INTRODUCTION

Please scroll slightly horizontally to make vertical scrollbar visible

Day Moran Fiona Groves Danielle Warman Nicola Jackson Naomi Hyland

Jason Hopkins Danielle Edgar Zak Warren Rosie Mcloskey Amy Munro Crisyn Smith

Timetable

EQUIPMENT

Multiprobe (T/S)	Niskin Bottles	Conductivity, Temperature, Depth Sensors (CTD)	Acoustic Doppler Current Profiler(ADCP)	Zooplankton Nets	Video	Side Scan Sonar	Secchi Disk	Van Veen Grab
			Provides data on current velocity magnitude and direction of flow as its primary function. Information can also be gained from the backscatter of sound waves within the water column.			Sidescan sonar sends out a sound signal at a set frequency from a transducer in the towfish. The signal creates a horizontal swath and is reflected back where it hits the seabed or an object to a receiver.	Light attenuation. Dropped into the sea and human records when disk is no longer visible.

LAB TECHNIQUES

Phytoplankton Zooplankton Water samples were fixed with Lugols iodine and allowed to settle overnight so that sedimentation of plankton could occur. Each sample was concentrated by siphoning off 90ml of excess Lugols iodine with a siphon pump, leaving 10ml of concentrated sample (the sample was concentrated by a factor of 10x.). From each concentrated sub-sample of 10ml, 1ml was extracted and transferred to a Sedgewick rafter cell. The cell was then viewed under an optical microscope (10x). Individual species were identified and quantified by counting the number of phytoplankton within each square. At the time of the sample, 10ml of Formalin was added to each 1L bottle sample, which cured the zooplankton allowing it to be analysed at a later date. Subsequently, each sample was concentrated from 1L down to 500ml aliquots. From each 500ml bottle, a 5ml or 2ml sub-sample (depending on how concentrated the zooplankton appeared) was extracted and transferred into a Bogorov chamber. This was then viewed under a light microscope (0 – 3.5x magnification). The contents of each subsample was then counted and different species identified using “Coastal Plankton: Photo Guide for European Seas” by Otto Larink and Wilfred Westheide, 2006. Each bottle was counted 4 times and the data averaged and with reference to the flow through the net, the number of zooplankton per meter cubed was determined by way of the following calculation. Number of revolutions x 0.3 x opening area of bongo net			Fig. 1. Group 1 analysing zooplankton and phytoplankton (30/06/2010)
Nitrate 2ml of sample was injected into a steady flow of artificial seawater (seawater without nitrate) and passed through a block that contained copper cadmium catalyst. The nitrate in the sample is subsequently reduced to nitrite. Sulphanilamide and NEDH reactants were added to the flow, which reacted with the nitrate to produce azo dye. The concentration of azo dye was then determined by way of transmissometer (any blocked light was recorded as a peak below a base line of 100% of light transmitted through reagents). This was then used to calculate nitrate concentration.
Phosphate 10ml of sample was injected into a labelled centrifuge tube. 3 random replicates included (from total sample base of 7 bottles) and 1 blank (using MQ water) Make up a reagent using: 20% Ammonium molybdate 50% Sulphuric Acid (2.5 M) 20% Ascorbic acid  10% Potassium Antimonyl tartrate Add 1ml of reagent to each 10ml sample and mix. Leave for 1 hour. Using a 4ml cell measure the absorbance of the standards, replicates, blanks and samples at a wavelength of 882nm in a spectrophotometer. Absorbance values measured twice for accuracy.
Chlorophyll 50ml of sea water was filtered into sample bottles (required for nutrient analysis) and the filter placed into acetone. In order to analyse chlorophyll content, 6ml of acetone (in which the filter had been preserved in overnight) was transferred to a cuvette, placed into the fluorometer and analysed. The reading was the adjusted for the sample size by multiplying the reading by the ratio of sample size to volume of filtered seawater to give a reading in µg/L. Chlorophyll calibration In order to be able to use the fluorometry data from the CTD system to provide a meaningful interpretation of chlorophyll concentration, it is necessary to calibrate the output data from the fluorometer (that is in volts) to a chlorophyll concentration determined in the lab. Once the chlorophyll concentration for a certain depth had been ascertained, it could be related to the fluorometer output at that depth. Using a minimum of two readings from separate depths, a calibration plot could be calculated and then used to calibrate the rest of the CTD fluorometry data	Fig. 2 Chlorophyll filter tubes. (30/06/2010)
Silicate      Prior to analysis, it was necessary to produce standards in order to calibrate future analysis. In analysing Offshore samples, Standard B - 25x dilution was used. Blanks were also produced that consisted of water and other chemicals to give a value for zero silicon. This value was then subtracted from final results to give blank corrected data. Reagent was added to 5ml subsamples for further analysis. In order to provide confidence in results, replicates were also analysed.Prepared reagent: 10 parts Metol Sulphate 6parts oxalic acid 6 parts sulphuric acid 8 parts MQ water   Added 3ml of reagent to bottles, including blanks.  Mixed well, left to set for 2 hours. Put samples into 4cm long glass box (as opposed to 1cm). Used larger box as there was so little silicon.Placed into spectrophotometer to give absorbance value.Record absorbance value for each standard sample and water sample by pouring each into the 4cm cuvette one at a time. A single beam spectrophotometer U5625 was used (wavelength 810 nm).
Dissolved Oxygen Firstly, the sodium thiosulphate had to be standardised:   Added 50ml of MQ water. 1ml sulphuric acid 1ml alkaline iodine 10ml KIO3. Add MQ water to brim. Add magnetic stirrer. Repeat 3 times until difference is <5%  Divide average of burette readings by 50. *Thiosulphate normality = 0.1 / V (V = average titre for the standardisation procedure in ml) 22.490 ml            1st test           Average = 22.45     =    0.449.    0.1/0.449 = 0.22* 22.500 ml            2nd test                               50 22.360 ml 1ml of sulphuric acid was added to the samples to release the fixed oxygen into solution. The oxygen bottle was then placed between a light source and a detector in the titration system. A magnetic stirrer was then placed in the sample to aid mixing of the chemicals.   Sodium Thiosulphate was added incrementally to the sample and the sample gradually became colourless. The chart recorder plotted the light detected through the sample and once the graph reached a plateau the titration was complete and the figure in ml on the titration system was recorded. This figure was then used to calculate the concentration of oxygen that was contained within the sample.		Fig. 3 Magnet mixer inside sample between a titration detector system. Fig 4 Samples of water with oxygen fixed.

