with the flow (e.g. chain of marine sediments and the amount varies
Lundquist et al., 2004). This is often particularly with many factors, including the productivity of the
important for juvenile life stages where the organ- overlying water column. Food quality is a big issue
isms are small and easily transported. For example, and can be coarsely quantified by the carbon to
the bivalve Macomona when it is 0.5–3 mm long will nitrogen ratio. In general phytoplankton and bac
move onto the sediment surface and orientate itself teria have lower C:N ratios, typically <10, whereas
so that its shell behaves a bit like a wing; once it is macrophyte detritus typically has C:N ratios >20.
ready to go it excretes long proteinaceous threads Consumers prefer energy sources with lower C:N
ratios (ideally as close to seven as possible, the ratio be seen as a greenish or brownish tinge. In more
in animal tissue) because higher ratios mean more oligotrophic settings MPB production can exceed
time (and energy) are expended acquiring sufficient pelagic production because they have ready access
food to satisfy their N requirements. As well as to nutrients stored in the sediment porewater. Their
these coarse measures of food quality, it is the plants value in coastal foodwebs arises because they are
that synthesise the essential fatty acids needed by easily digestible, rich in lipids and proteins, have
animals (Antonio & Richouz, 2014; Galloway et al., high turnover rates and have not undergone
2012). Faecal pellets from animals living in the pre-processing by pelagic consumers and so do not
water column or suspension feeders living on the arrive as faecal pellets (Hope et al., 2020). In the Dutch
seabed are an important source of organic matter Wadden Sea a stable isotope study showed that MPB
input into seafloor communities. Faecal pellets have were the most important food source for benthic
much higher settling velocities (e.g. Giles & invertebrates and given these organisms support
Pilditch, 2004) than the food that produces them higher trophic levels (fish, birds and seals) this further
and even after digestion (and any decomposition underlines their importance (Christianen et al., 2017).
occurring on the way down) have a higher organic MPB are ecologically important beyond their
content than water column particles naturally set- value as food for higher trophic levels (Hope et al.,
tling out. This biological pump is an important 2020). Light is attenuated rapidly in sediments and
component of benthic–pelagic coupling: i.e. in this a lack of nutrients in the photic zone means MPB
context, the delivery of water column organic mat- undertake vertical migrations to access them
ter to the seabed where it is remineralised by bac (Consalvey et al., 2004). To aid these migrations,
teria, releasing nutrients that fuel pelagic production diatoms in particular excrete extracellular polysac-
(Graf & Rosenberg, 1997). charides (EPS), a sticky mucus-like substance that
binds the sediment together. In cohesive sediments
(or non-cohesive sediments with a substantial silt/
1.6 Light and benthic primary production
clay content) the EPS can fill the void spaces, bind-
In shallow coastal waters where light hits the sea- ing sediment and particles, thus leading to a marked
bed the microphytobenthos and larger macrophytes increase in sediment stability, making it less prone
(macroalgae and seagrasses) can flourish and give to erosion (see Chapter 2). Photosynthesis in surface
rise to local production. The amount of light hitting sediment layers can also alter the distribution of
the seabed is a function of atmospheric conditions, oxygen, increasing the volume of sediment that
latitude, time of day and coastal topographic fea- then supports more efficient decomposition of
tures that create shade, water depth and clarity. organic matter by aerobic bacteria, affecting nutri-
Water clarity is strongly affected by phytoplankton ent cycling (see section 1.8). MPB also trap nutrients
in the water column, dissolved organic matter like at the sediment surface, preventing their release
tannins from land that stain the water and import to the water column. In shallow coastal systems
antly the input and resuspension of fine sediments. undergoing eutrophication, this sink of nutrients
The amount of light hitting the seafloor regulates helps slow the eutrophication spiral where con-
benthic primary production and in turbid estuaries tinual release of nutrients from decomposing
the loss of this production has been a contributing organic matter in the sediments fuels further pelagic
factor to accelerating eutrophication (Chapter 11). production.
Although on a per-area basis primary production
by benthic macrophytes can greatly exceed that of
unvegetated habitats, it is the ubiquitous microphy-
1.7 Sediment biogeochemistry
tobenthos (MPB) that fuel many coastal foodwebs
(e.g. Christianen et al., 2017; Jones et al., 2017). MPB Even at small scales (m2) coastal marine sediments
consist of diatoms, dinoflagellates and cyanobac are extremely heterogeneous with respect to their
teria (McIntyre et al., 1996) growing within the first physical properties (e.g. grain size, sorting) and
several mm of the surface sediment and can often concentrations of reactive solutes such as oxygen.
This heterogeneity arises primarily as a result of the human-induced changes in sediment organic mat-
interactions between the activities of the resident ter decomposition and nutrient cycling pathways
macrofauna community and the microbial commu- can extend into the water column, negatively
nity (both the bacteria that are decomposing organic impacting the entire ecosystem.
matter and the photosynthesising MPB). For If you were to carefully dig a small hole in a typ
ex ample, burrow irrigation by shrimps (e.g. ical coastal sediment you would most likely see
D’Andrea & DeWitt, 2009) may deliver oxygen three distinct layers distinguished by their colour
deep into the sediments whereas bulldozing heart (and smell). These represent substantial shifts in the
urchins leave faecal pellets that become hotspots of metabolic pathways of bacteria responsible for
bacterial activity (Lohrer et al., 2004; Solan & organic matter decomposition. The first major
Wigham, 2005). In Chapter 2 we explore more active zone in most coastal sediments is the surface
animal–sediment interactions but just as we have oxic layer which appears as a yellow/brown layer
described the physical aspects of the sediment, that morphs into grey before immediately being
there is value in considering the basic chemical replaced by reduced black anoxic sediment with a
implications of bacteria and organic matter down smell of rotten eggs (hydrogen sulphide). In the
the sediment column. decomposition pathways, aerobic respiration in the
The upper few centimeters of the sediment are surface yellow/brown layer releases the most
one of the most extreme chemical gradients on the energy and aerobes will outcompete other respir
planet where transition occurs from an aerobic to an ation pathways. The concentration of oxygen in a
anaerobic environment. These gradients are driven microbially dominated sediment decreases expo-
by the physical characteristics of the sediment as nentially from the sediment surface to the redox
well as the microbial communities and, in a world potential discontinuity (RPD) where no free oxygen
without large plants and animals, are vertically exists (Figure 1.5). The availability of oxygen is
structured according to the bacterial respiration measured by the redox potential (Eh); once the oxy-
pathways during the decomposition of organic gen is used up anaerobic processes dominate and
matter. The coastal sediments (which comprise control chemical speciation.
<10 percent of the oceanic seafloor) are estimated The thickness of the oxic reaction zones in sedi
to be responsible for processing ~30 percent of the ments is variable and as a consequence so too is the
world’s oceanic carbon (Smith & Hollibaugh, 1998) efficiency with which organic matter is remineral-
and during the decomposition regenertating essen- ised. The thickness of the oxic layer is a balance
tial nutrients. As we will see later in the book, between supply and demand, the sediment grain
Sediment surface
Eh pH O2 Fe+e+ CO2 NO3–
5 10 15 Yellow layer
mg/l
NO2–
Gray
RPD layer
Fe+e
NH3
CH4 Black layer

