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TRANSCRIPT
Hydrographic Measurements with a CTD
from Research Vessels Common Module in Multidisciplinary Offshore
Operations in Marine Science
Dr Martin White ([email protected]) and Dr Rachel Cave ([email protected])
National University of Ireland, Galway
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This section will introduce to you the basic use of the CTD and rosette system and relevant
sampling considerations to measure the physical and chemical properties of the coastal
environment from a research vessel.
Introduction
To fully understand biological and chemical processes, whether acting in the deep ocean or
coastal waters, a good appreciation of the environmental conditions is a basic requirement.
These physical processes are, for example, turbulence (which mixes temperature, freshwater
and chemical properties), tidal and other currents and wave or wind induced dynamics. These
processes occur on a myriad of time and space scales resulting in a complex dynamical
environment which will control subsequent chemical and biological processes. The physical
time/space scales involved vary from the very small (seconds and sub-mm) up to large basin-
scale processes related to atmosphere-ocean forcing scales covering years and 1000s of
kilometres (Figure 1). There will be an overlap between physical and biological/chemical
process scales related to the biogeochemical response to physical forcing. This necessitates a
detailed understanding of the environmental conditions present to develop an optimal
approach to sampling strategy, particularly when if the research is of a multidisciplinary
nature.
One must keep in mind that ship-based surveys are a one-off ‘snapshot’ of the environment
experiencing a number of dynamical and biological processes (Figure 1). Whilst in the deep
ocean lateral and vertical property changes may be small, in the coastal ocean these may be
very large and occur over relatively short length scales. This is partly due to amplified tidal
influence that will enhance horizontal and vertical mixing but will also advect coastal ocean
features (e.g. river plumes), or the influence of freshwater inputs to the coastal zone creating
fronts or strong haloclines and density stratification (e.g. Figure 2).
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Figure 1. Schematic illustrating the typical length and time scales of (a) relevant physical
processes and (b) selected biological processes within the ocean environment of relevance.
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Figure 2. Examples of small length scale structures in the coastal ocean. Left: Four aerial
photo ‘snapshots’ of the R. Avoca plume outside Arklow taken over a 90 minute period (from
White et al., 2006). Note the sharp frontal structure and the variation in colour due to
dissolved organic matter in the plume (Each photo is 800x800 m). Right: Windrows created
by Langmuir circulation spaced 2-10 m apart and creating small scale vertical motion in the
upper layer of Killary Harbour.
Measurements from a research vessel are Eulerian measurements, i.e. they are a series of
point measurements at a location or grid of stations made over time (i.e. survey duration).
Eulerian measurements measure both a local change in environmental conditions (temporal)
plus what spatial properties changes are being transported past them (i.e. due to horizontal
gradient in the property, e.g. temperature, salinity etc.). This is different to Lagrangian
observations when the measurements are made by a sensor that is following the same piece of
ocean water so measures only the local change the parcel of water experiences as it moves.
This difference in the measurements needs to be appreciated when interpreting results, i.e.
whether changes in a property, e.g. temperature, is a result of local atmospheric driven
heating/cooling, or if it is just the result of a parcel of warmer/cooler water has been advected
past the measurement point by the currents. An appreciation of the relevant length and time
scales of the likely processes and coastal ocean structure present is therefore crucial, both to
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interpret results but also to develop a measurement strategy beforehand that will be able to
resolve these features.
Consider the influence of tides as an example. Tides are a periodic process, typically semi-
diurnal (e.g. the biggest semi-diurnal tide (M2) has a period of 12.421hrs). Tides are a global
ocean process but are amplified in shallow seas, both in terms of the tidal range and in the
currents created by the tidal forcing. Tides in the deep ocean have a range of up to 1 m and
generate currents typically of order 10 cm s-1. The tidal range is very small relative to the
ocean depth (> 200 m). The currents produced may be similar to the currents produced by
forces in the deep ocean, but play a relatively minor role in moving ocean water big distances
relative to the large scale ocean currents produced by the wind or density differences (e.g. see
Figure 1). In coastal waters, especially for depths < 50 m, tidal amplification may cause tides
that have a range up to 5 m and this then becomes a significant proportion of the total water
depth, especially in estuaries where the depth may be 20vm or less. Currents will also be
amplified and often reach up to 50 cm s-1 (1 knot=51.5 cm s-1). These coastal tides with
strong currents will dissipate their energy through turbulence due to frictional forces at the
seabed and hence are the main contributor to the horizontal and vertical mixing length/time
scales shown in Figure 1.
