Who gave you that golden dollar?!

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My experience here has been INCREDIBLE! I can’t believe how fast it’s gone by and that tomorrow we will all be leaving. 🙁 I have loved every moment here and to be honest, I don’t really want to leave. The connections and memories I’ve made here this summer will stick with me forever. It was so great getting to know all of the fellow REUs and working with so many awesome mentors and professors. If you ever get an opportunity to participate in an REU, do not hesitate to accept! It will be the greatest decision you ever make! It’s been fun Port A, hopefully I see you again soon. <3

– Andrea

 

Elucidating small leucine-like peptides in marine dissolved organic matter using liquid chromatography mass spectrometry

Presenter: Andrea Reynolds – Minnesota State University Moorhead – Biochemistry & Biotechnology

Mentors: Kaijun Lu & Dr. Zhanfei Liu

Dissolved organic matter (DOM) is important in the biogeochemical processes of the ocean. Annually, there is between 15 and 25 Pg of DOM that is added to, and removed from, seawater by various processes. Labile DOM such as peptides and proteins are key factors that support the growth of bacteria. Identification and characterization of DOM is essential because it can provide insight into the functions and metabolisms of microbes that direct the ocean carbon cycle. Preliminary data in Liu Lab (Kaijun Lu) showed that two peptide-like compounds, dileucine and trileucine, were present in Ship Channel seawater using high resolution liquid chromatography mass spectrometry (LC/MS). The objectives of this study were to determine if the compounds found previously in the seawater were in fact dileucine and trileucine by comparing it to known standards using LC/MS, tandem MS (MS/MS) and Ion Mobility (IM). An incubation experiment was also performed to investigate the degradation of trileucine. The presence of dileucine in the ship channel seawater was confirmed and its concentration ranged from 15 nM to 20 nM between different seasons, while an exact signal of trileucine could not be detected. However, the molecular weight of the trileucine-like compound in Ship Channel shared a very similar retention time and fragmentation pattern with the trileucince standard, suggesting that this natural DOM compound may share a similar structure with trileucine. It may be a cyclic trileucine peptide yet could not be confirmed in the duration of the program but will be studied further in the future. Trileucine was found to fully degrade within 96 hours at a rate of 0.0165 μM h-1. Bacteria abundance followed a natural trend of increasing and then decreasing after 24 hours. Overall, this study showed that peptides are an important component of marine DOM and play an important role in carbon and nitrogen cycling in marine environments.

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So Long Port A

Beyond Recycling: A Closer Look into the Association Between Algae and Bacteria

Charles Davis1, Dr. Deana Erdner2

Rice University1, University of Texas Marine Science Institute2

Although phytoplankton and bacteria exist in two separate domains of the phylogenetic tree of life, the two have not only evolved together but also lived in close association over millions of years. Bacteria in ocean water ecosystems are found as free-living organisms, as organisms attached to detritus, or as algae associated bacteria. Although it is known that phytoplankton and bacteria live in close association, the nature of the relationship between the two requires more analysis. Previous studies in the Erdner lab have shown that a bacterized (xenic) culture of the toxic dinoflagellate Alexandrium tamarense experience higher growth rates, cell yield, cell volume, and toxin content compared to an axenic sub-culture. To test whether bacteria could “rescue” the axenic strain, bacterial communities from the xenic culture were added to the axenic culture. The resulting “rexenic” strains were monitored at 9 and 15 months after inoculation. Even though the reintroduction of the bacteria to the algae was shown to “rescue” the culture this effect was observed over a long 15-month period. One of the two rexenic cultures physiologically resembled their xenic parent at end of the 15-month period, and the other rexenic culture was healthier than the axenic parent but not as much as the other rexenic culture. This study examines how the composition of these free and attached communities change over time. To determine community composition, we sequenced the V4 region of the 16S RNA gene as a taxonomic marker. The sequence data was processed using the program QIIME. This consisted of quality filtering of the sequences, clustering into Operational Taxonomic Units (OTUs) at 97% sequence similarity, removal of chimeric sequences, and rarefaction of samples to an equal sequence depth. There were differences between free and attached communities in both the xenic and rexenic samples. The attached communities’ composition initially resembled the xenic parent, but diverged over time. Since one of the two rexenic cultures resembled the xenic parent at the end of the 15-month growth period, we conclude that bacterial communities can have different composition yet still have similar effect on the physiology of the algae.

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“That’s All, Folks!”

