Madeleine Brasier

Thomas Clarke

Freya Garry

Alex Kesser

Figure 1.1

Lucy Martin

Louisa Payne

Michael Pownall

Julia Robinson

Suzie Tooke

This webpage provides an overview of the scientific procedures and findings undertaken by Group 6 (Figure 1.1) during a field course in the Falmouth Estuary. The field course aim was to gain an overview of the physical chemical and biological systems in the Falmouth area (Figure 2.1). Three boat practicals were undertaken throughout the fortnight, one in the Falmouth Estuary, one offshore and one side scan habitat mapping exercise (Table 2.1). The physical, chemical and biological data collected during the surveys are processed and integrated to give an understanding of the estuarine and offshore systems. Particular aims of each exercise are outlined in the relevant sections below.

The Fal Estuary is an area of high conservation value with important biological habitats, for instance maerl beds. The estuary was formed as the river valley/ria became flooded. As a consequence there is a deep channel in the centre of the estuary. The geology of the area which principally comprises of Carnmellis granite and other metamorphic rocks to the west of the Fal influence the characteristics of the estuary. Due to the high levels of mining in the past, Restronguet Creek -which leads onto the Fal Estuary- has become the most metal polluted estuary in the UK and this has caused contamination of the sediments in other parts of the Fal. The Wheal Jane mine discharge in 1992 is a notable source of contamination, but residual drainage and leakage from spoil heaps lead to contamination of Restronguet and therefore the Fal (Langston et al. 2003).

The Fal Estuary, a busy harbour economically and recreationally, is subject to various pressures from pollution, for instance from organotin contamination originating mainly from Falmouth Dockyard. Industry and dredging, as well as sewage and contamination from tri-butyl tin, are additional anthropogenic factors that affect the physical, chemical and biological characteristics of the estuary. The Fal Estuary is generally high in nutrients, leading to hyper nutrification and risk of eutrophication in parts of the estuary (Langston et al. 2003).

Falmouth is additionally an ideal base from which to conduct offshore surveys in the Western English Channel. The vertical mixing processes in the Channel can be studied whilst aiming to discover how this affects the plankton communities in the region, with particular reference to the change in stratification around tidal fronts.

Figure 2.1

Table 2.1

1.   1. Preparation of phosphate working standard   The standard must be freshly prepared. The stock solution was diluted 400 fold by taking 1ml and made up to 100ml with MQ water in a volumetric flask. Then 25ml was separated and made up to 100ml with MQ water, giving a solution containing 15µmol per litre which is used to prepare the calibration standards.

2.   2. Preparation of Calibration and Blank solutions    Using a 5ml hand pipette, 10ml of MQ water was carefully added to three tubes labelled as blanks. Using appropriate pipettes, 50µl, 100µl, 200µl, 500µl, 1000µl and 2000µl was added each to 3 separate sample tubes, giving 21 test tubes. All tubes were made up to 10ml using MQ water. These tubes were treated the same as the sample tubes and then the analytical methods below were followed. These calibration tubes will have the following phosphate concentrations as in Table 4.1.

Fresh mixed reagent was prepared by combining  20ml Ammonium Molybolate, 50ml Sulphuric Acid (2.5M), 20ml Ascorbic Acid, 10ml Potassium antimonyl tartrate producing 100ml total. 1ml mixed reagent was added to every sample tube (blanks, calibration tubes and samples alike) then mixed well and left for 1 hour.
Then the spectrophotometer set at 840nm was used to determine the absorbance of each sample, calibration and blank tube. The calibration and blank tubes are used to calculated the phosphate concentration of the sample tubes based on the measured absorbencies.

The laboratory analysis to determine the amount of silicon present in each sample was carried out as in Mullin & Riley (1955); a slight modification was that the river end member samples were diluted by a factor of 5. A sub-set of standard samples were used to perform a calibration using silicon solutions of known concentrations, which were also placed into the spectrophotometer and their absorbencies measured.

1. Standard preparation    A stock silicon solution of 35.6mmol l^-1 was diluted using a 25 times dilution to create the working standard solution.
Further dilution was then carried out to create the following standards:
1.4μmol l^-1 , 2.8μmol l^-1 , 7.1μmol l^-1  , 14.2μmol l^-1, 21.4μmol l^-1.