OFFSHORE Boat practical
29/06/2010

Introduction to Offshore Practical The aim of the offshore cruise was to attempt to map the extent of the front offshore of Falmouth. Tidal mixed fronts are characterised by horizontal gradients in temperature and salinity. Fronts are often sites of high biomass, particularly phytoplankton and related zooplankton populations. The position of a tidally mixed front is determined by the interaction of surface heating and tidal mixing.Away from the influence of major sources of fresh water, in the summer months, temperate shelf seas are separated into thermally stratified and well mixed regions (Sharples & Simpson, 2009). In order to determine the extent of the front, it was necessary to obtain the physical characteristics of the water column to aid in identifying the mixed side and the stratified side. Such a division is noticeably visible in CTD profiles and ADCP backscatter images.   Offshore, during periods of increased insolation, shelf seas can exhibit a horizontal thermal gradient, where deeper water columns that are not influenced by tidal mixing become thermally stratified compared to the tidally mixed water in shallower areas. This is physically represented as a horizontal gradient in temperature (and possibly salinity) and is known as a tidal mixing front. These physical gradients are normally accompanied by similar rapid changes in chemical and biological features. Fronts are therefore important oceanographic features with defining physical, chemical and biological characteristics. The mixed side of a front can be identified by physical and chemical parameters that do not vary to any great extent vertically in the water column. However on the stratified side, the development of a vertical thermocline that results from insolation and the reduced influence of tidal mixing produces more pronounced changes in the same physical and chemical parameters through the water column. On the mixed side of the front it would be expected that primary productivity is limited. Phytoplankton require a certain light level in order to photosynthesize efficiently and thus mixing will limit how long they can remain in the euphotic zone. However, provided the critical depth remains below the mixed depth, net positive photosynthesis is still possible. As the water becomes thermally stratified, any nutrients above the thermocline may be rapidly utilized by primary producers resulting in a nutrient depleted upper layer and increased nutrient concentration in the lower layer due to remineralisation. This would also normally be associated with depleted oxygen concentration in the lower layer. By looking at these parameters in totality, it may be possible to identify the extremes of either side of the front and thus chart its extent.	Vessel Go to Vessels RV Callista Date 29/06/2010 Time of departure 0800 GMT High Water 0650 GMT 6.0m Low Water 1320 GMT 1.2m Instruments used Go to Equipment CTD ADCP Secchi Disk T/S Probe Heading 125° Weather at departure 8/8 cloud cover. Light showers. Low winds. Fig. 5. Track data of Offshore trip. (mouse over for full size)
Aim Procedure Map the position of the offshore front   To achieve the primary aim of mapping the front, continuous surface sea temperature was recorded as the ship navigated offshore. A relatively sharp increase in SST indicated the transition into stratified waters, and the depth at which the front occurred was noted. The ship's track was then set to zig zag along the noted depth contour, which was the predicted position of the front (see figure x.). Along the track, data was gathered by CTD, identifying whether the point was stratified or mixed. The actual position of the front was interpolated between stratified and mixed sample points. Determine the vertical profile of temperature, nutrients and chlorophyll on the mixed and stratified sides of the front, and compare conditions to current thinking on frontal systems In addition to the CTD profiles recorded around the front, comprehensive samples were taken at two stations; a stratified station was chosen offshore, and a mixed station at Black Rock. At these stations, niskin bottles were used to take water samples. In the light of the CTD profile, water samples in the stratified zone were taken from below (61m), at (27m), and above (5m) the thermocline. At the mixed station, samples were taken at 2.5m and 18.4m depth. For each sample, nutrient concentrations of nitrate, phosphate and silicon were determined, as well as dissolved oxygen and chlorophyll (used to calibrate the onboard fluorometer). The parameters at both stations were contrasted in the context of frontal system. Identify plankton species and abundance with respect to depth on either side of the front; identify and quantify the plankton community at the front The plankton community was sampled using nets. At the mixed station (Black Rock) a vertical trawl from 10m to surface was carried out with a 200µm net. At the stratified station, to differentiate between plankton above and below the thermocline, a closing net- again 200µm mesh size- sampled plankton between 40-35m and 20-0m. Plankton were sampled across the front during a 5 minute trawl at 2 knots, with a bongo net (double net with two mesh sizes: 200µm and 100µm) deployed at 2m. To determine temporal variability in vertical parameters (temperature, nutrients, chlorophyll and plankton) at Black Rock To compare parameters at Black Rock temporally, sampling was carried out at two seperate times; the first samples were taken at 08:25GMT on an ebb tide, and the seond were taken at 15:11GMT on a flow tide
Station Lat Long Time at departure (GMT) Weather at departure Tide Height (m) True Wind Water Temp (ºC) Procedures carried out and comments Fig. 6 Google Earth showing all stations (mouse over for full size) (Download Google Earth file) 1 050.08.476N 005.01.534W 0819 8/8 cloud cover 4.4 318°, 3.4 m/s 15.6 CTD deployed at 0825 GMT Secchi disk deployed at 0839 GMT, Secchi depth 7m 0954 GMT vertical plankton net 200 µm mesh, depth 10m. 2 050.07.007N 004.59.411W 0913 8/8 cloud cover 3.9 326°, 2.0 m/s 15.2 CTD deployed at 0918 GMT. No defined features, unclear thermocline, no water samples taken here 3 050.05.933N 004.57.360W 0937 8/8 cloud cover 3.6 317°, 1.9 m/s 15.3 T/S probe used to find the front. 15.4°C, increase of 0.2°C in a few seconds at 50.06N, 004.57W. CTD dropped to 60m. Clear thermocline on edge of the front 15.4- 12.3°C 4 050.05.040N 004.55.742W 1000 8/8 cloud cover 3.3 311°, 1.3m/s 15.8 CTD dropped to 60m. Temp very stratified, chlorophyll maximum clear just below thermocline.Secchi disk deployed at 1007 GMT Secchi disk depth 10.5m PLANKTON TRAWL 5 050.08.017N 004.55.005W 1135 8/8 cloud cover 1.9 181.1°, 2.4m/s 15.8 CTD drop depth: 48m. Current: 214.9° 0.4knots Secchi depth: 8.5m 6 050.10.684N 004.54.725W   1212 8/8 cloud cover 1.5 198.3°, 3.1m/s 15.2 CTD drop depth: 30m Current: 203.1° 0.4knots Secchi depth: 7.0m 7 050.09.953N 004.46.805W 1259 5/8 cloud cover 1.2 195.5°, 3.6m/s 15.9 Current: 213.0° 0.4knots Secchi depth: 11.5m No CTD drop. 8 50. 11.378N to 50.11.458N 004.47.449W to 004.47.819W 1326 to 1331   1.2m 192.6°, 3.8m/s 15.9 PLANKTON TRAWL (Bongoes) Current: 215.1° 0.4knots CTD drop depth: 42m 9 050.08.412N 005.01.351W 1511 5/8 cloud cover 2.3 240.1°, 5.8m/s 15.6 PLANKTON TRAWL (Vertical) CTD drop depth: 13m Current: 016.0° 0.6knots Secchi depth: 6.5m