–200 0 +200 +400 0 2 4%
mV
6 7 8
0 100 200 300 400
H2S mg/l
Figure 1.5 Sediment profiles of redox potential, pH, oxygen, hydrogen sulphide, iron, methane, carbon dioxide and nitrogenous species.
size which determines diffusion rates, and the qual- Table 1.2 Organic matter (CH2O) oxidation pathways mediated by
ity and quantity of organic matter which determine bacteria in the sediment and their free energy yields (ΔG°). Table
adapted from Boudreau and Jørgensen (2001)
the rates of bacterial metabolism. In finer-grained
sediments diffusion rates are slower and oxygen
Reaction kJ mol−1
decreases more rapidly. In permeable sediments
diffusion rates are higher but there is also advective Oxic respiration:
CH2O + O2 → CO2 + H2O −479
porewater exchange driven by pressure differen-
tials. If organic loading is high, then the RPD can Denitrification:
5CH2O + 4NO3− → 2N2 + 4HCO3− + CO2 + 3H2O −453
extend all the way to the surface and the sediments
(and even the overlying water) become anoxic, Mn-oxide reduction:
CH2O + 3CO2 + H2O + 2MnO2 → 2Mn2+ + 4HCO3− −349
limiting the higher and larger lifeforms. The loss of
the oxic sediment layer also decreases the efficiency Fe-oxide reduction:
CH2O + 7CO2 + 4Fe(OH)3 → 4Fe2+ + 8HCO3− + 3H2O −114
of organic matter degradation metabolism and alters
Sulphate reduction:
the cycling of key nutrients (see section 1.8). In
2CH2O + SO42− → H2S + 2HCO3− −77
terms of impacts in coastal waters, increased sedi
Methane production:
mentation in many parts of the world plus eutrophi
HCO3− + 4H2 + H+ → CH4 + 3H2O −136
cation are impacting on the biogeochemistry (see CH3COO− + H+ → CH4 + CO2 −28
Chapter 11). The presence of MPB can also induce
diurnal changes in oxygen availability and during
light reactions the production of oxygen can lead to the quantity of carbon stored in the sediment
a sub-surface maximum which disappears at night. (Middleburg, 2019).
Fluctuations in light intensity result in temporal The by-products of anaerobic respiration/decom-
variations in oxygen availability (similar fluctuations position include reduced inorganic compounds in
are seen through the activities of larger fauna—see the porewater that diffuse upwards toward the
Chapter 2) and may influence nitrogen cycling, a sediment surface. It is interesting to note that as you
process that depends on coupled reactions in the move deeper in the sediment more free energy
presence and absence of oxygen (see section 1.8). (once oxidised) is tied up in the reduced com-
Beneath the RPD, in the absence of oxygen, other pounds, a point highlighted by the fact that methane
terminal electron acceptors (oxidants) are utilised is a by-product of the fermentation processes at
by anaerobic bacteria sequentially with depth based depth. As these reduced compounds diffuse toward
on their standard redox potential and yield of free the RPD chemosynthesis can occur whereby bac
energy (Table 1.2; Figure 1.5). This creates a depth teria mediate the oxidation of reduced iron, manga-
sequence in the oxidants consumed for the mineral nese and in particular sulphides to release energy
isation of organic matter by bacteria, from oxygen that is then used to fix inorganic carbon. This form
to nitrate, manganese oxide, iron oxides, sulphate of primary production is similar to that which fuels
and finally carbon dioxide. The by-product of hydrothermal vent ecosystems in the deep sea. In
sulphate reduction is hydrogen sulphide, which
shallow water depths where the RPD extends to the
gives the sediment that rotten eggs smell. Hydrogen sediment surface and light penetrates to the seabed
sulphide and sulphide ions are toxic to nearly all phototrophic sulphur bacteria and cyano bacteria
metazoans so organisms living beneath the RPD are also capable of carbon fixation, utilising the dif-
layer obviously need to pump oxygen down. fusing sulphides (see Jørgensen et al., 2019 for a
Because the oxic layer in sediments is relatively recent review).
small in most of the coastal ocean it is estimated
that most of the organic matter is decomposed via
1.8 Nutrient cycling
manganese, iron and sulphate reduction in anoxic
sediments (Canfield, 1993; Jørgensen, 1982). The The decomposition of organic matter within the
fate of organic matter as it passes through these dif- sediments results in the regeneration of inorganic
ferent levels determines burial rates and ultimately nutrients essential for primary production. It has
been estimated that in some coastal and shelf eco- stage of the transformation process inorganic N can
systems up to 30–50 per cent of the pelagic primary diffuse upwards where it can be utilised by MPB at
production is supported by nutrients regenerated the sediment–water interface and, if not trapped
from within the sediments (Nixon, 1981; Pilskaln there, by pelagic primary producers. Ammonium,
et al., 1998). It is beyond the scope of this section to nitrite and nitrate can also diffuse downwards (the
describe in detail the cycling of all biologically direction is dependent on the concentration gradient
important elements and we refer readers to excel- and therefore a function of solute sources, sinks and
lent summaries in Aller (1994), Middleburg (2019; diffusion rates) into the anoxic sediment where it
carbon), Jørgensen et al. (2019; sulphur) and can undergo a series of reduction reactions.
Delaney (1998; phosphorus) for entry points into Of particular significance to systems experien
this literature. We have chosen however to provide cing excess N inputs are the pathways that reduce
some detail on the sediment nitrogen (N) cycle N to biologically inert forms. Denitrification con-
because it is the main nutrient limiting primary pro- verts nitrite and nitrate to nitrogen or nitrous oxide
duction in coastal waters, of which the sediment is gas which are not readily assimilated by primary
a key source (Nixon, 1981). Also, the sediment rep- producers and are ultimately released back into the
resents the most important biological pathway to atmosphere. In the anoxic zone, dissimilatory
remove excess N, which is the cause of eutrophicat nitrate reduction to ammonium (DNRA) can also
ion (see Chapter 11). occur where it can diffuse back into the oxic sedi
Bacteria in the sediment mediate multidirectional ments or in the presence of nitrite be converted via
oxidation and reduction reactions that transform anaerobic ammonium oxidation (anammox) to
organic N into a number of different inorganic nitrogen gas (see Devol, 2015 for a review). The
forms. A key feature regulating these transforma importance of anammox as a pathway of N removal
tions is the tight coupling between the oxic and remains relatively unknown in marine sediments,
anoxic zones in the sediment. The sediment porewa- whereas in coastal sediments denitrification tends
ter is rich in ammonium from the decomposition to be quantified more frequently. The small number
process (ammonification) and excretion by organ- of studies focussed on anammox in coastal sedi
isms. Nitrification, purely an aerobic process, trans- ments suggest it can account for 10–40 per cent of
forms the ammonium into nitrate via nitrite. At each the total N2 production (Devol, 2015). The removal
water column
N2 PON NH4+ NO3– N2O N2
A Nitrification
oxic
PON NH4+ NO2– NO3–
A DNRA
N2 PON NH4+ NO2– NO N2O N2
anoxic
Denitrification
Anammox
Figure 1.6 A conceptual model of the sediment nitrogen cycle in coastal sediments showing transformations specific to the oxic and anoxic
sediment layers. Note that nitrification is carried out by aerobic bacteria and provides the nitrate that is converted to inert forms of N in the anoxic
sediments. When the oxic layer is lost from sediments (e.g. due to organic loading) the ability of the sediments to remove bio-available N is
compromised. A: ammonification; Anammox: anaerobic ammonium oxidation; DNRA: dissimilatory nitrate reduction to ammonium; PON:
particulate organic nitrogen. Adapted from Devol (2015).
of nitrogen through denitrification in estuaries can Therefore, although these processes have been
account for 10–80 per cent of the inputs, thereby under study for many years, there is still plenty of
representing a significant sink providing resilience work to be done. However, physico-chemical pro-
to eutrophication (Nixon et al., 1996). cesses do not operate in a vacuum. Although there
The ability of sediments to remove excess N via are ‘dead’ zones in our marine systems, they are for-
denitrification is dependent on the presence of an tunately rare and instead physico-chemical pro-
oxic–anoxic interface. The simple one-dimensional cesses interact with, and are often driven by, the
picture of N-cycling in coastal sediments shown in plants and animals that live in and on the sediment
Figure 1.6 masks the complexity introduced by the (see Chapter 2). The interplay between these factors
activities of larger fauna that can greatly extend this is an area rich in opportunities for future research.
interface through building and irrigating burrows
or bulldozing their way through sediment, both
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C H A PT ER 2
Benthic animals and plants