The tidal period provides and immediate timescale of variation of any property in the water
column under study, whether it is being changed directly by the tidal currents (e.g.
turbulence) or advected past the measurement point. But how far will the tide move water
back and forth past a measurement location? This can be estimated through a simple
calculation and assuming a simple sinusoidal variation in the tidal currents.
If the tidal current strength (V) is assumed to vary as a sin wave, i.e. V=Vo*sin(2*π*t/T),
where Vo is the tidal amplitude (maximum current), t=time and T=tidal period (12.421 hrs),
then the resulting displacement (X) of a water parcel over the tidal period will be the integral
of this, i.e.
X= [Vo*T/(2* π)] *cos(2*π*t/T), and will therefore have a magnitude of Xo= Vo*T/(2* π).
For the M2 period of 12.421 hrs and a tidal current magnitude of 50 cm s-1, this displacement
amplitude (or tidal excursion) is ~3558 m or about 3.5 km. Therefore the water will move
about +/- 3.5 km from a central point, or 7 km end to end. This provides a basic length scale
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of variation one might expect for coastal water properties based on tidal movement. There
will be a number of consequences for these different timescales when considering your
sampling strategy. If one desires to look at the tidal variability in a property (e.g. salinity) at a
fixed location, it is likely that a minimum of 5 to 6 observations per period/wavelength of
variability will be required to resolve the tidal changes adequately, say a measurement every
2 hours. One must then also consider how far the tidal currents might move water past the
measuring point in the 2hr interval between measurements. Other measurements should then
be made at locations ‘up and downstream’ of your main station of interest, but a distance that
will also resolve the variability caused by the tidal excursion (as calculated above). Of course,
your sampling time is limited and there may be a number of measurements to be made in a
multi-disciplinary survey. You have to plan very carefully, therefore, your sampling strategy
to get the best trade off between adequate observation points in space/time and the time taken
to complete the survey. Appropriate resolution in the measurement interval and duration,
therefore, is vital to properly ‘sample’ the environment under investigation. One off
(essentially instantaneous) surveys, therefore, can be misleading and not representative of a
long-term steady or quasi-steady state of the ocean. This may lead to over-interpretation of
data.
The Conductivity, Temperature and Depth (CTD) Profiler
The real-time CTD instrument is the workhorse instrument for hydrographic observations
when sampling the ocean from research ships. CTD electronic systems have developed from
the mechanical era instruments of reversing thermometers and water sample bottles, triggered
by weights attached to the winch line (Lawson and Larson, 2001). A basic CTD package
comprises a temperature sensor (fast response thermistor), conductivity cell and pressure
sensor that can be connected to a conducting cable for real time use or as a self recording
instrument (Lawson and Larson, 2001; Williams, 2009). Additional sensors may also be
attached to the sensor recording package, such as those that measure fluorescence (to
determine chlorophyll); optical transmission (turbidity) and oxygen (see Table 1). The basic
sensor measurements (conductivity, temperature, pressure) enable secondary variables to be
calculated (e.g. salinity, depth, density). On a shipboard, vertically profiling CTD with real
time data transmission via conducting cable, the CTD package will have the electronic
sensors located near the bottom of the containing frame. The CTD may also include a rosette
of sampling bottles attached to the frame. These bottles, open at the start of any vertical
profile, may be ‘fired’ from the desk command to close at chosen depths to allow water
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samples to be taken for both calibration of the electronics or to take biological/chemical
measurements on board or back in the laboratory.
Table 1. Basic, derived and supplementary water column properties that are typically
measured by CTDs and additional attached sensors for coastal ocean observations.
