Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

Bravo, Andrea G.; Peura, Sari; Buck, Moritz; Ahmed, Omneya; Mateos‐Rivera, Alejandro; Ortega, Sonia Herrero; Schaefer, Jeffra K.; Bouchet, Sylvain; Tolu, Julie; Björn, Erik; Bertilsson, Stefan

doi:10.1128/aem.01774-18

Cited by 57 publications

(51 citation statements)

References 82 publications

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“…An increasing number of recent studies detailed below have intended to evaluate the biotic Hg II methylation by studying the biodiversity and activity of hgcAB + microorganisms (Gionfriddo et al ; Bravo et al , a ; Bowman et al ; Jones et al ; Villar et al ). Nevertheless, it is established that net MMHg production also depends on other concomitant processes, including (1) the composition and activity of the whole microbial community that in turn modulate the activity of hgcAB + microorganisms (Bravo et al ), (2) physico‐chemistry that controls Hg II bioavailability (Schaefer and Morel ; Jonsson et al ; Chiasson‐Gould et al ), and uptake in microorganisms (Schaefer et al ), and (3) biotic and abiotic MMHg demethylation (Du et al ).…”

Section: The Mercury Problemmentioning

confidence: 99%

Biotic formation of methylmercury: A bio–physico–chemical conundrum

Bravo

Cosio

2019

Limnology & Oceanography

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115

102

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Mercury (Hg) is a natural and widespread trace metal, but is considered a priority pollutant, particularly its organic form methylmercury (MMHg), because of human's exposure to MMHg through fish consumption. Pioneering studies showed the methylation of divalent Hg (HgII) to MMHg to occur under oxygen‐limited conditions and to depend on the activity of anaerobic microorganisms. Recent studies identified the hgcAB gene cluster in microorganisms with the capacity to methylate HgII and unveiled a much wider range of species and environmental conditions producing MMHg than previously expected. Here, we review the recent knowledge and approaches used to understand HgII‐methylation, microbial biodiversity and activity involved in these processes, and we highlight the current limits for predicting MMHg concentrations in the environment. The available data unveil the fact that HgII methylation is a bio‐physico‐chemical conundrum in which the efficiency of biological HgII methylation appears to depend chiefly on HgII and nutrients availability, the abundance of electron acceptors such as sulfate or iron, the abundance and composition of organic matter as well as the activity and structure of the microbial community. An increased knowledge of the relationship between microbial community composition, physico‐chemical conditions, MMHg production, and demethylation is necessary to predict variability in MMHg concentrations across environments.

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Section: The Mercury Problemmentioning

confidence: 99%

Biotic formation of methylmercury: A bio–physico–chemical conundrum

Bravo

Cosio

2019

Limnology & Oceanography

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115

102

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“…One drawback is the limited number of hgcAB + organisms that can be identified (50-100 clones/library) as well as inherent protocol bias. Direct amplicon sequencing is desirable given the increased data-output and lower labor (Bravo et al, 2018a;Liu et al, 2018b). Here we include direct hgcAB amplicon sequencing which was validated using a mock community and tidal salt marsh soils spiked with the mock community.…”

Section: Discussionmentioning

confidence: 99%

“…Raw sequences were filtered and trimmed using Trimmomatic, and only forward hgcA reads were used (Bolger et al, 2014). We adapted OTU clustering methods applied to functional genes from Bravo et al (2018a) and Pelikan et al (2016). For this study, hgcA sequences were trimmed (201 nt bp), dereplicated, and singletons removed with USEARCH (Edgar, 2010).…”

Section: High-throughput Sequencing Of Hgcab Ampliconsmentioning

confidence: 99%

“…Early hgcA primers could be biased towards Deltaproteobacteria, Methanomicrobia, and Firmicutes (Liu et al, 2014;Schaefer et al, 2014), often identifying Deltaproteobacteria and Methanomicrobia as dominant with less representation from Firmicutes, Chloroflexi, and unclassified clades (Liu et al, 2014;Schaefer et al, 2014;Du et al, 2017;Bravo et al, 2018a). While sulfate-reducing bacteria may be significant Hg-methylators (Compeau and Bartha, 1985;Kerin et al, 2006;Gilmour et al, 2018), it is unclear what role confirmation bias has had in their association with Hg cycling.…”

Section: Potential Biases In Identifying Key Hg-methylatorsmentioning

confidence: 99%

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An improvedhgcABprimer set and direct high-throughput sequencing expand Hg-methylator diversity in nature

