Who Are We?

...5 Oceanographers...

...5 Marine Biologists...

From left to right:

Tommaso Bendoni, George Grant, Lisa Holton,

Matt Hawksworth, Rachel Cook, Sam Gill, Becci Owen,

TJ Kearney, Ellie Hoolahan, Emily Last

Figure 1.  Simple overview map of Falmouth and its surroundings

Introduction

An investigation into the biological, chemical and physical processes in the Fal Estuary in Cornwall, England (see Figure 1) was carried out from the 26^th of June to the 6^th of July. Observations were made in three primary sessions, on research vessels, around the estuary and consisted of an ‘Offshore’, an ‘Estuarine’ and a ‘Geophysical’ investigation.

The Fal estuary can be geomorphically classified as a classic ‘Ria’, or drowned river valley, and is thought to have been formed from the beginning of the Holocene as a result of sea level rise (Langston et al, 2003). The Fal Estuary forms part of the Carrick Roads, which is the deepest natural harbour in the world, with a maximum depth of 35 m (Langston et al, 2003). These types of estuaries are usually large shallow inlets and bays, and the diluting effects from freshwater inputs are minimal. The harbour is subject to many anthropogenic, industrial and recreational pressure, such as dredging, sewage inputs, mining and industrial runoff.

The Fal Estuary is affected by south-westerly Atlantic winds and experiences macrotidal conditions at the mouth (Falmouth), with a maximum spring tide of 5.3m, and mesotidal conditions at the head (Truro) with a maximum spring tide of 3.5m (Pirrie et al, 2003).

 The west of the estuary is surrounded predominantly by Carnmellis granite and other metamorphic rock. The large input of China clay waste from St Austell has a major silting impact on the upper estuary and the salt marshes (Langston et al, 2003). The Fal is a designated special area of conservation and is a site of protected habitats such as maerl and seagrass beds as it is the site of many habitats such as maerl beds.

The area has a substantial history of mining, peaking in the 19^th century. Much of the tailings and wastage were deposited in Restronguet Creek, resulting in the highest concentration of polluting metals found in the UK (Langston et al., 2003).

Schedule

Equipment

Tables 1 and 2. Meteorological data and tide times for offshore work

28/06/2011	Tide Times GMT	Tidal Height (m)
Low Water	0629	1.30
High Water	1226	4.40
Low Water	1857	1.40

Figure 2.  Transect map for Offshore Stations

Abstract/Background

The aim of this investigation is to determine how vertical mixing processes in the coastal waters of the English Channel off Falmouth affect, directly and indirectly, the structural and functional properties of plankton communities.

Vertical mixing has a profound influence on the properties of the surface layer, which largely controls the planktonic productivity and distribution (Kiorboe, 1993). This investigation was carried out in the summer months (June), when the surface waters tend to be nutrient depleted and the deep waters are nutrient rich and therefore will focus on the rate at which nitrate and silicate can be mixed upwards across the thermocline. This occurs as there are lower rates of surface mixing and higher irradiance levels in the summer months. Fronts form in the regions where the well mixed, nutrient rich coastal waters meet the well stratified waters.  Planktonic productivity is high in this region due to the abundance of nutrients found along these frontal systems. Nitrate is an essential nutrient required by all types of phytoplankton and silicate is required specifically by diatoms for growth and formation of their siliceous skeletons.

Data was collected from stations listed in the table below. A full sample included a CTD cast to obtain physical measurements, sample collection in order to determine chemical properties such as nutrient and dissolved oxygen levels.  The CTD was deployed from the back of RV Callista and was lowered down to the required depths via a winch system. It contained a temperature and salinity probe, light sensor, fluorometer and a series of Niskin bottles on the Rosette sampler which collected the water samples. These samples were used to obtain the dissolved oxygen, chlorophyll, silicon, nitrate and phosphate data, and were stored in smaller glass bottles, apart from the silicon ones which were put into plastic bottles, ready to be transferred to the lab for analysis. It is unfeasible to put any samples for nitrate and phosphate analysis into plastic bottles because they are made of organic materials, which may contaminate samples, thus providing inaccurate results.  Glass contains silica, so can therefore not be used to contain the dissolved silicon samples, as the eventual silicate concentrations were analysed in the laboratory. 

Biological data was obtained through phytoplankton and zooplankton sampling, using a closing net with mesh size 200µm. This was deployed via a winch from the back of Callista, and lowered to depths defined on the CTD fluorometer and ADCP data as being significant.  It was raised over the pre-defined depth range, for example from 30m to 20m, and then closed via messenger weights. The water samples collected in the 500ml bottle attached to the bottom of the net were then placed in plastic containers for consequent identification in the laboratory.

The ADCP is permanently on the hull of Callista, and so was switched on at the beginning of the survey. Therefore the velocity and direction of the current was recorded over the entire survey time, enabling the creation of horizontal profiles.  

Two survey routes were planned in order to allow for weather interferences. Plan A was to be carried out if the weather was suitable, which would involve RV Callista travelling straight outwards from the coastline in a south easterly direction. Plan B would involve RV Callista travelling along the coast in the shelter of Lizard Point, as this would still allow the investigation to be carried out if conditions were unsuitable for work further offshore, for example with the presence of extreme fog. Plan A was carried out, and an overview of the route is listed in Table 3 below.

                                                        Table 3.  Positions and details of offshore sampling stations

Chemical Analyses

During nitrate analysis, pre-existing standards were used that were known to be accurate and correctly made up. From these peaks, we were able to calculate the relative amount of nitrate in our samples of seawater. Three stations were tested at different points along the offshore data sampling, allowing us an effective cross section from the mouth of the estuary, right out to our furthest sampling point offshore at station 2. The majority of samples contained very little nitrate, below the detection limit of the apparatus. This was to be expected from the high salinities present in all of our samples. Only one sample that had a measurable nitrate concentration was from station 3. This sample only just had peaks that were repeatable and also measurable, but they also confirm what was expected, for nitrate to be very low in offshore environments. It was surprising however, as it wasn’t our lowest salinity value, but one of our highest. Surface mixing and variable light over the previous few days will have lead to local variation.