Physical Results Offshore from Falmouth Mouse over graphs to enlarge on page.    Fig 7. Well mixed Station 1 - Black Rock Fig 8. Developing stratification Station 3   Fig 9. Weak thermocline Station 4 The CTD probe helped to find and map the leading edge of the front. CTD probes were dropped at nine different positions and the water column structure was analysed. Figure 7 shows a well mixed Station 1- Black Rock, with a well mixed water column, water temperature is constant throughout and no thermocline can be seen. Here chlorophyll is constant with depth. As we moved across the front, CTD profiles were taken to see the differences in thermocline structure. Figure 8 was at Station 3, which was taken closer to the leading edge of the front. It shows a CTD profile with a weak thermocline, density also increases slightly with depth. Figure 9 shows Station 4 which is in waters well within the front. Here there is a well defined thermocline as well as a steep Chlorophyll maximum which occurs a few meters above the 1% light intensity. The CTD was an important tool for finding frontal systems relatively quickly, overall there were nine CTD stations and using these data the frontal system was shown to run parallel to the coastline. The depth of the Chlorophyll maximum could be estimated by using values from the CTD system. Parameters such as light intensity and density could be seen throughout depth, these helped to explain the reasons for chemical and biological characteristics seen at the site.   Generally, stations on the mixed side of the front showed homogeneous characteristics with depth. Temperature and salinity followed straight, near-vertical lines on the plots of stations 1, 2, 5, 6 and 9, suggesting a mixed system. Mixing was the result of tidal currents generating shear stress with the seabed, and wind shear stress at the surface. In shallower waters, these two mixed cells meet, and the entire water column becomes mixed; the mixed side of the front is therefore always the shallower side. Recorded temeperatures were around 15 degrees celsius for the mixed water column. In terms of light and chlorophyll, station 1 showed uniform distribution of chlorophyll with depth, at 0.75µg/L. The 1% light level was 21m (see station 1 plot, figure 7) Stations 3, 4, 8 and 7 were stratified, with stations 4 and 7 showing strongest stratification. On the deeper side of the front, bottom shear with tidal currents and surface shear with wind still exist, except the depth involved keeps the two mixing cells apart. Thermal energy is not mixed evenly throughout the water column, creating layers of different temperatures, and therefore density. Warmer, less dense water overlies colder, denser water, and stability is reinforced by the fact extra energy must be provided to mix stable layers. This density change was evident at station 4; the plot showed less dense water (1025.7kg/m^3) at 5m, on top of denser water (1027.0kg/m^3) at 40m. The density change was a result in a change in temperature, evident as a thermocline between 4m and 20m at station 4. Temperature change between these two depths was 4.5 degrees celsius. The thermocline was also responsible for an increase in surface sea temperature (SST) at stratified stations, as thermal energy was kept in the surface layers rather than being dissipated throughout the water column. SST at station 4 was 17 degress celsius compared to 15 degrees celsius at station 1 (mixed station). At station 4, there was a chlorophyll maximum between 20m and 30m, with peak chlorophyll concentration of 1.7µg/l at 25m (see station 4 plot, figure 9). At this time of year, nutrients were depleted from the top layer by the spring bloom, reducing production at the surface. Below the thermocline, mixing brings up nutrients to support primary productio. As the plot shows, chlorophyll was restricted to below the thermocline (increasing availability of nutrients), but above the 1% light level (below which light intensity is too low to support high rates of primary production). Comparing 1% light depths between station 1 and 4 showed the 1% light level to be 10m deeper in stratified water (31m at station 4). This was due to no bottom resuspension in deep water, and low chlorophyll levels in nutrient depleted water above the thermocline. In conclusion, shallower stations were found to be mixed, whereas deeper water stations were found to be stratified. Mixed stations were typified by constant temperature, density and homogeneous chlorophyll distribution with depth; stratified stations exhibited a thermocline with a deep water chlorophyll maximum below the thermocline, but above the 1% light level. The area between mixed and stratified stations represented the area where the front was located.	ADCP & Richardson Number (Mouse over images to enlarge) Utilising the current velocity data from the ADCP the Richardson Number could be calculated. The Richardson Number (Ri) is the ratio of stratification to the square of shear in horizontal current. A Ri below 0.25 is indicative of mixing, a Ri value above 1 suggests stratification, and a Ri value between 0.25 and 1 indicates transition between a state of mixing and stratification. Station 1 (Mixed region) Fig. 10 ADCP profile for mixed region. Station 1   For station 1 the Richardson Number was calculated to be 0.094, which is well below the critical value of 0.25 and so it suggests a well mixed region. This is also presented by the backscatter image. Station 2 (Stratified region) Fig. 11 ADCP profile for stratified region. Station 4 For station 4 the Richardson Number was calculated to be 1.430, which is well above the critical value of 1 and so it is indicative of strong stratification in this region. This is also presented by the backscatter image.