Gionfriddo

Wymore

Jones

et al. 2020

Preprint

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The gene pair hgcAB is essential for microbial mercury methylation. Our understanding of its abundance and diversity in nature is rapidly evolving. In this study we developed a new broadrange primer set for hgcAB, plus an expanded hgcAB reference library, and used these to characterize Hg-methylating communities from diverse environments. We applied this new Hgmethylator database to assign taxonomy to hgcA sequences from clone, amplicon, and metagenomic datasets. We evaluated potential biases introduced in primer design, sequence length, and classification, and suggest best practices for studying Hg-methylator diversity. Our study confirms the emerging picture of an expanded diversity of HgcAB-encoding microbes in many types of ecosystems, with abundant putative mercury methylators Nitrospirae and Chloroflexi in several new environments including salt marsh and peat soils. Other common microbes encoding HgcAB included Phycisphaerae, Aminicenantes, Spirochaetes, and Elusimicrobia. Gene abundance data also corroborate the important role of two "classic" groups of methylators (Deltaproteobacteria and Methanomicrobia) in many environments, but generally show a scarcity of hgcAB+ Firmicutes. The new primer set was developed to specifically target hgcAB sequences found in nature, reducing degeneracy and providing increased sensitivity while maintaining broad diversity capture. We evaluated mock communities to confirm primer improvements, including culture spikes to environmental samples with variable DNA extraction and PCR amplification efficiencies. For select sites, this new workflow was combined with direct high-throughput hgcAB sequencing. The hgcAB diversity generated by direct amplicon sequencing confirmed the potential for novel Hg-methylators previously identified using metagenomic screens. A new phylogenetic analysis using sequences from freshwater, saline, and terrestrial environments showed Deltaproteobacteria HgcA sequences generally clustered among themselves, while metagenome-resolved HgcA sequences in other phyla tended to cluster by environment, suggesting horizontal gene transfer into many clades. HgcA from marine metagenomes often formed distinct subtrees from those sequenced from freshwater ecosystems. Overall the majority of HgcA sequences branch from a cluster of HgcAB fused proteins related to Thermococci, Atribacteria (candidate division OP9), Aminicenantes (OP8), and Chloroflexi. The improved primer set and library, combined with direct amplicon sequencing, provide a significantly improved assessment of the abundance and diversity of hgcAB+ microbes in nature. Contribution to the Field StatementThe gene pair hgcAB is essential for microbial production of the neurotoxin methylmercury. In recent years these genes have been used as biomarkers to determine the potential of a microbiome to generate methylmercury via PCR amplification using degenerate primers from several research groups. However, improved techniques for capturing hgcAB diversity are necessary for identifying the major environmental p...

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“…The potential presence of photoferrotrophs in Boreal Shield lakes has substantial implications for understanding Boreal Shield lake biogeochemistry, as well as for the evolution and ecology of anoxygenic photoautotrophy and the iron cycle. Boreal Shield lake biogeochemistry may be more tightly linked to the iron cycle than previously assumed, making iron a potentially understudied factor affecting the function and management of boreal 515 ecosystems (e.g., [76,77]). In addition, the new diversity of cyc2 among Chlorobia reported here implies that substantial unmined environmental cyc2 diversity exists.…”

Section: Anoxic Zone Boundaries Of the Lakes Several Authors Have Rementioning

confidence: 99%

Genomic potential for photoferrotrophy in a seasonally anoxic Boreal Shield lake

Tsuji

Tran

Schiff

et al. 2019

Preprint

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Abbreviations used throughout text: Chl. = Chlorobium; Cba. = Chlorobaculum; Che. = 15 Chloroherpeton; Ptc. = ProsthecochlorisThe authors declare no competing financial interests. Abstract 20Photoferrotrophy, the direct photosynthetic oxidation of ferrous iron, is thought to have contributed to primary production within Earth's early anoxic oceans yet is presumed to be of little modern environmental relevance. Here we use genome-resolved metagenomics and enrichment cultivation to provide first functional gene evidence that photoferrotrophic bacteria are important photoautotrophs in the anoxic water columns of globally abundant Boreal Shield 25 lakes. We recovered six high-completeness, low-contamination draft genome bins belonging to the Chlorobia class. Half of these genome bins contained the cyc2 candidate gene marker for iron oxidation, and one containing cyc2 lacked the sulfur oxidation gene pathway altogether. Using a custom profile Hidden Markov Model, we recovered distinct cyc2 homologues from our metagenome data and doubled the known diversity of Chlorobia-associated cyc2 genes. 30Metagenome data also showed that potential photoferrotrophs co-occurred with sulfide-oxidizing populations of Chlorobia in one lake but that only sulfide-oxidizing populations were present in a neighboring lake, implying that strong ecological controls govern the favourability of photoferrotrophy in ferruginous lakes. Our results greatly expand knowledge of photoferrotroph ecology in natural aquatic systems, demonstrating modern environmental relevance for this iron-35 oxidizing photosynthetic mode and supporting future investigations into early Earth microbial communities. expands capabilities to explore the role of photoferrotrophy and other forms of iron cycling in nature.Additional photoferrotrophic bacteria are also being isolated in the laboratory. For example, among the Chlorobia class (i.e., "green sulfur bacteria"), the only known photoferrotroph was 65Chlorobium ferrooxidans strain KoFox, which was enriched from freshwater lake sediments [18].Recently, two additional Chlorobia-associated photoferrotrophs were cultivated. Chlorobium phaeoferrooxidans strain KB01, a bacteriochlorophyll e-containing member of the Chlorobia, was isolated from the anoxic water column of the meromictic and ferruginous Kabuno Bay (see below; [19]). In addition, Chlorobium sp. strain N1 was isolated from marine sediments [20]. 70Both Chl. ferrooxidans and Chl. phaeoferrooxidans oxidize ferrous iron as their sole photosynthetic electron donor, assimilating sulfur as sulfate [18,19]. Chl. sp. N1 is capable of oxidizing either ferrous iron or sulfide as the photosynthetic electron donor [20].Phylogenetically, Chl. ferrooxidans and Chl. phaeoferrooxidans are sister groups to one another, whereas Chl. sp. N1 is closely related to Chl. luteolum, a sulfide-oxidizing species of Chlorobia 75 with genomic potential for photoferrotrophy [19][20][21]. Draft genome sequences available for Chl. ferrooxidans, Chl. phaeoferrooxidans, and Chl. sp. N1 show that...

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Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

Cited by 57 publications

References 82 publications

Biotic formation of methylmercury: A bio–physico–chemical conundrum

Biotic formation of methylmercury: A bio–physico–chemical conundrum

An improvedhgcABprimer set and direct high-throughput sequencing expand Hg-methylator diversity in nature

Genomic potential for photoferrotrophy in a seasonally anoxic Boreal Shield lake

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