Table 4.  Nitrate results and corresponding relevant information during the analysis stage

Station	Lat	Long	Depth (m)	Salinity (psu)	Bottle No.	Nitrate (μM)
Standard	Standard	Standard	N/A	N/A	Standard	10
3	50°03.169	004°59.306	0.874	35.346	51	Below Detection
3	50°03.169	004°59.306	14.543	35.251	45	Below Detection
3	50°03.169	004°59.306	41.109	35.244	20	0.714
3	50°03.169	004°59.306	20.913	35.194	6	Below Detection
2	49°59.561	004°56.071	60.606	35.344	56	Below Detection
2	49°59.561	004°56.071	26.325	35.286	55	Below Detection
2	49°59.561	004°56.071	0.826	35.203	54	Below Detection
5	50°08.701	005°01.500	24.8	35.183	50	Below Detection
5	50°08.701	005°01.500	11.1	35.102	48	Below Detection
5	50°08.701	005°01.500	0.811	34.724	7	Below Detection

 

When analysing samples for their phosphate contents, it is important to remember that stations 1 and 5 were both taken at Black Rock at 50o 08.214N and 005o 01.225W at the mouth of the estuary, but were taken at different times.  The samples for station 1 were taken at 09:05-09:41 UTC, whereas the samples for station 5 were taken at 14:56-15:01UTC. As a result of this, the same site was sampled at differing times in the tidal cycle.  This may explain why an increase in phosphate concentration was seen when the Black Rock site was sampled for a second time. With the tide starting to fall when the samples from station 5 were collected, water with higher phosphate concentrations will have been entering the system from the estuary. The influence of nutrient rich fresh water explains the high surface concentrations of phosphate, and as Black Rock is relatively shallow, the whole water column will be tidally mixed and well lit providing suitable conditions for algal growth leading to the concentrations decreasing with depth. Station 2 shows increasing concentrations of phosphate with increasing depth, with the maximum concentration being seen at 60m. Stations 3 and 4 also show decreasing concentrations with depth, with maximums at each station occurring at the deepest depth sampled. The station does however show an area of mixed water between 10-30 metres, and this is also seen when looking at the CTD casts for this station.

Figure 4.  Phosphate concentrations for all five stations plotted against depth. Stations 1 and 5 show decreasing concentrations in phosphate with depth. Stations 2-4 all show increasing concentrations with depth.

Again as in the phosphate figure, it is important to bear in mind for the silicate measurements that both stations 1 and 5 are taken at Black Rock at differing times in the tidal cycle. The samples taken at station 1 were collected towards high tide, whereas the samples from station 5 were collected as the tide was falling. This has yielded silicate results similar to the phosphate profiles, with station 5 having higher concentrations at all depths when compared to station 1. The reasoning for the increased concentrations, is the result of nutrient rich freshwater entering the marine system from the estuary.  The trend of decreasing concentrations at both stations 1 and 5 are due to Black Rock being in a tidally mixed body of water provides enhanced conditions for phytoplankton growth, and this coupled with the Black Rock being relatively shallow and well lit leads to the continued uptake of nutrients at depth.           

The samples collected at stations 2 and 3 show an increase in the concentration of silicate with depth, which is to be expected as both stations are from stratified waters. Although station 2 shows a slight increase with depth hinting at a relatively large mixed layer, station 3 has a very small stable layer extending down to about 16m and the silicate concentrations increase with depth.            Station 4 has a slightly unusual profile, as for the first 15m, the silicate concentrations decrease with depth.  This is more than likely due to phytoplankton activity. From around 15m to 28m there is a slight increase seen in the concentration of silicate and then from 28m until the deepest sample taken, the concentrations increase. This unusual behavior may be the result of a number of different water bodies mixing at this station, supported by the fact that this irregularity is also seen in the depth profiles generated from the CTD casts at this station. Figure 5.  Silicate concentrations for all five stations against depth. Stations 1 and 5 show higher silicate concentrations at the surface when compared with depth. The plateau seen in station 5 at the maximum depth is as a result of replicates being carried out with differing values being generated. For stations 2 and 3 increases in silicate can be seen with increasing depth. Station 4 shows an initial decrease in silicate concentration down to about 16m and then the concentrations increase with depth.

 

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Biological Analyses

Phytoplankton Abundance:

The greatest abundance of phytoplankton is found at station 4, with 1196 cells found per 4ml of sample, over twice the number found at other sites. The lowest count of cells, just 156, was found at station 1; Black Rock at the mouth of the estuary, though upon return survey later in the day, 538 cells were found in the samples from a similar location, as shown on the trackplot (figure 6). The high abundance at site 4 can be attributed to the effects of both the Fal and Helford estuaries, which feed into the sea towards this area, bringing nutrients such as phosphates and nitrates, along with sweeping phytoplankton out of the estuaries in bad weather conditions and receding tide. Here, the water is deeper than in the estuaries, allowing phytoplankton to make full advantage of downwelling irradiance and for stratification to occur, which is not usually possible in estuaries due to the combined effect of marine and riverine inputs. Measurements at station 5 were taken at slack water, meaning the water was incredibly still compared to earlier in the day when station 1 measurements were taken. This may account for the difference in cells at the two stations, whereby cells were mixed down by tidal input at station 1 but much less so at station 5, resulting in higher abundance later in the day, despite the similarity of the locations. Stations 2 and 3 were the furthest offshore and contained a moderate abundance of phytoplankton in the samples; 552 and 432 respectively. Again, stratification of the water column plays a vital role in the abundance of phytoplankton cells and perhaps had the weather conditions been better in recent weeks or months, the sample counts would be much higher due to stronger stratification along with increased temperature and sunlight.

