Tuesday, December 7, 2010

10.04.2010: Plankton Sampling Cruise

For this lab exercise, we had this opportunity to go on a sampling cruise to perform some net tows targeting plankton (animals that can’t swim fast enough to swim against water currents). A plankton tow is a very common method of capturing smaller planktonic life forms; oceanographers use this method often in studying the open oceans. Plankton tows use conical nets which are towed at low speed. Plankton is captured in the cod end; a cup at the end of the net which has three small openings covered in 500 µm mesh, the mesh allows water to flow all the way through the net and partially into the cup to prevent specimens from escaping.

Our journey began on Savannah State’s R/V Sea Otter, once the two large motors were fired up, we were off, slowly. On this beautiful day we were able to perform two different types of tows with the time we had. We used a bongo net, which has two separate nets that are attached at the ring openings. The first tow performed was a surface tow in which the net is pulled just below the surface of the water targeting organisms which stay or migrate near the surface. The location of the tow was near the SSU docks, but quite a ways down the Herb River in a long, straight, 30 ft deep area which allowed us to run the trawls with no impediments. The primary issue in using the bongo net is to get the nets even on the horizontal plane; once the nets are placed correctly the tow may begin. We ran our surface tow at .77 knots for 5 minutes, the collection cups were rinsed into our sample holders and samples were preserved in 70% ethanol. The second tow for the afternoon was an oblique tow, where the net is lowered to the bottom for the beginning of the tow and slowly pulled up sampling the entire water column from bottom to surface. For this second tow, the Sea Otter was run at 1.6 knots for 2 minutes. When the nets came up they contained a large amount of bottom sediment, our nets must have hit the bottom of the river at the beginning of the trawl. The samples were stored in ethanol and the Sea Otter and crew headed back for SSU docks. We viewed part of our sediment sample in a Plexiglas chamber, the only obvious specimen was a crab larvae with a very long spine. In the lab on campus, we observed several stages of crab larvae and phytoplankton was clearly visible.

Monday, November 29, 2010

Zooplankton Tow Sample Analysis

We conducted our second indoor lab assignment on October 11, 2010. We analyzed the two plankton tow samples (surface and oblique) from the October 4, 2010 outdoor lab assignment. Surface tows were characterized by being able to see the net at the surface. Oblique tows were characterized by the net being at least 4 m below the surface. The objective of this lab was to utilize dissecting microscopes to assess the abundance of copepods from two milliliter (ml) water samples from surface and oblique plankton tow samples.

Copepods are vital marine organisms that prey on phytoplankton in coastal ecosystems. They serve as important prey items for shrimp, small fish species, and crabs.
The plankton samples were collected using bongo plankton net with 1 mm (500 µm) mesh and collection container attached in the middle. The bongo plankton net was towed behind the boat at a speed of 0.77 m/s. After each tow, the bongo net was brought aboard and the collection container was removed from the net. We used saltwater to wash the plankton samples from the collection container into separate containers labeled either “surface” or “oblique”.

In order to assess the abundance/ number of copepods per sample, 1 ml pipettes were used to remove a 1 ml water sample from the surface and oblique plankton tow samples. One water drop of the plankton samples were placed in 36 miniature squares of a water sample tray. Each tray was observed under a dissecting microscope. The number of copepods per miniature square was calculated for both plankton tow samples.

Both the surface and oblique plankton tow samples produced low numbers of copepods and other zooplankton.

Monday, November 1, 2010

Estuarine Sediment Grain Size Determination

Marine geologists analyze sediment grain sizes to understand the composition of earth within a survey site. Through this analysis, they can predict sediment composition changes when the information is combined with other datasets (weather, land use). On September 20, 2010, the research methods class conducted an estuarine sediment grain analysis exercise.

Sediment cores collected from a previous survey (blog post 9-10-10) were procured for this exercise. A stacked series of cylindrical mesh sieves and water were used to manually separate the sediment grains according to the following sizes:

Coarse sand -1000 µm
Medium sand - 250 µm
Fine sand - 125 µm

The contents of each sieve were rinsed with water before they were transferred into pre-weighed collection dishes and dried in a laboratory oven for 7 days. The samples were weighed after drying.

The Station A core had a calculated dry weight of 8.41 g. Coarse sand was in 2.26 g (27%) of the sample. 3.06 g (36%) of the core was medium sand. 3.09 g (37%) of the core consisted of fine sand (Figure 1; Table 1).

The Station C core had a calculated dry weight of 62.13 g. Coarse sand constituted 14.57 g (23%) of the sample. 9.32 g (15%) of the core was medium sand. 38.24 g (62%) of the core consisted of fine sand (Figure 1; Table 1).