Basic
Measurements Method Biological significance
Conductivity (C)
Temperature (T)
Pressure (P)
Inductive resistance
Thermistor
Piezo-electric sensor
General water column structure, water mass
properties
Derived parameters
Depth Use pressure and latitude Location in water column
Salinity (S) Using C,T, P (Practical
Salinity Scale – PSS 78)
Salt content and for calculating density
Density (ρ) Using S, T, P (Eqn. of state) Water column structure and dynamics
Main additional
measurements
Oxygen Optode Oxygen levels, Anoxia, O2 minimum layer.
Fluorescence Fluorescence Chlorophyll levels (plankton abundance)
Turbidity Light transmission Suspended particulate concentrations
Water chemistry &
calibration
Rosette Bottles Water chemistry, plankton, suspended
particulates, salinity, oxygen
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Figure 3. Illustration of the depth profile of a CTD package with time to show typical
deployment methods; (a) The CTD is lowered at constant speed to the seabed or target depth,
before being raised and stopped at target depths for discrete water sampling. In (b) the CTD
is lowered to the target depth and then repeatedly raised/lowered over a smaller depth range
to increase temporal resolution in the target depth range. The firing of rosette bottles on the
CTD descent is shown in (c) and might be used for specific chemical sampling in relatively
shallow water.
For real time vertically profiling CTDs two principal deployments are commonly used. For
general applications, the CTD package is lowered at a constant speed to close to the seabed
and back to the surface. For hydrographic observations, typical lowering speeds of between
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0.5-1 m s-1 (30-60 m per minute, Figure 3a) are used. Slower speeds might be used if strong
vertical gradients in either temperature or salinity are expected. Generally the down profile is
used for the water column structure measurements and the up profile for stopping the CTD to
sample the water column using the rosette to obtain discrete water samples. The 2nd
common way to use the CTD is to ‘yoyo’ the package with repeated descending and
ascending profiles over a target depth range whilst the ship is fixed at a location or slowly
drifting (Figure 3b). This helps to improve the temporal resolution of the water column
structure, for example to resolve tidal variability at a particular location. If bottle sampling for
chemical parameters is the most important aspect of the CTD cast, then bottles may be
programmed to fire as the CTD is descending (Figure 3c). In deep water this may be a
problem as increasing water pressure as the CTD gets deeper may allow water to be forced
into the closed bottle and contaminate the original sample. However if in shallow enough
water that increased pressure is not an issue, closing bottles on the descent will allow a closer
match of the bottle sample to the measurements made by the electronic samples and this may
be important for some chemical oceanographic aspects, particularly oxygen.
Modern CTD systems generally record data many times per second, typically 24 Hz, which
would suggest a possible vertical resolution of 2-4 cm per measurement at typical profiling
speeds of 0.5-1 m s-1, but this is never achieved. This is due to a number of factors including
the response times of the individual sensors to adjust to the surrounding environment and the
fact that the CTD package may be disturbed significantly by surface wave/swell action. With
appropriate data treatment a vertical resolution of measurements O(1 m) for general
hydrography and O(0.1 m) for some fine scale structure may be achieved if the CTD is
profiled slowly. There are a number of errors that are associated with such a complex
instrument and an appreciation of this will help in appropriate data interpretation and
identification of problems that may arise when sampling. Sources of error with CTD data
arise for a number of reasons;
i) It takes time for each of the sensors to adapt to the changing environment and a ‘true’
measurement, and this varies with sensor resulting in two particular characteristics;
(a) water column features will often seem deeper/shallower than in reality for the
down/up portion of the CTD cast respectively. This may be particularly apparent for
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oxygen as typical O2 sensors have long response lags; (b) different lags in the
response of the temperature (T) and conductivity (C) sensors may result in the spiking
in the resultant calculated salinity (S) as essentially the measurements of T and C
come from different parcels of water. This may be important in regions of strong
vertical property gradients (temperature and conductivity).
ii) There are also effects related to the movement of the CTD package through the water
column, such as physical mixing and heating effects – both related to the contact of
the CTD with the water and self heating by the electronics. Also for large CTD
packages, water may be ‘trapped’ within the package and dragged up/down the water
column and may contaminate a water sample. In addition, the sea is restless and both
surface wind/wave actions, as well as the currents within the water column, will
disturb the descent of the CTD.