Each station contained a relatively high abundance of Chaetoceros, Guinardia f., Leptocyndrus d. and Rhizosolemia sp. Chaetoceros (figure 17) is a colony-forming diatom found largely in the surface waters receiving high sunlight, which goes some way to explain its fairly high abundance in each of the samples taken as it is probably present in the samples nearest the surface. Guinardia f (figure 18) is found in greatest number at station 4, with 354 cells compared to 60 at station 3, the second highest abundance. This could be in accordance with the high combined input of nutrients from the two estuaries causing high growth, along with that of other species in this area. Guinardia s., on the other hand, is found only at station 5, though in significantly high numbers of 112 per 3ml of sample. This may be due to this particular species having a late diurnal cycle, occurring later in the day and in the still water provided here at slack water, compared to the more turbulent waters found at the other stations, combined with the outflowing nutrients from the Fal estuary, most notably a rise in silicate as compared to the morning. Leptocyndrus d. (figure 19) is the most abundant phytoplankton found in total, with 570 cells found in total from the entirety of the samples. Occurring in high numbers at stations 2, 4 and 5, this species appears to thrive in still and stratified waters rather than more mixed waters. This has resulted in nutrient boundaries, where nutrients such as silicate and phosphate have accumulated at depth and may be mixed upwards at a later date to promote further phytoplankton growth when the stratification breaks down. Rhizosolemia so. is also found heavily in samples from stations 2 and 4 though little elsewhere, suggesting again a preference for deeper, stratified water columns rather than the more mixed waters of the estuary, given none of these cells were found at either stations 1 or 5, at the mouth of the estuary.

Figure 6. Chaetoceros	Figure 7. Guinardia flaccida	Figure 8. Leptocylindrus danicus
Figure 9. Abundance of phytoplankton species found at sample stations	Figure 10. Percentage composition of phytoplankton species found at each station	Figure 11. Other phytoplankton found - Rhizosolenia stoiterfothil
	Figure 12. Other phytoplankton found - Guinardia strata

Zooplankton abundance:

As with the phytoplankton, samples from station 4A held the greatest number of zooplankton, at 105 cells found in a 10ml sample from 35-25m in depth. The abundance of phytoplankton to feed on at this site is the most probable cause for the zooplankton numbers though as this sample was taken at the greatest depth of between 35 and 25m, thus suggesting the zooplankton follow a diurnal cycle, retiring to depths during the day to avoid predation then rising towards the surface as night to feed. This is reinforced by the two samples taken at station 2, where more zooplankton were found in a 5m stretch between 30 and 25m depth than were found between 25 and 15m, at 47 and 41 per 10ml respectively. Such vertical migration is not possible to the same extent at station 1, at the mouth of the estuary where the water is not as deep. However, station 1 contains the second highest abundance of the samples, at 82 per 10ml sample, perhaps indicating that, due to the rather low abundance of phytoplankton in this station, zooplankton keep the numbers low by grazing. Upon sampling higher in the water column at station 4, the total zooplankton found per sample was only 24 and the phytoplankton population significantly larger, suggesting the zooplankton had retreated to lower than the 10m depth of the net.

The most frequently found group were copepods, particularly in the samples taken further offshore, such as sample 2A, in which 70% of zooplankton found were copepods, compared to only around 20% for each station 1 and 4B. Copepods are an incredibly abundant group of zooplankton throughout the world’s oceans and the Falmouth area is no exception, given the availability of phytoplankton food supply. Copepod nauplii were also common, though usually only in stations where copepod numbers were lower, for example at stations 1, 3 and 4A. Estuaries such as the Fal and Helford would be used as spawning and nursery grounds for copepods and other zooplankton, giving a high proportion of larvae nauplii here and a wide range of groups found at both stations 1 and 5, both at the mouth of the Fal Estuary. Stations 3 and 4 both also have large populations of copepod nauplii, though these were both located near the entrance to both estuaries and thus would be affected by both, including the output of young copepods and other larvae. Both samples taken at station 2, located furthest offshore contained no juveniles, only adult individuals, as once they have reached this far from the estuaries they have fully grown and are able to feed further out into the ocean. A further abundant group was the Appendicularia, found in all samples apart from that at station 3. These tunicates are free-living in the pelagic zone, thus are found at all depths sampled, though may be absent at station 3 due to competition from copepods which are far the most abundant there. As they are in their smallest numbers at station 1, it can be inferred that they much prefer more stratified water further offshore from the estuary and are able to thrive there.

Figure 13. Abundance of zooplankton species found at sample stations	Figure 14. Percentage composition of zooplankton species found at each station

Physical Characteristics Analyses

Figure 15 shows offshore temperature variability with depth. These stations are very similar because they are very close to each other (see chart of station locations and station map). These locations in the estuary mouth are strongly mixed by both wind and tides, leading to the homogenous temperature distribution and no discernable water column. These stations are much shallower than the other stations, so the mixing can go through the entire water column at this point. For stations 3,4 and 5, a thermocline can easily be seen. At station 3, the thermocline is constant from 13.25 down to 11.5, suggesting mixing between only 2 water masses, the deeper cooler water and the warmer surface waters. Stations 4 and 5 have more complicated thermoclines with small plateaus, suggesting more complicated mixing between other water masses and a possible mixed layer at around 18m. This can be confirmed by checking our other parameters that we have sampled. It was hypothesized that wind driven water currents from around Lizard Point may have been causing this, although with our current samples we cannot prove this.

Figure 15.  Offshore temperature profile, changing with depth

The vertical profiles seen in the figures 16-20 represent the data collected from the CTD at the five stations, the locations of which can be seen in table 2 and figure 2, the transect map.

