Matt Green

Ross Deadman

AJ Recupido

Lewis Stagnetto

Anna Belcher

Ella Darlington

William Mills

Anthony Pyper

Boats and Equipment

Introduction

RV Callista
RV Callista is suited to offshore surveying with a large working area and has three deployment points. There are both wet and dry labs located onboard the vessel allowing for in situ processing of samples.
 

CTD and rosette:  The CTD is used to take vertical profiles of the water column (figure 3.3) by measuring conductivity (which is a proxy for salinity), temperature, depth, fluorescence and irradiance. All these parameters are recorded to a computer in real time. The CTD is usually mounted onto a rosette. The rosette allows other equipment such as Niskin bottles and other probes to be mounted.

Offshore

Estuarine

Geophysics

CCD Video Camera: A CCD video camera was trialled to observe the seabed and confirm sidescan outputs (figure 3.6) provides an undisturbed image of the surface sediment. Image quality was not always that high due to turbidity. It did however provide an overview of the surface benthic habitat at the grab sites.

Acoustic Doppler Current Profiler (figure 3.1): Using the principles of Doppler shift the ADCP is able to determine current speed and direction.  Mounted to the hull of the craft, the ADCP sends out an acoustical signal; this signal reflects off particles in the water and returns to the ADCP unit.  If the particle is moving towards the ADCP, the returning sound wave is compressed and will have a higher frequency.  If the particle in the water is moving away from the ADCP, the sound wave is stretched and will have a lower frequency.

Method:

A benthic survey was undertaken in the Carrick Roads section of the Fal estuary, on the 01/07/2008.  A transect line was plotted at the following coordinates; Start: 50º10.00N, 005º02.40W; Finish: 50º09.00N, 005º01.90W.  Two subsequent transect lines were plotted parallel to the original transect, 100m apart, see figure 4.3.

The side scan sonar was towed (~4 knots for maximum resolution) on each of the three transect lines: G2, G3, and G4.  The data was used to produce a track plot from which a mosaic of the area was created.  Areas of interest on side scan printout were selected as possible sites to take samples of benthic communities using a Van Veen grab.  The collected samples were examined with the aid of a 1mm mesh sieve to accumulate the fauna from within the grab.  Collected fauna were photographed to scale for further identification in the lab.  At each grab site a temperature and salinity profile was conducted, along with an in-situ observation of the sea bed using a remote video camera on the T/S probe.

Description of side scan features:

Sand Wave Area:

At the north end of transect line G2, between 11:25:27 and 11:28:27 there is an area of sand waves with a ~2.8m wavelength (figure 4.9) . The wave orientation is at 100° which is perpendicular to the predominant tidal currents (011°). Interpolating from the average tidal currents obtained from chart data, expected currents in this area are between 0.1ms^-1 and 0.2ms^-1. This combined with interpreted grain size analysis (0.1-0.2mm) from both sidescan data and grab samples suggests that the sand waves are a result of tidal currents. There is also a possible influence of waves on these forms.

Anchor Drags:

There is a patch of anchor drag marks at the north end of transect line G4, between 12:07:23 and 12:10:26 approximately 300m in length (figure 4.10). They can be seen on the sonograph as ~1.3m depressions. Transect G4 is located in the main channel at Carrick Roads and large ships have been seen to anchor here, corresponding well to the data from the sonograph.

Rock Outcrop:

There is a clear bedrock outcrop between 11:33:51 and 11:35:45 predominantly on transect G2, but also visible on transect G3 (figure 4.11). Large shadow zones and areas of high return show the elevation of the rocks ranging from 4.35 – 8.77m. The rock outcrop may form part of the submerged section of the Saint Mawes headland, and surveying further east may reveal further areas of bedrock.

Finer Sediments:

There is an area of weaker reflection on the sonograph which has been interpreted as an area of finer sediment (figure 4.12). This corresponds to the location just to the west of the main channel from 12:15:06 and 12:19:04 on transect G4. Current patterns are likely to be complex in this area due to reflection and refraction from headlands. It is possible that there may be deposition due to slowing velocities of vortices on the banks of the main shipping channel. Further investigation using an ADCP should be carried out to more thoroughly map the currents in this area.

There is a trend between the three grabs samples, which suggests that there is an increase in the organic/fine sediment content in the samples towards the head of the estuary. This is reflected in the reduced oxygen content of the sediment and increased diversity, which is related to the availability of organic matter. Grab sample 1 which was closest towards the mouth of the estuary consisted of poorly sorted coarse sediment, which had a low organic content and diversity of fauna.
Progression towards the head of the estuary saw an increase in the amount of fine sediment/organic content in the samples. This change in the diversity of fauna, which altered from suspension feeders (Serpulid spp.) at site 1 to deposit feeders (Siphunucula spp. & Echinoidea ssp.) at site 3. This is reflected in the availability of food and stability of the sediment.

Results and discussion

A benthic survey of the Carrick Roads area of the Fal estuary illustrates that the sediments show a degree of homogeneity.  Further investigation using the Van Veen grab showed that the composition of the sediments varied towards the head of the estuary.  There was an increase of fine particles/silt in the sediment, from coarse sediment at the mouth of the estuary. 

The Grab sample 2 consisted of coarse, moderately to poorly sorted sediment. The sample had a greater fine sediment content than site 1; the colour of the sediment was darker which suggests a reduced oxygen content. The sediment also contained a large volume of broken Maerl (P. calcareum). The fauna observed in the sample was greater than site 1, and included examples of epifaunal and infaunal species. A specimen of a sand mason worm, (Lanice conchilega), was identified, along with another polychaetes. Other biota observed in the sample included sponges (Demospongiae spp.), crabs (Decapoda), and a juvenile periwinkle (Mesogastropoda spp.).

