The Benthic Boundary Layer Transport Processes and Biogeochemistry

by Boudreau, Bernard P.; Jorgensen, Bo Barker

• ISBN13: 9780195118810
• ISBN10: 0195118812
• Format: Hardcover
• Copyright: 2001-03-22
• Publisher: Oxford University Press

Summary

The benthic boundary layer is the zone of water and sediment immediately adjacent to the bottom of a sea, lake, or river. This zone is of considerable interest to biologists, geochemists, sedimentologists, and engineers because of very strong gradients of energy, dissolved and solid chemicalcomponents, suspended matter, and the number of organisms that live there. It is, for example, the sink for anthropogenic substances and the home of microscopic plant life that provides the nutrients that determine fish populations--and ultimately the size of the fisheries. This book of originalchapters edited by Professors Boudreau and Jorgensen, both leading researchers in the field, will meet the need for an up-to-date, definitive text/reference on measurements, techniques, and models for transport and biochemical processes in the benthic boundary layer. Each chapter provides acomprehensive review of a selected field, with illustrated examples from the authors' own work. The book will appeal to professionals and researchers in marine biology, marine chemistry, marine engineering, and sedimentology.

Table of Contents

Contributors	xi
Introduction	1	(3)
Bernard P. Boudreau
Bo Barker Jorgensen
Physics of Flow Above the Sediment- Water Interface	4	(40)
W. Brian Dade
Andrew J. Hogg
Bernard P. Boudreau
Elements of Benthic Boundary Layers	5	(2)
Structure	5	(1)
Energy Cascade and Coherent Motions	6	(1)
A Historical Perspective	7	(2)
Benthic Boundary Layer Hydrodynamics	9	(9)
Governing Equations	9	(3)
The Logarithmic Layer and Coriolis Deflection	12	(2)
Structure of the Constant Stress Layer	14	(4)
A Hierarchy of Hydrodynamic Models	18	(4)
Local Closure	18	(1)
Eddy Viscosity Formulas	19	(1)
Nonlocal Closure Schemes	19	(2)
A Model for Discrete Turbulent Elements Near the Bed	21	(1)
Boundary Conditions	22	(6)
The Brinkman Layer and the No-Slip Condition	22	(1)
Roughness	23	(3)
BBL Development, Spatial Averaging of Roughness, and Flow Separation	26	(1)
Local Effects of Roughness and Bed Mobility	27	(1)
Biological Effects	28	(1)
Benthic Boundary Layer Stratification	29	(2)
Topographic Effects	31	(2)
Turbulent Wave-Current Boundary Layers	33	(1)
Estimating Bed Shear Stress	34	(3)
Quadratic Drag Laws	35	(1)
Semi-logarithmic Velocity Gradient	36	(1)
Near-Bed Reynolds Stress and TKE	36	(1)
TKE Dissipation Rate in the Inertial Subrange	37	(1)
Prospects	37	(7)
Fine-Scale Flow Measurements in the Benthic Boundary Layer	44	(34)
Arzhang Khalili
Markus Huetell
Wolfgang Merzkirch
Thermal Anemometry Technique	44	(7)
Sensor Design	45	(2)
Heat Transfer Correlations	47	(1)
The Anemometer Circuit	48	(1)
Calibration of Hot-Film Probes	49	(1)
Problems Associated with Hot-Film Measurements in Water	49	(1)
Hot-Film Measurements in a Boundary Layer	50	(1)
Examples of Thermal Anemometry in BBL Research	51	(1)
Laser Anemometry	51	(10)
Laser Doppler Anemometry	52	(2)
Examples of LDA Applications	54	(2)
Particle Image Velocimetry	56	(3)
Examples of PIV Applications	59	(2)
Positron Emission Tomography and Flow in Sediments	61	(3)
Setup and Basic Principles of PET	62	(1)
Examples and Limitations of PET	62	(2)
Acoustic Devices for Large-Scale Measurements	64	(1)
Flumes as Experimental Tools for BBL Research	65	(13)
Characterization of Open Channel Flow	65	(2)
Practical Considerations around Flume Experiments	67	(1)