Figure 16.  Profile for Station 1	Station 1	Station 1 shows fairly homogenous conditions through the water column, demonstrated in particular by the very small variation in temperature. The irradiance levels follow the same exponential decrease due to the absorption and scattering of light by particles in the water column as at the other stations, but there are much lower values at station 1; the highest irradiance level at the surface was ~1600PAR, but all the other stations range from ~2000 to ~5500PAR. The salinity has little variation in any of the profiles, as offshore salinity values have very few outside influencing factors. The turbidity is recorded on the transmissometer, and the lower the values, the higher the turbidity. So at station 1, it can be seen that there is very high turbidity at the surface and then fluctuates down through the water column to ~3NTU. The chlorophyll is fairly stable, but in comparison to the other stations, station 1has higher chlorophyll levels than the others. This could be due to the higher inputs of nutrients from the inflowing river (station 1 is closest to the estuary mouth). Also, it could be due to the high amounts of mixing caused by tidal activity, as further offshore stratification affects the transport of nutrients into the euphotic zone. The other characteristics of these profiles indicate a well-mixed environment.
Figure 17.  Profile for Station 2	Station 2	Station 2 was located at the furthest point offshore on the transect. The depth profile shows the most stratification across the stations, as there is a well-defined thermocline between the ~2m and ~30m. The chlorophyll remains roughly at about 0.06µg/L through the water column. The lower values than those of station 1 could be due to the nutrient limitation in the euphotic zone caused by the stratification in of the thermocline. The turbidity is higher at the surface, which is most probably due to wind stress, and then decreases quickly to just less than 4NTU, and then remains homogenous. Irradiance decreases exponentially with depth again, but has higher values at the surface, which could be indication of more UV rays. Salinity spikes can be seen on the depth profile, and these are most likely caused by the time-lag between the CTD temperature and salinity measurements.
Figure 18.  Profile for Station 3	Station 3	Station 3 depth profiles also represent a well-stratified environment, but the thermocline reaches to almost 40m and decreases in steps, so there is less stratification and therefore more mixing, as tidal influences are having more of an effect closer to the coast. Turbidity is again higher at the surface because of wind stress, but reaches down to a slightly greater depth before becoming vertically consistent at about 20m. Salinity spikes can also be observed on this profile, as the conductivity is recorded before the thermistor has had time to warm up at the same rate. Irradiance levels have a high at the surface of  ~4000PAR and decay to roughly 20m before primary productivity would be no longer possible. This correlates with increased mixing. Chlorophyll levels are again consistent at about 0.07 µg/L, but are unusually high at the surface to about 3m compared to the other stations. This is most likely linked to the increase in turbidity and decrease in irradiance. The more particles in the water column, the less light can attenuate, so with the increase in chlorophyll it is probable that there is a large patch of plankton.
Figure 19.  Profile for Station 4	Station 4	The stratification decreases more again at station 4, as the tidal mixing increases. The thermocline has become steeper, and although the turbidity at the surface has decreased slightly. The main feature of this profile is the correlation between the turbidity spike and the irradiance at about 3-4m; the turbidity increases and the irradiance decreases, so this shows a large patch of noise, caused by marine animals, anthropogenic features or other objects that would produce backscatter. There is no increase in chlorophyll this time however, so it is unlikely to be linked to plankton.
Figure 20.  Profile for Station 5	Station 5	Depth profiles for all the data acquired from the CTD cast at station 5 are shown. This station is very well mixed and the depth profiles reflect this fact. From just below the surface the turbidity is fairly homogeneous all the way to the seabed. The chlorophyll is also evenly distributed throughout the water column. Temperature and irradiance also follow steady curves however the temperature change at depth is much less than at other stations, proving the homogenised water column. The salinity shows some large spikes, caused by the time lag; however the scale of the graph exacerbates these.  The spikes occur over a very short spatial period and may be the result of incomplete mixing of the fresh water input in the estuary.

Water Column Stability

The Richardson number (Ri) is a calculated dimensionless value of the stability of the water column. It is the ratio of the stabilising effect of the density gradient to the destabilising effect of the velocity shear. A Ri number greater than 1 describes laminar flow and a number less than 0.25 reflects turbulent flow. A number between these two values is determined by gravitational shear. The Richardson number is calculated using:

  

All stations show increasing Ri numbers within the first 5-10 meters, and this indicates that with an initial increase in depth moving out of the wind and wave driven mixing, the water column increases in stability. After this depth, the individual characteristics of each site dominate the stability.  Both stations 1 and 5 were taken at Black Rock and the variation seen between these two stations is a direct result of the tidal cycle. Station 1 was sampled around slack tide resulting in a well mixed turbulent water mass, whereas station 5 was taken just after low water and has thus resulted in the appearance of two water masses: a turbulent freshwater layer extending down to 15 meters and a laminar stable water mass from 15-20m. The Ri numbers seen at station 2, although not reaching the laminar threshold, do agree with the CTD data for this station showing a clear thermocline.  At station 3 the majority of the data points fall below the turbulent threshold indicating that the water mass is well mixed probably due to the stations proximity to the coast increase the effects of tidal mixing. The water mass sampled at station 4 is predominantly stable, and this may be due to the tidal state, just being after low water, when the station was sampled.

Figure 21. The Ri numbers at station 1 are all below the turbulent threshold indicating a well mixed water mass.	Figure 22.  The Ri profile of station 2 shows an initial increase from 5-25 meters however the values do not reach the laminar threshold. From 25- 35 meters the Ri number falls and eventually falling below the turbulent threshold at 35-40 meters. From 40-45 meters the Ri number increases but again not reaching the laminar threshold. From 45-55 meters the Ri number falls again below the turbulent threshold.	Figure 23. The Ri profile at station 3 is initially turbulent but does increase from 20-35 meters but not actually reaching the laminar threshold before falling again to become turbulent.
Figure 24. The Ri profile for station 4 is predominantly laminar and stable as the majority of the dats points are either above or around the laminar threshold.  However, from 35 metres the Ri falls, eventually falling below the turbulent threshold.	Figure 25.  The Ri number for station 5 increase with depth over 5-20 meters showing a change from a turbulent well mixed water mass in the upper water column to a more stable laminar flow in deep water. The reduced Ri number at 25 meters could be the result of increased friction from the bottom of the sea floor.

 ADCP Analyses

ADCP data gathered at the stations offshore indicate the state of the current present in the water body.  The contour plots shown below and their relevant descriptions highlight this information.  Station 1 is not included as an analysis area itself due to the fact that its location is the same as that of station 5. The ADCP figures for the transect between stations 1 and 2 show a sharp transition from high backscatter and velocity magnitude to lower backscatter and magnitude. This may be due to a front occurring at the boundary between the two. The velocity direction also changes from 50° to 360° with velocity higher on the left of the track at 0.125m/s compared to 0.250m/s to the right. These sudden changes may also be due to a deepening of the water column and change from coastal to offshore processes. The ships track also shows the change in velocity from transect start to finish. At station 3 the waters were well stratified with a seasonal thermocline descending to 30m where the waters become well mixed and uniform in temperature. There is also a band of high backscatter at 30m on the ADCP transect, this reflects a Doppler shift in the signal received by the ADCP. This may be caused by zooplankton populations which graze the phytoplankton held above the thermocline where light is high enough for growth.