and what they do to sediments
2.1 Introduction been known for a long time but the coining of the
term ecosystem engineer has more widely high-
In the previous chapter we presented an introduc- lighted their significance (Jones et al., 1994).
tion to the sedimentary environment focussing pri- So, in this chapter we move from the simple
marily on physical characteristics and how the microbial, geochemical world view presented in
activity of microbial organisms alters sediment Chapter 1 to consider the animals and plants that
chemistry. However, any cursory look at the sedi- live on and in the sediment (Figure 2.1). We intro-
ment surface will show traces of larger life forms in duce these and the general categories in which they
the sediment that underlie a much greater complex- are often studied. As these organisms frequently
ity. This can include tubes, burrows, mounds and alter the physical environment that surrounds
pits created by the infauna as well as the epifaunal them, in terms of sediment characteristics and sedi
animals and large plants living on the sediment sur- mentary processes and also alterations in benthic–
face. These surface features indicate the presence of pelagic coupling, we also discuss some essential
a complex three-dimensional structure extending characteristics that determine what, how and how
above and below the sediment surface that often much they alter their environment.
defines seafloor habitats and how they function.
Above the surface the spatial structure of emer-
2.2 Size
gent habitats interacts with the benthic boundary
layer and in combination with the feeding activities Size is particularly important for studies of benthic
of the animals dramatically alters benthic–pelagic organisms, in part because sampling strategies are
coupling (i.e. the flux of dissolved nutrients/sol- dependent on size. For this reason, the communities
utes, inorganic/organic particles and organisms). that live in marine sediments are divided into dif-
For example, in sufficient densities these structures ferent groups based on size, and these groups are
can stabilise the sediment and promote the settle- often studied separately.
ment of organic matter. In areas devoid of emergent The microbial communities are composed of uni-
biogenic structure, the feeding, movement and irri- cellular organisms (e.g. protists, archaea, diatoms).
gation activities of large infaunal organisms can They are found throughout the sediment column
radically alter the sediment properties such as grain and are especially important in driving the trans
size distribution and the availability of oxygen, formation of organic matter in the sediment and the
creating a 3-D mosaic of microhabitats that affects processes of remineralisation (see Chapter 1). These
biogeochemistry and rates of organic matter decom- organisms can form colonies or mats that create
position and nutrient cycling. Sometimes single large structures, for example stromatolites and bio-
species are important and these are usually the films or mats consisting of microphytes or under
larger species. The role of these large species had reduced conditions Beggiatoa, or they can function
Ecology of Coastal Marine Sediments: Form, Function, and Change in the Anthropocene. Simon F. Thrush, Judi E. Hewitt, Conrad A. Pilditch and Alf Norkko,
Oxford University Press (2021). © Simon Thrush, Judi Hewitt, Conrad Pilditch, and Alf Norkko.
DOI: 10.1093/oso/9780198804765.003.0002
Figure 2.1 Plants and animals change the topography of the sediment surface, providing clues to burrows, tubes and processes beneath the
sediment surface. Tubes, burrows, faecal mounds and feeding traces are linked to sediment type and the action of physical forces on the seafloor.
(Photo credits ST, Rod Budd and Jenny Hillman.)
as individual cells. The composition and activity of usually based on how important the juvenile vs
microbial communities are influenced by their adult life stages are to the individual researcher. For
environmental conditions and in particular whether instance, if you are interested in recruitment and
the sediment is oxygenated or anaerobic. early benthic life stages that settle at 0.2–0.3 mm, or
For the larger multicellular fauna, size classes are if you are sampling a community dominated by
conventionally defined by the mesh size of sieves on small species you would select a smaller mesh size;
which the animals would be retained. Meiofauna are however, if your interests are in the adult life stages
the smallest; they pass through a 0.5-mm mesh sieve of larger organisms, or you want to sieve samples
and are retained on a mesh larger than 0.062 or 0.031 more quickly, a coarser mesh would be used. The
mm. These are not animals you can see with the naked early life stages of some of the larger macrofaunal
eye, and they usually live in the interstices between species are classified as meiofauna until they grow
grains of sediment. They graze on detritus, microbes to larger than 0.5 mm. Most kinds of marine inver-
and recently settled macrofauna and can contribute to tebrates are represented in the macrofauna, but
sedimentary processes and functions (Bonaglia et al., polychaetes, bivalves, gastropods, amphipods, iso-
2014; Coull, 1999). Nematodes, harpacticoid cope pods and ophiuroids are among the most common.
pods, turbellarians and gastrotrichs are commonly These are the organisms that are big enough to start
represented in meiofaunal communities, but there are moving sediment particles and pumping water into
representatives of almost all marine invertebrate and out of the sediment, so that they have a strong
phyla within the meiofauna. influence on ecosystem function and the sediment
The macrofauna are classified as organisms larger ary environment. There is no common definition of
than 0.5 mm, although some researchers use 0.3 the upper size limit to macrofauna, but the practi-
mm, whereas others use 1.0 mm. This distinction is calities of sampling come into play. Macrofauna are
THE BENTHOS AND SEDIMENT INTERACTIONS 21
usually collected by core or grab samples and there- living on the seafloor; infauna, living within the
fore are commonly less than 10 cm. sediment; and fringing vegetation, living in high
Larger fauna are called megafauna; these are upper tidal zones.
often animals like fish, large crustaceans and octo-
puses that burrow in sediments or the large pred
2.3.1 Epibenthos
ators which feed in and disturb the sediments—which
can include very large animals like grey whales and Epibenthos live on the sediment surface, and are
walrus. However, the cut-off point of 10 cm means comprised of both plants and animals. Epiflora
that many polychaetes, ophiuroids, echinoderms (plants) are comprised of macro-algae and sea-
and even some bivalves could be considered mega- grasses. They range from individuals to extensive
fauna in their adult stages. For this reason, it is beds and from encrusting to erect forms. They are
important not to take these categories too strictly. generally anchored (at least in the beginning) to
Apart from microalgae, a variety of plants inhabit small hard items, such as rocks, cobbles or shell. An
the soft-sediment seafloor; these range from macro- exception to anchoring is the rhodoliths. These are
algae (seaweeds) to seagrasses and vascular plants. red algae but they build calcium carbonate deposits
Although there are some species of red and green (much like the unrelated encrusting corallines).
macroalgae adapted to grow in relatively sheltered Also known as living stones, rhodoliths roll across
soft sediments, they do not reach the biomass and the seafloor until they reach a size where they can
forest-like structure associated with rocky substrate no longer be transported by the prevailing waves
kelp forests. For example, the temperate red alga and currents.
Ademsiella chauvinii form patches of several m2 in Seagrasses are the only marine angiosperm (ter-
extent and extend a few tens of cm off the bed restrial plant) to invade the marine habitats and
(Kregting et al., 2008). Seagrasses and vascular have been the subject of an extensive array of stud-
plants generally extend farther off the seafloor, but ies. Seagrass fronds can trap passing fine sediment
this is strongly species-dependent. particles, altering the sediment type beneath the
Still, these different size classifications of benthic bed (De Boer, 2007; Hendriks et al., 2010). The pri-
organisms are often studied by different research mary production from seagrass often enters the
groups with different objectives, approaches and benthic foodwebs via detritus. Beneath the sedi-
tools. To some extent this emphasises the practical ment surface the uptake of nutrients and release of
ities of sampling different kinds of communities organic compounds influence microbial commu-
(Gray, 1981). But these different size spectra do exist nity structure and sediment biogeochemistry.
and fundamentally represent organisms with dif- Epifauna consist of reefs of shellfish that sit on
ferent functions and different turnover rates that the sediment such as mussels and oysters, and
operate on different space and time scales. other sedentary species such as sponges, bryo
No matter what your study objectives and avail- zoans, soft corals and sea pens. Epifauna can also
able sampling techniques, it is important to remem- be mobile species such as small amphipods that
ber that all these different size-based classifications scoot around the sediment surface or larger crust
of benthic communities interact. For example, the aceans, gastropods and echinoderms that roam
microphytobenthos forms part of the microbial across the sediment surface. Their major contribu-
community, but is an important food resource for tions to modifying the physical environment
meiofauna and macrofauna that in turn are eaten by will be covered in the feeding, habitat formation
fish and shore birds. and mobility sections below (sections 2.4–2.6).
Regardless of whether the epibenthos are plants
or animals or a mix, in soft sediments they can cre-
2.3 Living position
ate an oasis of stability and provide an important
Three categories that we need to mention for com- transition between rocky reef and soft-sediment
pleteness are related to living position: epibenthos, habitats.
2.3.2 Infauna activities at an individual level that, when scaled

