LABORATORY FOR MICROBIAL & ENVIRONMENTAL GENOMICS
Join Us:

Detecting antibiotic resistant bacteria in our bays.

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.

blog-post-picture7

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

Plastic-microbe interaction study is underway!

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

Ran Tong Elephant Rescue

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.”

Culture Sculptures

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.”

 

Sheila Rogers: Oceans of Plastic

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

A Beguiling Aesthetic: Shelia Rogers and Her Oceans of Plastic

The ocean lures us to play, provokes us to awe, and makes us wary of its force. These colossal waters demand our reverence. And yet humans have become most intimately connected to this geography by way of our trash, by way of our thoughtless use of the ocean as an oversized garbage disposal.

I recently moved to the town of Corpus Christi, Texas, which sits directly on Corpus Christi Bay, a short reach from the Gulf of Mexico—the beloved Third Coast. Every day the locals breathe air from this water, finding sweet relief from the heat compliments of the steady breeze that rolls off the water. There is a consciousness here regarding the marine environment that can only arise from a nearness to the coast. The beaches and the Corpus Christi Bay function as the front-yard view to a home, a daily destination for recreation, a faithful landscape during the commute, a research center, or a storm tracker. There is even a university—Texas A&M-Corpus Christi—that sits on its own island, surrounded by both Corpus Christi and Oso Bays. Now that I have become a local, I can confirm that the sea is always present here, always on our minds.

Yet one glance along the bottom of the seawall steps or across the lengths of the sandy beaches and one can’t miss the filth and trash that accumulates from the sheer mindless practices of locals and tourists alike. Plastic grocery bags and other single-use plastic containers, fast-food Styrofoam drink trays, and an unbelievable mass assemblage of other material gather in these places. Some of the trash comes from daily use and discard, some is washed into the bay during rains, and some washes ashore from other cities—or from deep at sea—after tropical storms. It is a terrible cycle of pollution in an environment that desperately needs conservation, but even still, many local grocery chains insist on offering multiple plastic bags for the purchase of one gallon of milk.

An artist who I met early in my time here, Shelia Rogers, calls Corpus Christi her hometown and finds these circumstances intolerable. A self-proclaimed beachcomber, she began collecting, cleaning, and then organizing the trash she found into her art practice. In an effort to highlight the considerable ecological harm that we are perpetuating on our coastlines, she turned these fragments into an entire exhibition, entitled Oceans of Plastic, which she recently presented at the Art Museum of South Texas.

From a distance, the pieces in Rogers’s show take on a life that’s beyond their source material. They appear innocently vibrant and joyful, like a child’s playground. One cannot keep from admiring the aesthetic candy presented at every turn, as each and every contribution sparkles under the gallery lights. Rogers exploits the colorful potency found within her plastic art objects as a seductive device by which to entice us closer and closer to her work.

So come closer.

Ensconced inside the plexiglass displays are the countless pieces of plastic Rogers beachcombed for over several years—fragments of single-use containers or bottles that will never decompose naturally. At the other end of the room are additional display cases, exhibiting plastic soda bottles with gaping holes made by the marine life who cannot differentiate the bottles from an actual food source—many of these animals die from starvation because the plastic fills their stomachs and they are then unable to receive nutrition from normal food. Finally, hanging from the ceiling is an entrancing cotton candyesque sculpture made entirely of monofilament fishing line that has been cut and left to float in the water. Rogers found every piece of this beautiful, horrifying detritus.

Close-up, this is haunting. There is an aesthetic appeal to this trash that can make a heart break, and by displaying this beguiling aesthetic, Rogers pulls back the curtain on a deeper reality of our situation: plastic is made pretty so that we will use it. And we will. We do. All of the time.

Considering the effortlessness with which this one dedicated artist finds plastic remnants on the beaches of Corpus Christi, it is easy to see how problematic our trash consumption and disposal is on a global scale. Rogers is one of many artists who are working in an activist vein to raise our awareness to this dire situation through the presentation of organized material. I find the hope of her exhibit is that she is not working in a vacuum.

Rogers has offered a visual witness to the significant work of local conservation teams and researchers, who are attempting to understand and restore the health of local marine life and who are pushing for changes, such as a plastic bag ban. By partnering with the Harte Research Institute Gulf of Mexico Studies of Texas A&M University-Corpus Christi, this dialogue has expanded among academics, conservationists, artists, museumgoers, and the supportive public alike. Together these individuals are laboring to safeguard the beauty of the place whose name is the Third Coast. This is an incredible conversation to have moved into and an incredible art exhibit to start my journey in South Texas. Thank you, Shelia Rogers—I feel the possibility of refreshing change just as I feel the breeze off of Corpus Christi Bay.

Editor’s Note: For further information regarding local conservation efforts within Corpus Christi, Texas, visit these resources:  Coastal Bend Bays FoundationCoastal Bend Bays and Estuaries ProgramCoastal Conservation Association, Corpus Christi ChapterHarte Research Institute Gulf of Mexico Studies; and Surfrider Foundation.

Authors:
Jen Grabarczyk-Turner
Jen Grabarczyk is a contemporary artist who works in abstract drawing, painting, installation, and film. She holds an MFA from Claremont Graduate University and an MA in theology and culture from The Seattle School of Theology and Psychology. She is also art editor for The Other Journal.

Shelia Rogers
Shelia Rogers is a contemporary artist who lives and works in Corpus Christi, Texas. She completed her postgraduate work at Texas A&M University-Corpus Christi. She has shown her work extensively within her local region of South Texas and has received several awards from the Art Museum of South Texas. Her most recent exhibition, Oceans of Plastic, received notable press and was displayed at the Art Museum of South Texas, the Historic Brownsville Museum, and the Texas State Aquarium. More information about Shelia Rogers can be found on her website: http://sheliarogersfineart.com.

Original Source: http://theotherjournal.com/2014/11/13/a-beguiling-aesthetic-shelia-rogers-and-her-oceans-of-plastic/nggallery/thumbnails