Figure 26. Average backscatter contour plot, station 2 Figure 27. Velocity direction contour plot, station 2 Figure 28. RV ship track, station 2 Figure 29. Velocity magnitude contour plot, station 2 ADCP transects for station 4 show low magnitudes and varying directions of flow, which increases shear between flows. This data was taken at slack tide causing lower speeds than the other stations with a maximum of 0.125 and varying directions due to the change from flood to ebb. The high backscatter stops at 30m this may be due to a reduction in down welling irradiance preventing growth of phytoplankton and therefore zooplankton below the threshold. Figure 34. Average backscatter contour plot, station 4 Figure 35. Velocity magnitude contour plot, station 4 Figure 38. Velocity direction contour plot, station 5

Figure 30. Average backscatter contour plot, station 3 Figure 31. Velocity direction contour plot, station 3 Figure 32. Velocity magnitude contour plot, station 3 Figure 33. Velocity direction contour plot, station 4 Station 5 represents a well mixed water column with a relatively uniform profile for direction and magnitude with a maximum of 0.2m/s at 180°. Some vertical shear flow is evident in the velocity direction plot. The backscatter is higher than at other stations as available nutrients from river inputs are higher than at the stratified stations, thus sustaining higher populations of phytoplankton and thus zooplankton throughout the water column. Figure 36. Average backscatter contour plot, station 5 Figure 37. Velocity magnitude contour plot, station 5

Irradiance

LUP 1% Depth (m) Station 1 * Station 2 44.92 Station 3 38.76 Station 4 47.25 Station 5 *               Table 5. LUP 1% light depths for stations 1-5. Stations bearing '*' indicate water too shallow to calculate a 1% light attenuation depth.

Figure 39 demonstrates an exponential trend in irradiance decrease with depth at each station. At station 4, the irradiance seems to still be high at lower depths than at other stations (47.25m), whereas both stations 1 and 5 (both taken at Black Rock) do not reach their LUP 1% light depths as there was not a deep enough water column. By observing the plots generated from the ADCP data, it is possible to see that there is more backscatter in the water column in stations 2 and 3 than station 4; this allows more penetration of light and a deeper LUP 1% irradiance depth. A higher stratification index at station 4 implies minimal mixing and more stability in the water column.

Figure 39. Log of irradiance down the water column for stations 1-5 with their LUP 1% light depths.

Conclusion

The offshore investigation has shown that the water extending from black rock away from the Fal estuary becomes progressively more stratified with distance offshore. This is due to the deepening of the water column which reduces the mixing effect of the tide on offshore waters. The degree of stratification was less than would be expected in July, as wind stress and subsequent mixing has been higher than an average year. Station 2 showed a seasonal thermocline above which phytoplankton growth was contained. The silicate and phosphate data was low at station 2 as the thermocline prevents upward nutrient mixing from the layers below and phytoplankton populations utilise any available nutrients for growth. The ADCP transect between station 1 and station 2 showed possible presence of a frontal system with a boundary formed between areas of stratified and mixed waters, which also marks the transition from coastal to offshore waters where tidal influence is reduced. Station 2, 3 and 4 therefore fall on the stratified side of the boundary with solar heating causing seasonal thermoclines to form in the upper 30m, whereas stations 1 and 5 are located on the well mixed side where tidal velocities and shallow depths break down any stratification from heating and therefore conditions remain relatively homogenous throughout the water column.

Station 1 and 5 show decreasing nutrient concentrations with depth as mixing and irradiance allow for growth throughout the whole water column, whereas nutrient concentrations from 2, 3, 4 increase with depth as nutrients are able to replenish below the thermocline as growth is limited by light. This is also reflected in the dissolved oxygen concentrations for each station.

For a future investigation more stations would be needed to provide evidence of a definite frontal system between stations 4 and 5 before firm conclusions could be made.

Geophysics Mapping - SV Xplorer 02/07/2012

Tables 6 and 7. Meteorological data and tides for geophysical work

                       Tables 9 and 10. Meterological data and tide data for estuarine work

A scientific boat trip was undertaken throughout the Fal estuary to determine the type of estuary and also the key chemical, physical and biological behaviour within it. The estuary is where fresh and sea water mix, leading to interesting chemical, physical and biological conditions. Similar factors will be measured to the offshore boat practical however very different results are expected. The data compiled on the boat coupled with the pontoon data will provide a comprehensive overview of the processes at work in the estuary.  In recent years, the Fal has had numerous problems with heavy metal pollution (Bryan & Gibbs, 1983) from mining run off; which have been known to have an effect on the trophic assemblages within it (Warwick, 2001). Mining operations at Wheal Jane and other mines have since ended but metals may still be leaching into the estuary and causing problems. Some of the pollution may still be present and the residence time of water in the estuary shall be calculated to see how much of an effect the past problems may still be affecting the sediments and associate assemblages (Somerfield et al, 1994). Brown seaweeds may be an indicator of continuing problems as they have been known to be indicators of trace metals (Luoma et al., 1982 & Bryan, 1983) For this work, the Bill Conway was used in order to take lagrangian measurements, simillar to those taken on the pontoon at stations throughout the estuary. ADCP transects of the river at 5 different locations gave a profile of the speed and direction of flow beneath the boat. Secchi disk measurements allowed the depth of the euphotic zone to be estimated and the light attenuation to be inferred from this. CTD profiles and niskin bottles at 3 different locations allowed a complete, salinity, temperature and chemical profiles with depth. From the water samples collected, sub samples were taken in order to calculate the chemical values of dissolved oxygen concentration, nitrate, phosphate and dissolved silicon; back in the lab. Data was taken throughout the day by two groups from both the top and bottom of the estuaries to give a full profile from the river to the sea. Samples in the morning were taken from the top of the estuary down, into the onrushing tide, so that the same pocket of water wasn’t follow, with the opposite being done in the afternoon for the same reason.