Aim:

To determine the benthic habitats of the Fal estuary by use of a Geo Acoustics 415kHz side scan sonar, Van Veen grab, and a T/S probe with an underwater video camera attached.

Introduction:

The Fal and Helford estuaries are classified as a Special Area of Conservation (SAC) which relates to the extensive Maerl (Phymatolithon calcareum) beds and other fauna found in the estuary. The data collected in the Fal estuary will be added to the benthic fauna database at Natural England, which monitor the communities living in the estuary.

Tide Times

Click to enlarge

Van Veen Grab: This is a device used to take a sediment sample of 0.25m³ from the sea floor (figure 3.5). Although the sediment collected is disturbed it serves as a way to verify the results from side scan data. They can also be used to study benthic community structure at selected sites. The samples obtained can be sieved to sort sediments and help expose benthic species.

YSI Probe: This is a multi-parameter probe (figure 3.7) which can measure temperature, salinity, depth (pressure), dissolved oxygen, pH, chlorophyll and turbidity. The device is lowered via a cable and continuous data outputted to a handheld device. Easy deployment, as well as small and compact size makes the YSI probe a good piece of survey equipment for use on smaller vessels.

Niskin bottles (see figure 3.4) are used to obtain water samples from specified depths in the water column, each bottle mounted on a rosette is remotely fired from the computer terminal onboard. Niskin bottles can also be deployed individually on a hydroline, or can be handheld for surface sampling.

Introduction:

Sedimentary bed forms identified by the side scan sonar transects were selected for benthic sampling. Sampling was conducted using a Van Veen grab, which takes a 0.25m³ sample from the benthos. Three locations were chosen for sampling which represented different regions of the estuary. A temperature/salinity profile was conducted at each grab site, in conjunction with a remote video camera attached to the T/S probe. This allowed an in-situ observation of the sea bed before the grab sample. The samples were emptied into a crate for an initial observation (figure 4.13), then sieved (1mm) for further analysis. Any fauna observed were photographed to scale for identification after the survey.

 

Secchi disk: The Secchi disk is comprised of black and white segments that are separated into alternating quarters (figure 3.2).  The disk is lowered into the water until it cannot be viewed from the surface.  This is known as the Secchi disk depth. This value can be used to estimate the limit of the euphotic zone.   The disk is lowered into the water by the same person to keep results consistent.

Figure 4.8: Side scan plots. Hard at work calculating bedform dimensions

Kettle: A life or death piece of equipment which is vitally important for preventing mutiny on board between staff, crew, and students (figure 3.10).

Sidescan sonar:A 415kHz side scan sonar, with 150m swath width, mounted on a tow fish was used to map the seafloor. A pulse is emitted and the return time can be used to calculate distance. The information from the side scan gives information on:
• Sea floor topography
• Sea floor lithology
Strong reflection will correspond to steep slopes facing towards the sonar and lower backscatter values to flatter areas. Areas of no return will be found where slopes face away from the sonar and are steeper than the angle of the incoming sonar beam.

Zooplankton net: A 50cm diameter, 200 micron nylon mesh net which can be towed behind a boat to collect samples of zooplankton. Vertical nets can be towed and horizontal nets lowered to the desired depth.

Grab sample 1 consisted of coarse sand and broken fragments of calcareous fauna. The sediment was poorly sorted and the individual clasts were angular. The sediment colour was light, suggesting the sample was oxic. The sediment contained broken fragments of bivalves and Maerl (Phymatolithon calcareum), a coralline algae. Fauna found within the sample was limited to a few epifaunal species. Serpulid spp. were found attached to larger fragments of rock within the sample. Flora included examples of Rhodophycae spp.(red algae). In general, grab 1 was a coarse, poorly sorted sediment, which had a low species diversity.
 

Grab sample 3 consisted of soft sediment, sand with a large silt/fine sediment content. The colour of the sediment was dark which suggests low oxygen content (anoxic). There was a significant increase in the fauna observed in the sample, which was more diverse than sites 1 and 2. This included examples of deposit feeders such as sea potatoes (Echinocardium cordatum) & Peanut worms (Sipunucula nudus).

Figure 4.18: Grab 2 :Brachyura spp. a crab. & Sabellidae spp. the sand mason worm (a suspension feeder) is a tube dwelling polychaete that constructs a tube out of coarse sediment including maerl fragments. Habitat inshore or shallow waters.

Figure 4.15: Grab 1 : Maerl Phymatolithon calcareum. A calcareous algae found in the litorral and sublittoral zones, unattached or encrusting on substrata.

Figure 4.16: Grab : 1 Polychaete worm Serpulidae spp. Tube dwellers, habitat associated with coarse sediment i.e. 0.5-1mm. Suspension feeders require a flowing current.

Figure 4.21: Grab 3 : Sipuncula spp. (Peanutworm). A deposit feeder associated with sediments of a high organic content.

Figure 4.20: Grab 3 : Ascidiacea spp. (Sea squirt) A common suspension feeder found in south coast estuarine environments.