up, are responsible for shifts in function. Broadly
Infauna are meio-, macro- or mega-fauna that live
these animals can be divided into three important
within the sediment. They are represented by most
categories: predators/scavengers; suspension and
of the taxonomic groups and range from individ
filter feeders; and deposit feeders/grazers. While
uals that are attached to small, hard substrates bur-
this is a very simple classification, although with
ied in the sediment, to species that move only rarely
many nuances for different species, it is neverthe-
or over very small spatial scales on a daily basis, to
less a useful one. However, it is important to
species that freely burrow through the sediment.
remember that, in some taxa, feeding mode is plas-
Some species will build extensive galleries within
tic and able to be switched depending on environ
the sediment and pump water and detritus, micro-
mental conditions. Regardless of the feeding mode,
algae and organic matter through the galleries.
the dilution of organic matter by indigestible sedi-
Some large shellfish will anchor themselves within
ment poses some unique challenges to energy
the sediment by threads and protrude above the
acquisition for benthic animals.
sediment surface. Other species create tubes that
stick up through the surface and feed and move
only within these tubes. Still others move freely 2.4.1 Suspension feeders
either within the sediment surface, or between the
Suspension feeding is a feeding mode that has
deep (sometimes anoxic) and the surface, transport-
evolved in multiple benthic phyla including poly-
ing sediment, oxygen and pore water. As you can
chaetes, anemones, corals, bryozoans, echinoderms,
see, the categorising of species into ‘infauna’ vs
crustaceans, hydroids and molluscs. Many suspen-
‘epifauna’ can be difficult.
sion feeders live on the sediment surface (epifauna)
but some also live buried in the sediment and pump
2.3.3 Fringing vegetation seawater down to their feeding structures via tubes
or siphons. The suspension feeders are broadly clas-
Fringing vegetation includes mangroves (tropical sified as active or passive. In passive suspension
and subtropical) and salt marshes (temperate). feeders, feeding appendages are exposed to the cur-
Binding and trapping of sediment by these plants rents and particles travelling in the water column
has an important role in the geomorphological evo- are trapped and transported to the mouth (e.g. cor-
lution of shorelines and providing resilience to cli- als, foraminifers and ophiuroids). Many of the poly-
mate change. On shorter time scales, areas covered chaete tube worms that form dense mats are also
by mangroves and salt marshes are productive passive suspension feeders. The energy require-
with the plants providing high amounts of organic ments of these passive suspension feeders are low
matter albeit of low nutritional (high C:N ratio) because they do not generate active currents and
value. The leaf litter often ends up being incorp so can persist in regions of low or sporadic food
orated into coastal foodwebs. In highly oligo- resources.
trophic (mainly tropical) systems mangrove Active suspension feeders are those that expend
production is an important contributor to second- energy to generate water flows across structures
ary production (often via bacterially mediated that capture particles or engage in other feeding-
decomposition pathways). related behaviours when they sense the presence of
nutritious particles (e.g. ciliates, sponges, crust
aceans and bivalves). Some active suspension feed-
2.4 Feeding modes of benthic animals
ers may be referred to as ‘filter feeders’ because
Benthic fauna can be classified by their feeding they pump water through a structure that functions
mode. How these animals feed drives a lot of what as a filter (e.g. sea squirts); however, benthic ecolo-
they do to modify the physical environment and gists do not generally make a distinction between
underpins much of the functionality of marine sedi- the precise ‘filter feeder’ and the more general
ments (see Chapters 9 and 10). It is often the feeding ‘suspension feeder’ term.
The feeding ecology of suspension-feeding enerally think of suspension feeders as feeding on