Chemical Results Offshore from Falmouth Fig. 12 - chemical properties for mixed water column Station 1 (ebb tide at Black rock) had low levels of phosphate (0.19µmol L-1) and silica (0.5 µmol L-1) but these were constant with depth whereas nitrate increased with depth (0.86 µmol L-1-2.2 µmol L-1). Station 1 was a shallow, well mixed region, close to the coast so we expected to see fairly constant values for nutrients throughout the water column. Station 4 shows that phosphate levels remain fairly constant with depth (around 0.30 µmol L-1) and silica increases slightly with depth (0.3 µmol L-1-1.25 µmol L-1). Nitrate decreases in the surface 25 metres from 1.04 µmol L-1-0.88 µmol L-1 and subsequently increases with depth up to 3.15 µmol L-1. Oxygen decreases with depth (111.7%-89.6%). Fig 13 - chemical properties for stratified water column We predicted that Station 4 would show characteristics of the frontal system which include a warm overlaying water body with low nutrient levels and a steep thermocline and increasing nutrients hereafter with depth, due to the position offshore. Surface depletion of Nitrate is due to high levels of primary productivity in the photosynthetic layer which is enhanced by the seasonal stratification. Nitrate concentrations return at depths that are below the optimum light levels for primary production. Also an increase in silica with depth suggests remineralisation beneath the thermocline. Oxygen decreases with depth due to biological activity. In the surface irradiated layer high primary productivity, increased numbers of zooplankton and high rates of metabolic activity cause rapid depletion of oxygen. Beneath the thermocline, oxygen levels continue to decrease due to remineralisation by bacteria (bacterial respiration).
Biological Results Offshore from Falmouth During the offshore boat practical four plankton net samples were taken. Stations locations were chosen to highlight differences in the plankton composition throughout the water column due to the physical and chemical characteristics of the region. A station at Black Rock allowed comparision of plankton types and abundance during ebb and flood tides, it also highlighted differences between the well mixed water column and stratified regions of the frontal system. Station Date Time of plankton sample (GMT) Net Type Mesh size Water Temp (ºC) Depth  (m) 1 29/06/2010 0954 Closed net (Vertical) 200µm 15.6 2.5, 18.4 4 1046 Closed net (Vertical) 200µm 15.8 0-20, 35-40 8 1326 Bongoes (Trawl) Net open area: 0.38m2 100µm, 200µm 15.6 2m trawl at 1.6knots for 5 mins 9 1521 Closed net (Trawl) 200µm 15.8 0-15 Phytoplankton Fig 14. Phytoplankton species at stations 1, 4 and 9. Station 1 at 2.5m depth showed Coscinodiscus to have highest of all phytoplankton recordings. Station 1 at 18.4m had no recorded phytoplankton species.   Station 4 the thermocline had a significant effect on the numbers and distribution of phytoplankton. In surface waters, nutrients have been depleted from past bloom events and no addition of nutrients due to stratification. Consequently very little photosynthesis can occur and low numbers of phytoplankton were observed; at 5m depth there were no recorded zooplankton. At 27m Chaetoceros was recorded with 250000 per m^3, this was the deep chlorophyll maximum, which occurs during periods of prolonged stratification. Further information on this can be found in the Zooplankton write up.   There was a significant difference between the number of species seen at Black Rock at ebb tide (Station1 ) and during the flood tide (Station 9); with only one species found at Station 1, and four species found at Station 1. Flood tide events will bring in a higher diversity of species than ebb tides. At Station 9; Black Rock during flood tide, at 2.6m depth Rhizolenia setigera, Coscinodiscus and Letocylindrus donicus were recorded. At 13.1m; Chaetoceros, Rhizosolenia setigera. Each species found at the two depths at Station 9 were present at numbers of 250000 per m^3. Station Depth (m) No. columns counted Volume viewed (ml) (x10 dilution) Species Abundance 1(A) 2.5 10 2 Conscinodiscus 2 1(A) 18.4 10 2 None 0 4(D) 5 15 3 None 0 4(D) 27 20 4 Chaetoceros 1 4(D) 61 15 3 Conscinodiscus 1 9(I) 2.6 20 4 Rhizosolenia setigera 1         Conscinodiscus 1         Leptocylindrus donicus 1 9(I) 13.1 20 4 Chaetoceros 1         Rhizosolenia setigera 1 Table 1. Phytoplankton species at all stations   Zooplankton   Fig 15. Zooplankton at Black Rock with Ebb and flood tide.   Fig 16. Zooplankton above and below thermocline at Station 4   Fig 17. zooplankton trawl results from stratified to well mixed water column. Plankton trawls were carried out at three stations, to highlight differences between species composition and abundance in and around the frontal system. Station 1 was at Black Rock during the ebb tide. Here Copepoda and Cladocera were found to be the dominant species, with Copepoda abundance being 1991 per m^3 and Cladocera being 205 per m^3. Station 1 has a well mixed water column, whereas Station 4 is within the stratified zone of the front. At Station 4 the water column temperature showed a strong thermocline at around 26m. Plankton trawls were carried out both below the thermocline from 35-40m and above it from 20m to the surface. There was a significant difference between the zooplankton numbers found at these depths. Dominant species remained to be Copepoda and Cladocera, but the abundance of copepoda below the thermocline was nearly double that recorded above the thermocline. Copepod abundance above the thermocline was 6181 per m^3 , this increased to 12329 per m^3 which was recorded below the thermocline. This difference in zooplankton abundance is due to the presence of the Deep Chlorophyll Maximum which occurs during extended periods of stratification. Depletion of nutrients in surface waters from previous phytoplankton blooms, reduce the abundance of phytoplankton and zooplankton. Higher nutrient levels at the thermocline and the fact that light intensity remains high enough for photosynthesis to occur, so phytoplankton can live at this depth. A zooplankton population will consume the thermocline phytoplankton population. A plankton trawl was carried out at 1.5m depth across the start of the front. Again, there was a large number of Copepoda and Cladocera recorded, however this was significantly less than the other stations. Another plankton trawl was taken at Black Rock- Station 9 during the flood tide. A much higher number of Copepoda and Cladocera were present during the ebb tide; Copepoda abundance increased from 1991 per m^3 to 4535 per m^3. High levels were brought in with the tidal flow, this maybe because of enhanced population growth in the frontal systems and the coastal system having a more stable and greater area of which zooplankton can populate.