Analysis

The abundance of dissolved oxygen (DO₂), is a means to measure the biological activity within a body of water. Phytoplankton and macro algae present in the water body produce oxygen via photosynthesis, whereas other pelagic organisms (zooplankton, algae, and fish) consume oxygen by way of respiration.
An analysis of DO₂ concentrations was carried out across several transects of the Carrick Roads of the Fal estuary. The DO₂ composition of the water is affected by parables such as:

• Zooplankton and Phytoplankton activity

• Salinity

• Temperature

• Depth

Concentrations of DO₂% varies from 104.2% to 107.6% at depths ranging from 0m to 11m depth, from the estuary mouth to head. Comparing samples at depth and those nearer the surface at each station shows increasing oxygen saturation near the surface (figure 5.43).
An anomalously low value of 99.1 % was observed at RIB station 6 and the lowest reading of 98.3% taken from a sample at 11m depth on transect 5. This could possibly be due to its location below the euphotic zone and a resulting in lack of phytoplankton activity combined with the salinity reading of 34.61 reducing the solubility properties for DO₂ in water.

Bill Conway

The lower estuary was surveyed using R. V. Bill Conway. Eight transects were carried out using an ADCP to observe the currents; seven across the estuary and one vertically down the estuary, see figure 5.8. A YSI probe attached to the Niskin bottle rosette was used to profile the water column, recording temperature and salinity every metre up to 10 metres depth and every 2 metres beyond this. Vertical profiles were taken in the central channel at each transect and water samples taken at a number of depths. Due to rough weather conditions no CTD profile was taken at transect line 1 for safety reasons. Three surface samples were taken, at the start, middle and end of the transect line but no depth data was obtained. The planned transect 4 was omitted as insufficient variations were expected and further transects were taken upstream. Transect 7 was planned above the mussel farm located at 50°12.80N, 05°.01.65W, just South of the King Harry Passage. However, it was established that the mussel farm was no longer in operation and hence transect 7 was relocated upstream. Transects 7 and 8 were carried out to observe the effect of the fresh water input from the Truro river and the River Fal (Ruan Creek).

Water samples were taken both at the surface using an onboard pump and at depth using Niskin bottles. These water samples were used for analysis of nitrate, phosphate, silicate and dissolved O_2.  These samples were collected from transects 2, 3, 5, 6, and 8. Phytoplankton samples were taken at transects 2, 3, 5, and profile 7/8.  Zooplankton trawls were carried out using a 200µm zooplankton net at transect 2 and at the location of profile 7/8. Secchi disk readings were made at every sampling station to determine the light attenuation co-efficient.

Aims:

To obtain an understanding of the chemical, biological and physical processes of the Fal Estuary and how they interact. Both R.V. Bill Conway and the RIB Ocean Adventurer were used to survey from Black rock at the estuary mouth to the Malpus pontoon six nautical miles north. 

The charts below (figure 5.8-5.11) show the survey transects and sample sites investigated by RV Bill Conway and RIB Ocean adventurer.

Tide Times

Ocean Adventurer

Aboard the RIB Ocean Adventurer, sampling was undertaken at 6 stations in the northern reaches of the Fal estuary.  Sampling started downstream of the mussel farm at Turnaware Point, and finished at the Malpus pontoon near a residential area. Due to poor weather conditions sampling was carried out moored up on pontoons.
 

At each of the sampling locations a YSI probe was used to measure temperature, salinity, dissolved O₂ and pH. A handheld Niskin bottle was used just below the surface to collect water samples for nitrate, phosphate and silicate. At locations 1, 3 and 6, samples were taken for dissolved O₂ analysis. At each station a water sample for phytoplankton was collected, and 1ml of lugols iodine solution added as a preservative. Zooplankton trawls were undertaken at station 1 and 6 using a 200mm zooplankton net.

Richardson Number
Data from YSI profiles combined with data from the ADCP can be used to calculate Richardson Number (Ri), which is a good measure of whether flow in the vertical direction is turbulent or laminar.
Ri ≥1 implies flow is laminar
Ri ≤0.25 implies flow is turbulent.

Ri is a measure of the balance of stabilizing buoyancy, N, and the destabilizing vertical shear, du/dz. However, simplifications can be made to the full equation for Ri, as measurements were carried out in a shallow estuary where maximum vertical shear is at the seabed. The following equation has been used for calculations:
 

Current directions were taken into account of by changing the sign of the current velocity. Plots of Richardson number are displayed in figures 5.26-5.31. In order to plot the data on a log scale, Ri values ≤0 were replaced by 0.001.

Transect 1
The rough conditions at this station meant that not only could no vertical profile be taken but also ADCP data is distorted due to large unsteady movements of the boat.

Transect 3
An area of slightly lower magnitude flow (0.1ms^-1) can be seen to the left of the main channel, and flow is more westerly (see figure 5.14). This is likely due to friction effects of the channel side and proximity of Saint Mawes headland, see figure 5.8. Flow in the central channel is towards the south east and of magnitude 0.3ms^-1.

Transect 5
The fastest currents are located in the surface 4m, with currents of slightly lower velocity (0.1ms^-1) below this, see figure 5.16. Faster currents would be expected away from the sea floor where friction forces will be greater. Currents are southerly, corresponding to the ebbing tide.

Transect 6
The plot of velocity direction in figure 5.18 shows the presence of two layers, the top 10m flowing westward and the lower 5m eastward. Surface flows are downstream but bottom flow is upstream as can be seen by comparison with the chart in figure 5.8. Temperature and salinity profiles as well as flow patterns match those of a partially mixed estuary, with landward flow to compensate for mixing of salt water upwards across density gradients.

Transect 7
Although current magnitude for transect 7 is quite homogenous, current direction plots again show the presence of two layers, see figure 5.20. Flow is downstream in the surface 5m, with upstream flow in the lower 4m of the water column. As with transect 6, this can be explained by the partially mixed state of the estuary and the process of vertical gravitational circulation.

Transect 8
This transect was located just upstream of where the Truro River joins the River Fal (see figure 5.8), and shows low current velocities of approximately 0.07ms^-1, even at the surface. The direction plot displays variable current directions and there is no clear two layer system. This could be due to the presence of eddies due to the narrow channel width or changes in sea floor topography.