Figure 42. Plot of transects taken within the estuary

Figure 43. Track plot of RV Bill Conway throughout the estuary

Pontoon

Eulerian measurements were taken at King Harry pontoon (50°12.970N, 005°01.659W) in conjunction with group 7 who took measurements in the morning, with group 6 (us) taking over in the afternoon. Salinity, temperature, pH, dissolved oxygen and chlorophyll data were recorded using a YSI probe at 1m depth intervals. A light meter and ADCP were also used to measure down welling irradiance and vertical current profiles. Each profile was taken every 15 minutes throughout the day to establish a full time series of vertical changes in the properties over a complete tidal cycle.

Figure 44. Temperature contour plot, pontoon	Figure 45. Salinity contour plot, pontoon	Figure 46. pH contour plot, pontoon	Figure 47. Chlorophyll contour plot, pontoon

Table 11. Detailing relating to figures 44-47 above

Physical Characteristics Analyses:

CTD Data
Note:  Stations are named 4 and 4a because the two groups sampling the estuary measured stations 1-4 then 4-6, where the last and first stations respectively were in the same position. 
Hence 4 and 4a for the split group sampling.

Figure 48. Station 1 estuarine depth profiles	Station 1	The depth profiles for station 1 were taken at the furthest point up river of the transect. The temperature values decrease from about 14.9⁰C at the surface to about 14.5⁰C at 6m, a few centimetres from the bottom of the riverbed. The salinity follows the opposite pattern, as the lowest value is at the surface and increases down through the profile, with the highest value at ~6m depth. There is little variation in the turbidity; it has slight fluctuations through the water column around 3.8NTU, but does show more of a slight increase where there is a sharp spike in salinity, at about 4m. The main feature of the fluorometer data is the spike of chlorophyll, as it increases suddenly at ~3.8m from ~0.3µg/L to 0.7µg/L, and then decreases back at ~4m.
Figure 49. Station 2 estuarine depth profiles	Station 2	There is an inverse relationship between salinity and temperature at Station 2. There appears to be a slight thermocline in conjunction with a possible halocline at around 2 to 3 meters, though the overall changes are relatively small (0.7°C). The turbidity changes throughout the water column are minimal, with no apparent, significant change with depth. The chlorophyll readings show peaks at around 4, 8 and 11 meters, this suggests potential phytoplankton activity at these depths and can be related to irradiance levels.
Figure 50. Station 3 estuarine depth profiles	Station 3	Station 3 profiles were taken further towards the end of the Fal River, closer to the open estuary. The temperature values decrease down the water column over a range of 0.4°C, in a similar pattern to all the other stations. Salinity also imitates the previous two stations and increases down the profile, but has a slightly steeper slope so does not become more saline until ~3m. The temperature and salinity profiles both roughly show small spikes and curves at the same depth; they are mirror of the other. The chlorophyll and turbidity both have small fluctuations through the water column but do not have very large changes in value, although chlorophyll does have a relatively large peak at the surface (of ~0.4µg/L).
Figure 51. Station 4 estuarine depth profiles	Station 4	Station 4 was taken at the mouth of the river and at the top of the open estuary. The temperature and salinity again exhibit an inverse relationship, and display the same small fluctuations at the same depths along the profiles. A slight thermocline and halocline can be seen at ~8m, although both are relatively steep. Turbidity decreases with depth, by ~1NTU. Small spikes down the chlorophyll can be seen, and one particularly large increase is present at ~10-11m; the values change from 0.2 to >0.5µg/L. There is also a well-defined, albeit smaller, spike at 4m.
Figure 52. Station 4a estuarine depth profiles	Station 4a	Station 4a is at the same location as station 4, but was repeated later in the day so as to gain a range of data over the day of the same point. The temperature at the surface is slightly greater than at station 3 (15°C), and starts to decrease down the water column, before increasing in a small bulge around 4m, and then returning to the familiar decreasing pattern and ending at 13°C at the seabed. The salinity increases fairly steadily from ~30.5 at the surface to ~34.5 at the bed, with the occasional small fluctuations. The turbidity decreases slightly down the profile, except for a sudden increase at ~5m, correlating with a chlorophyll spike at the same depth. The rest of the chlorophyll profile is fairly uniform, with a few smaller spikes towards the bottom.
Figure 53. Station 5 estuarine depth profiles	Station 5	Station 5 shows slight amount stratification, with a steep thermocline and halocline at ~4m. The salinity increases down the water column by about 3.5, and the temperature decreases by 1.6°C. There is a small increase in turbidity between the surface and 2m, which corresponds with an increase in chlorophyll. Both then decrease again between 2m and 4m. Smaller chlorophyll spikes further down the profile also correlate with changes in turbidity. For example between 6m and 8m, when chlorophyll values decrease from ~0.25 to ~0.15, and turbidity shows a small corresponding decrease.
Figure 54. Station 6 estuarine depth profiles	Station 6	Station 6 was recorded as the final location at the end of the transect closest to the open sea. The temperature and salinity profiles again are the inverse of each other, and demonstrate two slight thermoclines and haloclines at ~4m and then again at ~17m. This may be the result of mixing of three water masses rather than just two, which would construct only one thermocline. The water is much more saline at the surface than at the other stations, but there is not such a great increase down the profile. The turbidity also decreases in similar stages as the salinity and thermocline patterns, with larger decreases at 4m and 7m. The chlorophyll shows little variation, although there are slight increases in the size of the spikes between 10 and 15m.

The temperature in the estuary is coldest in morning and warmed throughout the day, whilst also becoming colder with depth. From both the pontoon and CTD measurements, similar results were gathered, though the data gathered on the pontoon was 0.2⁰C lower than those of the CTD. Although small, this difference shows a slight warming in the 8 days between the measurements being recorded. 

There are incredibly significant differences in chlorophyll measurements from the pontoon YSI probe and boat CTD, leading to discrepancies on the graphs for this data. The CTD measurements were recorded to be between approximately 0.22 and 0.26µg/L whereas at a similar time from the pontoon measurements fell between 3 and 5µg/L, largely due to issues in calibration of the instruments and also with Sigmaplot, the graph software used to create the contour plot of pontoon data extrapolating values to fill in gaps, which may not have been accurate.

