Gracilaria: A dynamic habitat

Nick Partington, St. Olaf College

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The findings: In my previous post, I described the methods we would be taking this summer to explore how the biodiversity of fishes differ among dense and sparse patches of the invasive alga Gracilaria vermiculophylla. We followed these methods, and we produced some interesting results!

We finally sorted and identified all of the fishes we collected from our samples this summer, and were able to measure the biodiversity between dense and sparse habitats. In particular, we were interested in four measurements of biodiversity. The first, abundance, is simply the overall number of fishes collected from each habitat type. The second, species evenness, measures how evenly individual fishes


Some of the fishes we collected this summer, separated by species and sample.

are distributed among the different species collected in each habitat type. Finally, diversity took into account species richness, which counts the total number of species collected, and the Simpson’s Diversity Index, which quantifies diversity based on the number of species and the relative abundance of each of those species.

These measurements provided us with some interesting results. In the end, we collected a greater abundance of individuals in sparse sites than in dense sites. We also saw both greater species evenness and greater species richness in dense sites. Additionally, the Simpson’s Diversity Index showed a greater diversity of fishes in dense sites.

As I mentioned, abundance of individuals and species richness were both calculated by simply counting the overall number of individuals and species, respectively, collected in each site. Species evenness, on the other hand, required a bit more analysis. Figure 1 shows rank abundance curves for both sparse and dense patches of G. vermiculophylla. These curves tell us how evenly individuals are distributed among the species collected from each site. For each habitat type, species are ranked from 1 to 10 in decreasing order of abundance. That rank is then compared with the abundance of each species. The slope of the resulting line is what we are interested in. Basically, the flatter the line, the greater the species evenness. In our analysis, the line representing dense sites had a flatter slope, signaling greater species evenness in dense sites than in sparse sites.

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Figure 1. Rank abundance curves for both dense and sparse habitats. The slope of the curve representing dense habitats is closer to 0, indicating greater species evenness in those sites.

As I mentioned, overall we found a greater abundance of individual fishes in sparse sites, while we had greater species evenness, species richness, and diversity in dense sites. These differences between sites are very interesting in themselves. But what is even more interesting is that these results are the complete opposite of what was concluded after this same study was conducted last summer. Therefore, there must be some factor(s) that changed between these two studies. We’re not exactly sure what these factors are, but nonetheless, this highlights the importance of long term studies, as well as the importance of continuing this study to see how these trends in biodiversity change and pan out in the long run. I think a very interesting takeaway from this project is that invasive species, like G. vermiculohylla, can potentially provide benefits and sustain biodiversity in ecosystems here in Charleston and throughout the world.

Special thanks to Tony Harold and Mary Ann Taylor for their guidance in this research project. This project is funded by the National Science Foundation and is supported by the Fort Johnson REU Program, NSF DBI-1757899.


Zetaproteobacteria: The Journey Continues

Lauren Rodgers, Rutgers University


Findings: This past summer, we have been working furiously with one goal in mind: measuring the concentrations of iron in the sediments around Charleston to identify if they would be a good habitat for Zetaproteobacteria. We scoured Charleston for the perfect muddy sampling sights and battled the pluff, almost losing a few boots in the process, while also gaining lots of bug bites. We then spent hours in the lab, making solutions, extracting iron, running the spectrophotometer, and collecting data.  And now, after 10 long weeks, it is coming to an end.

This summer of researching Zetaproteobacteria with Heather, Alejandra, and Sarg has taught me so many things. One of which is that science does not happen overnight. You may have an idea of how you are going to do something, but when it comes to actually carrying it out, odds are that it will not go as you think. Science is a dynamic process. You are trying things out, failing, brainstorming for other ways to do things, revising methods, and most of all learning. And this part of the process is what makes it exciting. I experienced this first hand when it came to conducting the ferrozine assay. Much of the research detailing methods for a ferrozine assay were only written for liquid samples, not for sediment samples, so we had to come up with methodology for extracting iron from the sediments. As you can imagine, this took a lot of trial and error. Trial and error such as figuring out the hard way that the water you are using to make up the solutions is actually contaminated with iron, or that glass cuvettes tend to contain their own concentrations of iron in them as well. It was frustrating at times,  but this process was so important for me because it was one of the first times that I was able to take in ideas from many different sources and develop something of my own. It was hard work, but it was all worth it in the end. We were able to collect samples, successfully extract the iron, and measure the iron concentrations, gaining some very exciting results in the end.

What’s next for Zetaproteobacteria?

Now that we have optimized the ferrozine assay for measuring the concentrations of iron in the sediments, we can continue our research on Zetaproteobacteria. The first objective that we will work towards is identifying if Zetaproteobacteria are actually present in the sediments. If they are found, we will then quantify how many Zetaproteobacteria are actually present.