2. Sample preparation      2ml of molybdate reagent was added to 5ml of each silicon sample and left to stand for 10 minutes. 2ml of molybdate was also added to 5ml of MQ water to be used as blanks. A mixed reducing agent (MRR) was prepared by mixing metol sulphite, oxalic acid, sulphuric acid and MQ water. 3ml of the MRR was added to all samples, standards and blanks, and left to stand for 2hours. The absorbance of the samples were measured on a spectrophotometer (U1800) at a wavelength of 810nm, a 4cm cell was used.

Glass bottles are used for dissolved oxygen measurements in order to prevent contamination.  Samples were taken from Niskin bottles before any other samples were taken to avoid contamination, and were siphoned through rubber tubing with a tight seal on the valve. Air bubbles were removed from the tubing and the glass bottles were filled to a third and rinsed then emptied to clean which avoids contamination. The bottles were then filled to overflowing to avoid trapping any air within the bottle. Winkler reagents were added to the sample; 1ml manganous chloride and 1ml alkaline iodide solution using a pipette. This fixes the oxygen in the bottles, which are then stored in water to prevent leaching from air through the stopper until lab analysis.

In the lab, 1-2ml of sulphuric acid 10M was added to and mixed in each bottle to release the oxygen, turning the solution to a clear yellow. The bottles were placed into the end point detector and sodium thiosulphate (normality 0.22) was added using a metrohm device until the solution began to clear. Further additions were monitored on the Servoscribe 1s until the needle ceased movement and plateaued. The metrohm reading was recorded. As the amount of sodium thiosulphate added to the sample was known, the dissolved oxygen concentration could therefore be calculated.

Chlorophyll a concentration is currently the best index for estimating phytoplankton biomass (Huot et al., 2007) although the fluorometry readings obtained in the fieldcourse did not correlate very well to the CTD fluorometer readings; the CTD readings should be assumed to be the more accurate reflection of chlorophyll. In order to chemically analyse water samples for chlorophyll however, seawater was filtered into glass and plastic bottles for oxygen and nutrient analysis respectively on the boat. The porous glass fibre filters that the water was filtered through was then stored in 90% acetone; the acetone acts as a solvent and extracts the chlorophyll. The test tubes were frozen overnight. Using a fluorometer in the laboratory the following day, the fluorescent properties of the chlorophyll pigment in the acetone were measured and determine the amount of chlorophyll present using the following equation:

Chlorophyll (µg l^-1) = ( Volume acetone / Volume seawater filtrate ) * Fluorometer Reading

As there were two filters for each water sample taken, the results gained in the lab could be compared to give a reasonable indication of the chlorophyll levels in the sample generally.

Formalin was initially added to each 500ml zooplankton sample bottle in order to preserve the zooplankton. In the laboratory after mixing the sample by simply inverting the bottles, 10ml of the sample was pipetted into a measuring cylinder.  Then 5ml of this sub-sample was pipetted into a Borgorov chamber and viewed under a light microscope, and each zooplankton was identified with the aid of photo guide books.  The individual organisms were tallied into a table under the major taxa groups found in the area: Copepoda, Copepoda Nauplii, Cladocera, Mysidacea, Chaetognatha, Hydromedusae, Siphonophorae, Ctenophora, Appendicularia, Decopoda, Cirripedia, Polychaeta, Gastropod, Echinoderm and fish larvae. 

Water samples were added to bottles containing Lugols solution which preserved the phytoplankton.  100ml of solution was then left in a settling column overnight to allow the phytoplankton to settle.  In the laboratory the top 90ml of each sample was removed with a vacuum pump to leave a concentrated sample.  From this 10ml sample a smaller subsample of 1ml was taken and added to a Sedgewick-Rafter Counting Chamber which was placed under an optical microscope to be viewed. 5 vertical transects of 20 1μl squares were viewed with the number of cells in each square being recorded and the different species were identified and logged.