Salinity increases with depth at this station with measurements from both the CTD and probe off the pontoon, though, like salinity, there is a slight difference between the data, whereby the CTD recorded results approximately 2 salinity units below those of the probe off the pontoon, throughout the depth of the estuary. This may be due to calibration issues, or more likely due to the significant difference in salinity measurements because of the change in tidal state at this time on the two different days, indicating whether the river is at that moment marine or riverine dominated.

Discussion

The Fal estuary is a well-mixed estuary and is tidally dominated, with a semi-diurnal tidal cycle. High tide on 04/07/12 was at 05:19UTC and low water was at 12:04UTC, so stations 1 to 4 were taken as the tide was going out and stations 4a to 6 as the tide was coming in.

As temperature and salinity have an inverse relationship at the majority of the stations, it is appropriate to say that the tide has the greatest influence over both, and dictates the extent of mixing between the overlying freshwater from the riverine inputs, and the underlying saline water. This is why at stations 1 and 3 located towards the top of the river, salinity is lower at the surface and greater at the bed, and the temperature is greater at the surface and decreases down the profile, yet there are no identifiable thermoclines and haloclines due to the extent of mixing during the ebb tide.

Even though station 2 was located in between those two stations, the water body is much deeper, meaning that the same amount of mixing would not be possible. The salinity increases from the start to the end of the transect, as stations closer to the mouth of the estuary will evidently be more influenced by saline water than fresh river water. After station 3, the thermoclines and haloclines begin to become more defined, due to the increased depth of the water column and other influencing factors. Station 4 was taken at low water, so less tidal mixing would occur and so slight stratification could develop. Station 4a was taken as the tide was coming in, and less of a thermocline and halocline are present, which further proves the extent of the tidal mixing. Station 6 was taken at 13:58UTC, so the tide had started to come in, demonstrated on the graph as a breakdown in stratification developing during slack tide.

The general pattern between chlorophyll and turbidity is that with an increase in chlorophyll, there is also an increase in turbidity. This is because thicker layers of phytoplankton are present, meaning that there are more particles in the water column, increasing the turbidity values; an example of this is at 5m at station 4a. The chlorophyll spikes correspond with the level of stratification and the depth of the euphotic zone. From the riverine end to the marine end of the transect, the euphotic zone becomes deeper and so primary production increases. It is common in estuaries for the phytoplankton production to mirror the distribution of suspended sediments (Cloern, 1987). The distribution and availability of nutrients is also a factor in phytoplankton growth and therefore also the chlorophyll production. Stratification affects this, and so the more well stratified the station, the more likely it is for there to be increased chlorophyll at the thermocline, although the extent of tidal mixing in this estuary will usually counteract this.

Richardson Number

Biological Characteristics Analyses

Phytoplankton Abundance

The afternoon samples taken at station 4a and 6 contained the highest concentration of phytoplankton, at 430 and 380 per ml compared to a mere 29 per ml at station 4 in the morning. Earlier in the morning, in the riverine sample at station 1, no phytoplankton were found at all. This is testament to the effect of the tide, which, in the morning, was on its way out, flushing the phytoplankton out along the estuary whereas in the afternoon was its way back in, bringing with it a large concentration of phytoplankton. Furthermore, the afternoon irradiance was much greater due to better weather conditions and less cloud cover, which would promote phytoplankton vertical migration towards the surface. As phytoplankton trawls were carried out only at 1-1.5m depth, this vertical migration to take advantage of the sunlight near the surface makes a measurable difference to concentration of cells.

Furthermore, there was a greater species diversity found at station 6, with a wide range of cells in this sample, taken from near the estuary mouth where the water is much that of the ocean, suggesting a preference for most of the organisms to be in fully saline water rather than the more brackish water of the estuary. However, station 4 and 4a at the top of the estuary are far less diverse, and dominated mostly by Rhizosolenia spp. and Leptocylindrus d. in the morning and Coscinodiscus spp. and Alexandrium spp. in the afternoon, suggesting that these groups much prefer the slightly fresher water provided here and have carved themselves a niche in this area, allowing them to thrive in greater numbers, particularly in the case of station 4a.

Figure 62. Percentage abundance of phytoplankton species in the estuary	Figure 63. Species abundance of phytoplankton in the estuary

Zooplankton Abundance

Morning samples were taken both at station 1, where the Fal River meets the Truro and station 4; the top of the estuary, as shown by the map (figure 44). Samples by the afternoon group were performed at a similar location by the top; station 4a and at the bottom of the estuary near the mouth; station 6.

At 102, 94 and 84 individuals per 10ml of sample, the three stations on the river and top of the estuary contain a similar concentration of planktonic organisms. In these cases, copepods and their nauplii account for approximately 70% of the individuals found (figure 64), though the nauplii account for a greater proportion at stations 4 and 4a at the top of the estuary. Being nearer the sea, they are composed of far more saline water, and thus contains a greater number of certain organisms found rarely in lower salinity water up the river, such as Hydromedusae, Ctenophora and Siphonophorae. These are far more common in saline and brackish water than they are in fresher water and are also found in considerable numbers at station 6, with Hydromedusae being the most significant group behind copepods and their nauplii, 38 specimens found in the sample, more than twice that found at station 4a. Coupled with the much greater abundance of zooplankton at station 6, this suggests a far greater tolerance by zooplankton to seawater, given the salinity of 35.5 at this station compared to the fresher water found further up the estuary and river. An interesting feature of station 6, and to a lesser extent station 4a was the much greater abundance of copepod nauplii compared to adult copepods; almost four times the amount at station 6. This may be explained by the copepod breeding season usually occurring from December to March annually (Conover, 1967), meaning that many nauplii will be almost fully grown, and some copepods will have just reached maturity so are being flushed out towards the ocean from their estuarine nursing grounds, especially given how the salinity varies relatively little along a large portion of the estuary. The relatively small quantities of Polychaeta, Gastropoda and Decapoda larvae, amongst others, present in samples taken at all stations suggests that these have most likely settled or fully grown and as such are rarely found as planktonic larvae.

