For the 2018 summer months, I was fortunate enough to receive an internship working with Dr. Robert Nowicki at Mote’s International Center for Coral Reef Research and Restoration in Summerland Key, Florida. While there, I was able to learn from a wide variety of experiences, such as fieldwork, lab work, literature reviews, R data visualization, and recreational diving.

Upon first arriving at Mote, my advisor Robert Nowicki had started a preliminary project analyzing whether seagrass beds had the potential to act as a filter for coral pathogens since there has been an outbreak of an unknown disease affecting the majority of the reef. For data collection, we sampled the water column right above eight seagrass beds and eight adjacent sand habitats. Back at the lab, we pipetted 150 microliters of the water sample onto TCBS plates and then used plating beads for colonies. After 48 hours of letting them sit at room temperature, we counted the number of colonies — specifically, it was broken up into yellow colonies and all other colonies seen. With that data, we imported it into R. Unfortunately, we did not find a strong correlation for seagrass beds reducing Vibrio abundance. In the future, Dr. Nowicki is waiting on a permit that will allow him to place coral directly along the seagrass beds so he can see if there is a more direct filtering response.

Dr. Nowicki also is working to create a long-term database of shark populations in the lower Florida Keys. To assist his research, I was able to tag a shark and collect data on it! To catch them, we set out 10 drum lines with bait attached, waited for a couple hours and then visited the lines again to see if a shark was on the hook. In the handful of times I was able to go out on Dr. Nowicki’s research boat, we were able to catch two 7ft nurse sharks, one 6ft lemon, and a 7ft lemon shark. Once the shark was captured, we proceeded to collect data on the shark’s length, sex, location, species, girth, and any notes of the animal’s health.

A third project I was able to work on was his ongoing assessment of much damage Hurricane Irma caused to seagrass beds. For this, we conducted a literature review to gather information from other papers about past seagrass bed damage caused by hurricanes. Finding out the resiliency of seagrass beds during hurricanes was a major point of the review. Another point he wanted us to look at was if human impacts caused more of a destruction then a hurricane alone. Our findings were that seagrass beds unaffected by human impact were resilient enough to withstand a hurricane with minimal loss. But when seagrass beds had a large disturbance by humans, a hurricane was very destructive and almost caused the majority of the seagrass to be lost.

The most recent project I was working on for Dr. Nowicki is a nurse shark bycatch problem by lobster traps in the Dutch Caribbean. For this project, we housed and cared for 18 spiny lobsters and recreated the lobster traps used in the Dutch Caribbean. In the future, Dr. Nowicki should receive the nurse sharks so that he can start an experiment looking at the ways lobsters and sharks both enter the trap, the interaction between the two animals, and determine possible designs that could eliminate the nurse sharks from not being able to exit.

Overall, this was an incredible experience as an undergraduate student. I interned along side other students from across the U.S. and as far away as Australia. It solidified my desire to further my marine sciences education and seek out additional research opportunities next summer.

By now, you’ve probably heard that antibiotic resistant bacteria (ARB) are a global human health concern. They’ve been found in high numbers in hospitals and schools and a lot of work has been done to investigate their presence in these built environments. It turns out ARB can also be found in natural environments, such as lakes, rivers, and coastal bays. The main way we contribute to their spread in these environments is through… our poop. Wastewater that flows into aquatic environments carries both ARB (which can transfer their resistance to other non-antibiotic resistant bacteria) and residual antibiotic compounds we’ve taken (low levels of exposure to antibiotics selects for the survival and spread of ARB).

So, why do we care about ARB being in a natural environment? In a system such as a coastal bay, ARB can cause seafood- and recreation-related human infections that are essentially untreatable. Important wild and aquacultured fishery species (such as sportfish, shrimp, and other tasty invertebrates) are also harmed by ARB, which can increase their mortality.

To help tackle the spread of ARB, we are using next-generation metagenomic DNA sequencing and bioinformatics to detect ARB, specifically, antibiotic resistance (AR) genes, in three Texas coastal bays: Galveston Bay, Copano Bay, and Nueces Bay (Packery Channel, which receives relatively little freshwater, is our control site). Each bay receives a different major type of wastewater inflow based on its surrounding human development. Freshwater inflows to these bays are largely urban (Galveston Bay), agricultural (Copano Bay), and industrial (Nueces Bay). Each type of inflow carries unique compositions of chemical inducers of AR.

We’ve sampled oysters (an ideal sentinel species since they concentrate contaminants via suspension-feeding) and ambient water from each bay, extracted total bacterial metagenomic DNA from each sample, and sent the DNA out for sequencing. I’m currently analyzing the data and will complete my analyses and the project itself in the coming weeks. Until then, here is a figure detailing the overall abundance of AR genes in each sample type per site as well as the list of antibiotic drugs AR genes in the samples conferred resistance against.