The Control core had a calculated dry weight of 82.36 g. Coarse sand was in 2.11 g (3%) of the sample. 10.66 g (13%) of the core was medium sand. 69.59 g (84%) of the core consisted of fine sand (Figure 1; Table 1).
Figure 1 - Estuarine sediment grain size to weight composition. 
Skidaway Island, GA

Table 1 - Dry sediment weight of sieved samples.  Skidaway Island, GA.

Station A
Station C
Coarse sand
1000 µm
2.26 g
14.57 g
2.11 g
Medium sand
250 µm
3.06 g
9.32 g
10.66 g
Fine sand
125 µm
3.09 g
38.24 g
69.59 g
Total weight
8.41 g
62.13 g
82.36 g

In conclusion, the sediment cores in this exercise contained high quantities of fine and medium grain sand.

A plausible theory: This area experiences high tide differentials (8 feet / 2.4 meters twice daily); yet the energy of the water as it enters and leaves the study site is low. As a result, sediment grains of smaller size are able to settle and accumulate since the water is flowing at a relatively steady rate.

Friday, October 8, 2010

CTD Cruise on Country Club Creek

On August 30, 2010 the graduate research methods class left the Savannah State University creek side dock to embark on a CTD cruise.  A CTD is an essential oceanographic tool used to measure various water parameters such as Conductivity, Temperature and Depth of sea water.


The CTD can be considered as a device designed to take vital signs of the ocean and house a multitude of sensors which can measure a host of water characteristics at different water depths. The CTD can also record data continuously both vertically as it descends through the water column and horizontally at different depths as it is pulled behind a boat.  Information recorded by the sensors on the CTD are electronically sent via a data cable to an on-board computer system (laptop).  

One major goal of this research trip was to deploy the CTD and record temperature, conductivity (salinity), density, depth, fluorescence, PAR (Photosynthetic Active Radiation), and oxygen saturation. This information was continuously gathered as the CTD was lowered into the water column to a depth of 1 m above the bottom.  

 The exercise was structured so that every student had an opportunity to have hands on experience on deploying the CTD, operating the laptop program and retrieving the recorder. One drawback of this device was that it was necessary to have “sea legs” to deploy the recorder without causing damage to the sensors.  In rough or choppy waters this may be impossible unless a crane or some other mechanical deployment device was used.
We recorded GPS coordinates to mark the locations of CTD deployment. This is a very important step to perform especially when recording along various transects. The data collection went without any glitches and we obtained a good data set.  My part in data analysis was to investigate the photosynthetic component in the water columnPhotosynthetic cells in pelagic plants (1-70 µm) such as phytoplankton absorb sunlight to produce necessary sugars required for life, during this process they emit a type of radiation known as fluorescence.  The intensity of fluorescence emitted by these plants is recorded by the CTD as it descends through the water column.  The fluorescence intensity data sent back to the laptop can therefore give an indication of the abundance and vertical distribution of phytoplankton in the water column. Fluorescence (phytoplankton abundance) was maximum (35.8293 mg/m³) at a depth of 1 m, was lowest between 3 and 6 m, but increased near the bottom at 8 m. These results suggest that there were three layers within the water column that differed in the abundance of phytoplankton, with the lowest abundances occurring in the middle of the water column.

The second part of this activity was to obtain grab samples of benthic substrate by deploying a Ponar grab. 
The Ponar grab was very light weight and easy to handle.  It was so easy to handle that J.J. slung it out as if she was playing a game of horseshoe! Of course as far as she appeared to throw it—it some how ended up going off 2 inches from the stern of the boat. 
Not all Ponar pulls resulted in sediment grabs.  There were a few areas that seem to have rocky outcrops or compacted sediments that the grab could not penetrate.

The first couple of tries with the Ponar grab were quite successful! We got a healthy serving of sediments and other benthic organisms which were immediately placed in ziploc bags and kept in a secure place for future analysis.

If you want to get a taste of the lab research experience (with a hint of Island music in the background) simply click on this link:  Enjoy!!!!!!!!

Wednesday, October 6, 2010

Spectrophotometry –long name easy procedure

Our first indoor lab assignment was conducted on September 13, 2010. The objective of this lab was to use the spectrophotometry technique to determine the phosphate concentrations for water samples collected from three different marine/aquatic environments.

Phosphate is an essential but limiting nutrient required for marine and aquatic plant/algae growth. Phosphate occurs naturally in the environment, usually in sediments and rocks. However, surface runoff (water) mainly caused by rainwater that is unable to infiltrate the soil, creates a way for phosphate as well as other nutrients to enter marine/aquatic systems. High concentrations of phosphate usually result in over-enrichment (eutrophication) of the marine/aquatic system, causing the phenomenon called algal blooms. These blooms use up so much oxygen that fish and others species die. However, when phosphate concentrations are low there is very little productivity (algal growth) and the environment is considered nutrient poor (oligotrophic).