Figure 5.10 Temperature

Figure 5.11 Salinity

Figure 5.12 Chlorophyll

Figure 5.13 Turbidity

Figure 5.14 Temperature

Figure 5.15 Salinity

Figure 5.16 Chlorophyll

Figure 5.17 Turbidity

Variation in East and West measurements from the pontoon

The measurements taken using the YSI probe on the East and West side of the pontoon show variations in data collected, despite their close spatial proximity.  It is important to analyse the differences between these two sites before any assumptions are made about the relationship between measurements made on the pontoon and on RV Bill Conway. Variations on this small spatial scale can be used to assess the significance of variations seen between stations sampled on RV Bill Conway. The East and West sides of the pontoon experience differing levels of disturbance from passing vessels: the East side of the pontoon being disturbed and mixed by ferries every 15 minutes or so whereas the West lies relatively undisturbed which may have lead to the stabilisation of water layers that were unable to develop on the East side. The two sides may have been affected in different ways by tidal forcing due to the interruption of the tidal flow by the pontoon structure. There was also the issue of depth; the West side of the pontoon was approximately 2m shallower than the East side so the development of layers in the column would be affected.

The Secchi disk measurements (Figure 5.18) show a clear trend between the upper sampling stations and the lower stations. The shallowest Secchi depth was measured at station 1 with a depth of 1.26m and the deepest at Group 11’s station 5 with a depth of 7.5m which partly reflects the deepening of the natural river channel and hence the varying proximity of the euphotic zone to the sediment of the seabed. Group 11's station 5 was sampled 14 minutes before high water therefore the Secchi depth is deeper due to reduced bottom turbidity, as highlighted by the pontoon time series. There is a very slight decline in depth between station 3 and 4 of 0.1m but all other measurements show an increasing trend which reflects a larger euphotic zone (recognised as approximately three times the Secchi disk depth unless this exceeds the depth of the bed).

The attenuation coefficient, k, is an indication of the rate at which light is absorbed within the water column. The highest k value and therefore fastest attenuation rate is shown at station 1 with a value of 1.14 (Table 5.3). There is then a general decline down the estuary towards the mouth, with the lowest value at group 11 station 5 with a k value of 0.19 indicating a deeper euphotic zone.

Table 5.3

Figure 5.18

Figure 5.19

The mixing diagram is a diagram which shows the concentration of a solute against an index of conservative mixing in the estuary - salinity is commonly used.  The diagram can be used to understand the behaviour of solutes, in this case phosphate, as they flow through the estuary.

The four assumptions for estuarine mixing diagrams were met: the constituents were assumed to be at steady state, the end member concentrations are constant on a timescale somewhat greater than the residence time of the estuary, there is only one riverine and one end member and there were no additions of pore waters.

Samples taken at stations up the estuary were taken over a relatively narrow salinity range as this was the extent of the estuary that could be surveyed in the R.V. Bill Conway; the low number of riverine inputs mean that the estuary is relatively saline for quite some distance up the estuary. Freshwater riverine end members were obtained by staff members separately.

The theoretical dilution line in the graph (Figure 5.19) between the riverine and saline end members represents the conservative behaviour of solutes - changes in concentration are solely due to mixing. If there is deviation of the data points away from the TDL addition or removal of the solute is indicated. The graph shows that there is a dramatic increase above the TDL. This demonstrates that phosphate is behaving non-conservatively  and is being added to the water column. This could be a result of possible anthropogenic factors such as sewerage outfalls and agricultural inputs further up the estuary. A mussel farm near King Harry pontoon may also cause a change in levels of dissolved phosphate in the water column. Mussels have been farmed near the King Harry Pontoon and close to station 3 by West Country Mussels of Falmouth since 1993 (accessed: www.westcountrymussels.co.uk, 7^th July 2011).

An example of an input of phosphate in the Fal Estuary is a survey of the mussel farm by Envirogene which used DNA to establish that there was persistent contamination of the waters by human and bovine faeces (there are a large number of cattle/dairy farms in the area). In addition significant inputs of human faecal matter were detected entering the Fal at the King Harry Ferry.                                                         (accessed: www.envirogene.co.uk/downloads/casestudies/envirogene_case_fal.pdf , 7^th July 2011).

Figure 5.20

Phosphate Time Series at King Harry Pontoon

Low tide was at 09:52GMT and salinity was at its lowest following this because the influence of salt water was lowest at low tide, although a small tidal lag was observed. With the flood tide, the salinity began to increase again with a peak around high tide (Figure 5.20).

Phosphate concentration increased from low tide reaching a peak at 13:00GMT of 5.9µm. From low tide to high tide the increase in phosphate could be due to nutrient inputs further downstream being washed up the river. Nutrient inputs could be due run off from agricultural practices in the region and sewage treatment farms. Phosphate in the Fal Estuary is also known to be discharged from mine drainage sites, notably in the Carnon Valley.