Flow Generation in Flumes	68	(1)
Flume Designs for Special Purposes	69	(1)
Examples of BBL Studies Using Flumes	69	(9)
Suspended Particle Transport in Benthic Boundary Layers	78	(26)
Paul S. Hill
I. N. McCave
Sinking Speed	79	(6)
Eddy Viscosity and Diffusivity	85	(3)
Boundary Conditions	88	(10)
Concentration Bottom Boundary Condition	90	(1)
Flux Bottom Boundary Condition	91	(2)
Bottom Boundary Condition for Nonzero Es (O+,t)	93	(1)
Models with Nonlocal Injection from the Bed	94	(3)
Effect of Nonlocal Injection on Estimates of γ0	97	(1)
Summary of Bottom Boundary Conditions	97	(1)
Conclusions	98	(6)
Solute Transport Above the Sediment-Water Interface	104	(23)
Bernard P. Boudreau
Solute Transport Near a Flat Solid Surface	104	(8)
Classical Eddy Diffusion Theory	104	(5)
Periodic Boundary Layer Models	109	(2)
Higher Order Closure Models	111	(1)
Mass Transfer with a Porous Interface	112	(8)
Effects of Porosity and Permeability	112	(2)
Effects of Surface Roughness	114	(3)
Unequal or Changing Reactivity of the Sediment Surface	117	(3)
Mass Transfer in the BBL with Reaction	120	(3)
Influence of the Time Scale of Reaction	120	(1)
Turbulence and Nonlinear Reactions	121	(2)
Summary and Some Directions for Future Work	123	(4)
The Fine Structure and Properties of the Sediment Surface	127	(17)
David M. Paterson
Integrated Studies	127	(1)
Visualization of the Sediment-Water Interface	128	(2)
Towards a Correlative Approach	130	(3)
Fine-Scale Properties of the Sediment Surface	133	(1)
Temporal Variability in Sediment Properties	134	(2)
Optical Properties	136	(3)
Conclusions	139	(5)
Porewater Flow in Permeable Sediments	144	(36)
Markus Huettel
Ian T. Webster
Introduction to Advective Transport	144	(3)
Molecular Diffusion Versus Advection	144	(1)
The Physics of Porewater Transport and Darcy's Law	144	(2)
Advective Transport in the Marine Environment	146	(1)
Mechanisms of Advective Transport	147	(15)
Current-Induced Advective Transport	147	(7)
Wave-Induced Advection in Sediments	154	(6)
Density-Driven Convection	160	(2)
Consequences of Advective Transport	162	(8)
Spatial and Temporal Zonation Due to Advection	162	(2)
The Impact of Advective Flows on Sediment Geochemistry	164	(5)
Consequences to the Natural Environment	169	(1)
Summary and Suggestions for Future Research	170	(10)
Biogeochemical Microsensors for Boundary Layer Studies	180	(31)
Michael Kuhl
Neil peter Revsbech
Electrochemical Microsensors	181	(13)
Reference Electrodes	181	(1)
Ag/Ag+ Half-Cell Microelectrodes	181	(6)
Ion-Exchange-Based Microsensors	187	(2)
Simple Microsensors with Continuous or No Polarization	189	(2)
Gas Microsensors with Ion-Impermeable Membranes	191	(2)
Instrumentation for Electrochemical Microsensors	193	(1)
Optical Microsensors	194	(5)
Field Radiance Microprobes	194	(1)
Irradiance and Scalar Irradiance Microprobes	195	(1)
Microprobes for Fluorescence and Surface Detection	196	(1)
Fiber-Optic Microsensors: Micro-opt(r)odes	197	(1)
Instrumentation for Fiber-Optic Microsensors	198	(1)
Microbiosensors	199	(3)
Methane Microbiosensor	200	(1)
Nitrate Microbiosensor	200	(2)
Microsensors for Diffusivity and Water Velocities	202	(1)
Diffusivity Microsensor	202	(1)
Flow Microsensor	203	(1)
Physical Disturbance Caused by Sensor Insertion	203	(1)
Summary and Some Directions for Future Work	203	(8)
Diagenesis and Sediment-Water Exchange	211	(34)
Bo Barker Jorgensen
Bernard P. Boudreau
Biogeochemical Processes and BBL Interactions	212	(14)
Processes with Direct BBL Interaction: Oxygen Uptake	213	(6)
Processes with Indirect BBL Interaction: Denitrification	219	(3)