Overall, the offshore survey and corresponding data collection proved successful, as the two extremes of the tidal mixing front were located offshore of the Fal estuary, with their extent mapped onto a Google Earth image (See Fig. XXX). As expected, CTD profiles and plankton trawls revealed a mixed water column on the relatively shallow side of the front, and a stratified water column on the deeper side of the front. Due to the zig-zagging nature of the ship’s track, the location of the front was not located exactly, but only confirmed to be between two regions either side of the front. CTD profiles helped to confirm either a mixed or stratified water column; hence the front was assumed to be between these regions.

It would appear that the spring phytoplankton bloom had occurred prior to the offshore survey, as there was a significantly lower phytoplankton abundance compared to zooplankton abundance. This suggests that much of the phytoplankton had already been consumed by the large numbers of zooplankton that were discovered in the plankton trawls. Nutrient data from the shoreward side confirmed the homogeneous nature of the water column compared to the data from the stratified side. In addition, the distinction between the two sides of the front was confirmed by calculating Richardson numbers, with the mixed side having an Ri of 0.09 and the stratified side having an Ri of 1.43.

In summary, the waters offshore of Falmouth exhibit the physical, chemical and biological characteristics to be able to determine the boundaries of the tidal frontal system.

GEOPHYSICS Practical
02/07/2010

Introduction to Geophysics Practical Mawes Harbour, as part of the Fal Estuary, is a designated Special Area of Conservation (SAC), due to the presence of ecologically important biotopes including maerl and seagrass beds. Both habitats encourage increased biodiversity, and provide nurseries for juvenile species, hence maintaining recruitment rates to adult populations. Mapping such habitats is an essential step towards conservation and estuary management. Maerl is a calcareous algae and coloured red by phycoerithrin photosynthetic pigment. It exists as loose beds of branched colonies that interlock, and it is this complicated structure that provides diverse niches for other algae and invertebrates (Foster, 2001). Dead maerl keeps its skeleton, and also provides a similar habitat. Maerl is used as a soil conditioner on acidic soils. Dredging for maerl for this industry has affected stocks in the Fal Estuary (Grall and Hall-Spencer, 2003), so mapping beds is necessary to create legislation that balances economic need with habitat vulnerability. Seagrass is a marine flowering plant that forms ecologically important meadows. As well as providing food for herbivores (Heck and Valentine, 2006), seagrass provides shelter for juveniles and adults (Connolly, 1994; Horinouchi, 2007), and stabilizes sediment in the coastal zone through root systems. It is widely recognised mapping and protecting seagrass is important to promote sustainability of coastal ecosystems (Yap, 2000). Previous studies have successfully used side scan sonar and video analysis to sense seagrass (Norris et al. 1997). The last habitat sampled in the survey was kelp forest, another highly biodiverse habitat (Christie et al. 2003). The fronds provide shelter for nurseries, and a substrate for edible, epiphytic algae; destruction of the algae reduces fish stocks, and impacts top consumers (Lorensten et al, 2010).

Vessel Go to Vessels SV Xplorer Date 02/07/2010 Weather   High Water   Low Water   Instruments used Go to Equipment Van Veen Grab Video Camera Sector Scan Sonar Side Scan Sonar Fig. 18 Google Earth showing all stations (mouse over for full size) Download Google Earth file