The estuarine mixing diagram (Figure 5.21) shows that dissolved silicon was behaving conservatively between the salinity 0 and 25; this suggests that the extent of mixing between these two points was the determining factor for the concentration of dissolved silicon at this time. This observed conservative behaviour does not guarantee that no biological uptake was occurring; there could have been a low rate of uptake which was not observable as non- conservative behaviour. This slow removal could be due to turbidity caused by the heavy rainfall during June 2011, this could affect the growth of diatoms; such effects have been shown in the River Zaire (Cadee 1978). Another suggestion could be made that the behaviour is conservative but has been represented as slightly non-conservative due to long term temporal changes of dissolved silicon concentrations at one of the end member. If this change occurs on a different scale to the residence time of the estuary then a conservative solute can be plotted as non-conservative on estuarine mixing diagrams (Lorder & Reichard 1981).

There may, however, be some removal of dissolved silicon between salinities 30.2 and 34.8 indicated by the slight bowing of the data points beneath the Theoretical Dilution Line (TDL). Biotic uptake by siliceous diatoms may be the reason for this due to late spring phytoplankton growth.

Figure 5.21

Figure 5.22

Figure 5.23

Figure 5.24

Figure 5.25

Figure 5.26

Figure 5.30

Figure 5.31

Figure 5.32

The offshore boat practical aimed to investigate the vertical mixing processes in the waters of the Western English Channel off Falmouth. They usually become vertically stratified during the summer months due to lower wind mixing and higher irradiance levels, but the shallow waters next to the coast remain mixed. Fronts therefore form in the channel, with warmer water above cold water on the stratified side and mixed cooler water on the coastal side. Fronts often tend to have large plankton communities due to the nutrients provided by the mixed side but the stratified waters allowing the plankton to remain in the high irradiance surface waters. The systems offshore along the coast around Falmouth were therefore investigated to observe how the vertical processes affect the plankton communities. The physical measurements made by instruments aboard a CTD would be compared with chemical data from water sampling and the biological data from phytoplankton samples and zooplankton trawls to observe how the physical processes control the biological productivity.

The primary plan for the offshore day was formulated based on data from the previous day's group (Group 3) who had travelled west from Falmouth along the coast towards Lizard Point and discovered frontal systems along the 30m contour. Based on this, Group 6 planned to zig-zag across the frontal system out to 50m and back in to 20-30m along the coast from the Manacles to Lizard Point. Samples were collected from stations along the frontal systems appropriate to the findings in the field indicated by the thermo-salinometer and the acoustic doppler current profile. An overview of each station is provided below in Table 6.1. Although a number of stations were fully sampled, due to time constraints only a CTD drop occurred at others in order to gain a larger set of physical data relating to the front.

In case of the primary plan not yielding a change in physical processes (being constantly monitored onboard by the ADCP and thermo-salinometer) the secondary plan would be to head out directly offshore until a change from mixed waters to stratified waters was observed and then to sample either side of and on the frontal system. In the event, the secondary plan was not required and the path taken is displayed in Figure 6.1.

Figure 6.1

Figure 6.2 - Station 1

Figure 6.3 - Station 2

Figure 6.4 - Station 3

Figure 6.5 - Station 4

Figure 6.6 - Station 5

Figure 6.7 - Station 6

Figure 6.8 - Station 7

Figure 6.9 - Station 8

h= depth (m) over which density/ velocity are compared

g=9.81 m s^-1 (gravitational force)