g
bivalves is particularly well studied. Oysters, mus- phytoplankton, in reality particles fed on can
sels, clams, scallops and many other bivalves are include zooplankton, larvae, bacteria, detritus and
culturally important food resources for humans. suspended microphytobenthos. Thus, some sus-
These energetic feeders live in regions of abun- pension feeders are carnivores (including some
dant food resources and at least historically they sponges), and others that feed at the sediment–
often dominated harbours and estuaries. These water interface are primarily detritivores. Sponges
active suspension feeders often form distinct and may be the most diverse feeders of the suspension
dense beds, they create habitat for other organisms feeding group, ranging from feeding on phyto-
(see Chapter 7) and their feeding activity can be an plankton to being carnivores, to using spicules to
important regulator of both benthic and pelagic sys- garden diatoms (Bavestrello et al., 2000), to directly
tems, as demonstrated below. consuming dissolved organic carbon (Wooster
Suspension-feeding bivalves use cilia on their gill et al., 2019; Yahel et al., 2003).
structures to generate water currents that draw An important consequence of the suspension-
water in. This process can remove particles sized feeding processes is the particle transformations
from several μm to hundreds of μm and depending these organisms undertake. Faeces and pseudofae-
on size achieve filtration rates of several litres per ces can change the flux of organic matter to the sea-
hour. When densities reach several thousand per m2 bed, these particles have a lower C:N ratio than the
this represents an important biological filter on bulk sediment. Where dense aggregations exist this
water clarity and removal of water column prod added flux alters microbial activity and community
uctivity. The water flow on the gill surface acts not structure (Norkko et al., 2001), and, interestingly,
like a filter mesh taking particles out; rather, particles suspension feeders are more likely to form aggrega-
are bound in mucus and transported toward the tions than deposit feeders (Herman et al., 1999).
mouth. Prior to ingestion particles are sorted on the
labial palp and those not selected for ingestion are
2.4.2 Deposit feeders
rejected through the exhalent current as pseudo-
faeces. This sorting process provides a way to reject Deposit feeding is generally the most abundant
non-nutritional particles prior to ingestion and feeding type in soft-sediment systems (Lopez et al.,
can increase the quality of the ingested material by 1989). Deposit feeders include holothurians, echin
up to a factor of 15 (Kiorboe & Mohlenberg, 1981). oids, gastropods, bivalves, ophiuroids, decapods
But at the same time, it also removes suspended and polychaetes. They were so called because it was
sediment from the water column to the sediment thought that they fed on organic matter that had
surface, bound in a protein-rich mucus. The ability drifted down through the water and settled (been
to sort and reject particles is species-dependent and deposited) on the bottom. However, similar to sus-
also varies within species dependent on particle pension feeders, deposit feeders feed on many dif-
quality, type and size (Safi et al., 2007). The gill is a ferent types of particles originating from many
sensitive organ and the ability of suspension feed- different places. The one thing they have in com-
ers to deal with suspended sediments is a critical mon is that they are feeding either on the sediment
factor in their energetics. If the turbidity is too high surface or in the sediment.
gill structures can become damaged and/or simply Many of them are bulk processors, that is, they
food is diluted to a point where they cannot acquire ingest sediment, absorb what organic matter they
enough energy for growth and reproduction, so can and process the rest as faeces. Others are spe-
they die. There are several good summaries of cialist grazers on microphytobenthos and bacteria.
bivalve feeding that readers should consult (Bayne They use a variety of methods to collect the sedi-
et al., 1993; Jørgensen, 1996; Rosa et al., 2018). ment and pull it into their mouths, including tent
Many suspension feeders display strong prefer- acles, arms or nets, and digest and assimilate a
ences for certain particles according to size, shape fraction of the microbial community living on those
or chemical properties. Moreover, although we particles. Deposit-feeding bivalves generally use
siphons, often with the inhalant and exhalent siphons environment by respiration and excretion, it also
separated, and the length of the inhalant siphon provides some organic matter for further break-
controls the depth in the sediment to which the ani- down by microbes as not all of a prey item is
mal can live. Tentacles, arms and siphons can be consumed. Furthermore, excavation of, or burrow-
used to stir the sediment, helping separate microal- ing through, the sediment by predators seeking
gae and detritus from the sediment surface. their prey creates sediment disturbance and turn
Deposit feeders also employ a variety of strat over. Localised feeding pits, often formed by crust
egies in where they feed. Conveyor belt deposit aceans, birds or fish, which expose other infauna to
feeders, or head-down bottom-up, eat at depth and predation, can range from mm to m and cover large
defaecate at the surface. Subductive feeders, or areas. The sediment disturbance and rate of turn
head-up bottom-down, eat on the sediment surface over (bioturbation) is controlled by size and mobil-
and defecate at depth. However, there are also ity and its effect on the biogeochemistry of the