To reduce these errors, a number of steps can be completed in the processing of the data.
The steps below may be used as a guideline as to a basic strategy for quality control, but
are not hard and fast rules. CTD instruments will have manufacturer software that will
accomplish similar steps.
1) Alignment of temperature and conductivity sensors. This accounts for different lag
of the temperature and conductivity sensors on a real time CTD. Salinity may be
calculated for a number of data samples with the conductivity sample offset by
different measurement lags relative to the temperature to obtain the ‘least spiky’
salinity dataset.
2) Run a median filter through the data. A median filter is used instead of a normal
running mean to remove noise/spikes in the data, as this does not artificially change
or smooth real vertical structure in any of the variables.
3) A temperature calibration is preformed if calibration data is available.
4) Calculate salinity and other secondary variables. Using the filtered temperature,
conductivity and pressure. Use an approved and tested routine for calculation of
salinity, e.g. a UNESCO formula.
5) Filter salinity data. Use a median filter through the salinity data with the same
window size as previously used.
6) Salinity Calibration. Perform a salinity calibration of salinity using bottle data.
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7) Checking for looping in Pressure signal. Data is discarded during the CTD up-cast
or parts of the down-cast when CTD is passing through a depth that has already been
obtained. This is because the sensor package is usually located at the bottom of the
CTD rosette system and therefore it is the downcast that is passing through water that
is relatively undisturbed by the CTD package.
8) Data Averaging. Average the data to required vertical (profiling CTDs) or horizontal
resolution (for towed and self recording instruments).
A typical upper layer profile of T, C, S (Figure 4a-c) and density (Fig. 4.4d) can be used to
illustrate some of the issues raised above. The untreated profiles indicate a surface mixed
layer and seasonal thermocline. Temperature and conductivity profiles are similar and also
show smaller mixed layers (steps in the profile) of a few meters in vertical extent through
depth range of the seasonal thermocline. The salinity profile is spiky, however, in particular at
the top (~35 m) and bottom (~60 m) of the seasonal thermocline when the mismatch in
temperature and conductivity measurements is greatest in the raw data. The treated profiles
smooth out the salinity errors but retain the water column structure, including the unusual
decrease in salinity just below the mixed layer (the profile of density in Figure 4d indicates
this is not an artefact but the water column is stably stratified at that depth). Figure 4e and 5f
show the effect of ‘looping’ of the pressure records (this problem was eliminated in the
profiles in Figure 4a-d for clarity) from the same CTD profile. In the surface layer, surface
wave action and ship movement significantly affects the CTD descent. The apparent
periodicity of 4 cycles in about 800 samples (or ~32s at 24 Hz) indicates a modulation at a
period of 8 s, a typical ocean swell period. Modulation of the descent is apparent at deeper
depths (Fig 4.4f) but is much reduced.
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Figure 4. An example vertical CTD profile showing the upper 120 m of; (a) temperature, (b)
conductivity, (c) salinity and (d) density from deep water in the Rockall Trough, NE Atlantic.
The thin line shows the unaveraged, untreated data and the thick line treated data, offset in
value for clarity. The variation of pressure with sample number for the same downward CTD
profile is shown for portions of the cast in (e) and (f).
BOTTLE SAMPLING
Niskin bottles were developed early in the 20th century and they consist of open ended tubes
(typical capacity 5-10L) equipped with spring loaded cups that can close at required depths at
both ends with the help of a “messenger “(weight that travels down a wire). Niskin-type
bottles are now often mounted on CTD frames (with varying capacity up to 20L per bottle)
and fired electronically. Similar types of bottle include Nansen bottles and NIO bottles. The
rosette bottles on a CTD are a very useful sampling tool, although discrete samples of a finite
number and volume can be taken depending on the size of the CTD frame (and hence bottle
number/size) being employed. It is usual to close these bottles during the up cast of a vertical
profile, as the rosette is typically housed in the upper portion of a CTD frame. It can
sometimes be hard to position the CTD bottles at the exact depth preferred by the scientist,
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and one should be realistic about the accuracy to the vertical location at which samples are
taken, even in shallow water. This is due to inherent characteristics of the CTD, particularly
those involving response times of sensors which result in vertical offset in features for both
up/down profiles (see next section), and not least because of the heaving/rolling of the CTD
tethered to a ship at the surface of a restless ocean!