Processes with Reaction in the BBL: Manganese and Iron Cycling	222	(4)
Processes Independent of the BBL	226	(1)
Quantitative Modelling of Solute Profiles and Fluxes	226	(8)
Overview of Diagenetic Models	226	(3)
Dissolution or Precipitation of a Solid	229	(1)
Oxygen Uptake in Sediments	230	(3)
Transport with Reaction in Sediments and the DBL	233	(1)
Modeling the Solids Exchange	234	(4)
Parting Thoughts	238	(7)
In Situ Sampling in the Benthic Boundary Layer	245	(24)
Clare E. Reimers
Richard A. Jahnke
Lairenz Thomsen
Methodologies	245	(7)
Particle Transport Measurements	245	(3)
Solute Flux Measurements	248	(1)
Deployment Platforms and Vehicles	249	(3)
Limitations	252	(3)
Problems of Spatial Scale and Temporal Variability	252	(1)
Instrument Effects	253	(2)
Examples of Emerging Experimental Strategies	255	(8)
An Unresolved Shallow-Water Question	255	(6)
A Deep-Sea Example: BIOPROBE	261	(2)
Concluding Remarks	263	(6)
Transport and Reactions in the Bioirrigated Zone	269	(33)
Robert C. Aller
Average Transport Properties in the Bioirrigated Zone	269	(2)
Excavation, Irrigation, and Sediment Fluidization	271	(2)
Biogenic Turbulent Diffusion Analogy	273	(4)
Biogenic Advection	277	(1)
Apparent Source-Sink or Nonlocal Exchange Models	278	(4)
Diagenetic Reaction Distributions in the Bioirrigated Zone	282	(1)
Average-Microenvironment-Analog Transport Models	283	(6)
Interactions Between Solute Transport and Reaction Kinetics	289	(2)
Biogenic Sediment Fabric and Microscale Transport	291	(3)
Structure and Biogeochemistry of the Bioturbated Zone	294	(1)
Summary and Conclusions	295	(7)
Constraining Organic Matter Cycling with Benthic Fluxes	302	(18)
Richard A. Jahnke
Seafloor Solute Exchange Mechanisms and Rates	302	(3)
Biogeochemical Cycling on the Continental Shelf	305	(4)
Biogeochemical Cycling on the Continental Slope	309	(2)
Biogeochemical Cycling on the Abyssal Seafloor	311	(9)
Macroscopic Animals and Plants in Benthic Flows	320	(28)
Peter A. Jumars
James E. Eckman
Evamaria Koch
Flow Modification of Sensory Fields	321	(4)
Chemosensing	321	(2)
Other Sensory Cues	323	(2)
Flow Effects on Momentum and Mass Transfer	325	(5)
Mass and Momentum Transfer to and from Macrophytes	325	(4)
Momentum and Mass Transfer in Other Benthic Settings	329	(1)
Benthic Populations and Larval Dynamics	330	(7)
Spawning and Fertilization	330	(2)
Dispersal	332	(2)
Settlement and Recruitment	334	(2)
Settlement Probability	336	(1)
Conclusions	337	(11)
Life in the Diffusive Boundary Layer	348	(26)
Bo Barker Jorgensen
A Viscous World	348	(3)
Moving at Low Reynolds Numbers	349	(2)
Transport by Diffusion	351	(3)
Solute Transport to Moving Particles	351	(1)
Diffusion Field Around Particles	352	(2)
The Benthic Diffusive Boundary Layer	354	(12)
DBL Visualization by Microelectrodes	355	(2)
DBL Dynamics	357	(2)
Surface Roughness	359	(2)
Microelectrode Interference with the DBL	361	(3)
Diffusive Boundary Layer Thickness	364	(2)
Overcoming the Diffusion Limitation	366	(8)
Gradient Sulfur Bacteria	367	(7)
Interfacial Microbial Mats and Biofilms	374	(21)
Dirk de Beer
Michael Kuhl
Structure and Composition of Biofilms and Mats	377	(3)
Techniques for Structural Analysis	377	(1)
Staining of Structural Components	377	(2)
Case Study of a Model Biofilm	379	(1)
Function of Biofilms and Microbial Mats	380	(9)
Role of Boundary Layers	381	(2)
Diminution of Mass-Transfer Resistance	383	(2)
Measurements in a Model Biofilm	385	(3)
Diffusional Mass Transfer in Biofilms and Mats	388	(1)
New Approaches to Mass Transfer in Biofilms and Mats	389	(6)
List of Common Symbols	395	(2)
Index	397