Thesis: Ecophysiology of mercury-methylating microorganisms in freshwater ecosystems

Methylmercury (MeHg), the toxic bioaccumulative form of mercury, is produced by microorganisms living in anoxic environments. Identifying the processes that lead to MeHg accumulation in freshwater ecosystems is a key step in understanding MeHg accumulation in aquatic food webs. MeHg production is limited by bioavailability constraints on inorganic Hg and the Hg methylation capacity of the microbial community. My research focus was primarily on understanding the in situ microbial communities that directly and indirectly mediate the production of MeHg and how their capacity for Hg methylation interacts with factors controlling bioavailability. While I specialized in using metagenomics data, I ultimately used a multi-disciplinary approach that also included biogeochemical field measurements, microbial activity assays, and stable isotope incubations. Below are some of the studies I have published as part of my Ph.D. thesis.

Ecophysiology of mercury-methylating microbes in Lake Mendota

Our initial study focused on a genome-resolved metagenomic approach to identify potential mercury-methylating organisms in potential hotspots for MeHg production in the water column of Lake Mendota. Sulfate-reducing bacteria, which are typically associated with MeHg production, only accounted for small percentage of the hgcA+ organisms we identified. Most hgcA+ genomes were associated with obligately fermentative organisms, including the relatively uncharacterized Kiritimatiellaeota. This work showed that even in a sulfate-rich lake with abundant evidence for sulfate reduction, SRBs may not be the dominant Hg methylator, at least not directly.
Citation: Peterson, Benjamin D., Elizabeth A. McDaniel, Anna G. Schmidt, Ryan F. Lepak, Sarah E. Janssen, Patricia Q. Tran, Robert A. Marick, et al. “Mercury Methylation Genes Identified across Diverse Anaerobic Microbial Guilds in a Eutrophic Sulfate-Enriched Lake.” Environmental Science & Technology 54 (December 15, 2020): 15840–51. https://doi.org/10.1021/acs.est.0c05435.
We are currently testing several of the hypotheses developed in our initial metagenome study using enriched stable-isotope Hg methylation assays adapted from other studies in aquatic ecosystems (Eckley et al, 2005; Malcolm et al, 2010). This will be paired with molecular sequencing data to further probe how different functional guilds of putative Hg methylators impact MeHg production.

Metabolic diversity of Hg-methylating microbes under nitrate-reducing conditions

For part of my Ph.D. work, I collaborated with a large working group of scientists from the U.S. Geological Survey and from Idaho Power company as part of a large study to develop qualitative and quantitative studies of mercury cycling within the Hells Canyon Complex, along the Snake River between Idaho and Oregon. This ten-year study has resulted in unprecedented understanding of Hg cycling in a reservoir, which facilitated a comprehensive study of mercury methylation within a highly complex and variable system.
We showed that Hg methylation within the water column was a prominent source of MeHg to the reservoir. Biogeochemical measurements and functional gene profiling showed that nitrate reduction was the dominant terminal-electron accepting pathway within the water column where MeHg accumulation was occurring, indicating that MeHg production can occur under relatively high redox conditions. Using assembly-based and genome-resolved metagenomic methods, we identified putative mercury-methylating microbes that could perform nitrate reduction, as well as many obligate fermenters.
Overall, we suggest that MeHg production may be more dependent on overall microbial activity (with carbon degradation as a proxy) than on any specific terminal-electron accepting process such as sulfate reduction. There is a great deal of interest in managing MeHg levels within reservoirs. Many of these efforts have focused on increasing the redox status of the reservoir hypolimnion, either by oxygenation, nitrate amendment, or manganese oxide amendments, to reduce sulfate reduction and therefore reduce MeHg production. However, the results of our study show that this may not be effective in some systems, depending on the microbial community that is carrying the methylation gene hgcA.

Citation: Peterson, Benjamin D., Brett A. Poulin, David P. Krabbenhoft, Michael T. Tate, Austin K. Baldwin, Jesse Naymik, Nick Gastelecutto, and Katherine D. McMahon. “Metabolically Diverse Microorganisms Mediate Methylmercury Formation under Nitrate-Reducing Conditions in a Dynamic Hydroelectric Reservoir.” The ISME Journal, July 26, 2023. https://doi.org/10.1038/s41396-023-01482-1.

Microbial and abiotic constraints on methylmercury production in peat sediments

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The Florida Everglades have been a testing ground for identifying environmental drivers of Hg pollution, particularly the production of toxic methylmercury, for three decades. While we know that mercury methylation can be controlled by biotic factors (microbes carrying hgcA) and abiotic factors (ligand complexation of inorganic mercury) we still have little understanding of how these two variables, and the environmental factors that underlie them, interact under environmentally relevant conditions to control mercury methylation. To gain insight into this balance, we performed mercury methylation assays using enriched stable isotope tracers with a full factorial design using intact peat cores (representing the microbial community) and filtered porewater for tracer equilibration (representing abiotic complexation). Our results clearly showed that both biotic and abiotic factors could limit MeHg production under environmentally relevant conditions. We also showed that the relative abundance of the mercury methylation gene hgcA correlated to the ability of the microbial community to produce methylmercury.

Citation: Peterson, Benjamin D., David P. Krabbenhoft, Katherine D. McMahon, Jacob M. Ogorek, Michael T. Tate, William H. Orem, and Brett A. Poulin. “Environmental Formation of Methylmercury Is Controlled by Synergy of Inorganic Mercury Bioavailability and Microbial Mercury‐methylation Capacity.” Environmental Microbiology, March 5, 2023, 1462-2920.16364. https://doi.org/10.1111/1462-2920.16364.