Wetland Vegetation Sampling

 9/28/2013 - Wetland Vegetation Sampling Lab

Wetland vegetation above the oyster restoration site

Jesse measuring and marking quadrats

The class was separated into 3 groups. Brian, Jesse, and I decided to analyze wetland vegetation north of the oyster restoration site. Vegetation was analyzed using the transect line method with four quadrats positioned at 3 meter intervals (0, 3, 6, and 9). One meter square quadrat was used to measure the total abundance of individual plant species and their percent coverage. The transect began at the edge of the shoreline where the vegetation started (0 meters) and ended 9 meters from the starting point. Global positioning system (GPS) coordinates were collected at both the starting and ending points of the transect. Vegetation within the quadrat was identified by both the common and scientific name. Unidentified vegetation was bagged and labelled appropriately so that the species of vegetation could be determined when we returned to the laboratory at University of North Florida. Our group had one unidentified species of vegetation that we determined to be Sporobolus virginicus (marine couch).

Rough Periwinkle on Spartina alterniflora

We found that Spartina alterniflora (smooth cordgrass) was the dominant vegetation from 0 to 6 meters, but did not grow 9 meters from the marsh-edge. In quadrat 4, Batis maritima (saltwort) was the dominant vegetation, but shared the quadrat with Salicornia virginica (glasswort), Sporobolus virginicus (marine couch), and Avicennia germinans (black mangrove - pneumatophores). 

In this photo, Batis maritima (Saltwort) is the dominant vegetation

Taking Core Samples

The first sampling method employed by my group was the use of sediment corers. In total, twelve sediment core samples were taken from both sites, 8 from the restored site and 4 from the non-restored site. In the restored site, six sediment core samples were taken from behind reef 3, 6, and 8 as well as from between reefs 3-4, 5-6 , and 7-8 for faunal analysis, and two cores were taken for sediment analysis, one behind reef 6 and one between reef 5-6. In the non-restored site, three sediment cores were taken, one near each settlement tray for faunal analysis and one sediment core was taken at 110m for later sediment analysis.The cores taken from the non-restored site were a little more difficult as the soil was covered with large loose shell. Each of the nine sediment core samples designated for faunal analysis were preserved for 1 week in formalin and a Rose bengal stain. After 1 week, the samples were drained for the formalin using a 300 micrometer sieve and transferred to 70% ethanol for analysis. The samples were carefully examined and all benthic organisms (infauna) were separated and preserved in 70% ethanol for later identification. We were able to find a number of organisms both in the restored site and within the non-restored site. 

As expected, species abundance was greater in the restored site. The core samples from the restored had a higher species abundance in oligochaetas, polychaetas, amphipodas and gastropoda w Total species abundance for the restored site was approximately 479 individuals while in the unrestored site the species abundance was only 66 individuals. Measures of biodiversity were also calculated for the core samples, including a Shannon’s and Simpson’s index as well as a measure of Pielou’s evenness.

This is the core we used to extract samples

Core samples after Rose-bengal treatment and being run through a seive

Jars used to hold core samples before being worked up

Unidentified polychaetes and oligochaetes

What we had to look through to find the microscopic organisms 

Overview of the project

Though it has been a while since I posted last, I will do my best to catch up on what we have been working on. I am in the Benthic Fauna group and we are working to see the differences in species richness and diversity of invertebrates. Three sampling methods were used to analyze and compare species diversity and abundance of benthic organisms between a restored and non-restored sites along the Tolomato River: sediment cores, fiddler crab burrow transects and settlement trays.
The first sampling method we chose to deploy was to take core samples behind the reefs, between the reefs and in designated spots along the non-restored coastlines where the settlement trays were to be located (75m, 110m,and 145m from the restored coastline) . With this the overall productivity of the sediment near the settlement trays was able to be assessed. 

Another method that was used to try to quantify the oyster reef’s effects on its ecosystem is that of counting the burrows of fiddler crabs in multiple sites along a transect in both restored and non-restored systems. 