If Zetaproteobacteria are found in the sediments around Charleston, it could have many implications. The first implication is that they could be affecting the local iron cycle around Charleston through their transformations of Fe(II). Zetaproteobacteria have also been shown to be able to live on solid metal and use the Fe(II) present in it, quickening the metal’s rate of rusting. If they are found in Charleston, they could be speeding up the rusting of ships or even metal pipes. Lastly, their presence in Charleston would add evidence to their potential worldwide distribution.

The project from this summer may be finished, but the Zetaproteobacteria journey has just begun!


The Fullerton Lab Team stopping to pose while sampling at Kearns Park on the Wando River. (p.c. Heather Fullerton)

I would like to thank my mentor, Dr. Heather Fullerton, for guiding me through this research, and my Fullerton Lab members for assisting me in the field and in the lab throughout the summer. I would also like to thank the National Science Foundation for funding this research as well as the College of Charleston and Grice Marine Lab for their support.


Expect the Unexpected in Science


Alessandra Jimenez, Whitworth University

As this internship has recently come to an end, I now begin to reflect on the wonderful yet challenging experience I had conducting observational research on Atlantic brown shrimp (Farfantepenaeus aztecus). In the last few weeks of this 10-week summer program, there was a fascinating yet unexpected turn of events. In particular, results of the experiment pointed to conclusions that I initially found myself unprepared for!

In summary, the focus of this experiment was to test effects of immune response on the ability to escape predators in shrimp. The escape mechanism, called tail-flipping (see video below) is actually powered anaerobically. However, recovery from this energetic behavior absolutely requires oxygen (is aerobic). As further explained in previous blog posts (click here and here), a recently discovered consequence of mounting an immune response against bacterial infection involves depression of aerobic metabolism. So, my mentor and I decided to focus on the recovery aspect (aerobic) of the escape response and predicted that this aerobic process would be impaired in shrimp injected with bacteria. At the same time, we predicted that the anaerobic part of this mechanism would be significantly impacted.

A slow-motion video of an Atlantic brown shrimp juvenile tail-flipping in an experimental tank (c) Alessandra Jimenez

The last few weeks of the internship mainly consisted of analysis, arriving at conclusions, and publicly reporting results. After testing tail-flipping ability (click here for an explanation of how this was tested) in a total of 42 shrimp juveniles, 30 of these were chosen for final analysis. Using a statistics software called Sigmaplot (version 12.5), I conducted tests that basically compared experimental groups based on the two variables I investigated: treatment type (bacteria or saline) and time given after injection (4 or 24 hours). Afterwards, results were deemed important based on significance values assigned by these Sigmaplot tests.

Significant results were very surprising!  Overall, results suggested that metabolic depression (indirectly caused by the immune response) did not have an impact on recovery (aerobic). At the same time, the most unexpected finding of all suggested that bacterial exposure actually increased anaerobic tail-flipping activity in Atlantic brown shrimp juveniles! Thus, this result called for a complete change in focus from the aerobic part to the anaerobic part of this particular escape response.

So, how could I possibly explain the increase in anaerobic processes found through this experiment? After much pondering and going through scientific literature, I formulated a new hypothesis. An important enzyme in crustaceans called arginine kinase is involved in the storage and creation of anaerobic energy that can be used for tail-flipping. Recent studies involved injecting bacteria into live crustacean tissue and comparing arginine kinase expression levels with controls. Results indicated a significant increase in expression in bacteria-injected tissue, especially in abdominal muscle (important for tail-flipping!). Based on these investigations, I now think that there may be a link between immune response and levels of anaerobic metabolism. Further research is required to explore this.

The final stages of the internship included creating and presenting a Powerpoint presentation of our work, and submitting a manuscript of my summer investigation. Overall, this REU internship experience has been challenging yet exciting, and has confirmed my love for marine biological research. As I mentioned at the end of my presentation, “expect the unexpected in science”.

powerpoint presentation - REU 2015

Picture of me right before giving my Powerpoint presentation (c) Alessandra Jimenez


Burnett, L. E., Holman, J. D., Jorgensen, D. D., Ikerd, J. L., & Burnett, K. G. (2006). Immune defense reduces respiratory fitness in Callinectes sapidus, the Atlantic blue crab. Biological Bulletin, 211(1), 50-57.

Gruschczyk, B., Kamp, G., 1990. The shift from glycogenolysis to glycogen resynthesis after escape swimming: studies on the abdominal muscle of the shrimp, Crangon crangon. J Comp Physiol B, 753-760.

Scholnick, D. A., Burnett, K. G., & Burnett, L. E. (2006). Impact of exposure to bacteria on metabolism in the penaeid shrimp Litopenaeus vannamei. Biological Bulletin, 211(1), 44-49.

Yao, C., Ji, P., Kong, P., Wang, Z., Xiang, J., 2009. Arginine kinase from Litopenaeus vannemai: Cloning, expression, and catalytic properties. Fish Shellfish Immunol 26, 553-558.

Many thanks to College of Charleston for hosting my project, Dr. Karen Burnett and Hollings Marine Laboratory for guidance and work space, and NSF for funding the REU program.