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Dissolved organic matter (DOM) is a complex mixture of organic compounds found in all natural waters. Its composition affects its reactivity towards numerous processes. Its composition is a function of both its source (e.g., allochthonous or autochthonous) as well as the extent of environmental processing it has undergone (e.g., chemical or biological degradation). Ultraviolet-visible (UV-vis) spectroscopy is an analytical technique commonly used to assess the composition of dissolved organic matter in water samples. Here, we present spectra from Lake Mendota samples collected from June - November in 2017 at the surface of Lake Mendota as well as at specific depths within the water column. All samples were collected near the NTL-LTER research buoy. Absorbance values are listed for wavelengths 200 - 800 nm for each sample. 

Dissolved organic matter (DOM) is a complex mixture of organic compounds found in all natural waters. Its composition affects its reactivity towards numerous processes. Its composition is a function of both its source (e.g., allochthonous or autochthonous) as well as the extent of environmental processing it has undergone (e.g., chemical or biological degradation). Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) allows for the characterization of dissolved organic matter at the molecular level. The water sample was collected near the NTL-LTER research buoy on Lake Mendota. Formula assignments were made to raw mass to charge ratios detected in the mass spectrum using a custom processing script and resulting in a list of chemical formulas making up the DOM sample. 

Methylmercury (MeHg) production is controlled by the bioavailability of inorganic divalent mercury (Hg(II)_i) and Hg‐methylation capacity of the microbial community (conferred by thehgcABgene cluster). However, the relative importance of these factors and their interaction in the environment remain poorly understood. Here, metagenomic sequencing and a full‐factorial MeHg formation experiment were conducted across a wetland sulfate gradient with different microbial communities and pore water chemistries. From this experiment, the relative importance of each factor on MeHg formation was isolated. Hg(II)_ibioavailability correlated with the dissolved organic matter composition, while the microbial Hg‐methylation capacity correlated with the abundance ofhgcAgenes. MeHg formation responded synergistically to both factors. Notably,hgcAsequences were from diverse taxonomic groups, none of which contained genes for dissimilatory sulfate reduction. This work expands our understanding of the geochemical and microbial constraints on MeHg formation in situ and provides an experimental framework for further mechanistic studies.

 

ABSTRACT Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment. IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria , Firmicutes , and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem. 

Atmospheric delivery of mercury (Hg) is important to the Upper Great Lakes, and understanding gaseous Hg exchange between surface water and air is critical to predicting the effects of declining mercury emissions. Speciated atmospheric Hg, dissolved gaseous Hg (DGM), and particulate and filter passing total Hg were measured on a cruise in Lake Michigan. Low mercury levels reflected pristine background conditions, especially in offshore regions. In the atmosphere, reactive and particle-associated fractions were low (1.0 ± 0.5%) compared to gaseous elemental Hg (1.34 ± 0.14 ng m–3) and were elevated in the urbanized southern basin. DGM was supersaturated, ranging from 17.5 ± 4.8 pg L–1 (330 ± 80%) in the main lake to 33.2 ± 2.4 pg L–1 (730 ± 70%) in Green Bay. Diel cycling of surface DGM showed strong Hg efflux during the day due to increased winds, and build-up at night from continued DGM production. Epilimnetic DGM is formed from photochemical reduction, while hypolimnetic DGM originates from biological Hg reduction. We found that DGM concentrations were greatest below the thermocline (30.8 ± 13.6 pg L–1), accounting for 68–92% of the total DGM in Lake Michigan, highlighting the importance of nonphotochemical reduction in deep stratified lakes. 

Dissolved organic matter (DOM) is an intermediate between organic carbon formed by primary producers and carbon dioxide (CO₂) produced through respiration, making it a key component of the carbon cycle in aquatic ecosystems. Its composition influences the routes of mineralization. Here, we evaluate DOM composition as a function of time and depth in Lake Mendota, a highly productive eutrophic lake that stratifies in warm months and is located in Madison, Wisconsin, USA. Dissolved organic carbon concentrations and optical properties are presented for 73 samples collected at a single location at varying depths within the water column from June to November. A subset of samples is analyzed by Fourier transform‐ion cyclotron resonance mass spectrometry (FT‐ICR MS) to investigate DOM composition at the molecular level. Temporally, increases in more oxidized formulas are observed in both the epilimnion and hypolimnion. At the surface, correlations between DOM formulas and both chlorophyll concentrations and light intensity show that photochemical reactions contribute to DOM oxidation. In the hypolimnion, redox conditions and interactions with sediments likely influence temporal compositional change. Our results show DOM composition varies with depth with more highly oxidized formulas identified deeper in the water column. However, DOM composition varies more temporally than by location within the water column. This work has implications for climate change as DOM photooxidation in lakes represents an understudied flux of CO₂to the atmosphere. Additionally, lake eutrophication is increasing due to warming temperatures and this data set yields detailed molecular information about DOM composition and processing in such lakes.

 

Mercury (Hg) 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 ofhgcgenes from metagenomes. Our Hg‐cycling microorganisms in aquatic and terrestrial ecosystems (Hg‐MATE) database, a catalogue ofhgcgenes, 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 ofhgcgenes from environmental samples. We compared the recovery ofhgcgenes from environmental metagenomes using the marky‐coco pipeline with an approach based on coassembly 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 coassembly approach was preferred. Finally, we discuss the definition of truehgcgenes and methods to normalizehgcgene counts from metagenomes.