Transect 9
A transect down the estuary from 50°13.473 N, 005°01.088 W, to 50°12.428 N, 005°02.943 W, see figure 5.9 was carried out showing the varying topography of the sea floor down the estuary. The velocity does not change much throughout the profile, ranging from 0-0.25ms^-1. Looking at the direction plot, see figure 5.24, there is distinct stratification of flow between about 6m and 8m depth, particularly in the centre of the transect. Flow is southerly (seawards) in the surface layer and northerly in the deeper layer. This corresponds to the ebbing state of the tide, with bottom inflow of saline water showing the vertical gravitational circulation of the partially mixed areas of the estuary.

ADCP

An ADCP was used to produce cross sectional profiles of the estuary at a number of locations, giving information on the current flow and the effect of the banks and the seabed on it. Settings on the ADCP mean that only current information down to 15m was obtained. A general trend from well mixed waters near the mouth of the estuary to partially mixed waters landwards.

Transect 2

The temperature profile taken in the channel (figure 5.32) shows a slight temperature gradient from the surface down to 4m, and more homogenous at depth. The plot of Richardson numbers (figure 5.26) suggests a turbulent well mixed surface layer and a lower well mixed layer from 5.5-8m. This can be seen as Ri numbers are all below the critical value of 0.25. The area between these layers has Ri >1, showing a dynamically stable layer which corresponds approximately to the base of the surface temperature gradient. This is a stable layer which prevents mixing between the two layers. There is no YSI information below 8.15m due to rough conditions and concern over proximity to the banks.

Transect 3
The temperature-salinity (T-S) profile (figure 5.33) shows that salinity is fairly constant with depth, where as there is a temperature difference of about 0.5°c between the surface and at depth. There is a slight gradient at 5m with a more pronounced gradient at 15m. This corresponds well to the dynamically stable layers (Ri>1) shown on the plot of Ri number (figure 5.27) at 6m and 12m. This suggests the presence of three mixed layers with the deepest layer located in the deep main channel, although there is no YSI data from below 14m to support this.

Transect 5
A change in flow dynamics can be seen in figure 5.28, with laminar stable flow at approximately 4m. This layer prevents mixing between the turbulent and well mixed flow above and below. Figure 5.34 displays a temperature gradient between 2m and 4m which corresponds to the two layers observed on the ADCP profile.

Transect 6
The Ri number plot (figure 5.29) displays two turbulent layers separated by a region of laminar flow. The boundary between these layers corresponds to the slight pycnocline due to changes in both temperature and salinity (see figure 5.35). This occurs at about 6m corresponding to the change in Ri number to 5.9. This stratification can be seen in the ADCP profile showing the partially mixed state of the estuary at this location. The two layers consist of more saline water at depth flowing landwards and fresher water flowing seawards at the surface.

Analysis

The nitrate samples were analysed using flow injection analysis, incorporating the reduction of nitrate to nitrite by a column containing cadmium and copper. This method of analysis is based on the Johnson and Petty method (1983).The full scale deflection was 100mV and the standards used were 1, 5, 10 and 25µM.

Nitrate samples obtained using the RV. Bill Conway and Ocean Adventure (RIB), ranged from a low value riverine end member of 361.47 μM to a seaward end member of 0.389 μM. Using these end members a theoretical dilution line (TDL) was produced. This TDL shows how concentrated nitrate should be diluted at any given salinity moving from the head of the estuary to the mouth of the estuary (figure 5.37). Since the Fal estuary is an open system there are many ways and reasons for collected samples to not fall on this line. The obtained samples indicated that nitrate was acting non-conservatively in the Fal estuary and hence are well below the Theoretical Dilution Line, suggesting removal from the system.
 

Transect 2
The ADCP profile, (see figures 5.12 and 5.13) shows a well mixed water column down to 15m with currents of about 0.4ms^-1 flowing southwards. However, limitations with the maximum depth reached by the ADCP means no information about currents deeper in the main channel can be obtained. Considering the ebb stage of the tide it is likely that these more saline waters are also moving southwards.

Transect 7
Again two layers can be seen at this location, corresponding to the ADCP profile suggesting a partially mixed estuary. At about 5m, Ri values exceed the critical value showing stable flow. Above and below this flow is turbulent implying two well mixed layers with shear occurring at the boundary across which mixing is prevented.

Transect 8
The shallow depth at this station combined with the lack of surface data from the ADCP means there is not much information about the gradient in flow in this region. Richardson numbers imply that the waters are well mixed, with turbulent flow throughout the water column. Richardson number is increasing towards the seabed, suggesting flow is becoming more stable towards the seabed.

Although there were no vertical profiles taken at transects 7 and 8, a profile was recorded between the two which shows a more complex temperature and salinity structure. This is likely to reflect the fresh water input from the Truro River. Density values from this profile were used for calculations of Ri number for both transect 7 and transect 8 so obviously there will be errors due to differences in density.

Analysis

Samples obtained using R.V. Bill Conway, and Ocean Adventure (RIB), had a range of concentrations between 1.012 μmol/L and the riverine end member which was 90.432 μmol/L. Most of the sample sites lie very close to the theoretical dilution line (TDL). The silicon concentration in the Fal estuary decreases whist moving towards the mouth. This is to be expected as all the small rivers open up into the larger estuary.