deposit feeders that eat and defecate within the sediment is discussed in section 2.5.1.
sediment; these are more likely to be bulk proces-
sors. These are all important for particle transport
2.5 Mobility
within the sediment and aeration of the sediment
(see section 2.5.1). Deposit feeders can also directly The seafloor is a busy place. Many of the fauna are
alter the sediment grain size, either by palletisation mobile, scurrying over or ploughing through the
(larger particles produced by excretion) or by par sediment surface, digging burrows or burrowing
ticle size selection during feeding. For ex ample, through sediment. Mobile organisms moving
many maldanid worms are conveyor belt deposit around, in or on the sediment, have multiple effects
feeders. As they excavate at the bottom of their on both sediment characteristics and sedimentary
tubes, fine sand from the sediment surface falls into processes either directly (bioturbation) or indirectly
this excavation, changing the grain size of the sedi- (sediment destabilisation).
ment surface (Levin et al., 1997).
Importantly, many deposit feeders, with the
2.5.1 Bioturbation
exception of bulk processors, can switch to suspen-
sion feeding. This switch is usually driven by loca- Since fauna first developed in the Cambrian era, the
tion of resources and modified by current. More seafloor has changed from the system described in
generally, all these fauna respire, releasing CO2, and Chapter 1 to a bioturbated environment, with on
excrete, increasing NH4. They influence biogeo- average the upper 5–10 cm being biologically mixed
chemistry, affecting the carbon and nitrogen supply (Boudreau, 1998). Studies of sediment reworking by
at different depths in the sediment column animals have a long history, moving from studies of
(Middelburg, 2017). rates of particle transport by specific species
(Cadee, 1979; Rhoads, 1963, 1974) to understanding
the effects of this particle transport on the surround-
2.4.3 Predators and scavengers
ing environment (Aller, 1982; Lohrer et al., 2004).
Predators/scavengers is the other main feeding Sediment reworking occurs through a number of
mode in soft sediments. They are generally con activities: burrow construction and maintenance;
sidered together, both because many species do ingestion and excretion, especially of bulk proces-
both, but also because it is difficult to know which sor deposit feeders; and through larger epifauna
they do. Rough categorisation is usually based on ploughing through the sediment. This reworking
jaw structures (Fauchauld & Jumars, 1979). Multiple results in particles moving vertically or laterally,
trophic levels are created by predation and scaven- burying or exposing organic matter and microbial
gers, generally related to both size of the predator organisms (Figure 2.2).
and more specifically the size of its jaws and the However, animals do not just rework sediments,
size of prey it can consume. Although it is obvious they can also affect porewater flow (advection
that this group does modify the sedimentary or bio-irrigation) through feeding activities.
Echinocardium
(urchins graze microphytes,
consume bacteria & POM, require
oxygen)
sink
Biotu
n
teria
fusio
tion
rbatio
d bac
c
O dif
v e
n: po
d
Excre
a
Grazin
ly
ity, D
M an
(+) D
: DO
supp
rosity
tion:
poros
g: Po
O pro
ation
g mic
POM
, nutr
NH 4–
feedin
ventil
tion:
ductio
rophy
tion:
ient e
N sup
turba
rrow
faeca
posit
te sin
n
fflux
ply (+
(+)Bio
(+)Bu
(–)De
(+)De
k (–)
( +)
)
Organic matter Benthic primary
remineralisation DIN & DIP supply (+) production
(bacteria regenerate (microphytes utilise
dissolved inorganic dissolved inorganic
nitrogen & phosphorus, nitrogen & phosphorus
oxygen increases rate) (+) DO production and generate oxygen)
Figure 2.2 Effect of a burrowing urchin on sedimentary processes. From Figure 1, Lohrer et al. (2004). DIN: dissolved inorganic nitrogen; DIP:
dissolved inorganic phosphorus; DO: dissolved oxygen; POM: particulate organic matter.
Crustaceans or polychaetes often pump water (2010) found that the area influenced by an areni-
through their burrows (e.g. Aller, 1988; Kristensen, colid polychaete experienced transient bursts of
2001) which, particularly if the burrows are closed, activity, bio-hydraulic sediment cracking, forward
or burrows are permeable, generate pressure waves and reversed advective pulses, and long-term flow
through the sediment (Wethey & Woodin, 2005; reversals.
Volkenborn et al., 2010). Similar porewater move- However, many animals that contribute to
ment generated by pressure waves has been particle reworking also contribute to porewater
observed for bivalve feeding with excurrent siphons advection—often by the same activities. For this
below the sediment surface (e.g. tellinid bivalves: reason Kristensen et al. (2012) suggested that the
Reise, 1983; Woodin et al., 2016; see Figure 2.3). This term bioturbation should be standardised as cover-
porewater bioadvection, driven by animal activity, ing ‘all transport processes and their physical effects
moves anoxic and oxic water through the sediment on the substratum’. The study of bioturbation and
and varies with time in both rate and direction its effects on the physical and chemical composition
(Krueger, 1964). Changes in direction can lead to of sediment has been covered in many books
redox oscillations on the scale of minutes to hours (Aller, 1982; Kristensen, 2000; Rhoads & Boyer, 1982)
(Volkenborn et al., 2010), with important conse- and will be covered in more detail in Chapter 9.
quences for sediment biogeochemistry (Aller, However, generally, bioturbation has been demon-
1994; Timmermann et al., 2006). Volkenborn et al. strated to affect the flux of nitrogen and oxygen,
(a) Macomona liliana