Finally the last sampling method utilized was that of settlement trays. Three settlement trays were used for both the restored site and non-restored site. The first thing done with the trays was to identify and measure the benthic invertebrates using the synthetic reef as habitat. We used a sieve to separate the invertebrates from the oyster. Then these organisms were collected and frozen to later be worked up in the lab. As well, the settlement trays will be used to analyze spat settlement. Measurements of spat settlements will be taken using oysters in the settlement trays that were attached to bricks.

Core Samples: After Rose Bengal Addition

Najda and Julianne analyzing fiddler crabs

Collin and I saving organisms caught in settlement trays to be identified in the lab

Oyster Spat

Vegetation, Transects, and PVC

The vegetation analysis is in full swing! We have collected all the data needed for the project and are now in the process of analyzing it using sample point. Which brings me to my point today:

One of these quadrat transect methods is not like the other!

One of the projects of the vegetation analysis is to compare two different quadrat transect methods. The first one involved a one meter square PVC quadrat being placed along a vegetation transect every 4 meters for 16 meters. In each quadrat we would count the number of individuals in each plant species and determine the average height of each plant species. This was all done by sight and it was very labor intensive. That aside, the data for the quadrats seemed to vary widely because of human error. Each time sight was the method used to determine the abundance and height. Jesse and I both estimated what we thought was the measurements for the quadrat and then averaged the numbers.

On the other side of the project, Jason from GTM and Sharylin quickly zipped through transects using the image analysis transect method. This procedure used a camera mounted above a stand to take a picture of a 1 meter square quadrat below. The method took two days to complete, mostly because of weather restraints since our camera was not water resistant. The measurements for the quadrats were made a program called sample point (www.samplepoint.org). Once the images were cropped to only show the quadrat sections sample point was used to select 64 random points/pixels. Each point determined to be a type of plant or not and then the data for abundance was put in a excel file to be analyzed with a statistical process. By the time of this writing, all of the transects are completely cropped and only one transect is left to be run through sample point.

All 17 transects were measured using the Image analysis method while only the first 3 transects were measured using the visual method. After doing three transects with the visual PVC method it was obvious that it was not nearly as accurate as the Image method. The transects have not been compared as of yet but we believe that the camera and sample point method will be much more accurate.

Last sampling day (fish group)

The last day of sampling for the fish group went very smooth. 

We seined four times and collected several samples. Even though the tide was incoming and not going out we got a nice amount of data. We worked as efficiently and hard as we could to make sure no mistakes were made and that we would finish sampling on a high note. I think we accomplished this. 

Here are some pictures that I wanted to share with you of the last day at the restoration site. 

Waiting for high tide we took a little hike 

Fish Group use B-shaped traps

The set up: The traps sit with the opening facing the incoming tide. Two plastic mesh wings are secured at the opening of the traps to direct fish into them. The traps fish for two hours during incoming tide.

The opening is somewhat small so the main fish collected are small fish and shrimp. Fiddler crabs and hermit crabs are also found inside the trap a lot, for the purpose of our study these are not identified and processed. The amount of fish collected using this method is not nearly as much as the data we collect while seining.

Both times while using the these traps we were able to see the wake energy approaching the shore. Some wakes were strong and damaged wings, moved traps or turned them. The wakes this shore is hit by is a constant problem and we have been able to see what recreational boating does to some of our shorelines.

Vegitation Data

This past Friday and Saturday my group (the vegetation group) went out to the GTM NERR. Despite bad weather conditions we were able to collect all the data we needed. What we did was on Friday we set up all of the markers for the quadrants that we were to be sampled; however due to rain and the non-water proof camera none of the data could be collected. So Saturday afternoon we went back out and took the photos and measurements for each of our 17 transects. We based this number of transects on the sites that a previous experimenter had set up using her markers as the base points for our transects. We took quadrant samples for five quadrants along each transect at 0, 4, 8, 12, 16 meters. We used the camera set up provided by the NERR which allows for aerial photos to be taken. We also measure the average canopy height of each species within each quadrant as well as the distance between the base point markers and the edge of the shoreline. This was done with the intent of it being the initial reference distance to determine whether the shoreline is eroding behind the reefs or if is is accreting. Now we have to use the computer program provided by the NERR to quantify the photos that were taken and analyze the trends in the data.

