New Mexico Tech, Socorro, NM
Dr. Rebecca Reiss is a genomic scientist interested in the application of next-generation sequencing techniques to environmental and materials engineering projects. She has a Ph.D. in Genetics from Cornell University and over 20 years of experience as a Professor of Biology at New Mexico Tech (NMT) in Socorro, New Mexico. Her involvement with environmental engineering started in 2010 with shotgun metagenomic analysis of a tetrachloroethylene-contaminated EPA Superfund site. Now retired (emeritus) from NMT, she started a company, Hexadecaroon Genomics Consulting LLC, to facilitate continued research on environmental microbomes. Currently she is applying her experience to a trichloroethylene-contaminated site. She predicts that recent refinements to metagenomic techniques that eliminate the uncertainty in DNA fragment assembly will be the next milestone in environmental microbiomics by accelerating the rate at which microbes with novel functions can be identified.
Bio-Prospecting for PFAS-Degrading Microbes in Fluorspar Deposits
The scarcity of characterized microbes capable of degrading Per-and Polyfluoroalkyl Substances (PFAS) are currently a major barrier to the establishment of bioaugmentation protocols for these important emerging contaminants. Analogous to the finding that microbes capable of respiring chlorinated solvents exist in nature where chlorine is found, we hypothesize that fluorinated chemical degrading-microbes might exist where fluorspar is found. Fluorspar, also referred to as fluorite, or calcium fluoride, commonly exists in deposits in the Rocky Mountains. Near these sites water sources are often high in fluorine, indicating that there may be biological activity associated with fluorspar. Fluorspar has been found to be rich in fluorocarbons including CF4, CF2Cl2 and CFCl3. The presence of carbon fluorine bonds in fluorspar has the potential to select for specialized microbes that utilize these compounds as metabolic growth substrates, which if found, would be candidates for bioremediation of PFAS. Currently, we are using the resources of the Colorado and New Mexico State Geological Bureaus to identify potential collection sites by locating fluorspar deposits and nearby water sources with high fluorine levels. Once potential sites are identified, the logistics and permissions necessary to acquire appropriate geological samples will be established. Once sampling of selected sites is completed samples will be subjected to microbial enrichment techniques in microcosms with media amended with selected PFAS compounds and electron donors and other compounds with potential to enhance PFAS degradation. Microcosms that exhibit declines in PFAS concentrations relative to sterile controls will be selected for further enrichment and characterization. The microbial composition of the enrichments will be determined using standard 16S rRNA amplicon and shotgun metagenome sequencing protocols, and a novel technique, in which the DNA is cross-linked in a duplicate sample prior to DNA extraction and sequencing. When compared to a non-crossed linked sample, it is possible to determine the association of DNA fragments to specific genomes, eliminating most of the uncertainty in assembling DNA fragments into genomes. High-quality metagenome-associated genomes (MAGs) can be annotated and examined for genes coding for proteins with the potential to degrade PFAS. Annotated genomes can also indicate effective conditions for culturing. While attempting to enrich PFAS degrading microbes from PFAS contaminated groundwater is certainly worthwhile, the relatively short duration of this contamination (i.e., decades) may be insufficient for natural evolution of PFAS degradation. Relatively ancient fluorspar deposits may offer a unique opportunity to find important carbon-fluorine bond breaking microbes.