Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes

Abstract

Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota's Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.

An improvedhgcABprimer set and direct high-throughput sequencing expand Hg-methylator diversity in nature

“…Interestingly, hgcA amplicons and clones closely related to Bacteroidetes and Chloroflexi were prevalent in both tidal marsh and freshwater sediments, while nitrogen-cycling Nitrospirae were prevalent primarily in freshwater sediment (Figures 5,6). Several Chloroflexi, Bacteroidetes, and Nitrospirae containing hgcA have been sequenced (Baker et al, 2015;Podar et al, 2015a;Anantharaman et al, 2016;Jones et al, 2019) but none have been tested for Hg-methylation. Nitrospirae are often found alongside sulfate-reducing bacteria, and can perform sulfate-reduction (Henry et al, 1994;Teske et al, 1994;Zecchin et al, 2018).…”

“…This expanded phylogeny of potential Hg-methylators includes metabolic clades associated with nitrogencycling, fermentation, and chemoheterotrophy. Members of these metabolic clades have previously been connected to Hg-cycling in environmental metagenome studies (Podar et al, 2015a;Gionfriddo et al, 2016;Jones et al, 2019).…”

“…In addition to the Hg-methylators confirmed in culture, sulfate-and iron-reducing Deltaproteobacteria, acetogenic and syntrophic Firmicutes, and methanogenic Archaea (Compeau and Bartha, 1985;Fleming et al, 2006;Kerin et al, 2006;Ranchou-Peyruse et al, 2009;Gilmour et al, 2013;Yu et al, 2013;Gilmour et al, 2018;Goñi-Urriza et al, 2019)genomic analyses have identified hgcAB (and thus inferred the ability to produce MeHg) in many other lineages including Chloroflexi, Chrysiogenetes, Aminicenantes (Candidate Phylum OP8), Atribacteria (Candidate Phylum OP9), Nitrospira, Nitrospina, Elusimicrobia, Thermotogae and Spirochaetes (Podar et al, 2015a;Gionfriddo et al, 2016;Liu et al, 2018a;Bowman et al, 2019;Christensen et al, 2019;Jones et al, 2019). The occurrence of hgcAB in Bacterial and Archaeal genomes is rare but widely dispersed across phyla (Parks et al, 2013;Podar et al, 2015a;Jones et al, 2019). Hg-methylating microorganisms often constitute less than 5% of the bulk microbial community (Christensen et al, 2019), yet in these same environments MeHg can comprise up to 10% of the total Hg within a system (Christensen et al, 2019).…”

“…PCR primers and reference libraries for hgcAB have improved with the increasing number of hgcAB sequences identified. Early studies relied on sequences from a small number of cultured methylators (Bae et al, 2014;Liu et al, 2014;Schaefer et al, 2014) while more recent work has captured a wider diversity (Christensen et al, 2016;Bravo and Cosio, 2019;Christensen et al, 2019;Jones et al, 2019). Improved techniques for capturing hgcAB presence and diversity are necessary for identifying both the major players in environmental MeHg production as well as the evolutionary history of the gene pair.…”

Mercury dynamics in the pore water of peat columns during experimental freezing and thawing

“…Methylmercury is the most toxic form of Hg found in the environment and can bioaccumulate in fish, animals, and humans that consume aquatic organisms (Driscoll, Mason, Chan, Jacob, & Pirrone, 2013). Mercury methylation is mediated, in part, by anaerobic bacteria (e.g., sulfate‐reducing bacteria) that convert Hg to MeHg (Branfireun, Roulet, Kelly, & Rudd, 1999; Gilmour & Henry, 1991; Jones et al., 2019). Temperature is also an important factor in this process (Celo, Lean, & Scott, 2006): warmer conditions lead to faster sulfate reduction (Sokolova, 2010) and presumably higher rates of Hg methylation.…”