Image of the aerial camera set up in the field

November 16, 2013

On November 16, 2013 the benthic group met up at the University of North Florida for a lab day in which we would attempt to identify the organisms, as best we could, that were found in the core samples. This was a very tedious process that took us around five to six hours to complete. Also the furthest we could classify the worms to was class. We didn't have the experience or microscopes to really give us the ability to classify them any further. I also personally had some trouble moving the worms from the petri-dish to a microscope slide, a few were mutilated in the process. Within the cores we also found a couple arthropods as well as a few gastropods. Once the organisms were counted and stored in the correct vials in 75% EtOH, we wrapped up our day discussing the final aspects of our project. We decided on a poster layout as well as how we were going to display a lot of our results. We also discussed how we were going to finalize our paper and who was going to work on which parts. I'm personally happy we are finished analyzing all of our samples and that now we only have to focus on the presentation side of our results. By next Saturday I believe we should have our results analyzed and should be wrapping focusing on finishing up our paper. So far we are making great progress and I'm interested in what our data is going to tell us. 

November 9, 2013

On November 9, 2013 we arrived on site, at GTMNERR, around 8am. Our main focus was collecting our settlement trays for oyster spat settlement and benthic fauna. We began by pulling up our trays behind the restoration site and moved down the shoreline pulling up all the trays. When we pulled up the trays we removed the bricks, then put the oyster shells for oyster spat in bags and then stored them on ice. After the bricks were removed we poured the contents on the trays into a mesh filter to remove the oyster shell and allow the organisms to fall through. In some of the trays we found a couple fish and a few crabs, but most of the organisms consisted of shrimp. Dr. Smith was able to identify one of the crab species to be an exotic species of interest. All of the organisms were bagged and put on ice to be identified back at the lab. We were also fortunate enough to get our transects of fiddle crab burrows, thanks to Julianne and Nadja. Once all of our data was collected we went back to the lab to try and finish up our core samples as well as start on our identification of the organisms found in the settlement trays. Overall it was another long day, around seven hours, but we were able to get a lot accomplished. We still have a good amount of work left, but we are moving at a good pace and have an efficient flow within our team.

Field Day - Settlement Trays and Fiddler Crab Burrows

            On 11/9/13 we finished our field sampling which included pulling up the settlement trays and completing the fiddler crab burrow transects. We learned how to process the settlement trays in the field which was a very involved and messy process. It definitely required all 4 group members and Dr. Smith at times, but we got better at it with practice. We emptied the contents of the tray into a set-up of layers of trays and mesh.

Sifting through the contents of the settlement trays
Courtesy of Dr. Smith

            Once all the contents were emptied out of the settlement tray we had to rinse the oyster shells with water and sift through to separate the benthic organisms into a labeled bucket which were then later collected into Whirl pak bags for further identification in the lab. Two species of shrimp that were identified from the samples taken from the settlement trays were Palaemonetes pugio (shore shrimp) and Alpheus heterochelis (big-clawed snapping shrimp).

Alpheus heterochelis (top)
Palaemonetes pugio (bottom)

            While Collin and Kierstin were measuring and sorting through the benthic organisms collected, Julianne and I started to measure out the transects for counting the fiddler crab burrows. One 12 m transect was measured out behind each settlement tray in each site (3 per site). 0.25 m² quadrats were placed at 0 m, 4 m, 8 m, and 12 m along the transect and each fiddler crab burrow that fell within the quadrat was counted.

Julianne and I counting fiddler crab burrows
Courtesy of Dr. Smith

            After a long day of sampling we brought back a lot of samples that need to be worked-up including analysis of spat settlement on the oyster shells that were attached to the bricks in the settlement trays. This will be done by using a 4 cm x 4 cm grid and placing it on the oyster shell while looking under a dissection microscope.
    Overall, there is still a lot of identification to do, but I'm excited to see what kinds of organisms we were able to collect. 

