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

Capo, Eric; Peterson, Brittany F.; Kim, Minjae; Jones, Daniel S.; Acinas, Silvia G.; Amyot, Marc; Bertilsson, Stefan; Björn, Erik; Buck, Moritz; Cosio, Claudia; Elias, Dwayne A.; Gilmour, Cynthia C.; Goñi-Urriza, Marisol; Gu, Baohua; Lin, Heyu; Liu, Yurong; McMahon, Katherine D.; Moreau, John W.; Pinhassi, Jarone; Podar, Mircea; Puente-Sánchez, Fernando; Sánchez, Pablo; Storck, Véronika; Tada, Yuya; Vigneron, Adrien; Walsh, David A.; Vandewalle-Capo, Marine; Bravo, Andrea G.; Gionfriddo, Caitlin M.

doi:10.1101/2022.03.14.484253

Cited by 4 publications

(12 citation statements)

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“…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.…”

Section: Phylogenetic Distribution Of Thementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132

Gionfriddo

Soren

Wymore

et al. 2022

Preprint

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ThehgcABgene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg-methylatorPseudodesulfovibrio mercuriiND132, we specifically evaluated transcriptional control ofhgcABby a putative ArsR encoded upstream and co-transcribed withhgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosyl-homocysteine (SAH) responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR inPseudodesulfovibrio mercuriiND132. Using qPCR and RNA-seq analyses we confirmed this ArsR regulateshgcABtranscription, and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link betweenhgcABactivity and arsenic transformations byPseudodesulfovibrio mercuriiND132, with significant up-regulation of other ArsR-regulated arsenic resistance operons alongsidehgcAB. Interestingly, wild-type ND132 was less sensitive to AsV (but not AsIII) than anhgcABknockout strain, supporting the idea thathgcABmay be linked to arsenic resistance. Arsenic significantly impacted Hg-methylation rates by ND132, however, responses varied with culture conditions. Differences in growth and overall metabolic activity did not account for arsenic impacts on methylation. One goal of this research is to better predict MeHg production in nature. However, we found thathgcABgene and transcript abundance was not a good predictor of Hg-methylation rates. Our finding thathgcABactivity is linked to arsenic may hold clues to the possible environmental drivers of horizontal transfer ofhgcAB.

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Section: Phylogenetic Distribution Of Thementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132

Gionfriddo

Soren

Wymore

et al. 2022

Preprint

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Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation

Zhang

Aris‐Brosou

Storck

et al. 2023

ISME Communications

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Methylmercury (MeHg) is a microbially produced neurotoxin derived from inorganic mercury (Hg), which accumulation in rice represents a major health concern to humans. However, the microbial control of MeHg dynamics in the environment remains elusive. Here, leveraging three rice paddy fields with distinct concentrations of Hg (Total Hg (THg): 0.21−513 mg kg−1 dry wt. soil; MeHg: 1.21−6.82 ng g−1 dry wt. soil), we resorted to metagenomics to determine the microbial determinants involved in MeHg production under contrasted contamination settings. We show that Hg methylating Archaea, along with methane-cycling genes, were enriched in severely contaminated paddy soils. Metagenome-resolved Genomes of novel putative Hg methylators belonging to Nitrospinota (UBA7883), with poorly resolved taxonomy despite high completeness, showed evidence of facultative anaerobic metabolism and adaptations to fluctuating redox potential. Furthermore, we found evidence of environmental filtering effects that influenced the phylogenies of not only hgcA genes under different THg concentrations, but also of two housekeeping genes, rpoB and glnA, highlighting the need for further experimental validation of whether THg drives the evolution of hgcAB. Finally, assessment of the genomic environment surrounding hgcAB suggests that this gene pair may be regulated by an archaeal toxin-antitoxin (TA) system, instead of the more frequently found arsR-like genes in bacterial methylators. This suggests the presence of distinct hgcAB regulation systems in bacteria and archaea. Our results support the emerging role of Archaea in MeHg cycling under mining-impacted environments and shed light on the differential control of the expression of genes involved in MeHg formation between Archaea and Bacteria.

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Ecological consequences of climate change in boreal marginal seas

2024

Frontiers Research Topics

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Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

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

Cited by 4 publications

References 72 publications

Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132

Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132

Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation

Ecological consequences of climate change in boreal marginal seas

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