Well, I’ve reached the end of my ten weeks and the REUisMe program, I’ve had the time of my life! I’ve learned so much in the academic and personal aspects, I’m extremely happy I came here and that I had the opportunity to experience research up close and personal. I am extremely thankful to Dr. Deana Erdner, director of the program and my mentor for choosing me to be a part of this experience. My fellow REUs already feel like family. I think that this program also has opened my eyes to a lot of opportunities in the marine science field and I’m excited to see what else I can learn and the new chances I’ll have to explore new areas of this field, being graduate school and other opportunities. I’ve really had experience of a lifetime being here in Port Aransas, having fun with my roommates/REUs and working on my project!
Speaking of my project; here’s my abstract, so that you can see what I’ve worked in these 10 weeks!
How to Clean Phytoplankton: A Guide to Natural Sample Separation
‘Phytoplankton interact closely with bacteria, both those free in the water and those that are closely associated with the phytoplankton cells themselves. Most of our knowledge about phytoplankton-bacteria interactions come from culture studies, and we do not know if this reflects what happens in nature. The few studies focusing on natural attached bacteria, have examined “particle attached” bacteria in general. This is due to methodological limitations, as the easiest and most efficient way to collect enough biomass is to use filters of different sizes to separate “free” bacteria (most often defined at the 2µm. This project focuses on designing a method to separate phytoplankton from other particles in a natural sample of seawater.
Our method is based upon two previously published studies that used density gradient centrifugation to separate phytoplankton cells and cysts. We created linear density gradients using a cell-friendly colloidal silica solution (Percoll) and a high osmotic strength buffer system (sucrose). To get an understanding of where phytoplankton would sediment on the gradients, we tested cultures of 9 different phytoplankton species (3 diatoms, 3 dinoflagellates, 3 other). Cultures showed that different groups and species have different yet characteristic sedimentation properties. We also tested a mock field sample, and it proved that interactions with other species in the sample don’t affect sedimentation behavior. When separating wild samples, the dominant species behaved as expected based on the culture results. Most input samples contained detritus, but when the gradient fractions were examined, they were clear of detritus and dominated by diatoms. Our recommendation for optimizing this kind of separation is to target a natural bloom (preferably dinoflagellates), in fairly clear waters. This project’s ultimate goal is to produce phytoplankton-only samples to study wild phytoplankton-bacteria interactions, but the project has multiple applications in the phytoplankton field.’

Thanks to everyone who was a part of this project and all those who made this summer one to remember forever! 🙂

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Amazing Friends, Fantastic Research, Final Bog Post: Oh My Time Sure Does Fly By!

I can’t believe that is the last week, time sure does fly by when you are having fun and working hard! This summer has truly been one of my best, meet and made great friends from in lab to my totally awesome fellow REU students. I am going to miss ya’ll so much, from all the adventures, support, and just relaxing we have done together the past 10 weeks. I have learned so much by working in Dr. Erisman’s lab from how to age fish to figuring out what reproductive phase they are in. I have a new niche in marine biology that I know that I would what to do work in once I graduate. This whole experience has helped me see what the research side of marine biology is like, I do enjoy it alot; yet I can see myself doing work also in educating others about the dangers fish and the marine environment face.  Just yesterday I presented my findings in front of  people from the institute as well as family, boy was I super nervous but in the end it was great. Here is my abstract encapsulating all the work I did in 1o weeks:

Sheepshead (Archosargus probatocephalus) are a very popular recreationally fished species in many regions, especially in Texas. Despite them being very popular in South Texas little is known about their growth patterns in this region. Having knowledge of any fish species growth patterns are important in managing their populations, but it’s especially important for exploited fishes. The objectives of this study were to fit the von Bertalanffy growth model to length at age data, and compare South Texas Sheepshead growth with Sheepshead growth in South Carolina, Georgia, and Florida. We hypothesize that the t0 and L parameters would be different, while k value will be like that of other Sheepshead studies. Differences in growth parameters can be explained by regional differences in nutrient availability, exploitation status, and temperature. To determine the age of each fish otoliths were extracted, sectioned, and then aged by counting annuli under a camera equipped microscope. Von Bertalanffy growth parameters were estimated by nonlinear squares regression in R Studio. Our growth parameters came to L=400.11, k=0.38, and t0= -2.54.  Our estimates of t0 and L are substantially lower than values reported in previous Sheepshead age and growth studies. Specifically, t0 was biologically implausible, suggesting a sampling deficiency. Data was simulated using mean length at age calculated using growth parameters from Dutka-Gianelli and Murie (2001), and standard deviation for ages one to three. Combining our data with our simulated data showed that our parameter estimation for t0 and Lwill improve when more samples are collected. Therefore, this work is an important foundation for describing Sheepshead age and growth in South Texas, but more sampling must be done to accurately characterize this relationship.

Here are some photos from the past couple weeks:


                                                       

Thank you to everyone in Dr. Erisman’s lab, Deana, Yida, and of course my REU fam for making this research experience amazing. Keep in touch Andrea, Aileen, Adriana, Ally, Charles and Kwame will miss you guys a bunch!!

   An experience I will never forget!

-Sam Vanderhoof

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And That’s a Wrap!