An inverse relationship was observed between [Si] and salinity (Figure 5.39). Since an estuary is an open system there are many inputs and outputs that will impact upon the environmental variables. The data collected display non-conservative behaviour; when plotted above or below the TDL, [Si] has been added or removed, respectively. There is slight fluctuation from above the TDL to below. This oscillates six times whist moving towards the marine end member. This shows that there are inputs and outputs all along the estuary. Examples include are weathering of rocks and clay that are rich in silicon running off into the estuary; an output could be the utilization by diatom populations within the estuary.

The depth profiles showing change in concentration of silicon vary largely from the mouth of the estuary to the head. There is little change between surface samples and samples taken at depth when closer to the mouth of the estuary. The sample furthest from the mouth of the estuary shows the greatest change with depth. The sample taken from transect 8 ranges from around 20.6 μmol/L to 9.3 μmol/L at 10 metres. Furthermore, the lowest concentration, 8.5 μmol/L silicon, was taken from a depth of 5.5 metres. This area – Transect 8 – has the highest fluorescence reading out of all the transects completed on Conway, and all samples taken from Ocean Adventure. This is most likely dues to a bloom of diatoms in the area.
 

Analysis

Phosphate samples collected on board the R.V. Bill Conway and Ocean Adventure (RIB) were found to be non-conservative. The samples range from a high of 2.71 μmol/L to 0.496 μmol/L. Overall, phosphate has an inverse linear relationship to rising salinity (figure 5.41). The data from the RIB has a much more obvious decrease with increasing salinity but is very distant from the Theoretical Dilution Line (TDL). The same is true for samples taken on the Conway . Phosphate in the Fal estuary has a much higher concentration than predicted by the TDL.

Phytoplankton analysis of the Fal estuary has shown that the community changes from Rhizosolenia spp. dominated in the lower estuary, to Coscinodiscus spp. in the upper estuary. The estuary in general is dominated by diatom species.
Transect 2 (Black Rock) (Figure 5.44) the dominant species found was Rhizosolenia setiger with an abundance of 23 cells ml-1 of seawater. Other species present included Rhizosolenia imbricata and Chaetoceros.
Transect 3 (Figure 5.44) was similar in species composition in that it was dominated by Rhizosolenia spp.
Transect 5 (figure 5.44) is dominated by another diatom species Leptocylindrus danicus. A few examples of Rhizosolenia spp. were observed in the sample, there was an increase in Coscinodiscus (1.67cells ml-1).
Transect 8 showed a significant increase in Coscinodiscus (12 cell ml-1 seawater). Although chain diatom species were dominant at this stage in the estuary.
RIB stations 1-3 were similar in that Coscinodiscus was the dominant species throughout (figure 5.45), however there was an increase in the dinoflagellate Alexandrium at site 1 (15 cells ml-1) There was a similar increase in the diatom Thallasiosira spp. at station 3 (57 cells ml-1).
RIB stations 4-6 were dominated by Coscinodiscus to a maximum of approximately 600 cells ml-1 (figure 5.45). This could be due to the increase in the concentration of silicate related to the riverine input. Coscinodiscus thrive and utilise the silicate to produce their silicate frustules.

Chlorophyll data, calculated from fluorescence readings taken in the lab show that as you travel further up the estuary chlorophyll concentrations increase, from about 1.5 μg/l to 11.6μg/l, suggesting there is an increasing number of phytoplankton in the water samples.

There was limited number of samples with depth due to misfiring of Niskin bottles making it difficult to make any conclusive statements about the varying levels with depth. A euphotic zone of 6m at transect 6 reflects lower chlorophyll levels (~3 μg/l) below this depth compared to surface values of 4.18 μg/l.

The Secchi disk readings taken on Bill Conway show decreasing euphotic zone depth with movement upstream (Table 5.1). This may be due to the fact that seabed depth is decreasing and may also be due to increased turbidity upstream.

Four zooplankton net samples were collected; two on RV Conway and two on Ocean Adventure (RIB) (figure 5.48 and 5.49). The results collected identified copepods as the dominant throughout the estuary. Samples take at the two RIB stations highlighted copepods as the dominant species by a large margin; however trawls conducted at the two Conway stations also showed amplified levels of Siphonophore spp (figure 5.56). These heightened levels reflect phytoplankton grazing expected in the lower estuarine environment. Other noteworthy features include increased levels of Cirripedia larvae (figure 5.51) found at Station 6 on the RIB. There was also a notable presence of Hydromedusae throughout the estuarine system as well as a small increase in Gastropoda larvae (figure 5.52) towards the river end member.

ADCP profiles of the four transects carried out are displayed below and key features highlighted.

Introduction
Offshore surveying onboard R.V Callista was undertaken on 08/07/08. Our initial transect was across the mouth of the Fal estuary at Black Rock and after this surveying was planned along a single transect line southwards of the eastern side of Mounts Bay, west of Falmouth starting near shore and working out to the offshore region, see figures 6.1 to 6.3

The tidal flow in this area is affected by the peninsula which was of particular interest to our physical survey. An ADCP was used to measure the flow velocity and backscatter where the backscatter is an indicator of areas of high zooplankton concentration. A CTD which was attached to a Niskin bottle rosette was used to measure temperature, salinity, fluorescence and light. Niskin bottles were fired at depths of interest, such as at the chlorophyll maximum. Vertical zooplankton trawls using a closing net were also taken at the locations of CTD measurements. The closing net enabled sampling of zooplankton populations at specific sub surface depth ranges. CTD and zooplankton sampling stations had been planned every 1.5miles of the ADCP transect. Due to increased wind and poor weather conditions our initial survey off the Mounts Bay region had to be abandoned after an hour. We returned to the Fal Bay and continued an ADCP survey with CTD and zooplankton sampling stations from Manacle Point across the bay to Black rock.

