Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

Abstract

Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment. IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea

“…Some syntrophic microbes were recently suggested to be involved in the Hg methylation process (Gilmour et al, 2013;Yu et al, 2018;Hu et al, 2020), but we did not identify hgcAB genes from known syntrophic microorganisms in the Baltic Sea. Instead, we identified hgcAB-carrying bacteria closely related to various groups that are still poorly described (McDaniel et al, 2020) including members of Spirochaetes and Kiritimatiellaeota phyla. For instance, among the predominant hgcAB-like genes detected in Baltic Sea, the hgcAB genes BARM-01, -07 & -09 were clustered together and found close to a number of Spirochaetes (Figure 3).…”

“…The two procedures resulted in the recovery of the same hgcA genes and hgcAB gene clusters from the BARM dataset. For phylogenetic analysis, we used the amino acid sequences of the 650 hgcAB gene clusters identified as putative Hg methylators by McDaniel et al (2020). These 650 hgcAB gene clusters were obtained from the analysis of publicly available isolate genomes and metagenome-assembled genomes (Supplementary Datasheet S2, McDaniel et al, 2020).…”

“…In order to taxonomically identify each Hg methylation gene detected in the BARM dataset, we constructed phylogenetic trees using the 650 hgcAB gene clusters generated by McDaniel et al (2020). For the nine hgcAB-like gene clusters concatenated, we performed a phylogenetic analysis with the 650 hgcAB gene clusters (Figure 3, Supplementary Figure S1).…”

“…https://www.frontiersin.org/articles/10.3389/fmicb.2020. 574080/full#supplementary-material FIGURE S1 | Maximum-likelihood phylogenetic tree of concatenated hgcAB amino acid sequences of 650 hgcAB gene clusters (McDaniel et al, 2020) and BARM hgcAB genes. Gene clusters detected in the Baltic Sea water column (BARM) are displayed in bold.…”

“…It is broadly established that the capacity for Hg-methylation is limited to specific microbial lineages, with the most commonly reported groups found in the Deltaproteobacteria and Methanomicrobiales (Gilmour et al, 2013;Podar et al, 2015;Bravo et al, 2018;Yu et al, 2018). However, recent work has expanded this view and unraveled a higher phylogenetic diversity of microbes carrying the hgcAB genes than previously expected (McDaniel et al, 2020) calling for further analyses of microbial Hg-methylation in aquatic environments.…”