Irradience

Table 12. Calculated secchi disk values

Station number	Depth	Secchi disk depth (m)	Depth of euphotic zone- 1% light level (m)	Attenuation coefficient (k)
1	6	2.8	8.4	0.51
2	14	3.4	10.2	0.42
3	14	3.6	10.9	0.40
4	14	4.0	11.9	0.36
5	8	2.3	6.9	0.62
6	20	3.8	11.4	0.38

The secchi disk data show that the depth at which the disk can no longer be seen increases as you move from riverine to marine end of the estuary, with the exception of station 5. Increasing channel depth reduces the effect of flow shear on the sea bed, lowering the effect of suspended particulate material causing absorption of light in the water column.

The attenuation coefficient, k, measures how quickly light is absorbed in the water column; the highest value is seen at station 5 which corresponds also to a reduction in secchi disk depth. The channel depth is lower at station 4 than station 5, whilst the tidal state was flooding into the estuary. High tidal flow and shallow depth would increase attenuation as sea floor sediments are suspended. This would cause a high k value as light is absorbed by suspended matter reducing the secchi disk depth.

Figure 66. Graph to show the depths at which the secchi disk could no longer be seen when lowered into estuarine water

Residence Time

T_res=[1-(S_mean/S_sea)*V_total)/R

T_res is residence time of the estuary

S_mean is mean salinity of the estuary

S_sea is the salinity at the furthest point of the estuary, closest to the sea

V_total is the total volume of the estuary

R is the river flux into the estuary

 The residence time is the amount of time a substance remains in a system, so in this case the length of time a molecule of water stays in the Fal estuary after entering from a river and before entering the ocean. It is a vital component when calculating the time a pollutant or contaminant will remain in the estuary after accidental excessive anthropogenic inputs. An estuary with an efficient residence time is often more healthy in terms of water quality and marine life than a poorly flushed estuary. In order to calculate the residence time, it is assumed that the estuary is in a steady state; there are no changes in volume, temperature etc.

In order to obtain the residence time for the Fal estuary, the salinity values along the length of the estuary were measured via a CTD on board RV Bill Conway during the estuarine investigation (see estuary data for exact locations). Seven cross sections of the estuary were also recorded by the ADCP as the stations moved from river end to marine end. From this it was possible to access the areas of each of these cross sections by using the ADCP data in WinriverII, and the distance between the cross section transects were measured in order to then work out the total volume of the estuary – 26789460.7m³ = 2.7*10⁷m³. The mean salinity was calculated from the CTD values (30.6725), and the final salinity reading that was taken at station 6 was used as the sea salinity (35.1).

The data for the river fluxes into the Fal estuary were acquired from the Centre for Ecology and Hydrology website. The three rivers that feed into the estuary are the Kennal, Kenwyn and Fal, and their average annual fluxes have been recorded from 1968-2010 for the Kennal and Kenwyn, and from 1978-2010 for the Fal. These gave results of 0.51m³, 0.378m³ and 2.028m³, respectively, which were then added together to give a total riverine flux of 2.916m³.

All of these values were then entered into the equation, and finally divided by 86400 (number of seconds in a day):

    T_res=([1-(30.6725/35.1)*26789460.7)/2.916)/86400

                                                          =(3379211.87/2.916)/86400

                                                          =1158851.813/86400

                                                          =13.41days

This is however an estimate of the residence time rather than en exact calculation, partly due to the necessary assumptions, but also because the final ADCP transect did not fully record all the data as the depth was greater than 20m and so the sonar beam could not reach the bottom. The area of this cross section was then approximated from the existing data of the shallow edges of the estuary on WinriverII.

Conclusion

From our investigation of the Fal estuary it can be concluded that the tidal mixing is the dominant force within the estuary, influencing biological, chemical and physical processes, and producing a well mixed estuary.

                The data collected from the time series on the King Harry Ferry pontoon and during the river cruise on the R.V Bill Conway show the complex nature of the estuary and the extent of the tidal mixing. The extreme diurnal changes in temperature and salinity seen in the pontoon data and ctd cast are a direct result of a large tidal range and the mixing of salt and fresh water dependant on certain stages in the tidal cycle. During an inflowing tide lower temperatures and higher salinities are found higher up the estuary, in contrast to higher temperatures and low salinities at low tides. This constant change also has large influences on biological activity with both phyto and zooplankton being found in higher numbers towards the marine end of the estuary. This leads to the non-conservative removal of nitrate and silicate seen at higher salinities. However, as previously mentioned the increases in phosphate are the result of anthropogenic inputs into the system. Tidal mixing also effects the distribution of nutrients as there is little stratification to limit their availability in the euphotic zone. Even with the well mixed nature of the estuary all stations sampled had under saturated dissolved oxygen concentrations. This indicates a highly active microbial system resulting from increased terrestrial organic inputs to the system, as seen in the increased leaf litter present in the video trawls taken during the geophysics survey and excessive sediment resuspension throughout the estuary, although this does decrease towards the marine end. This also mirrors the depth of the euphotic zone. The residence time within the estuary is roughly 13 days which could be linked to the Springs-Neaps tidal cycle and the increased mixing and flushing associated with this cycle.

Future Investigations

To further the conclusions made in this webpage an increased number of stations for estuary, offshore and geophysics investigations would be required. This would allow for more in depth analyses of the water column structure both vertically and horizontally which would help secure the physical, biological and chemical patterns identified.  A future larger temporal and spatial investigation would increase the ability to form secure conclusions on the processes occurring and the general state of the Fal estuary and offshore environment. Another element that was not studied during the fortnight was the effects of metal pollutants. Having been a problem the in past, the residence time data collected among other parameters could be used to model and prepare for other pollution problems in the estuary in the future.

Errors and limitations

Differences in calibration of instruments and human error in calculations and analyses may have presented errors in the data recorded. Changing weather and tidal patterns between collection times made linking data together difficult and the use of different equipment and people for comparable data may have caused errors within the final graphs and results.
 

References

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All figures and photographs have been produced by the named students unless otherwise stated.