Data collected from YSI probes and the ADCP show a change in water column structure from well mixed near the estuary mouth to partially mixed until transects 7 and 8. In partially mixed areas the stratification between landward flow at depth and surface outflow is clear. Calculations of Richardson Number confirm the presence of mixed layers separated by stable boundary layers of laminar flow. The dynamics of the water column correspond quite well to gradients in density shown on the temperature and salinity plots. Small gradients in temperature and salinity can be observed lower down in the estuary. Results from the RIB show a homogenous water column due to increased mixing and turbulence with shallower water depth. The small fresh water input to the Fal estuary is seen by the lowest salinity of 28.6 found at RIB station 6. Temperatures decrease with movement downstream with highest temperatures of 18.5°c further up the estuary due to the warming effect of the land.

Biological removal, coincidental with the end of the diatom bloom due to nutrient limitation in the system, may explain nitrate levels observed in the estuary. Silicon also decreases with increasing salinity because of increased utilisation by diatoms. Phosphate results show increased concentrations at the estuary mouth, which most likely reflect inputs from sewage treatment works such as those in St.Just and St.Mawes. Phosphate levels are generally higher in the Fal in the summer when river inputs are lower and dilute anthropogenic sources to a lesser extent.

Although there are limited number of sample points for dissolved oxygen, analysis of the data shows that oxygen is more saturated in surface waters. This is due to increased phytoplankton activity in surface waters. An anomalously low value can be seen in surface waters at station 6 at Malpas. There is a sewage treatment works located here and hence bacterial action may have led to decrease O₂.

Analysis of phytoplankton samples shows an abundance of diatoms, in particular Coscinodiscus, higher up the estuary. Diatoms are adapted for lower light levels and favour well mixed conditions. This may explain the fact that fluorescence was seen to increase up the estuary, despite decreasing euphotic depth. High abundances of copepods were seen throughout the estuary, most likely due to the high levels of phytoplankton at this time of year. Siphonophorae was noted in surveying of the estuary but not further upstream as this group favours salt water.
 

Lab Methods

Transect 1
The plots from the ADCP, particularly the direction plot, shows four main areas of flow, see figures 6.4 to 6.6. At the limits of the transect towards the banks there is easterly flow where as at the middle of the transect easterly flow can be found in the surface layer. This could be explained by flow leaving the Fal estuary combined with the final part of the flood tide. There is northerly flow at depth (below 10m) representing the residual landward flow of more saline water. Flow of greatest magnitude, 0.25ms^-1, is found at the surface. A region of high backscatter can be seen in the centre of the plot which could represent the high amount of sediment being removed from the estuary.

Transect 2
Figure 6.1 shows the location of the transect which is west of Lizard Point. Flow is greater in the surface 15m, with westerly flow overlying northerly flow, see figures 6.7 to 6.9. With movement away from the reaches of the headland, the body of water becomes well mixed with westerly flow throughout. This reflects the ebbing state of the tide at the time of this transect. The high backscatter seen at the surface could partly be due to the rough state of the sea interfering with the surface readings.

Transect 3
Flow along this transect is predominantly southerly, displaying the final part of the ebbing stage of the tide in Falmouth Bay. The area of higher flow magnitude, (0.35ms^-1) towards the centre of the transect, see figure 6.10, may correspond to flow from the Helford River. Comparison with T/S profiles shows there is an influence of fresh water at CTD station 5. Changing direction of flow with depth illustrates the beginnings of an Ekman spiral. There are a few areas of higher backscatter located in the water column, particularly at the end of the transect towards CTD station 5. ADCP, CTD and zooplankton trawl data confirm the location of zooplankton at 15m depth.

Transect 4
Transect 4 was carried out just as high tide was reached, and with movement closer to the mouth of the River Fal there is a change in flow direction from southerly to westerly, see figures 6.13 to 6.15. This may be representative of flow leaving the River and the beginnings of the ebb tide. An increase in flow magnitude and CTD profiles confirm this influence of the fresh river water. Again there is an area of high backscatter at about 15m depth suggesting the presence of zooplankton.

Richardson Number
As with the estuarine survey, data from the ADCP and CTD was used for calculations of Richardson number at each CTD station.

CTD Station 1
A slight gradient in both temperature and salinity from surface to about 6m reflects a surface turbulent layer with a 7m. An increase in Ri from 0.1 to 13.8 between 4m and 7m shows the stable boundary created by the pycnocline, see figures 6.16 and 6.17. Mixing is prevented across this layer maintaining the stratification of the water column. Another mixed layer lies beneath this with a more stable layer of laminar flow at the sea bed.

CTD Station 2
Figure 6.19 shows sharp temperature gradient of about 1°c at about 13m depth, with peak temperatures of almost 14°c. The deep water depth at this location, despite proximity to the headland may have prevented stratification from being eroded by tidal currents. There are tidal streams around Lizard Point which may have directed stronger flows away from this point allowing stratification to build. Sampling by other groups locates the Western English Channel front along the 50m contour offshore from Falmouth bay and so this station may have been located near the front. As expected salinity is almost constant with depth due the lack of fresh water influence in this area. The Ri plot (figure 6.18) shows laminar flow at about 15m coinciding with the thermocline and well mixed layers above and below this. A stable boundary can also be seen at about 24m which may correspond to the shear between flows of different direction seen in the ADCP plot at this station.

CTD Station 3
Station 3, see figures 6.1 to 6.3, has a shallower thermocline at about 7m than that observed at CTD Station 2. The pattern of a shallowing thermocline would be expected with movement from the stratified to shallower well mixed side of the front, so it is unusual that this pattern has been observed with movement offshore. This may be due to the slight erosion of stratified waters due to increased storm events in the days proceeding sampling. Figure 6.20 shows upper well mixed waters separated from lower well mixed waters by a stable boundary layer at about 23m.