Figure 6.10 - Station 1

Figure 6.11 - Station 3

Figure 6.12 - Station 5

Figure 6.13 - Station 6

Figure 6.14 - Station 8

Figure 6.15 Backscatter

Figure 6.16 Velocity Direction

Figure 6.17 Velocity Magnitude

Figure 6.18 Stick

Figure 6.19 Backscatter

Figure 6.20 Velocity Direction

Figure 6.21 Velocity Magnitude

Figure 6.22 Backscatter

Figure 6.23 Velocity Direction

Figure 6.24 Velocity Magnitude

Figure 6.25 Stick

Figure 6.26

Figure 6.27

The stratification parameter log(h/u^3) (where h is the depth and u the tidal current) gives an indication of the degree of mixing in the water column due to tides and wind or the degree of stratification enhanced by heat input, freshwater inputs, and increased water depth. As a general rule, the stratification parameter tends to be < 2 at mixed stations and >3 at stratified stations. At a tidal front the value may be approximately log (h/u³) = 2.7± 0.3 for a tidal front (as suggested by Simpson and James (1986)). At station 1, the station was well stratified: the stratification parameter value 3.65 (Table 6.2) is corroborated by the CTD data. Stations 3,5 and 6 are all relatively close to the tidal front and so show stratification parameter between 2 and 3. For example, station 5 was observed in the CTD data to have a stratified water column with respect to temperature, but high chlorophyll levels throughout the water column suggested that the water column had been recently mixed. This demonstrates how the tidal front moves as the balance of mixing due to tide and winds and heat input varies. Station 8, offshore of Lizard Point, was well stratified and the stratification parameter corroborates the data gained from the CTD at this station. As R. V. Callista neared station 8, a temperature of >17°C was recorded on the thermo-salinometer which was the highest surface water temperature that had been recorded offshore for the preceding week. This illustrates the increasing solar irradiance/heat input and how its balance with the tidal and wind mixing would affect the position of the tidal front during the fieldcourse (especially as the weather was generally fine with low winds).

Table 6.2

Secchi disk measurements were used to estimate the depth of the euphotic zone for the offshore stations. This is defined as the area with sufficient light for photosynthesis. The LUP measurements from the CTD can also be used as a euphotic depth estimate by finding the 1% light level. Both estimates suggested that the deepest euphotic zone was found at station 8 (Table 6.3), this station also had the lowest k value and therefore slowest attenuation of light. Station 8 was strongly stratified suggesting lower mixing in the surface layer so reduced turbidity. As shown in Figure 6.28 there is a difference of 11m between the Secchi and LUP estimates, the LUP 1% is considered to be more accurate, and the fluorescence CTD readings indicated the presence of chlorophyll at the LUP depth as shown in Figure 6.9.

These estimates should be used as a rough guide to the euphotic depth and this cannot be understood fully until chlorophyll and fluorescence are analysed. In all cases the LUP depth should be considered as the most reliable when identifying relationships.

Note that the Secchi disk euphotic depth estimates for station 6 and 7 are deeper than the water column. Therefore the entire water column was contained within the euphotic zone and could expect to receive sufficient light for photosynthesis from the surface to the bed. However the LUP 1% was much shallower at station 6 suggesting an inaccurate Secchi estimate. The 1% light level was not reached for stations with marked * in Table 6.3.

Table 6.3

Figure 6.28

Station 1 (Figure 6.29) showed a decrease in measured dissolved silicon concentration at 17m which increased down to 20m to 4.8 µmol l^-1. On the CTD data a strong thermocline was illustrated down to 21m, this prevented the dissolved silicon mixing below the thermocline. This correlates with Figure 6.32 which shows an increase in phytoplankton abundance at this depth and suggests that they are utilising the silicon source, resulting in a decreased silicon concentration at this depth.

At station 3 measured dissolved silicon concentration increased to 6.4 µmol l^-1 at 18m, then decreased with depth. The CTD data showed a very shallow surface warmed layer and a deep thermocline, below which chlorophyll increased (Figure 6.4). An increase in chlorophyll is a proxy for phytoplankton abundance and suggests the decrease in silicon concentration at 32m may have been due to the utilisation of dissolved silicon.

At station 5 silicon concentration increased to 5.2 µmol l^-1 at 17.3m. The shallowest warmed layer at station 5 (Figure 6.6) may have forced the immotile phytoplankton to the very surface which is where lower silicon concentrations were observed indicating utilisation. The dissolved silicon concentration showed an increase at depth at 17m indicating replenishment just below the thermocline.

From surface to 14.3m, measured silicon concentrations at station 6 decreased by 0.5 µmol l^-1. Figure 6.7 showed that the water column at this station had weak stratification. This was reflected by the low concentrations measured as there is no strong stratification keeping the silicon in the shallower depths sampled.

At station 8 silicon concentration showed no measured changes with depth after 3.5m, with slight depletion in the surface waters. Figure 6.9 showed a strong thermocline down to 20m below which temperature and salinity data indicated well mixed waters. Also below 20m fluorescence remained homogenous with depth, suggesting phytoplankton were also mixed within the water column, which may have explained the lack of measured changes in dissolved silicon concentrations.

