Research ArticleBIOCHEMISTRY

Global prevalence and distribution of genes and microorganisms involved in mercury methylation

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Science Advances  09 Oct 2015:
Vol. 1, no. 9, e1500675
DOI: 10.1126/sciadv.1500675
  • Fig. 1 Global frequency and abundance of HgcA based on the metagenomic projects evaluated.

    Overlay is the estimated continental emission of Hg (in tons) based on “UNEP Global Mercury Assessment 2013: Sources, Emissions, Releases and Environmental Transport” (2). Diamonds represent pelagic ocean water samples, whereas circles represent all other samples. The abundance of Hg emissions and hgcA is colored according to the accompanying legend.

  • Fig. 2 Distribution and relative abundance of HgcA in metagenomic projects, by environment type.

    Each metagenomic project includes a wide-ranging number of metagenome sequencing data sets. Each bar represents a metagenome project. Gray bars indicate metagenome size. Colored bars represent HgcA abundance normalized to 1 Gb of metagenomic sequence. Overall, about two-thirds of 3500 metagenomes and 140 of 203 metagenome projects did not reveal any hgcA. PCE, polychloroethylene.

  • Fig. 3 Maximum likelihood phylogeny of HgcA proteins in complete genomic and metagenomic sequences.

    Open circles at major nodes denote bootstrap support values >50. Gray-shaded clades represent the fused HgcAB sequences. Sequences with colored circles and color naming indicate full-length HgcA from metagenomes, with the color corresponding to the metagenome classification in Fig. 2.

  • Fig. 4 Closest family and genera assignments for metagenomic HgcA genes/fragments for metagenomic data sets containing hgcA.

    Assignments were made using MEGAN.5, a program that evaluates the taxonomic and functional content of short-read metagenomic data sets. Circle size represents the relative abundance (square root–transformed) of taxonomically assigned hgcA sequence types in each metagenome. The metagenomes are arranged by environment type, as classified in Fig. 2. PCE, polychloroethylene.

  • Fig. 5 Maximum likelihood phylogeny of the cobalamin binding domain of HgcA and the WL pathway carbon monoxide dehydrogenase/acetyl-CoA synthase γ subunit.

    HgcA and HgcAB clades were collapsed. Bootstrap support at nodes is indicated by black circles (>75) or white circles (50 to 75). Some archaeal and bacterial taxa were collapsed and color-coded. Blue and yellow branches indicate archaeal and bacterial lines of divergence that would suggest a potential archaeal origin for bacterial CFeSP. Cand, candidate phylum.

  • gnl|SRA|ERR260153.9799443.11 TKGINVWGAAGKGTFGTDELVGRISETGLSTKG+NVW AAGKGTFGT+ELV RI +TGL+
    M. luminyensis B1077 TKGVNVWCAAGKGTFGTEELVRRIEDTGLA 106

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/1/9/e1500675/DC1

    Table S1. List of metagenomic projects with hgcA counts.

    Table S2. Identity matrix of sequence similarities.

    Fig. S1. Whisker plot distribution of genomic and metagenomic PFam3599 protein hits to various hidden Markov profiles.

    Fig. S2. Distribution of HgcA and WL pathway–associated CFeSP encoding genes in methanogenic Archaea.

    Fig. S3. Distribution of HgcA, HgcB, and WL pathway–associated CFeSP in genomes of Deltaproteobacteria and Firmicutes.

    Fig. S4. Hg methylation assays for M. luminyensis B10.

    Fig. S5. Repeat methylation assay for M. luminyensis B10.

    Fig. S6. Schematic representation of the domain architectures of HgcA, HgcB, and the fusion HgcAB.

    Fig. S7. Hg methylation assays for P. furiosus.

    Fig. S8. MEGAN-based co-occurrence profiles of the closest genera-assigned HgcAs based on all metagenomes.

  • Supplementary Materials

    This PDF file includes:

    • Fig. S1. Whisker plot distribution of genomic and metagenomic PFam3599 protein hits to various hidden Markov profiles.
    • Fig. S2. Distribution of HgcA and WL pathway–associated CFeSP encoding genes in methanogenic Archaea.
    • Fig. S3. Distribution of HgcA, HgcB, and WL pathway–associated CFeSP in genomes of Deltaproteobacteria and Firmicutes.
    • Fig. S4. Hg methylation assays for M. luminyensis B10.
    • Fig. S5. Repeat methylation assay for M. luminyensis B10.
    • Fig. S6. Schematic representation of the domain architectures of HgcA, HgcB, and the fusion HgcAB.
    • Fig. S7. Hg methylation assays for P. furiosus.
    • Fig. S8. MEGAN-based co-occurrence profiles of the closest genera-assigned HgcAs based on all metagenomes.

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    Other Supplementary Material for this manuscript includes the following:

    • Table S1 (Microsoft Excel format). List of metagenomic projects with hgcA counts.
    • Table S2 (Microsoft Excel format). Identity matrix of sequence similarities.

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