CTD Station 4
A slight gradient in temperature between 11m and 13m corresponds to the salinity spike seen at this depth, see figure 6.23. Above and below this temperature is fairly homogenous, as is salinity. The Ri plot , figure 6.22, shows a stable layer at 7m which is shallower than expected considering the position of the temperature gradient. However, the temperature gradient is not that strong and differences in stability may be due to changes in shear.

CTD Station 5
There is a temperature change from 13.2°c to 12.4°c between 6.5m and 9.5m depth, see figure 6.25 A slight fresh water input can be seen due to proximity to the Fal River. The Ri plot , figure 6.24, shows a layer of laminar flow at about 3.5m which when comparing to the ADCP plot of Transect 3 may reflect the increased flow velocity at the surface due to fresh water outflow. Another stable layer can be seen at about 10m depth, corresponding to the base of the temperature gradient. Well mixed waters can be seen below this shown by Ri values less than 0.25.

CTD Station 6
There is quite a large difference in surface and depth temperature (1.2°c), which occurs over a depth of 10.5m. Considering the location of this station, surface water will reflect river water as the profile was carried out at low tide. The Ri plot, figure 6.26, suggests that the water is completely well mixed which is surprising considering ADCP data at the end of Transect 4. This could be due to inaccuracies in matching up CTD and ADCP data in the calculation of the Richardson Number but it is also important to consider that the critical values are not absolute and are a guide to the state of the water column. Considering the state of the tide and the T/S profiles some stratification in the water column would be expected.

Data Manipulation

Initially we wanted to see how the nitrate, silicate and phosphate concentrations change with increase in chlorophyll biomass. However due to there being a lack of correlation between the parameters nothing could be determined from the graphs. The N:P ratio showed that nitrate was below the standard 16:1 ratio and therefore was seen to be a limiting factor. Therefore we have plotted our nutrient values against the CTD data for temperature and fluorescence against depth as seen below.

Analysis

The CTD profiles of temperature and fluorescence against depth show that a seasonal thermocline has formed. The thermocline is seen to be shallowest at station 1 (figure 6.29) at 5m, where the water depth was shallowest. Further offshore in the Mounts Bay area the thermocline deepens to around 10m (figures 6.30 and 6.31). Our final transect from Manacle Point to Black Rock shows that the decreasing depth of the water column causes the thermocline to be pushed up from 11m to 7m (Figures 3.32, 6.33, 6.34). At each station the drop in temperature with depth could be a factor in the reduced chlorophyll levels due to photosynthesis being an enzymatic process.

The chlorophyll levels generally peak around the depth of the thermocline and the extracted chlorophyll data correlates to this. Stations 1, 2, 3 and 6 had a chlorophyll maximum at around 5m, where stations 4 and 5 (further offshore) had deeper chlorophyll maxima between 7 and 10m. The chlorophyll levels then decreased with temperature as the water column became deeper.

At stations 1 and 2 (Figures 6.29 and 6.30) the NO₃, PO₄ and Si concentrations are highest at the chlorophyll maximum, around 5m. At 22m depth where the temperature is much lower and chlorophyll has significantly dropped, the concentrations are also much lower. This is likely to be due to the nutrients having been plentiful at the thermocline and having been depleted by this depth.
In comparison at station 3 (Figure 6.31) the nutrient levels are relatively low at the thermocline. This was our most southerly point offshore and thus the nutrients are likely to be diluted. At this station only one sample was taken, causing comparison difficulties.
The last three stations (figures 6.32, 6.33 and 6.34) the euphotic zone became shallower with increasing proximity to the shore ranging from 18.74m-12.94m. The data for station 4 does not go below the euphotic zone, and hence it appears that chlorophyll is high throughout the water column. At 7m there is a peak in chlorophyll indicating the possibility of a large bloom. The drop in chlorophyll below this could be due to the bloom creating a shielding effect and reducing the light level. At station 5 the chlorophyll again peaks at the thermocline and drops with the reduced temperature. Station 6 is again completely in the euphotic zone so that chlorophyll again remains high.

Data collection and analysis methods

From each Niskin bottle (R.V. Bill Conway-1.25L and R.V. Callista-3L) 50ml water sample for both nitrate and phosphate analysis was filtered through a glass fibre filter into a numbered glass bottle. A 50ml sample for silicate analysis was also filtered into a numbered plastic bottle to avoid silicon contamination from glass. Bottles were first flushed through with the water sample in order to prevent contamination from a previous sample. The filters were then placed in numbered tubes containing 6.0ml of acetone for analysis in the lab. A glass bottle was used for the dissolved O₂ water sample, and these had 1ml of each manganese chloride and alkaline iodide added, ensuring no air entered the bottle. The bottle was then sealed and submerged into a container of water to avoid contamination. The following analysis methods were used in the lab:
 

• The dissolved O₂ analysis using the Winkler method as per: Grasshoff et al, 1999
• Chlorophyll was analysed as per: Parsons et al, 1984.
• Silicate and phosphate were analysed as per: Parsons et al, 1984.
• Nitrate analysed using Flow injection analysis as per: Johnson and Petty, 1983.

Phytoplankton taxonomy analysis method
• 100ml water samples were placed in glass bottles, with Lugols 1ml of iodine solution added as a preservative.
• These samples were then placed in a measuring cylinder and left overnight allowing the phytoplankton to settle at the bottom.
• The water sample was removed using a glass inverted pipette leaving the bottom 10ml of the sample for analysis. Care must be taken to ensure that the phytoplankton are not re-suspended and therefore lost from the sample.
• 1ml samples were placed under a microscope to count the organisms and to make taxonomic identifications.
• This process was repeated for each of the Niskin bottle samples, for both the estuarine study and the offshore study.
 