a3
4 a1
a2
2
–2
–4
4860 5040 5220 5400 5580 5760 5940 6120
a1 feeding/respiration and a2 feeding/respiration with fecal a3 burrowing

siphon movement and pseudofecal expulsions
3 5
2
2
0 0
1
–2
0 –5
5130 5140 5150 5560 5580 5600 5620 5960 5980 6000 6020
Figure 2.3 Different animal behaviours generate different pressure signals in the porewater. From Figure 2 in Woodin et al. (2016). Reprinted
under Creative Commons Attribution 4.0 International (CC BY 4.0) licence.
improving conditions for production by micro- may otherwise stabilise the sediment and allow
phytobenthos, and changing surficial sediment both sediments and microphytes to be picked up
characteristics. and moved by waves and currents. Animals dig-
It is also important to remember that not all par ging and clearing burrows both lift sediment into
ticle reworking or porewater pressurisation is due the water, allowing it to be carried away, or create
to animal behaviour. As described in Chapter 1, mounds on the surface that can be washed away.
waves and currents are both drivers of these pro- Different-sized particles are eroded and transported
cesses and the relative importance of physical and differentially, resulting in changes to the sediment
biotic drivers is a fascinating area of study particle size and organic content of the sediment.
(Grant, 1983). Regardless, except in extremes of
these physical drivers, modification by benthic 2.6 Habitats formed by organism–
plants and animals is, at the least, of equal import
environment interactions
ance and frequently more important.
Habitats in soft sediments are frequently described
by the physical environment. Despite this, the
2.5.2 Sediment destabilisation
majority of habitats in soft sediments are created by
Another effect of mobility on the soft-sediment sea- species living in or on the sediment. These species
floor is sediment destabilisation (Needham et al., are variously called ecological engineers, habitat-
2012; Rhoads & Young, 1970; Volkenborn et al., formers or key species. Habitats formed by eco
2009). Animals scurrying across or bulldozing logical engineers include some of the bioturbators
through the sediment disturb microphytes which we have discussed, for example, areas dominated
by pits, burrows, galleries and holes or by heavy The next element came from considering the spa-
bulldozing of the surface sediments, or even by the tial structure of tube worm patches, seagrass and
faeces of head-down bottom-up deposit feeders. bivalve beds (Gambi et al., 1990; Green et al., 1998).
However, there is another very important habitat As the areal density increases and patch length
type that has multiple effects on sedimentary and increases from the leading edge, a phenomenon
water column processes; relatively immobile struc- known as skimming flow is induced. In essence the
tures that protrude above the sediment–water inter- benthic boundary is now raised to the top of the
face (often called 3-dimensional habitat structure). structural elements, with a transition zone occur-
These can be structures created by infauna or epi- ring between the structural elements—a zone of
fauna such as the sand grain tubes or calcium low flow and turbulence. This transition results in
deposits built by polychaetes, or they can be the the structural elements moving from being sedi-
plant or animal itself. Generally, these are intended ment destabilisers to being sediment stabilisers
to give better access to resources. In the case of where the sediment surface is protected from high
plants, growth away from the sediment surface bed shear stress upon turbulence (Figure 2.4). The
will give them better access to light and higher density of structure required to induce skimming
water flows that break down diffusional boundary flow is a function of the vertical height, frontal area
layers and limit solute exchanges across blades. For exposed to the flow and flexibility (especially import
others, such as suspension-feeding polychaete tube ant in terms of macrophytes)—a good description
worms and bivalves such as mussels and oysters, of this can be found in Eckman (1983) and Nepf and
the move off the sediment surface means that less Koch (1999).
of the particles encountered are inorganic (sedi- This work stimulated many more field and labora
ment) and thus the food is of higher quality. But for tory studies as technology for visualising and char-
both plants and animals the consequences of pro- acterising flows has developed. In turn this has led
truding into the water column are exposure to to a better understanding of the implications. The
higher velocities and the potential to affect hydro- alteration of the hydrodynamic regime in patches of
dynamic and sedimentary processes driven by sufficient size fundamentally alters benthic–pelagic
alteration of the benthic boundary layer. This alter- coupling, changing settling of detrital matter to the
ation has important implications for the benthos seafloor and nutrient and oxygen fluxes into the
independent of any physiologically dependent water column. Reduced flows between structural
processes and has been an important area of study elements allow the sedimentation of finer-grained
for benthic ecologists. particles and enhanced organic matter deposition
The concepts of how structures alter and interact (Bos et al., 2007). These changes in the fluxes of fine
with boundary layer flows have been well estab- sediments can result in enhanced nutrient cycling
lished in the engineering/fluid mechanics literature within the bed. The alteration to the flow regime
for decades because of their relevance to bridge also has impacts on the settlement/recruitment of
design, drag on ships’ hulls etc. However, it is only benthic invertebrates (as discussed in Chapter 7).
comparatively recently that they have been applied A final habitat type formed by interactions
to benthic ecology. In a series of elegant papers in between organisms and sediments could be con
the 1980s, Pete Jumars and Arthur Nowell and PhD sidered as a subset of the 3-dimensional habitat
student Jim Ekman cast the engineering literature structure, although in this case the vertical dimen-
into an ecological framework through an investiga- sion is very small: encrusting organisms and rhodo-
tion of how individual and groups of tubes affected lith beds. Small encrusting organisms such as
flow. This work demonstrated that with individual coralline algae and surpulid worms can create a
tubes high-momentum fluid is transported down highly stable seafloor, inhibiting sediment resuspen-
toward the sediment surface, increasing the bed sion, in high-flow and coarse sediment areas. This
shear stress and destabilising the sediment (Carey, stability fundamentally changes the biogeochemistry
1983; Eckman et al., 1981). of these areas.
Independent flow
Interactive flow
Skimming flow
Figure 2.4 Effects of horse mussel density (Atrina zealandica) on benthic boundary layer flows. At low densities alterations to the flow caused
by a mussel have dissipated before it encounters the next individual. At high densities skimming flow occurs where a new benthic boundary is
established above the mussels and the zone between them becomes a low-flow area that promotes sedimentation. Figure modified from
Friedrichs (2004).
(such as sheltered intertidal mud flats and high cur-

