Research > Genomics-Aquatic Microbiology


The Genomics and Microbiology Program is diverse, with projects centered on bacteria, archaea, and eukaryota, ranging from studies on single genes or organisms to studies on whole genomes and metagenomes.  Most of our research projects are student-led. Many research projects involve some combination of genomics or metagenomics followed by bioinformatics to unravel the big data gathered and make informed conclusions.

Culture versus DNA-based detection of bacterial pollution indicator species

Our lab is comparing century-old culture-based detection of bacterial pollution indicator species with more current quantitative DNA-based detection methodology.  The study is being conducted using water samples collected on the Texas Coast in the summer of 2018.  The rapid DNA detection method has the potential to shorten the testing phase and provide more timely answers for public health officials.  The project is a collaboration with Dr. Larry Hauck of the Texas Institute for Environmental Research.

Microbial detection/source tracking with CRISPR/Cas systems

While CRISPR/Cas systems are in the news daily as tools for gene editing, we are using them for detection and genotyping of water microbes.  Two graduate students from Tarleton State University are working in our lab to develop extremely rapid, highly specific detection assays for waterborne pathogens. This project is a collaboration with Dr. Janice Speshock of TSU.

Genomics of important plant traits

We are developing genome-wide markers to characterize Little Bluestem ecotypes used in revegetation projects. The project is a collaboration with Forrest Smith of Texas A&M University, Kingsville, and Dr. Jim Muir of Texas A&M AgriLife Research.

The population genetics of the Comanche Peak prairie clover is currently being studied by a Tarleton State University graduate student in collaboration with Drs. Russell Pfau and Darrel Murray of TSU.

We are also evaluating transcriptomics of drought response intolerant/resistant peanut genotypes. This project is a collaboration with John Cason and Dr. Charles Simpson of Texas A&M AgriLife Research.

Finally, we are studying the population genetics of Pappophorum sp. from disjunct populations in Argentina and Texas. The project is a collaboration with visiting Fulbright Scholar, Lisandro Entio and with Jim Muir of Texas A&M AgriLife Research.

Soil microbiome response

Soil microbiome responses are a vast area of study at the Stephenville center and Dr. Anil Somenhally of Texas A&M AgriLife Research, and Dr. Barbara Bellow of the Texas Institue for Environmental Research is conducting independent studies on soil microbiomes. We also have a few Tarleton State University graduate students conducting studies in the following areas:

  • Establishing a mouse explant microbiome
  • The microbial metagenomics of water samples used for regulatory decision-making
  • Escherichia coli pathogenicity gene survey from water isolates
  • Enterococcus sp. antibiotic resistance gene survey from water isolates
  • The response of the horse microbiome to transport and exercise
  • Soil microbiome/plant interrelationships and soil microbiology
  • Biochar for purification of microbial pollutants
  • Microbiome studies of insect pathogens

These studies are in collaboration with Dr. Janice Speshock of Tarleton State University, Dr. Trinette Jones of Tarleton State University, Dr. Donald McGahan of Tarleton State University, Dr. Eunsung Kan of Texas A&M AgriLife Stephenville, and Dr. Forrest Mitchell of Texas A&M AgriLife Research.

Our own researchers are studying the goat rumen microbiome response to feeding on juniper with Dr. Travis Whitney, Texas A&M AgriLife Research, San Angelo and Dr. Whit Stewart, University of Wyoming. Another rumen study being conducted by Texas A&M Kingsville grad students and in collaboration with Dr. Natasha Bell of Texas A&M University Kingsville is focusing on the effects of monensin and other feed additives on rumen methanogens and the microbiome.

Dr. Jeff Brady

Research Scientist


  • Somenahally, A., Dupont, J., Brady, J., McLawrence, J., Northup, B., and Gowday, P. 2018. Microbial communities in soil profile are more sensitive to legacy effects of wheat-cover crop rotations than tillage systems. Soil Biology and Biochemistry 123, 126-135.
  • Shawver, S.E., Brady, J.A., and McGahan, D.G. 2018. Variation of prokaryotic and fungal soil communities across a vegetative transect. Agricultural Research and Technology 15 (3), 555953.
  • Elrod, N., Brady, J., Rathburn, H., and Speshock, J.L. 2017. Alteration of cytokine profiles inhibits efficacy of silver nanoparticle-based neutralization of arenaviruses. Toxicology: Open Access 3, 1-6.
  • Drugan, A., Brady, J., and Speshock, J. 2017. Ag-NP-induced interleukin-1beta upregulation in a lung co-culture model. Frontiers in Nanoscience and Nanotechnology 3, 1-5.