In order to assess what phosphate concentrations may be associated with varying marine/aquatic environments, water samples for this assignment were collected from the following areas: 1) a brackish water creek surrounded by marshlands that flows along the backside of Savannah State University (SSU), 2) a phytoplankton tank that is a part of a controlled biofuel study being conducted by a fellow graduate student, and 3) the effluent (outflow) of a wastewater treatment plant that receives high mineral and nutrient loads.

Collecting water sample from Phyto-tank

The Spectrophotometer
The technique used to determine the phosphate concentrations for each water sample was called spectrophotometry. This technique utilizes light absorption to determine the concentration of particles in solution. The instrument used for this technique was the spectrophotometer: a very sensitive by precise apparatus. Our first step was to calibrate the spectrophotometer with 10, 15, 20, 30, 50 and 100 µL standards of a known phosphate concentration (50 mg L-1 PO43-), using the molybbdate blue complex phosphate determination. This determination tells us how much and how well light pastes through a sample, therefore, the amount of light absorbed by the sample is equal to its concentration. For analysis, this determination required preparing a concentrated mixed phosphate reagent and a color developing solution, which were placed in 1-cm cuvettes. 2 mL of each standard was placed in the 1 cm cuvettes and 250 µL of concentrated mixed phosphate reagent and 100 µL of the color developing solution was added.. Each standard was placed one at a time in the spectrophotometer, and the phosphate concentrations were recorded.
Cuvettes containing water sample

This completed our calibration process. Our next step was to prepare the water samples collected from the three different sites. The preparation technique for these samples was exactly the same as for the standards: 2 mL of each sample was placed in 1 cm cuvettes and 250 µL of concentrated mixed phosphate reagent and 100 µL of the color developing solution was added. Each water sample was placed one at a time in the spectrophotometer, and the phosphate concentrations were recorded.
Courtney preparing samples for processing

The phosphate concentration data collected from the standards was used to construct a calibration curve, and the phosphate concentration data collected from the water samples were compared to this calibration curve. The unit used to represent concentration was absorption (arb), because that the amount of light absorbed by the sample was a reflection of its concentration. The major finding was that that wastewater effluent had the greatest concentration of phosphate with 0.291 arb, followed by the estuary with 0.022 arb and the phyto tank with 0.004 arb. These observations could lead to the hypothesis that high phosphate concentration may be associated with high nutrient loads. Hence, the result from the water sample collected from the wastewater treatment plant was as expected; it had the highest levels of nutrients. While the photosynthetic activity occurring in the phytoplankton tank, which was full of algae using up the nutrients, may have resulted in it having the lowest phosphate concentration.

Water Sample              Absorbance (Arb.)

Macrotank (estuary)    0.022

Wastewater (effluent)  0.291

Phyto tank                  0.004___________
Results table showing the water samples arb ratios.

Friday, September 10, 2010

Visiting the Oyster Restoration site at the Skidaway Institute of Oceanography campus

On August 10th, 2010 the research methods class visited the oyster restoration site located on the Skidaway Institute of Oceanography campus. The site was recently restored with pallets of oyster material in April and July of 2010 and is being monitored for the amount of sediment that accumulates over time. Four areas labeled (1, 2, 3, and control) within the site were designated and markers were placed at three different locations off of the beach. These three transects were located near the water, near the shoreline, and in between.

Our job was to measure the length of the markers at that specific time in all areas to determine if sediment is accumulating or eroding from the shore-line and using the measurements of previous months we can determine the sedimentation rate of the shore-line with or without the addition of the oysters. We also took 2 sediment core samples for each transect at the site so that we can examine the grain size distribution and the types of macroinvertebrate infauna that will be done at a later data. We placed all of our samples in Ziploc bags and when we arrived at the laboratory on campus we quickly placed our sediment samples in the freezer to preserve them and our macroinvertebrate samples in a mixture of formalin and rose Bengal in order to stain and preserve the living organisms that we want to identify.

The sedimentation rate for the land had the highest average at 0.53 ± 0.03 cm/day while the control site on land was at 0.02 cm/day (Table 1). The sedimentation rate for the middle area averaged 0.48 ± 0.36 cm/day while the control site had zero sedimentation during the 64 day period. The site closest to the water had the lowest sedimentation rate of 0.21 ± 0.32 cm/day while the control site had eroded at a rate of -0.04 cm/day. It is apparent that the sedimentation rate of the restored site is increasing compared to the control.

Table1: This table represents the sementation rates from July 19, 2010 to August 22, 2010 in three distinct areas of the site. The control site sedimentation rate is represented in red.

This is a photo taken of the oyster restoration site.

These are the markers that we used to measure the depth of sediment.

The sediment tubes that were used to captured the sediment near the depth markers.

The red liquid used was rose Bengal to preserve our sediment samples in the laboratory.

Monday, August 16, 2010

A New Year, A New Class

The new semester is underway at Savannah State and today is the first day of Research Methods in Marine Ecology. Throughout the semester, the students and I will be discussing our class activities in the field and lab and reporting what we learn.