Superfund Research Program

The Superfund Research Program (SRP) hosted a Risk e-Learning webinar series emphasizing new approaches to elucidate mechanisms responsible for bioremediation. The series featured innovative molecular, biochemical, cellular, and/or engineering tools to advance our understanding of the structural and functional properties of microorganisms or plants involved in the bioremediation of hazardous substances.

Session I - The Microbiome
September 30, 2019 • 1:00 – 3:00 p.m. EDT
To view the archive, visit EPA's CLU-IN Training & Events webpage.

The first session served as an introduction to the series and touched on opportunities to build linkages with other microbiome fields of study, such as the human microbiome.


  • William A. Suk, Ph.D., NIEHS Superfund Research Program
  • James Tiedje, Ph.D., Michigan State University
  • Raina Maier, Ph.D., and Paul Carini, Ph.D., University of Arizona
  • Moderator: Heather Henry, Ph.D., NIEHS Superfund Research Program

SRP Director William A. Suk, Ph.D., introduced the series, highlighting SRP grant recipients' contribution to innovation in bioremediation. The SRP funds multidisciplinary research to address the complex and evolving challenges associated with Superfund and related hazardous waste sites, including the development of new remediation technologies. Dr. Suk provided an overview of the findings from past SRP bioremediation research, from basic discoveries to cost-saving field applications, and introduced potential opportunities to expand the bioremediation toolbox.

James Tiedje, Ph.D., from the Michigan State University SRP Center, discussed the past and future of microbiome science, which transcends habitats. The major questions, methods, and underlying biology of microbiome science are very similar, so much is transferable among studies in the soil, gut, ocean, and other systems. There are important differences in the details, but the details are not the starting point. In this talk, Tiedje summarized what we have learned from the past in microbial ecology that helps us project the future and then speculated on that future and how it may impact and likely facilitate SRP-relevant microbiome research.

Microbial communities mediate important transformations of environmental arsenic. These biotransformations dictate the bioavailability and toxicity of arsenic in environments ranging from soil to the human gut. Raina Maier, Ph.D., and Paul Carini, Ph.D., from the University of Arizona SRP Center, discussed new integrative tools that combine plant transcriptomics, microbial meta(genomics), and high throughput microbial culturing to link key taxa to specific arsenic biotransformations important to both phytoremediation processes and human health.

Session II - Novel Omics Approaches
October 3, 2019 • 1:00 – 3:00 p.m. EDT
To view the archive, visit EPA's CLU-IN Training & Events webpage.

The second session highlighted innovative genomic approaches to enhance bioremediation by microbes and plants.


  • Claudia Gunsch, Ph.D., Duke University
  • Julian Schroeder, Ph.D., University of California, San Diego
  • Moderator: Michele Mahoney, U.S. Environmental Protection Agency (EPA) Technology Innovation and Field Services Division

At Duke University, Claudia Gunsch, Ph.D., leads a research team developing a framework for precision bioremediation. The team seeks to maximize biodegradation potential by identifying optimal microbial targets for biostimulation, bioaugmentation, and genetic bioaugmentation given a site's microbial and biogeochemical fingerprints. This work includes characterization of several Superfund sites in North Carolina and Virginia.

Julian Schroeder, Ph.D., from the University of California, San Diego SRP Center, discussed molecular mechanisms of heavy metal detoxification and remediation in plants. Many human diseases have been attributed to environmental contamination by toxic heavy metals, in particular lead, mercury, cadmium, and the metalloid arsenic. Plants play a key role in mediating human exposure to toxic metals and the metalloid arsenic in two ways: (1) people consume toxic metal(loid)-containing plants (diverse foods, tobacco products), and (2) non-crop plants can be used to remove heavy metals and arsenic from the environment for bioremediation. Extensive redundancy in plant genes has been an obstacle to understanding processes mediating toxic heavy metal(loid) accumulation in plants. Newly developed genome-wide artificial microRNA libraries were presented that can now identify the genes, signal transduction pathways, and mechanisms underlying heavy metal(loid) accumulation in plants. This knowledge is crucial to reducing human exposure to toxic heavy metal(loid)s.

Session III - Emerging Opportunities
October 11, 2019 • 1:00 – 3:00 p.m. EDT
To view the archive, visit EPA's CLU-IN Training & Events webpage.

The third session highlighted new and emerging tools to improve existing bioremediation approaches and improve human health.


  • Pedro Alvarez, Ph.D., Rice University
  • Dora Taggart, Microbial Insights
  • Ameen Razavi, Microvi Biotechnologies
  • Moderator: Cindy Frickle, U.S. EPA Office of Superfund Remediation and Technology Innovation

Pedro Alvarez, Ph.D., from Rice University, discussed opportunities for nanotechnology-enabled in situ remediation technologies to address soil and groundwater contamination. Complex subsurface contamination domains and limited efficacy of existing treatment approaches pose significant challenges to site remediation and underscore the need for technological innovation to develop cost-effective remedies. This discussion covered candidate nanomaterials and their applications to complement existing remediation approaches, as well as potential barriers for implementation and strategies and research needs to overcome these barriers.

Dora Taggart, an SRP Small Business grant recipient from Microbial Insights, discussed their work to understand how environmental microbes are protecting our health. Research has consistently shown that human health is deeply intertwined with the gut microbiome, and new studies are illuminating the ways in which environmental contaminants are affecting, and are affected by, those microbes – sometimes even increasing in toxicity throughout the process. Through qPCR, isotopic analyses, metabolomics, and other molecular biological tools, technology advancements and novel approaches are finally allowing scientists to understand the beneficial impacts that active microbial contaminant degraders can have on human microbiomes. This presentation highlighted the information that these tools can provide and discussed some of the new groundbreaking methods that will soon be common in the industry.

Ameen Razavi, an SRP Small Business grant recipient from Microvi Biotechnologies, discussed microenvironmental impacts on the induction kinetics of cometabolism for the bioremediation of chlorinated hydrocarbons. The effectiveness of aerobic cometabolism-based bioremediation strategies for chlorinated hydrocarbons is tightly linked to the sustained induction of specific enzyme classes using primary metabolites, or inducers. This presentation provided an overview of aerobic cometabolism with an emphasis on emerging concepts for enhancing induction kinetics. Data from laboratory-scale and field pilot systems were presented to illustrate translational applications and identify continuing research and knowledge gaps. The presentation also covered the early-stage development of a functional and predictive computational model based on microbiome-based sciences. Specific contaminants discussed included chlorinated solvents, 1,4-dioxane, and BTEX (benzene, toluene, ethylbenzene, and xylene).