Projects

Project #1: Land use Development and pollution -- Monitoring of stormwater quality from the nearby industrial warehouse

Lead Mentor - Dr. Den, support from Dr. Abongwa and Dr. Smyth

1. Motivation: The U.S. has seen a warehouse boom thanks to the convenience of e-commerce. While there has been growing awareness of the air quality impact and environmental justice associated with these industrial warehouses, their impacts on water quality deterioration have not been well-studied. Industrial buildings, such as mega-sized warehouses, are likely to pose a bigger threat to stormwater quality than other industrial facilities. This is attributed to industrial warehouses and parking lots adding more impervious surfaces, causing pollutants to wash off easily in each rainstorm instead of penetrating the ground. The TJX distribution center, a 1,700,000 sq ft warehouse whose boundary is about ¼ mile from the western edge of Cassin Lake, can be an unmonitored source of runoff pollution to soil and water in the down-gradient land and water. The lake, despite being designated as a floodplain zone, is also used for recreational purposes and thus the currently unmonitored water quality of the lake can be a public health liability.
2. Project Description: This research involves water and soil sampling and analysis at designated sampling points along the downgradient slope from the TJX warehouse to Cassin Lake. Pollutants can result from the loading and unloading of industrial materials, heavy truck traffic, HazMat spills, and dumpster management. The objective is to
   1. Estimate the warehouse’s contribution of nutrients and sediments to the lake.
   2. Establish a water quality profile, including physical (pH, conductivity, turbidity, total solids, total dissolved solids, dissolved oxygen, salinity), chemical (nutrients, total organic carbon, volatile organic compounds, heavy metals, ions), and biological (total and fecal coliform) parameters.
   3. Examine the quality of surface and subsurface soil at two distances (500 ft, 1000 ft) from the warehouse to Cassin Lake.
3. Undergraduate Research Opportunities: Three REU students will be involved in this project, each will be responsible for their assignments such as soil sampling, water sampling, and lab analysis. Water and soil sampling will be a weekly activity. Students will participate in the design of the sampling campaign, learn how to collect, store, preserve environmental samples, and make on-site measurements. They will also learn how to analyze data by using statistical and plotting tools.
4. Student Background: This project would be ideal for students who have completed at least introductory biology or chemistry. Training on the instruments and tools would be provided.

Project #2: Introduction of Invasive Species -- 3a. Water-borne surveillance for microbial contaminants

Lead Mentor - Dr. Smyth, support from Dr. Den and Dr. Teufel

1. Motivation: The continual monitoring of water quality across San Antonio is a critical endeavor as we are faced with ongoing water scarcity and insecurity. The city known for its river walk is nationally recognized for innovation in water treatment, reuse and sustainability. The PI has several ongoing projects looking at effluent and the Edwards Aquifer and she is developing pollutant source tracking methods that target known host-adapted microbes and is also developing sequence-based approaches to determine unknown emerging pathogens. Cassin Lake and the San Antonio river are located in Espada and this project will focus on developing a longitudinal water analysis program for microbial contaminants (bacteria, viruses and parasites). While minimal development has occurred at the site to date, there are plans in place to add residential units north of the lake and SARA and A&M-SA will also be developing the site. This human activity, along with animal perturbance as well as impacts on the lake will alter the microbial abundance. This represents an ideal site for ongoing surveillance and testing of methods.
2. Project Description: This project will focus on water bodies at ESPADA , and particularly the lake as develop proceeds. Sampling points will be identified, and grab samples will be collected over time, with parameters taken on site using probes and samples brought back to the BSL2 lab of Dr. Smyth on ice. There the samples will be cultured and total nucleic acids isolated. The levels of viable microbial contaminates will be recorded and the amount of detectable microbial nucleic acids will be measured by q-PCR. Metagenomic sequencing and targeted PCR will be used to look at community structure in the water. Students will use statistic and bioinformatic methods to characterize the communities present and to identify any trends over time.
3. Undergraduate Research Opportunities: Two to three REU students will be involved in this project and their role will be to assist in the field and laboratory experiments. They will assist the collection of Cassin Lake water samples, and field testing of water quality using probes and portable devices. Back at the lab, they will isolate genomic information, conduct RT-PCR for targeting host species and leverage next-generation sequencing to conduct metagenomic analyses. Data on coliform/E. coli counts will be shared, along with RT-PCR findings and metagenomic data via a data portal. This portal will be designed to be friendly to the public and shareable with SARA.
4. Student Background: This project would be best supported by students who have taken basic microbiology courses as the lab work will be conducted in the BSL2 lab of Dr. Smyth.

Project #3: Land-use change and anthropogenic impacts -- An ecological baseline for aquatic invertebrate communities

Lead Mentor - Dr. Borda, support from Dr. Valdez-Barillas and Dr. Teufel

1. Motivation: Cassin Lake, a 35-acre man-made lake is in the western region of the Espada Nature Park site. The proximity of the site to industrial and residential development and Phase 5 master planning of boardwalk and trail access to Cassin Lake, impacts to ecological communities are likely, but have not been evaluated. Thus, baseline data is needed to monitor ecosystem shifts over time, relative to anthropogenic and climate impacts. Monitoring of aquatic macroinvertebrates, such as Water Pennies, Riffle Beetles, Mayflies, and Caddisflies, serve as biological indicators and can provide insights into ecosystem health. Sampling protocols of aquatic macroinvertebrates typically use kick nets, rock brushing and/or hand collections, followed by sorting to the lowest possible taxon; the latter which can be limited by time and taxonomic expertise to generate species records. Direct environmental sampling from sediment and water to isolate DNA from meiofauna and zooplankton, can serve as a valuable complementary tool to monitor communities over time and characterize commonly overlooked and understudied invertebrate taxa in freshwater habitats of San Antonio, TX.
2. Project Description: This project aims to characterize benthic meiofauna (benthos/sediment) and zooplankton (water) communities of Cassin Lake and surrounding water bodies within (e.g., La Minita Creek waterway) and proximal (San Antonio River) to the Espada Nature Park. Sampling will include the collection of sediment and water along three north/south directed transects across Cassin Lake, from west to east, with sampling from Le Minita Creek and the San Antonio River from access points within the Park. Sample will be collected in duplicate, to include a sample for photo-documentation / digitization of invertebrates and a sample for DNA extraction and low pass whole genome sequencing. The objectives are to: a) establish community baseline data to document benthic and planktonic invertebrate diversity; b) use modern next generation sequencing tools to characterize biological communities; c) establish an image, genetic and environmental data reference library for small invertebrates of Espada Nature Park, to also serve as a resource for monitoring projects for aquatic habits in Texas.
3. Underground Research Opportunities: Up to two students per year will collect water and sediment samples and environmental data from each transect at the start of the project, where students will gain experience in field sampling, sample preservation and field data collection. Post collection students will engage in downstream sample processing including:
   1. DNA extraction;
   2. Picking for small invertebrates from environmental samples and digitization;
   3. Collection and organization of sample/species metadata; and
   4. Illumina sequence data processing, assembly, annotation and taxon characterization. Students will learn how to analyze and interpret ecological community patterns relative to environmental parameters.
4. Student Background: This project would be ideal for students who have completed at least introductory biology, genetics and/or ecology. Training in all field, lab and computational procedures will be provided by the PI and graduate students serving as mentors.