Since small water volumes are usually required for most chemical and biological analyses
(typically from 100s ml to 1-2 L), therefore water from the same bottle can be used for the
determination of many parameters. Typical parameters that would be routinely collected are
in Table 2.
Table 2. Water sample parameters routinely collected on research vessels. Lab gloves should
ALWAYS been worn when dealing with water samples, both to prevent you contaminating
the sample (e.g. your sweat contains both salt and nitrite, soap residue will contain phosphate,
you skin cells are particles rich in carbon, nail varnish contains trace metals), and to protect
you from reagents used to fix the samples.
Parameter - Water Volume Post-collection Notes
Oxygen
Use plastic tube to
direct flow to bottom
of bottle to prevent
air getting into
sample
250ml plus overflow
Clear or amber glass
oxygen bottle with
plastic stopper and
rubber bands to keep
stopper in place
‘fix’ with two
reagents, store at
room temperature
and under seawater
Water samples for
gas analysis are
collected first to
reduce the uptake of
atmospheric gas as
bottle gets emptied
Dissolved inorganic
carbon (DIC)
Use plastic tube to
direct flow to bottom
of bottle to prevent
air getting into
sample
500ml plus overflow
Schott Duran glass
bottle with glass
stopper, coated with
Apiezon grease.
Rubber bands to keep
stopper in place
‘poison’ with
mercuric chloride,
Store in refrigerator
As above
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Parameter - Water Volume Post-collection Notes
Salinity 150ml
Flat sided glass
bottle, plastic stopper
and screw cap
Store at room temp Next sample taken
after any gas
samples. Used to
confirm accuracy of
CTD salinity
Alkalinity 250ml or 500ml
HDPE. Overflow the
bottle before
capping.
Store in refrigerator Alkalinity can also be
measured on the DIC
samples (see above)
Dissolved Organic
carbon/nitrogen
60ml,
HDPE bottle
Syringe filter through
acid-washed GF/F,
freeze
Dissolved Nutrients
(nitrite, nitrate,
phosphate, ammonia,
silicate)
50ml x 2
Plastic red-top
Falcon tube
Vacuum filter
through 0.4micron
Nucleopore filter
(membrane) and
freeze
Use plastic filtration
unit if silicate
analysis require.
Otherwise can use
glass.
Coloured Dissolved
Organic matter
(CDOM)
Amber glass or
opaque HDPE bottle,
minimum of 100ml to
allow for triplicates
Filter through
0.4micron
Nucleopore filter
(membrane). Keep
dark at room temp,
Analyse on
spectrophotometer
within 24 hours
Can use same filtrate
as for nutrients.
Cannot be stored
beyond ~24 hours as
organic matter will
begin to break down.
Suspended
Particulate Matter
(SPM)
Use 47mm GF/F
filter paper which
has previously been
combusted at high
temp (450C) and
weighed on a high
precision balance
Rinse filter with DI
water to remove salt,
fold, put into labelled
plastic bag or petri
dish and freeze.
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Parameter - Water Volume Post-collection Notes
Chlorophyll-a,
phaeopigments
Use 47mm GF/F
filter paper
Fold filter paper and
store in red-top 15ml
tube, freeze
Particulate Organic
carbon/nitrogen
Use 25mm GF/F
filter paper
Syringe filter known
volume, fold filter
paper and freeze
Material is usually collected onto filters (commonly glass fibre filters but various membrane
filters can be used depending on types of analyses) after gentle vacuum filtration to avoid
particle disintegration or loss through the pore sizes of the filter. However there are issues.