Side Scan Sonar Results Patterns in the side scan output, coupled with ground truthing (grabs and video), were used to identify bottom habitats (see figure 19) The towfish used on Xplorer used two sound signal frequencies. The 100kHz signal had a longer range whereas the 415kHz signal gave a higher resolution image i.e. the 415 kHz signal was able to identify two small objects together on the seabed better than the 100 kHz signal. In order to interpret sidescan images it is necessary to calculate the wavelength of the transmitted sound pulse. This determines the resolution that can be detected from the backscattered sound. The wavelength is determined from:  v=fl where: v = velocity of sound in water (1500 m/s) f = frequency of soundwave pulse (Hz) and l = wavelength (m). Layback was calculated by Pythagoras's Theorem. Information from the side scan was plotted in Surfer contour software and used to generate sea floor habitat maps (see figure). As expected, maerl was confirmed in transect one, seagrass and small patches of kelp in transect two, and kelp and seagrass was found in transect three. In more detail, the maerl bed in transect one extended from 184650m East, 32750m North, to past the western limit of the transect. In transect two, the sidescan revealed rocks nearest the shore, giving way to sand, and then seagrass from 18500m East, 32250m North, extending to the eastern edge of the transect. A thin band of kelp was located on the southern border of the seagrass. Finally, in transect three, the seabed was found to be mainly bare sand. Kelp fringed the rocks at 184450m East, 31500m North, 184470m East, 31600m North, and 184450m East, 31850m North. Transect three also revealed a seagrass bed with dimensions 60m by 120m, centred around 184430m East, 31800m North. Transitions in seabed habitat appeared as clear changes of pattern on the side scan output, and so definite boundaries could be plotted on the charts. Due to blurring of the side scan readout along transect one, areas of transect one remained unknown. Video Camera The video camera was useful in that it provided continuous ground truthing when deployed. It was evident that changes in habitat occured as sharp boundaries occurred rather than a gradient of change (see figure). Video footage of different habitats consistently matched with changes on the sector scan output.	Fig. 19 Habitat map of Transect 3. Fig. 20 Dense seagrass shown on sector scan and video. Fig. 21 Seagrass boundary shown on sector scan and video. Fig. 22 Kelp bed shown on sector scan and video.	Sector Scan Sonar Results The reason for deployment of sector scan sonar was to assess its practicality as a tool for benthic habitat mapping. Whilst side scan sonar can produce wide area sea bed images, interpretation in isolation can sometimes prove problematic. Sector scan sonar can be used to provide a finer analysis of a much narrower swath (Bozzano and Siccardi, 1997). When used in conjunction with other remote sensing techniques, it may be possible to use sector scan images to determine transitions in underwater habitat boundaries that can then be used to calibrate a corresponding feature on a side scan plot. In addition the compact nature and its fixed location on the vessel means that the sector scan sonar can be used in more confined area to target regions of interest for further investigation (unlike a deployed towfish). In transect 2, at 184760m East, 32349m North, dense sea grass was found with the use of a video camera. This corresponded to a thick band of backscatter on the sector sonar data (see figure 20). At 184709E, 032309W, the seagrass bed boundary was identified using the video camera, as seagrass gave way to sand. This corresponded to a sudden change in the sector scan sonar data; a thick band of backscatter was recorded in the area of dense sea grass, and a thinner band was recorded over sand (see figure 21). As small patches of seagrass emerged on the video output, there was small occasional thickening of backscatter data. The sector scan was also able to detect kelp. At 184995m East, 31736m North, sector sonar backscatter became thicker and less uniform; video footage confirmed the transition from bare sand to kelp (see figure 22). The kelp backscatter signature was unique compared to the seagrass backscatter signature, highlighting the potential for sector scan to identify precise benthic habitat. Whilst seagrass was displayed as a thick, uniform band, backscatter off kelp appeared as a rougher band of backscatter seperate from the backscatter received off the bottom. This banding may be due to the relatively dense canopy of kelp fronds overlying a less dense substorey of stalks. On the other hand, there is no canopy in seagrass; seagrass blades are uniformly thick along their length.
Grab Results A mechanically operated Van Veen grab provided ground truthing. Samples were washed through a sieve stack for ease of analysis. At grab site 1 (32559E, 184296N), the grab picked up a layer of live maerl on top of fine mud. This information was used to analyse the side scan pattern, and map the extent of maerl. Also present in the grab were hermit crabs, gastropods, ophiuroids, errant polychaetes and green seaweed (Ulva spp.). (Figure 24) Grabs two and three (located at coordinates 31671E, 184503N and 31708E, 184504N respectively) sampled transect three (figures 25 and 26), typified by bare sand and rocks fringed by kelp. The grabs brought up medium coarse sand with shell fragments, bivalves and loose kelp fronds. As discussed in the limitations section, grabbing a kelp bed is difficult due to its patchy nature, and the rock substrate. The spatial difference between sector scan position and grab meant grabs and backscatter did not correlate exactly. Fig 23. Group 1 - Sieve analysis.	Hover over photos to enlarge   Fig 24. Grab site 1 LAT: 050°09.225N LONG: 005°01.260W DATE: 02/07/10 TIME: 0915GMT DEPTH: 6.99m CONTENTS: Mearl, Green Seaweed – ulva, Gastropods - Hermit Crab, Ophiuroida, Errant Polychaete, Red Seaweed, SEDIMENT TYPE: Fine mud   Fig. 25. Grab site 2. Transect 3 LAT: 050°08.751N LONG: 005°01.056W DATE: 02/07/10 TIME: 1135GMT DEPTH: .5m CONTENTS: Bivalves SEDIMENT TYPE: Just sand; grain size 375µm 1 ½ phi medium sand   Fig 26. Grab site 3. Transect 3 LAT: 050°08.771N LONG: 005°01.056W DATE:02/07/10 TIME: 1144GMT DEPTH: 7.0m CONTENTS: Few fronds and partial kelp fragments, Shell fragments SEDIMENT TYPE: Sand; grain size as grab 2  All photos were taken by group member Amy Munro.
Summary of Geophysical Practical Apart from transect one (due to blurring of side scan image), seabed biota was successfully surveyed, and accurate maps created. Habitats were found where expected; maerl was confirmed at transect one, seagrass and kelp at transect two, and seagrass and kelp were found at transect three. Definite boundaries of habitat were drawn up on charts. Sector sonar data corresponded with video footage and side scan (limitations in comparing video and sector scan are discussed under materials and methods). There is therefore potential to use sector sonar as a habitat mapping tool, although further work would be required to differentiate between a wider range of habitat signatures.

ESTUARIES PRACTICAL
06/07/2010

The Fal estuary is a drowned river valley, or ria, which formed at the end of the last glacial maximum (LGM)
approximately 18000 years ago. During deglaciation, large volumes of glacial meltwater eroded a deep river valley,
which has since been filled by high present-day sea-levels. As the glacial freshwater source is now depleted, the
fresh riverine input into the Fal estuary is very small, so we expect the estuary to be tidally dominated with
relatively small horizontal variations in salinity.

The overall aim of the survey was to gain an overview of the physical properties of the Fal
estuary, and to see how these characteristics affect the chemical and biological properties of the estuary.

A secondary aim was to classify the estuary in terms of its physical, chemical and biological properties. This would be
achieved by producing an estuarine mixing diagram once all data and water samples were collected, processed and
analysed. This diagram would enable us to understand the mixing characteristics of the Fal estuary in relation to
horizontal changes in salinity.

The survey was to begin at Black Rock and progress towards the head of the estuary with the flood tide.
ADCP transects, CTD profiles, and water samples were to be taken at key points along the main channel, specifically
at every 0.5 PSU change in salinity. Plankton trawls were also to be completed at the extremes in salinity, i.e. at
Black rock, Turnaware point and close to the riverine end member near Woodbury Point. From the water samples various
nutrients would be obtained, including nitrate, phosphate, silicon and dissolved oxygen. The concentrations of these
nutrients would be determined during lab analysis of the water samples.

Preliminary analysis of vertical nutrient profiles indicates that nutrient concentration in the water column appears to generally increase towards the head of the estuary.

Station 6 (see google earth image, figure 29) represents the furthest upstream sampling point and as expected this had the highest relative levels of nitrate, phosphate and silicon (see figure 37)

.

