Metagenomics reveals diverse community of putative mercury

Overview

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Key numbers

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preserved in liquid nitrogen and subsequently transferred to of MAGs. Only high-quality MAGs (completeness > 75%,
a − 80 °C freezer in the laboratory until DNA extraction. contamination < 5%) were retained for downstream analyses.
sodium phosphate (pH 8.0), 1.5 M NaCl, 1% (w/v) CTAB), the corresponding NCBI taxonomy using the built-in script
panol, followed by a wash with 70% (v/v) alcohol and finally (Graham et al. 2018).
detection limit. (Fig. S1A). Sulfide was undetectable above
and Li 2006) at a 50% sequence identity threshold, and the downward trend with increasing depth, with a concentration
derived through coevolution-based modeling. Root mean pleteness > 75% and contamination < 5% were derived, com-
lent × 100%’, representing the percentage of genomes in the MAGs belonged to seven different phyla, in which more than
sequences (1000 ultrafast bootstrap replicates; values > 90% are the hgcA sequences are labeled in the outer circle by different colors.
prising more than 60% of the YBH-HgcA dataset. Other
experimentally confirmed HgcA sequences using multiple genes at 0 m, while only 0.01% of the microorganisms were
for this analysis. All of these YBH-derived HgcA sequences organisms in the surface water. We found that 0.22% of the
(Fig. S3), which forms a “cap-helix” structure in the globular the percentage dropped to only 0.001% at 30 m but increased
facilitating methyl group transfer to mercury (Fig. S4). The microorganisms increased to 1.46% and 1.58% of the micro-
et al. 2020; Parks et al. 2013). Although certain regions of carrying microorganisms were estimated to occupy ~ 30%
the AlphaFold3 models exhibited relatively low pLDDT (30.87%, 28.42%, and 28.38% in the 120 m, 140 m, and
diction, all models demonstrated overall high pTM scores three PA samples increased along depth (15.18%, 24.26%,
(≥ 0.73). Importantly, the functionally relevant regions, and 30.55% in the 120 m, 140 m, and 170 m samples,
twelve YBH-derived HgcA models exhibited notable struc- exhibited higher levels at depths of 0 m, 50 m, 90 m, and
Habitat preference of different putative Hg of the microbial community, but it only occupied 0.07% in
microorganism, accounting for 4.31%, 5.16% and 3.85% intermediate water (Fig. 3B, C). In particular, Nitrospina
pied no more than 1% at the same depths as above in the
Meanwhile, the hgcA-carrying microorganisms to KEGG database (Fig. 4). Most MAGs also carried hgcB
gene in the PA sample at 170 m depth, accounting for 2.36% Complete operons of cytochrome bd complex encoding
methyltransferase catalyzing methanogenesis were found decreased to undetectable below a depth of 100 m, forming
More than 30% of the microbial community were found to metabolic adaptations enabling effective competition under
bases, particularly within the Delta-1, Delta-2, and Delta-3 at 170 m depths, accounting for 6.93% of the microbial com-
clades, with Delta-3 exhibiting the greatest divergence munity, but they only occupied 0.46% in the FL sample at
factors. Moreover, we found that while the abundance of Hg shared only ~ 40% sequence identity and were not located
(~ 30% of the microbial community) in the deep water, it findings suggest that the Hg methylators found in YBH
increased along the depth (from ~ 15% at 120 m to ~ 30% might possess alternative regulatory mechanisms govern-

Methods (brief)

Fig. 1 Map of the Yongle Blue Hole sampling site and illustration et al. 2018). Samples for hydrochemical analyses and metagenomic
age (Pante and Simon-Bouhet 2013). B Samples collected in this two different pore sizes
than the second deepest blue hole – Dean’s Blue Hole in samples from 29 different depths of YBH (111.768° E,
Long Island, Bahamas (Gonzalez et al. 2011). YBH features 16.525° N, Fig. 1A) from 0 to 190 m were collected to meas-
suggesting a potential habitat for Hg methylators. For this (2009) after the sample was fixed by 2 mol L−1 MnCl2 and
Hg methylation; (2) the distribution of Hg methylators in L−1. Sulfide samples collected from the Niskin bottles were
to investigate the genomic traits and phylogenetics of puta- analysis, samples were filtered through pre-combusted
tive Hg methylators. Relative abundance of the hgcA gene glass-fibre filters and the filtrates were collected and stored
(PA) samples was also assessed to study the distribution and using a Total Organic Carbon analyzer (Shimadzu, Japan).
were measured with depth and tested for correlation with Metagenomic sample collection
shed light on the distribution of Hg-methylating potential in Seawater samples (50 L) from seven depths (0, 30, 50, 90,
120, 140, 170 m) of YBH were collected in October 2019
(Xie et al. 2019). These samples were collected at specified merged and assembled with MEGAHIT v1.2.9 (Liu et al.
bottles was combined at each depth. The samples were then using metaBAT (Kang et al. 2015), metaBAT 2 (Kang et al.
sequencing of a total of 14 DNA samples was performed at The hgcA hmm profile provided in the Hg-MATE data-
and binning. First, every sample was assembled separately with the parameters “-c 1 -n 5”, and only one representative
ing approach. Second, the 14 samples were divided into was predicted using BLASTp against the NCBI-nr database.
samples collected from 0–50 m, 60–100 m, and 105–190 m All HgcA amino acid sequences derived from this analy-

Implications

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Update history

The five most recent substantive edits to this page, classified major (evidence or structure moved), correction (a published value or statement was wrong and has been fixed), or minor (narrative rewritten without changing the underlying evidence). Each description is derived from what the edit did to this page; the linked commit is the authoritative record, routine regeneration passes are excluded, and the full version history lives in git. When DOI minting comes online (see schema docs), each entry below will also link to a version-pinned DataCite DOI.

Commit	Date	Change	Description
b01ec52c	2026-08-04	major	2 sections added
d49e450f	2026-08-03	major	5 sections added; narrative text revised