Seine Day #2 for the Fish Group

Our day began Sunday November 10, 2013 out at the GTMNEER at 9 am. As a group we decided to make Sunday our seine day because with the tides we had to work with, it made it a better fit to seine. The four of us made it out on site a little after 9:30 and to our surprise the tide was a bit low still for us to do anything. So to make good use of our time though, we split up and began measuring out our sections of the on reef and off reef location, and we doubled checked our equipment and made sure everything was ready to go once the tide came in. After some time pasted, the tide finally came in enough for us to begin. Water quality, turbidity reading, and water samples were collected first from the on reef site and off reef site. After that, Jon and i had the task of dragging the net at each of our four locations (2 on reef and 2 off reef) while Shannon and Natalia recorded what was caught. Since this was our second go around seining, collectively as a group were able to get a pretty efficient system down that seemed to really make the whole collection process go by pretty fast. Overall, the day was very productive, I felt like we collected pretty good data.

Second encounter in the same weekend, I almost stepped on this one two!

Trap Day #2 for the Fish Group

Trap day #2 started bright in early for the fish group. Low tide for Saturday November 9, 2013 was at 6:50 am so it was important to get out there as soon as we could to get the traps set. As soon as were got out on site Jon and i got to work. We were kinda on a time crunch because we had to do the work of four people and the tide was coming in fast! Dr. Smith said something about a foot an hour so we had to move quickly! Since we were low on people to help set the traps, Jon and I made a game plan to set out all the B-Traps first in there specific locations (4 on reef and 4 off reef), and then one of us installed the wings while the other zipped-tied them the the traps to help save time. Due to the bentic groups trays on one of the reefs we were suppose to trap behind we had to deviate a bit from the proposal and set the traps in between the reefs which we made a note of on our data sheets. Once the traps were set, we set our timers for two hours and then begin to take our water quality and turbidity readings. By the time we collected all our data from the water quality and turbidity reading , it was time to pick up the traps and record what was caught. For two people, dragging all eight traps in about waist high water was a bit of a chore but thankfully Dr. Smith was able to start identifying, measuring, and recording while the two of us were bring in traps. Once all the traps were in and the three of as went to work it was long after that we were packing up and headed back to the shed. I'd have to say the day went pretty smooth with the amount of stuff that had to be done. 

Lab Day - Sediment Core Analysis

            Due to tide and weather constraints, we (the benthic group) started the work-up process of our sediment core samples taken the previous Saturday (10/26/13). However, it was only part 1 of the analysis. After being stained with a reddish/pink color and preserved in formalin for a week, we had to transfer the samples to 70% ethanol. The process was a bit messy and complicated at first, but it was interesting to learn a new sampling/analysis technique. The sediment core samples were put through a 300 micrometer sieve and the formalin was drained off and discarded in the appropriate waste container. Then, the sieve was taken over to a sink and using tap water, the sieve was rinsed through pushing the sediment down and only leaving behind the sediment and organisms larger than 300 micrometers. The remaining sediments/organisms were then rinsed into a labeled vial with 70% ethanol. We repeated the process with all 9 of our sediment core samples intended for faunal analysis.

            After all the samples were transferred to ethanol, we were able to start the work-up process. We used dissecting microscopes and small petri dishes to find any organisms that were present in our core samples and this was indicated by a dark pink color. We separated any organisms we found into small vials with ethanol for later identification. So far, we found mostly worms, but I did find what appeared to be a shrimp in one of the samples. The process takes a good amount of time, but I'm looking forward to see what else we will find. 

Looking through dissecting scopes for benthic organisms (pink color)

      

11-2-2013, Core Analysis

On 11-2-2013 we, the benthic group, removed our 9 core samples from the preserved whirl-bags for fauna collection and preservation. We were successful in sieving all the unwanted  material from the samples taken from our site at GTMNERR. The sediment and material that remained in the sieve was then stored in a labeled jar. From there 3 out of the 9 jars had all the remaining sample analyzed for fauna. In the previous week, when the samples were collected, they were preserved with a dye that binds to a particular protein staining fauna red. This made it far easier to identify organisms as we were sifting through the material under a dissection scope. The organisms that were collected were stored in a vial with 75% EtOH and labeled according to site. Before next Saturday we would like to have all our samples analyzed and all fauna preserved, as well as possibly begin the identification process. Everything seems to be going according to schedule and so far I've learned a few new lab skills. Also, I was impressed by the overall amount of organisms we've found so far in our 3 samples.