Zooplankton taxonomy analysis method
• A 500ml bottle was placed at the end of a zooplankton net with a mesh size of 200µm and a net diameter of 50cm. The net was placed and trawled for a certain period of time.
• Water samples were mixed to ensure even distRIBution of organisms
• A 5ml sample was put on a Bogorov Chamber.
• The samples were placed under a microscope to count the organisms and to make taxonomic identifications.
• This process was repeated for each of the zooplankton trawls, for both the estuarine study and the offshore study.

Analysis of the water column structure off the Lizard point from shows that in the main it is turbulent with all CTD casts showing an area of stability at around 5 metres. At Pennance point the same structure is observed showing that in a horizontal plane the water column has changed very little. Temperature decreases with depth and salinity increases with depth for both sites. Density calculations show that as expected the density increases with depth.

Nutrient analysis shows that there is a slight decrease with depth for stations 1-3. The opposite is true for stations 4-6 which conform to the expected results. The limitation with these results is mainly down to the lack of data points sampled which should have been increased to maximise resolution of the plots. Station 5 showed the lowest concentrations of all nutrients and had the highest concentration of chlorophyll at 3.2μgL-1. This combined result confirms a large phytoplankton bloom in this location which are using the available nutrients. Chlorophyll for all other stations was between 1.4-2.6 μgL-1 and varied according to the depth of the euphotic zone between sites.

Zooplankton counts showed that Copepoda was the most dominant sub-class in the water column with varied levels of Cirripedia larvae being determined by distance from shore. Samples closer to the Fal estuary showed increased numbers of Siphonophore and Gastropoda larvae possibly indicating an influence from the riverine water.

Phytoplankton counts did not show any conclusive results. This was due to the lack of similar depth samples which severely limited the comparisons between sites. However, certain species did remain dominant across samples irrespective of depth. Rhizosolenia setigera and Rhizosolenia alta had high counts for all samples. Alexandrium spp.was found in high numbers off the Lizard point but in low numbers off Pennace point. This could be attRIButed to competitive exclusion by Rhizosolenia spp.which are faster growing.

Bibliography

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The Zooplankton composition at station 1 (Black rock) was dominated by Copepods (509 per m³). There were examples of other groups in the sample, of which Polychaete larvae and Cirripedia were more prevalent.
Station 2 was situated west of Lizard Point. Plankton samples identified that there was an abundance of Cirripedia larvae at station 2 (752 per m³), which was situated close to the shore.
It can be suggested that the abundance of Cirripedia larvae at station 2 may relate to the proximity of the rocky shore, and recruitment of new individuals. The larvae are attracted to adult colonies on the rocky shore in order to settle and develop into adults.
Two Zooplankton samples were taken at station 4, which was situated east of Lizard Point in a sheltered cove. Z3 was taken from 14m to the surface and Z4 from 7m to the surface. By comparing the two samples the zooplankton composition of the water column above and below 7m can be compared.
Both samples are similar in that Copepoda are dominant throughout the water column. Polychaete larvae were more prevalent in the top 7m of the water column; however other zooplankton groups such as Siphonophores and Hydromedusae were more prevalent below 7m.
Two zooplankton samples were also taken at station 5, which was situated within the Fal bay area. An area of strong back scatter was identified during the ADCP transect at 12m, so samples were taken from 15m to the surface (Z5) and 10m to the surface (Z6) to compare the zooplankton community.
There was a significant increase in zooplankton below 10m. The plankton bloom identified by the ADCP transect was dominated by Copepods, there was an increase of 389 per m³ below 10m. Other groups which increased significantly below 10m include Hydromedusae (220 per m³) and Siphonophores (177 per m³). There was however an increase in most groups below 10m.

Analysis

The data collected from R.V. Callista showed interesting results from the samples collected. CTD station 1 was at Black rock at the mouth of the Fal estuary this relates to ST1 -1 to ST1-3 (as seen in table 6.1). The results show that the DO₂ concentration at this location is remarkably low. This could be due to the consistently stormy weather conditions prior to the survey. The stormy conditions result in the mixing of the water column. The poor irradiance levels result in lack of phytoplankton activity due to increased turbidity. Turbidity effects irradiance penetration which is required for photosynthesis. This would reduce the DO₂ concentration which explains the low levels. CTD station 6 samples taken from points ST6-1 to ST6-3 are also situated in the Black rock area. The latter results are higher than the previous samples taken. This is due to tidal influence; when sampling the tide had just begun to flood. This shows that there would be a high level of DO₂ due to riverine water flowing over the incoming saline sea water. This is further supported when taking different parameters into consideration. The results from CTD station 6 show that at ~1.35m depth the temperature was ~14.1°C, which is warmer than the prior sample of CTD station 1. This could have resulted in having sped up the metabolic rate of phytoplankton resulting in higher DO₂ production according to the Q₁₀ hypothesis. Furthermore, salinity was lower at 34.5 for CTD station 6 compared to previous sampling of 35.2 for CTD station 1. This rise in salinity lowers the solubility of O₂ in water and explains the rise from 93.3% to 100.5%.
The data collected from CTD station 5 at ST5-1 taken at 21.46m depth showed a DO₂ reading of 90.0% which may suggest that there be elevated O₂ removal due to respiration of zooplankton at this depth. Due to a combination of weather conditions, faulty equipment and problems with data sampling there evidence is lacking to support this theory.