I am so thrilled and sad that this program is over. I had such a great time creating bonds, learning about dendrochronology, and just living the island life in general. The REU symposium is tomorrow and I am so nervous and so excited to finally wrap up my project. My abstract is as follows:

In the northeastern Pacific Ocean, sea surface temperatures have shifted from warm to cool phases in 20-30-year cycles over the course of the instrumental record (1900-present) (Mantua et al, 1997). This pattern of Pacific Decadal Variability was originally described as the Pacific Decadal Oscillation (PDO), defined as the dominant pattern of sea surface temperatures in the North Pacific (Mantua et al. 1997). The PDO significantly affects ecosystem functioning in marine and terrestrial systems with implications for human societies.

We aimed to develop a new reconstruction of Pacific Decadal variability using all available tree-ring data in the International Tree Ring Data Bank (ITRDB)—one that includes the global trend in warming temperatures, collectively identified by Johnstone and Mantua in 2014 as the Arc pattern.

Research began with collating available chronologies from the International Tree Ring Data Bank. Then, raw measurement data available on the ITRDB were used to construct chronologies. Afterwards, all chronologies were compared to the Arc pattern using a regression analysis in SAS. Significant chronologies were screened for crossdating accuracy via COFECHA.

Later, all significant chronologies that are properly crossdated will be recreated and detrended using raw measurement data. These chronologies will then be averaged together in order to create a comprehensive look at patterns in pacific decadal variability.

At the moment, we have a preliminary reconstruction that indicates many areas of interest. First of all, the periodicity of the Arc pattern appears not to be 20-30 years as previously thought, but instead around 50 years. Additionally, there are no regime shifts in the 1800s, further evidence for a periodicity of 50 years. Lastly, sea surface temperature is at its record high in the twenty-first century.

 

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Ohio (Come Back to Texas)

I cannot believe how extremely fast this summer has passed by and I am so incredibly thankful that I was able to spend it doing something I really enjoyed. I had no idea going into this program if I would enjoy being in Texas, living in a dorm with roommates, or spending my entire summer doing research. Texas was a lot of fun this the summer and I got to have a lot of cool, new experiences. My REU family and I became extremely close over the course of 10 weeks and I found that I really enjoyed my project this summer. This program helped me gain the confidence to apply for graduate school, fellowships, and many other opportunities in the field of environmental science that I didn’t know about until I joined this program. I am extremely thankful to Dr. Erdner and Dr. McClelland for accepting me into the program this summer and allowing me to work with them at UTMSI. I am also thankful for the graduate students that helped me on my project: Hengchen Wei, Xin Xu, and Yida Gao. Here is my abstract from my project this summer:

TFZs are found at the lower reaches of coastal rivers, where tides influence flow characteristics but there is no mixing with saltwater. The tidal energy slows down the river flow and increases water residence times. Long water residence times allow phytoplankton populations to bloom within TFZs, but spatial variations in ambient nutrient concentrations and physical parameters may affect phytoplankton community characteristics within TFZs. We sampled the Aransas River TFZ in June and July at six sites and investigated the size composition of the phytoplankton community via size-fractionated Chl-a analysis (0.7-5, 5-20, and >20 μm) and flow cytometry (to enumerate pico-, nano-phytoplankton, and cyanobacteria). The ambient nutrient concentrations were measured as well.

The Chl a data show that total phytoplankton abundance is higher in the TFZ than inflowing water during both months. Within the TFZ, total abundance showed no systematic change from upstream to downstream in June but increased consistently in July. The phytoplankton communities were dominated by the 0.7-5 μm fraction in June and the 5.0-20.0 μm size fraction in July. The flow cytometry data showed more consistent spatial patterns for June and July. In both months, the proportion of cyanobacteria increased along the non-tidal/TFZ gradient. Despite the similar spatial patterns, the total counts were higher in June than July. These changes were accompanied by rapid depletion of water column DIN between the non-tidal site and the first TFZ site, which remained low within in the TFZ.  N appears to be the limiting nutrient in this system when comparing the inorganic N/P ratio and the particulate organic C/N ratio. Overall, this project showed that the TFZ supports substantial phytoplankton communities. Cyanobacteria become increasingly important from upstream to downstream of the TFZ. TFZs have the potential to export substantial amounts of labile organic matter as phytoplankton biomass to the estuary. Finally, this system is also a N limited system, therefore sensitive to increasing N loadings from the watershed.

