A consensus protocol for the recovery of mercury methylation genes from metagenomes

Abstract

Mercury methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce 'marky-coco', a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132

“…ArsR family regulators are also encoded with hgcAB in genomes from outside of the Desulfovibrionaceae family. In hgc+ genomes from the Hg-MATE-Db (7,11), we identified putative ArsR/SmtB family regulators of hgcAB in isolate and environmental metagenome-105 and is also made available for use under a CC0 license.…”

“…The copyright holder for this preprint this version posted October 18, 2022. ; https://doi.org/10.1101/2022.10.17.512643 doi: bioRxiv preprint methylator environments, sequencing coverage of hgcAB genes is often low compared to other functional genes (7). For example, the coverage of dissimilatory sulfite reductase genes (dsr) in metagenomic assemblies is often 3-34x higher than hgcAB (7).…”

“…The copyright holder for this preprint this version posted October 18, 2022. ; https://doi.org/10.1101/2022.10.17.512643 doi: bioRxiv preprint methylator environments, sequencing coverage of hgcAB genes is often low compared to other functional genes (7). For example, the coverage of dissimilatory sulfite reductase genes (dsr) in metagenomic assemblies is often 3-34x higher than hgcAB (7). Despite the association of sulfatereducing bacteria (SRB) with Hg methylation, the hgcAB gene pair is found in only ~12% of publicly sequenced SRB in the Deltaproteobacteria (although hgcAB is more common within some genera including Pseudodesulfovibrio) (8)(9)(10).…”

“…Despite the association of sulfatereducing bacteria (SRB) with Hg methylation, the hgcAB gene pair is found in only ~12% of publicly sequenced SRB in the Deltaproteobacteria (although hgcAB is more common within some genera including Pseudodesulfovibrio) (8)(9)(10). Of the roughly 3,078 sequenced Deltaproteobacteria genomes in the NCBI reference database, only 368 were identified as potential Hg-methylators when the Hg-MATE database was compiled (7,11). Within other phyla, especially environmental metagenome assembled genomes from the Bacteroidetes, Nitrospirae, PVC superphylum and candidate phyla radiation, hgcAB distribution further diverges from species trees but follows environmental patterns and suggests horizontal gene transfer of this capability (4,6).…”

“…Currently, we do not have a good metric for estimating the prevalence of the mercury methylation trait among microbiota. However, in environmental metagenomic studies of mercury methylator environments, sequencing coverage of hgcAB genes is often low compared to other functional genes(7). For example, the coverage of dissimilatory sulfite reductase genes ( dsr ) in metagenomic assemblies is often 3-34x higher than hgcAB (7).…”