Ecophysiological analyses of isolates representing key taxa at contaminated sites

Plasmid analysis of an isolate from the uranium and nitrate-contaminated subsurface of the Oak Ridge Reservation reveals a large number of metal resistance genes and transposable elements.

A significant goal of microbial ecology is the development of models that accurately predict how environmental perturbations will impact the structure and function of microbial communities. Identification of representative isolates is essential for the high-resolution physiological studies required for proper parameterization of these models. Frequently, pure-culture laboratory studies fail to select appropriate isolates that are relevant to an environment either in terms of taxonomic abundance or metabolic function. I am using 16S amplicon sequence data to identify isolates that have 100% 16S identity to prevalent amplicon sequence variants (ASV) in the toxic metals and nitrate contaminated subsurface of the Oak Ridge Reservation. Using a combination of laboratory experimentation informed by field-relevant geochemical parameters, genomic analysis, and proteomics, I am exploring how mixed waste contamination (i.e. nitrate and metals)  impacts the physiology of microorganisms at the site. 

Additionally I am interested in the evolution of microorganisms at this site. I am using genomic and metagenomic analyses to explore site-relevant adaptations with a particular emphasis on acquisition and expansion of mobile genetic elements.  

The video below is a recent poster talk discussing part of this project. 

Metal cofactor utilization at contaminated sites

The molybdenum cofactor and tungsten cofactor are synthesized via the same biosynthetic pathway. Thus, many organisms will synthesize only one or the other at any point in time. However, we have identified an isolate with measurable WOR activity during nitrate respiration-- a process which is dependent on the molybdenum cofactor.

The tungsten (W) oxidoreductase (WOR) family of enzymes is widely distributed in prokaryotes– both bacteria and archaea. Despite being a ubiquitous and diverse family of enzymes, WORs are very poorly characterized. I am studying the role of WORs within the contaminated Oak Ridge Reservation (ORR) subsurface environment. As in most environments, W concentrations are low in the contaminated groundwater of ORR. Interestingly, when we look at the metagenome data for several of these contaminated wells we see that certain W-related genes are enriched relative to background wells. I have identified isolates from this site with WORs in their genomes and am using a combination of genomics, whole cell activity assays, protein purification, and FPLC-MS to characterize the function of WORs at this site. 

In addition to my work on W cofactor utilization, I have recently been exploring how heavy metals impact iron cofactor utilization by microorganisms at the site.  We have found that mixed heavy metals disrupt the activity of iron-cofactor containing proteins, likely through mismetallation.
The video below is a recent seminar talk given on this project.

Tellurium microbiology

Tellurite adsorption onto microbial surfaces is facilitated by reaction with surface sulfhydryl groups within proteins. Picture from: Goff, Jennifer L., et al. "Tellurite Adsorption onto Bacterial Surfaces." Environmental Science & Technology 55.15 (2021): 10378-10386. DOI: 10.1021/acs.est.1c01001

Tellurium is an emerging environmental contaminant due to its increasing usage in thin film photovoltaic cells. However, we know relatively little about its biogeochemistry and how microorganisms interact with various tellurium compounds. My work has shown that sulfhydryl groups are important in microbe-tellurium interactions. Furthermore, the sulfate transporter can also transport tellurate intracellularly due to the structural similarity between the two compounds. 

Extracellular biogenic sulfur metabolites

Bacillus sp. JG17 was isolated from seleniferous soils. This strain was capable of solubilizing elemental selenium during active growth. This process was connected to the extracellular sulfur species released by the isolate. Figure adapted from Goff, Jennifer, et al. "Role of extracellular reactive sulfur metabolites on microbial Se (0) dissolution." Geobiology 17.3 (2019): 320-329.

Phylogenetically diverse bacteria will release low levels of reduced sulfur metabolites (e.g. thiols, sulfite, and sulfide) during heterotrophic non-sulfur-respiring growth. However, the physiological function of these metabolites is not well understood and their potential to influence biogeochemical cycles has not been extensively characterized. My work has shown that endogenous sulfite, sulfide, and thiosulfate released by cells during active growth can solubilize and facilitate the mobilization of elemental selenium minerals. Additionally, my work has suggested a possible physiological function for extracellular sulfite in mitigating extracellular hydrogen peroxide and antibiotics stress.