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Raising baby fish is harder than I thought

When they told me i was going to be raising fish I thought it would have been easy. I had some goldfish for a couple months and they practically raised their selves but this was something completely different. First off, larvae fish are extremely sensitive so water temperature, and the amount of air they are receiving must be checked and regulated daily. If they are then lucky to make it to three days after hatching, which for me has been unlikely, then feeding them is another factor. We feed them rotifers that have been enriched with fatty acids and another group we feed them rotifers that have been enriched with fatty acids and probiotics. The rotifers culture can suddenly crash because of a bacterial infection or some unknown factor. Same with the live algae we use for the study. We have not yet gotten them to survive past five days because of either poor egg quality or hard metal in the water. We recent drain the tanks and refilled them again so if anymore more fail water quality can be ruled out. Other than that everything has been great.

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Mid REU Update.

Hey everyone! I can’t believe we’re already halfway through the program and I’m excited for whats next. My project is well underway. So far we have successfully uploaded the sequence data, and used QIIME, a program for microbial ecology, to organize the data. QIIME is run through the terminal app on the computer, so when ever you mess up commands you get error commands, which becomes very disheartening when you spend an entire day trying to do one command. I am now using the program PAST which is used to analyze paleontological data to perform statistical analyses, because the interface is much more forgiving than QIIME. Even though the majority of my work involves me getting frustrated with a computer, the experience is worth it because I will have to lean these skills later.

It’s been a blast getting to know the other REU students, and hanging out in Port A on the weekend. A couple weeks back we went to Six Flags in San Antonio which was super fun because I had never been to either San Antonio or Six Flags. Last weekend, we went on the RV Katy with another group of REU students. While on the Katy we did several field tests that allowed us to get a closer look at marine life. I got to see a baby squid which was really awesome, because I got to look at its chromataphores.

This program has been very interesting so far, and I can t wait for what’s next.

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C1V1 = C2V2 (And other fun stuff too!)

My title is the chemical formula for diluting solutions. Why, you may ask? It’s because I am trying to make myself remember it any way I can, I use it all the time and every day I forget. My mentor must be very tired of repeating it to me!
My project, which is finding a way to separate phytoplankton from every other particle in seawater, has taken some twists and turns. Let’s just say we’re taking the scenic route and we’re walking before we can run. Between cracking the perfects solutions for the gradients, the gradient maker, and plankton tows, our samples weren’t separating as we had predicted. But, we haven’t given up, we attempted many alternatives, like changing the solutions and the gradients; we decided to make steps and even small cushions of different densities, to see what would pass through and what wouldn’t.
Other things we tried were multiple staining, to see our sample clearly, in which we stained a sample with two dyes and our phytoplankton cells emitted fluorescence in one color (blue), while detritus was another. And our last alternative was attempting to use the gradients with cultures (non-wild samples). It helped us to see where common species of the area would be found in the gradient. We are now getting ready to re-test our wild samples with the gradients, with new information about phytoplankton. I’m excited to see our wild samples with fresh eyes!
While it hasn’t been all work and no play, I’ve grown a lot closer to the other REU students; we’re like a little family, there’s no one else I would’ve wanted to have this experience with. We’ve done a lot of fun things, like movie nights, we visited the Texas State Aquarium, go the beach (of course), and we went to Six Flags! That day was amazing! Also, another REU program came to visit from UT Austin (the big campus) and we got to hear a little about their projects studying climate change, in many different approaches, which was very interesting. I met another student from the University of Puerto Rico from the other program, and it meant a lot to me that I could speak Spanish and someone understood me! We had a bonfire on the beach and we went on the RV Katy (boat) and did a plankton tow, mud grab and otter trawls! In which we saw a lot of organisms, like brittle stars, even a squid and a baby shark!
I’m very thankful for this REU program as it gives us a lot of experiences and information, such as seminars and discussions about grad schools and other projects, so we learn a little from everyone! Port Aransas has something special that I’ve grown to really appreciate, as well as the Marine Science Institute. Can’t wait to see what’s in store in the other half of this program!

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Ally’s Adventures on the Aransas River

Hello again! It’s hard to believe that I am already halfway through the program. I’ve gotten to experience so many fun things down here in Texas and the research feels like it is flying by. So far the other REU students and I have gotten to go to lots of awesome restaurants, Six Flags in San Antonio, the Texas State Aquarium, and we got to have a bonfire and go on the RV KATY with the REU students from UT @ Austin last weekend to do some sampling. I absolutely love how much fresh seafood I get to eat here since I’m from Ohio and I don’t get to enjoy it very often. I’m getting pretty close with the other REU students and they’re starting to feel like a family away from home.

My research project seems to be going pretty well. We’ve gone on one official sampling trip on the Aransas River to collect samples for flow cytometry, microscopy, chlorophyll and phycobilin analysis. The trip went great aside from some spiders that took the boat captive on the way to the first sampling site. We also got to see two alligators along the bank, which was awesome because I have never seen them in the wild. We’ve been able to process the first round of samples and we’re working through the data right now. I get to go sampling again next week and I’m excited to see what we find so I can compare the data from both trips. I really enjoy my research and I feel like I have already learned so much this summer.

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