Filtering is often a time consuming process, mostly due to filter clogging, that requires
considerable man-power and effort, particularly when different parameters are measured.
Filter clogging depends on pore size, location and/or water depth, for example it may take
several hours to filter 1L of particle-rich, productive, surficial water onto GF/F (nominal pore
size 0.7 µm) filters; this could lead to severe backlogs, leading to operator fatigue that could
ultimately affect sampling resolution and strategy. In addition the small filter volumes do
pose problems with respect to weighing accuracy, replication and small scale patchiness.
Many other parameters may be sampled for, requiring more specialised handling. Almost
every substance known to man is dissolved to some degree in the oceans, so somebody
somewhere will want to measure them.
SAMPLING ISSUES/STRATEGY
Two very different CTD sampling grids are shown in Figure 5 to illustrate the resolution of
scales discussed earlier. One is a CTD grid used to make observations over a carbonate
mound over a small area and rapidly to ‘sample’ motions within a tidal period. The other is a
transect across the south Pacific - the World Ocean Circulation Experiment (WOCE)
hydrographic transect P06. The yoyo technique of CTD deployment employed for Figure 5a
allowed high temporal resolution measurements of the near seabed approximately every 20
minutes to highlight tidal and short term variability in the benthic boundary layer and
associated suspended particulate material concentrations (see later Figure 6). Conversely the
WOCE P06 section was occupied to measure full depth physical and chemical water column
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parameters (Figure 5b). In total 259 stations were occupied during 70 days at sea occurring over a
period of 3 months and was conducted for the assessment of the long term state of the ocean,
driven by inter-annual or climatic forcing. Such a transect would not resolve either the tidal
motions or even the mesoscale (eddy) variability in the ocean either, which would appear as a
form of small amplitude noise within the large scale oceanic structure.
Figure 5. Examples of CTD station grid for measurements made (a) over a small carbonate
mound, NW Porcupine Bank (NE Atlantic), by ‘yoyo’ CTD from 400 m depth to bottom (the
north-south transect data are shown in Fig 4.5), taking just 4 hours and (b) World Ocean
Circulation Experiment (WOCE) line P06E,C,W occupied between 2-5-1992 and 30-7-1992
and undertaking 259 full depth CTD stations
Conversely the data from the yoyo profiles over the mound show how a CTD can be
manipulated to sample the water column adjacent to the seabed at relatively high temporal
resolution (Figure 6). Data are from a survey of the slope of the Porcupine Bank, NE Atlantic
to assess the dynamics over a carbonate mound (see Mienis et al., 2007). The CTD was
lowered to close to the seabed (depths 700-750 m) from a depth of 400 m. Between each
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up/down profile the ship was edged slowly by a few hundred meters in a transect so a profile
was made every ~20 minutes. The resultant temperature profiles show the variability in the
benthic boundary layer (BBL) height (Figure 6a). Use of a beam transmissometer indicated a
benthic nepheloid layer (BNL) or suspended particulate material associated with the BBL
(Figure 6b). The temperature profiles also indicated the likely presence of an overturning
internal wave in progress, seen as the inversion of temperature in 3 consecutive vertical
profiles between the depths of 650-700 m. If a single profile, perhaps made as part of a
coarser resolution transect across the slope, had shown this temperature inversion, it may
have been interpreted as a temporary mis-function (e.g. blocked sensors) as the associated
inversion in density would not be stable). Here the 3 consecutive profiles made within a time
of 40 min showing a consistent feature is persuasive, given the likely timescale for an
overturn to occur and particularly as the region is know as a region of high internal wave
energy (Dickson and McCave, 1986; Mienis et al., 2007).
Figure 6. Vertical profiles of near seabed (a) temperature and (b) light transmission across a
small carbonate mound on the NW flanks of Porcupine Bank, NE Atlantic (see Fig 4.9a for
local bathymetry and station locations). Values of each property are relative to the value at
the bottom, whose value is indicated by the short thin vertical line, and each profile is offset
relative to the distance across the mound. Data courtesy of Henko de Stigter, Royal NIOZ.