We are extremely excited by what we’re seeing in the samples so far and we can’t wait to uncover more.

I’ll keep you posted,

James

Well in truth our research focusing on the interaction between microbes and plastics in the marine environment has been underway for some time. However, the second part is just underway, and this is the first time I’ve written about it, so I think the title is fine.  Before I get into the details, let’s briefly go over what this research involves. The main focus is to investigate the relationship between nature’s first responders – microbes – and plastic debris in the marine environment. To do this we are deploying capsules containing polyethylene terephthalate (PET) and polyhydroxyalkanoate (PHA) pellets in the upper Laguna Madre. In case you’re wondering, PET is a petroleum-based plastic that is used to make water and pop (that’s what us Canadians call soda) bottles, and PHA is a bioplastic designed to promote bacterial growth and biodegrade rapidly. Since we know microbes respond quickly to contaminants in marine environments (eg. oil in the Gulf), we think it makes sense they will act similarly to the large amount of plastic ending up in our coastal waters. The question that remains is which microbes are responding to this plastic, and how? We’ve designed a study to help answer these questions.

There are two main parts of the study. The field/lab work portion of first part is done, but it involved incubating our plastic pellets (and ceramic pellets as a control) at the water-sediment interface in the Laguna Madre for one month. Following the incubation, we extracted the DNA from the biofilm associated with each type of pellet. We also extracted DNA from filtered seawater to include as a non-biofilm control. The DNA was sent for sequencing on an Illumina Hi-Seq instrument, which we’ve got the data back from and have begun analyzing. I’m not going share the results yet, but to quote a current person of interest, trust me – they’re great. I’ll post later to prove it. Part two is just underway, and the field/lab work aspect of it will run through Fall 2017. The process is very similar to the first part, except subsamples will be taken every month for 15 months, allowing us to track changes in the plastic-associated microbial communities over time.

That’s enough background information for now, and hopefully you get the gist of what we are trying to do. The main reason for this post is to share a video of us deploying our sampling devices that contain the plastic and ceramic pellets. This video was shot two weeks ago out at the Laguna Madre Field Station, which is run by the Centre for Coastal Studies here at TAMU-CC (http://ccs.tamucc.edu/facilities-equipment/laguna-madre-field-station). I’ve edited it together so that you can see the whole process, and hopefully it makes sense!

That’s it for now. I’ll post again shortly(ish) with some results and updates on the project.

Keep your stick on the ice,

Lee

Our talented students are traveling the world for conservation! Amanda Macías ventured to Thailand this summer to volunteer at the Ran Tong Elephant Rescue. Here’s what she wanted to share about the experience.

“Wildlife conservation has always been of great interest to me. I want to be part of the efforts to give some relief to disappearing species/habitats caused by human interference. I had a taste of conservation work through a program called EcoTeach where we traveled though Costa Rica to areas where restoration projects were underway. It was a great experience that helped raise my interest in a career in conservation. This past summer I was also able to travel to Thailand with International Student Volunteer. I spent a few weeks working at Ran Tong Elephant Rescue with other volunteers from around the world. Working with elephants was an incredible experience which only strengthened my desire to study conservation.”

I’m always attracted to art and sometimes that art is inspired by microorganisms. The colorful and psychedelic patterns created by Paenibacillus dendritiformis and P. vortex are among the most well known examples. I recently found inspiration in the sculptures of artist Rogan Brown. A recent NPR article entitled Is This Snowy Wonderland Or The World Inside A Petri Dish? showcased the artist’s micro-inspired paper sculptures. The level of intricacy and detail is astounding and more reminiscent of a scanning electron micrograph. I’m especially fond of the following quote from the interview. “We live in a world dominated by science,” Brown says. “Art needs to work hard to keep up or use the language and imagery of science for its own ends.”

The intent of Sheila Rogers’ captivating and colorful artwork is to raise awareness of one of the most pressing consumer and environmental issues that we face today – plastic pollution, particularly in our oceans. The 3-D pieces are made from debris she has collected along our area waterfronts. Motivated by her desire to educate and motivate the public, Sheila advocates for a reduction of single-use plastics by encouraging small lifestyle changes that will lessen the amount of waste we are putting into our environment.

More Info: http://www.artmuseumofsouthtexas.org/View/ExhibitDetails/tabid/164/articleType/ArticleView/articleId/52/Sheila-Rogers-Oceans-of-Plastic.aspx#Images