Figure 6.29

At Station 1 no measured changes in phosphate concentration were observed with depth (Figure 6.30). This is reflected in the CTD data (Figure 6.2) which shows no significant changes in fluorescence with depth, indicating very low biological activity at this point.

At station 3 measured phosphate concentration showed a general increase with depth. However at 32.5m phosphate decreased to 0.09 µmol l^-1. At this depth (Figure 6.4) shows an increase in fluorescence implying increase of phytoplankton abundance. Phosphate being a macronutrient may be being utilised at this depth and has the potential to become limiting over time.

Station 5 shows a measured increase of phosphate concentration of 0.6 µmol l^-1 at depth 30.8m. (Figure 6.6) shows that this depth is in the mixed layer below the thermocline suggesting that the increase in phosphate was due to remineralisation. However also at this depth the phytoplankton data show abundance in Thalassiosira. This genus of phytoplankton are surviving at this depth as they are in the photic zone, however it is likely they have not got sufficient light to utilise the phosphate to the point of depletion.

Phosphate concentration at station 6 increased from 0.02 µmol l^-1 at depth 1.7m to 0.12 at depth 14.3m. (Figure 6.7) shows that the thermocline exists down to about 15m, above which phosphate was more depleted than below where it is being replenished.

Measured phosphate concentration at station 8 showed a very similar profile to measured silicon concentrations (Figure 6.29); showing no measured change in concentration with depth from 19.8m. There was depletion in the surface waters, with 0 µmol l^-1 at 6.1m. (Figure 6.9) shows a strong thermocline down to 20m below which temperature and salinity data indicate well mixed waters. Also below 20m fluorescence remains homogenous with depth, suggesting phytoplankton are also mixed within the water column therefore unable to utilise phosphate which can explain the lack of observed changes in phosphate concentration.

Figure 6.30

Station 1 (Black Rock) was well-mixed with low background concentrations of chlorophyll and no significant chlorophyll peaks; this is reflected in the homogeneity of the oxygen measurements taken over the range of depths (7.3m to 21.1m) (Figure 6.31). Due to the attenuation of light through the water column, chlorophyll concentration decreases with depth as does rate of photosynthesis and therefore the drop in oxygen concentration may be explained.

Station 3 was offshore at a stratified water column with the strongest recorded thermocline of the offshore stations. The water was supersaturated with oxygen (260.1% at surface, 466.6% at 32.5m) and the peak in oxygen saturation coincided with the peak of chlorophyll at 32.5m (24.8µg l^-1).

Station 5 was inshore on a body of water that had recently been mixed and was weakly stratified at the time of sampling. Variation between the oxygen measurements taken across the warmed surface layer was small. A small rise in oxygen concentration was measured at 17.3m which coincided with a small peak of chlorophyll at the same depth.

Station 6 was inshore on a well-mixed body of water. The oxygen measurements showed little variation and CTD data show the homogeneity of the water column.

Station 8 was on a stratified water body and yet the oxygen data show there was little variation over a large depth range (6m to 69m). Despite the presence of a chlorophyll maximum, turbidity minimum and strong thermocline at 12.5m, the oxygen saturation remained stable.

Figure 6.31

Knowledge of variability in zooplankton biomass is important for understanding the ocean food webs and energy flow in the oceans; as  zooplankton contribute to the  transport of carbon and nitrogen to the deep sea via production of faecal pellets and active transport by vertical migration, which are important components of the biological pump (Longhurst et al., 1990). Using information displayed on the computer in real time from acoustic backscatter intensity derived from Acoustic Doppler Current Profilers (ADCPs) and zooplankton biomass from net collected zooplankton samples, variability in the distributions of zooplankton biomass are described. This is possible as zooplankton are large enough to provide an image on the ADCP. The zooplankton samples collected were taken from areas that showed high acoustic backscatter in relation to the surrounding areas.

Sample sites were also selected based on fluorometer readings, which indicated areas of high chlorophyll concentrations at various depths. This allowed comparisons of chlorophyll concentration with zooplankton biomass. All zooplankton samples were collected from stations where physical data from the CTD, chemical and biological (phytoplankton) data from Niskin bottles attached to the rosette system were all collected.

Samples were collected using a vertical closing net allowing specific depths within the water column to be targeted for sampling. All zooplankton samples were stored in the dark with formaldehyde added after collection to preserve the sample.