Vertical nutrient profiles remain fairly constant through the water column at the mouth of the estuary reflecting the amount of tidal mixing at these points (see figure 36). As the topography changes at the head of the estuary to narrower river channels, the effect of tidal mixing appears to be reduced as the vertical nutrient profiles indicate some variation, albeit on a small scale.

Chlorophyll concentration in the estuary follows the low concentrations discovered in offshore samples indicating that the phytoplankton bloom has occurred sometime in the past. Again, the highest relative chlorophyll concentration were identified at the most upstream sampling station. This is probably the result of the higher nutrient concentrations there (St6_nut plot]).

The 1% light level depth appears to increase towards the mouth of the estuary suggesting turbidity increases in the estuary although this would need to be confirmed from the turbidity data from the CTD samples.

In summary, the vertical nutrient profiles appear to indicate that the effect of mixing in the estuary decreases with distance from the mouth. Whilst there appears to be some vertical variation in nutrient concentration towards the head of the estuary, the limited number of sampling points and low nutrient concentration values make it difficult to conclude whether this effect has a biological cause or whether it represents some natural variation in sampling or analysis techniques. The vertical profiles would seem to agree with the horizontal profiles that nutrients are being diluted down the estuary by seawater.

Preliminary analysis of the mixing diagram constructed from the samples taken estuarine practical on 06/07/10 indicates that whilst salinity varies very little along the estuary there would appear that nitrate displays non conservative behavior (see Fig 39). Plotting of the sample points on the mixing diagram indicate a removal of nitrate from solution (fig 39), possible reasons for this may be due to the recent phytoplankton bloom utilizing the nitrate for metabolic processes.

Nitrate enters the marine environment via runoff from the land, and is then diluted as it is mixed. The highest nitrate values were found at station 6 (Max value 12.86 µmol/L), which corresponds to the furthest upstream location where samples were taken. This is what was expected.

Fig. 40 is an estuarine mixing diagram for phosphate concentration (µM) with riverine and marine end members connected by a theoretical dilution line.

Values for the riverine end member were salinity 0.00 and phosphate 1.16 µmol/L, at the marine end member values of salinity 35.02 and 0.12 µmol/L of phosphate were recorded. The majority of samples collected on RV Conway on the 06/07/10 were in the salinity range of 30.11 and 35.02

Water column depth restricted the range of RV Conway thus the samples at the top of the estuary were collected by ribs. Plotting the data on the mixing diagram revealed an input of phosphate (recorded value 3.23 µmol/L) at a salinity of 20.00, which was a sample given to us in the lab previously collected by the technicians. Phosphate is showing non-conservative behaviour as the points reside above the theoretical dilution line, so addition of phosphate is occurring. At salinity 20.00 there appears to be an outlier, which will need further investigation to determine the input source of phosphate at this point.

Biological Results

Phytoplankton Fig 41. Phytoplankton abundance over 5 different stations in the Fal Estuary on 6/07/10 Phytoplankton abundance in the Fal estuary was estimated by taking samples at 5 different stations. It was found that the highest abundance of phytoplankton was at station 6 which corresponds with zooplankton data (fig 42) and nutrient data (TDL plots above). At station 6 the most abundant phytoplankton were Chaetoceros sp. (estimated at 4.24x107/m3). The second most abundant species are the diatoms Alexandrium. High abundance of diatoms corresponds with TDL plots for silicon which show a non-conservative removal of silicon in the estuary. As previously mentioned the lowest nutrient values and zooplankton abundance were found at station 1. This corresponds with the graph (Fig 41) which shows that the lowest abundance of phytoplankton were also found at this station.   Zooplankton Fig 42. Abundance of Copepods over three different stations up the Fal estuary. Three stations were chosen A, B and C in the Fal estuary in order to estimate zooplankton abundance and species distribution. Station A (Black rock) is at the mouth of the estuary and station C is at the top of the estuary (off the pontoon). Station B occurs between these two points. The most abundant species of zooplankton were Copepods. Station A has the lowest abundance of zooplankton overall. This is due to low nutrient levels following utilization by biota (spring phytoplankton bloom). The highest abundance of zooplankton were found at station C. As station C is furthest up the estuary nutrient levels were expected to be high. The high abundance of zooplankton corresponds with figure 41 which shows a high abundance of phytoplankton and also with the TDL nutrient data. High nutrient levels caused by nutrient run-off and proximity to land fuel biological processes. Light data also supports this theory as the secchi disc depth decreased further up the estuary due to suspended particulates (which can be attributed to biological and chemical processes) in the water column. Station B is a midway point between the mouth of the estuary and the top of the estuary. The zooplankton abundance here supports the above theory ie. Higher nutrients further up the estuary correlates with high phytoplankton abundance (see fig 41) and therefore high zooplankton abundance.

Summary

Conclusion

The Falmouth field course provides an opportunity to explore the physical, chemical and biological characteristics of the Fal from offshore to estuary head. Although the course week was divided into three distinct data collection voyages, it is possible to draw some overall conclusions of the area.

The Fal estuary appears to be a partially mixed estuary that flows out into the Western approaches. It was characterised by a thermocline and halocline evident at the head of the estuary that diminishes towards the mouth. This suggests that the mixing influence of the tides decreases up the estuary.

As the estuary transitioned into open ocean, the homogeneous water column structure evolved into a distinctly stratified structure. This is indicative of a tidal mixing front located offshore. The characteristics of the mixed and stratified sides of the front allowed its extent to be mapped to some degree.

As was expected, the source of nutrients would appear to be from the river inputs along the Fal where concentrations were highest. Nutrient concentration decreased down the estuary and offshore suggesting dilution by mixing seawater away from the source.

The low chlorophyll concentrations and low numbers of phytoplankton recorded in the estuary and offshore suggest that the expected temperate spring/summer phytoplankton bloom had occurred at some point prior to the course. This supposition was supported by the relatively high numbers of zooplankton present in the estuary and offshore that would have fed on the bloom.

In 2003 the Fal was a candidate Special Area of Conservation as a result of features such as the maerl beds and seagrass meadows found in St. Mawes bay. Given the vulnerability of these features, accurate mapping of their extent is of vital importance. By referencing side scan sonar output and video, it would appear feasible to be able to use sector scaning sonar as an aid to identifying changed in benthic habitat.

