CAREER: Thermal proteome profiling applications for in-situ bioreporting of contaminant degradation in soils

Emerging contaminants, commonly referred to as contaminants of emerging concern (CECs), are anthropogenic chemical pollutants that are increasingly being detected in soils, surface water systems, and groundwater aquifers. In the United States, CECs pose a significant threat to the Nation’s drinking water resources. Microorganisms in soils play a critical role in the protection of drinking water sources by degrading anthropogenic chemical pollutants into harmless and nontoxic byproducts.

However, our ability to grow soil microorganisms and characterize/harness the enzymes responsible for the degradation of CECs has remained elusive. The overarching goal of this CAREER project is to advance the fundamental understanding of microbial enzyme-soil interactions with the goal of developing and validating proteomic-based assays and techniques to probe the microbial degradation of CECs in soils.

To advance this goal, the Principal Investigator proposes to combine soil characterization, active enzyme extraction from soils, predictive modeling, and thermal proteome profiling (TPP) to 1) probe and unravel the microbiological attenuation of CECs in soils and 2) detect and discover novel enzymes that can degrade CECs in soils. The successful completion of this project will benefit society through the generation of new fundamental knowledge on CEC microbial degradation pathways to support the development and deployment of natural and engineered solutions to protect drinking water sources.

Additional benefits to society will be achieved through student education and training including the mentoring of a graduate student and four undergraduate students at the University of Kansas.

Contaminants of emerging concerns (CECs) threaten the Nation’s drinking water sources and access to clean and fresh water. Understanding and harnessing the degradation of CECs by microbial communities in soils, surface water systems and groundwater aquifers could lead to greater source water protection. The goal of this CAREER project is to investigate and unravel the degradation pathways of CECs by microbial communities in soils using advanced proteomic techniques including thermal proteome profiling (TPP).

This innovative approach leverages protocols and assays developed and used extensively in drug discovery to identify a pharmaceutical's protein target. However, a barrier to applying TPP to environmental remediation problems is a lack of knowledge of how active enzymes interact with complex soil matrices, including a robust framework to assess and quantify the extraction of active contaminant-degrading enzymes from soils.

The specific objectives of this research are to: 1) probe and unravel the interactions of contaminant-degrading enzymes with complex soil matrices, 2) develop predictive models of soil-enzyme extraction efficiency based on sorption isotherms, proteolytic potentials, and machine-learning approaches, and 3) integrate model predictions and advanced “omic” techniques (e.g., metagenomics and meta transcriptomics) to validate the use of TPP as a platform for (i) identifying enzymes/proteins involved in contaminant degradation and (ii) in-situ bioreporting of contaminant degradation in soils. The successful completion of this project has the potential for transformative impact through the generation of new fundamental knowledge on enzyme-soil interactions to support the development and deployment of natural and engineered solutions to protect drinking water sources from CECs.

To implement the educational and training goals of this CAREER project, the Principal Investigator (PI) proposes to develop classroom and research-based education modules to increase the motivation and retention of junior college transfer students. This coursework will be paired with research opportunities provided by the University of Kansas Emerging Scholars Program.

Junior college transfer students will be identified through a network of eight Kansas community colleges. In addition, the PI plans to disseminate the education modules to Rose-Hulman Institute of Technology, a primarily undergraduate institution, to recruit and engage undergraduate students in environmental engineering research at the University of Kansas.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.