As seen in Figure 6.35 the highest abundance of zooplankton was measured at stations 3 and 8: 1613 m^-3 and 1103 m^-3, respectively. The dominant species at both of these stations were hydromedusae, 728 m^-3  at station 3 and  467 m^-3  at station 8. The phytoplankton data obtained (Figure 6.32) may explain the higher numbers of zooplankton at station 3 and 8.

Stations 3 and 8 have different secondary dominant species; station 3 has decapod larvae and at station 8 copepods are the second largest group recorded.

As zooplankton feed on phytoplankton in areas of well mixed coastal waters, with larger communities of phytoplankton more zooplankton can be supported. In this data the larger zooplankton samples collected were situated further offshore, this could be due to the chlorophyll maximum at depth and the development of  thermocline (Figure 6.9). Nutrients were constantly replenished from deeper waters, the phytoplankton were able to grow thus providing a food source for the zooplankton. This can be seen in the CTD data as the fluorometer reading at station 8 shows a minor increase at a depth of 20m, however there is a large amount of turbidity which could possibly be zooplankton which feed on the phytoplankton keeping the chlorophyll levels low.

At station 5, the zooplankton were sampled at two depths: 0-15m and 15-30m. High chlorophyll concentration throughout the water column suggested that the station may have been recently mixed allowing the chlorophyll concentration to rise in response. However the recent increase in levels of irradiance (http://www.metoffice.gov.uk/climate/uk/anomalygraphs) may have caused stratification of the water column with a shallow steep thermocline. High levels of acoustic backscatter were also observed. For these reasons two samples were taken from either side of the thermocline; to study any differences in zooplankton compositions. From 0-15m station 5 had a larger number of hydromedusae present (239 m^-3) with a smaller number of copepods (144 m^-3), whereas at 15-30m station 5 was dominated by copepods (167 m^-3). It could be suggested that this is due to the different communities of phytoplankton at the thermocline allowing for different niches for individuals to develop within.

Station 1 is situated at Black Rock near the mouth of the Fal estuary, there is a low amount of phytoplankton recorded at this station (Figure 6.32) although there is a high chlorophyll concentration (Figure 6.2).  This could possibly be due to phytoplankton cells having high chlorophyll content but are few in number therefore unable to support high zooplankton abundance.

Figure 6.33 - Teleost Egg photo from zooplankton sample

Figure 6.34 - Copepod photo from zooplankton sample

Figure 6.35

The chlorophyll measurements from the samples collected reflected the general characteristics at the different stations and the fluorescence readings on the CTD profiles. Stratified stations 3 and 8 (Figure 6.36) show a distinctive increase in chlorophyll l^-1 just beneath the thermocline (shown by comparison to the CTD profiles). The greatest chlorophyll concentration was at station 3 with a concentration of 25mg l^-1 at 32m. Both stations show a decline in chlorophyll after the peak as depth increased. Results at station 5, which was also stratified, suggested recent mixing within the surface water as there was no distinct increase in concentration surrounding the thermocline. The thermocline was also much weaker compared to stations 3 and 8. Mixed stations 6 and 1 showed an gradual increase in chlorophyll with depth.

Figure 6.36

The video trawls show that the habitat surveyed with the video was a sandy/shingle bottom, with a third to a quarter covering of empty larger shells. Red (for example Dudresnaya verticillata) and green seaweeds and some kelp covered approximately a tenth of the seafloor. There were occasional large features covered in kelp and rhodophyta. As the long trawl following the second grab progressed more of the seabed became covered in maerl and occasional shoals of juvenile fish were observed (maerl is known as an important nursery ground for juveniles).

Figure 7.18

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Accessed: www.envirogene.co.uk/downloads/casestudies/envirogene_case_fal.pdf , 7^th July 2011

Accessed: www.westcountrymussels.co.uk, 7^th July 2011

MarLIN - Marine Life Information Network [Online] Available:  http://www.marlin.ac.uk/speciesfullreview.php?speciesID=4284 [Accessed 2011, July 7^th]

JNCC – Joint Nature Conservation Committee [Online] Available: http://jncc.defra.gov.uk/ProtectedSites/SACselection/habitat.asp?FeatureIntCode=H1110 [Accessed 2011, July 7^th]

Tri tech innovative underwater technology. [online] Available: http://www.tritech.co.uk/products/info/products-info-sidescan_sonars.htm [Accessed 2010, November 23rd]