2.7 Close out
rent, coarse sediment) are of very limited value.
The sedimentary environment that would develop These descriptions do not even provide a useful
under a world with no plants and animals is funda- hierarchical categorisation of sedimentary pro-
mentally different than that seen in most soft- cesses such as organic matter remineralisation (see
sediment systems. Benthic species therefore strongly Figure 2.5), let alone ecological function or ecosys-
influence the balance between recycling vs seques- tem services (see Chapter 9).
tering of organic material. Increased oxic depth Many books describe biotic habitats based on
and enhanced particle transport and solute advec- different types of vegetation—e.g. seagrass, rhodo-
tion are common (Figure 2.5), but increased flux lith beds, kelp, coralline algae, fringing vegetation—
of organic material from the water column, but we need a much wider consideration of
changes in nutrient fluxes, increased carbon inputs biogenic habitats. However, differences in size, liv-
and increased microphyte activity also occur. ing position, feeding mode and mobility of the ani-
Simplistically, sediments with no fauna will not be mals that inhabit various places result in a
as efficient at processing organic matter, meaning large potential range of non-vegetated habitats.
that more material is buried. Although we have suggested the possibility of
These differences mean that descriptions of sea- additional categories based on degree of bioturb
floor habitats based on environmental descriptors ation, sediment stability (or lack of it) and erect
(a) (b)
Figure 2.5 The world of the sediment is very different without animals. From Figure 1, Snelgrove et al. (2018). Reprinted from Trends in Ecology
& Evolution, 33, Snelgrove P V R, Soetaert K, Solan M, Thrush S F, Wei C-L, Danovaro R, Fulweiler R W, Kitazato H, Ingole B, Norkko A, Parkes R J,
and Volkenborn H, Global Carbon Cycling on a Heterogeneous Seafloor, 96–105., Copyright (2017) with permissions from Elsevier Publication.
3-dimensional structure, different combinations of McCall P L and Tevesz M J S, eds. Animal-Sediment

key species will result in different types of habitats Relations, Springer, Boston, MA, pp. 53–102.
that are important not just for ecological function- Aller R C (1988). Benthic Fauna and Biogeochemical
Processes in Marine Sediment: The Role of Burrow
ing but, at least as importantly, for biodiversity
Structures. In: Blackburn T H and Sorensen J, eds.
(see Chapters 6 and 7) and for sensitivity to and
Nitrogen Cycling in Coastal Marine Environments, J. Wiley
recovery from natural dis turb
ances and human and Sons, New York, pp. 301–38.
activities. Aller R C (1994). Bioturbation and Remineralization of
Sedimentary Organic Matter: Effects of Redox
Oscillation. Chemical Geology, 114 (3–4), 331–45.
Bavestrello G, Arillo A, Calcinai B, Cattaneo-Vietti R,
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The sedimentary environment

1.1 Introduction we nearly always measure but it’s not a simple

(g)S Slightly gravelly sand

(g)mS Slightly gravelly muddy sand

gmS Gravelly muddy sand

1:9 1:1 9:1

in terms of the bulk volume of the sediment (VT; i.e.

Box 1.2 The benthic boundary layer

Clay Silt Sand Pebble

(c) 4 (d) 4 (e)

30 50 70 90 110 130 150 170 190 210 4 8 12 16 4 8 12 16

­iffusion physically dominates solute exchange,

CH4 Black layer

N2 PON NH4+ NO3– N2O N2

PON NH4+ NO2– NO3–

Benthic animals and plants

2.3.2 Infauna activities at an individual level that, when scaled

The feeding ecology of suspension-feeding ­ enerally think of suspension feeders as feeding on

(a) Macomona liliana

4860 5040 5220 5400 5580 5760 5940 6120

a1 feeding/respiration and a2 feeding/respiration with fecal a3 burrowing

(such as sheltered intertidal mud flats and high cur-

3-dimensional structure, ­different combinations of McCall P L and Tevesz M J S, eds. Animal-Sediment

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