The Fal and its surrounding area offers distinct oceanographic and biological features for marine scientists to study. In time, it may be possible to use the datasets collected to provide an in depth analysis of the physics, chemistry and biology of this unique area.

Potential further work

To extend this investigation other facets of the fal estuarine system and related offshore regions could be analysed in greater detail.

In the offshore regions more detailed mapping could be undertaken to get a more accurate positioning of features such as the frontal system, as well as taking a longer term time series of the front to see how it changes over time and the effects this has. Utilisation of satellite data can augment the data collected in the field to gain a better understanding of the features in this area. Another index number which could be used is the Simpson-Hunter index to aid in determining the front. A look into the turbidity of the water column and how it changes over time could also be considered. On the biological side a more detailed look at the standing stock of plankton could be embarked on, in particular a study into the change in biomass over time and the relationship with nutrient distribution. An examination of the controls and limits on primary productivity could also be considered. A useful aid for this would be the L4 and E1 buoys offshore from Plymouth from the western channel observatory, which provides data on nutrient fluxes and chlorophyll concentrations.

In the fal estuary further study could be undertaken to understand the effects of the different river systems on the estuary. The flushing times and its effects on nutrients, contaminants and pollutants could be examined, as well as the residence times. A longer term time series could be initiated to investigate the changes in the estuary, including the effects of the tide. Further investigation into the physical processes could be undertaken and the Richardson Number could be calculated at various points along the estuary to indicate whether the estuary is well mixed, partially mixed or stratified. Similarly to the offshore work, turbidity could be studied to try to understand the effects this could have on the estuarine system, with particular regard to the biology. An examination of the controls and limits on primary productivity could also be considered as well as a study into the change in biomass over time and the relationship with nutrient distribution. A further investigation could combine the data from both within the estuary and offshore to look at gradients from the top of the estuary to the related offshore regions.

On the geophysical side, a more detailed mapping project could be undertaken to gain a greater understanding of the extent of the various habitats in the region. A long term time series could be used to investigate how the extent of habitats, such as seagrass, changes over time and a look into the possible reasons for this. The sector scanner could be utilised on more habitat types to see if there is a significant change on the read out, which could be useful to find out if it could be used as a more prominent instrument for mapping various different types of habitat.

DOWNLOADS

Click to download any of the following files to save and open on your own computer.
 

REFERENCES

Bozzano R. and Siccardi A., (1997). Underwater vegetation detection in high frequency sonar images: A preliminary approach. Lecture notes in computer science, Vol 1311/1997, pp 576-583.

Christie, H., Jorgensen ,N.N., Norderhaug, K.M., Waage-Nielsen, E., 2003. Species distribution and habitat exploitation of fauna associated with kelp (Laminaria hyperborean) along the Norwegian coast. Journal of the Marine Biological Association of the United Kingdom 83, 687-699.

Connolly, R.M., 1994. A comparison of fish assemblages from seagrass and unvegetated areas of a southern Australian estuary. Marine and Freshwater Research 45, 1033-1044.

Dyer,K.R. (1973) Estuaries: A Physical Introduction 2nd Edition.John Wiley & Sons Ltd, England.

Foster, M.S., 2001. Rhodoliths: Between rocks and soft places – Minireview. Journal of Phycology 37, 659-667.

Grall, J., Hall-Spencer, J.M., 2003. Problems facing maerl conservation in Brittany. Aquatic Conservation: Marine and Freshwater Ecosystems 13, S55-S64.

Head, P.C., 1985, Practical estuarine chemistry, Cambridge University Press, Cambridge.

Heck, J.K.L., Valentine, J.F., 2006. Plant-herbivore interactions in seagrass meadows. Journal of Experimental Marine Biology and Ecology 330, 420-436.

Hodgkiss,I.J, Lu SH (2004) The effects of nutrients and their ratios on phytoplankton abundance in Junk Bay, Hong Kong. Hydrobiologia 512: 215-229.

Heiskary,S., Markus,S. (2001) Establishing, Relationships Among Nutrient Concentrations, Phytoplankton Abundance, and Biochemical Oxegen Demand in Minnesota, USA, Rivers. Journal of Lake and Reservoir Management, 17(4), 251-262.

Horinouchi, M., 2007. Distribution patterns of benthic juvenile gobies in and around seagrass habitats: effectiveness of seagrass shelter against predators. Estuarine, Coastal and Shelf Science 72, 657-664.

James, R. and Wright, J. 2005, Marine biogeochemical cycles, 2nd Ed, Elsevier Butterworth-Heinemann, Oxford.

Lorentsen, S., Sjotun ,K., Gremillet, D., 2010. Multi-trophic consequences of kelp harvest. Biological Conservation doi: 10.1016/j.biocon.2010.05.013.

Martin-Jézéquel, V., Mark Hildebrand, M., and Brzezinski, M.A.(2003) SILICON METABOLISM IN DIATOMS: IMPLICATIONS FOR GROWTH . Journal of phycology . Vol 36 I(ss 5) Pgs 821-840.

No Author. (2006) ‘Nutrients -- Nitrogen and Phosphorus’:From Voluntary Estuary Monitoring Manual Chp 10: Available http://www.epa.gov/owow/estuaries/monitor/pdf/chap10.pdf. Accessed 06/07/10.

Norris, J.G. Wyllie-Echeverria, S. Mumford, T. 1997. Estimating basal area coverage of subtidal seagrass beds using underwater videography. Aquatic Botany 58, 269-287.

Roubeix, V., Rousseau, V. and Lancelot, C. 2008, Diatom succession and silicon removal from freshwater in estuarine mixing zones: From experiment to modelling, Estuarine, Coastal and Shelf Science. Vol 78, Iss 1:14-26.

Sharples, J., & Simpson, J. (2009). Shelf Sea and Shelf Slope Fronts. Encyclopaedia of Ocean Sciences , 391-400.

Yap, H.T., 2000. The case for restoration of tropical coastal ecosystems. Ocean and Coastal Management 43, 841-851.