Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities.

The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.

Stable Isotope Fractionation Reveals Similar Atomic-Level Controls during Aerobic and Anaerobic Microbial Hg Transformation Pathways.

Mercury (Hg) is a global pollutant and potent neurotoxin that bioaccumulates in food webs as monomethylmercury (MeHg). The production of MeHg is driven by anaerobic and Hg redox cycling pathways, such as Hg reduction, which control the availability of Hg to methylators. Anaerobes play an important role in Hg reduction in methylation hot spots, yet their contributions remain underappreciated due to how challenging these pathways are to study in the absence of dedicated genetic targets and low levels of Hg0 in anoxic environments. In this study, we used Hg stable isotope fractionation to explore Hg reduction during anoxygenic photosynthesis and fermentation in the model anaerobe Heliobacterium modesticaldum Ice1. We show that cells preferentially reduce lighter Hg isotopes in both metabolisms, leading to mass-dependent fractionation, but mass-independent fractionation commonly induced by UV-visible light is absent. Due to the variability associated with replicate experiments, we could not discern whether dedicated physiological processes drive Hg reduction during photosynthesis and fermentation. However, we demonstrate that fractionation is affected by the interplay between pathways controlling Hg recruitment, accessibility, and availability alongside metabolic redox reactions. The combined contributions of these processes lead to isotopic enrichment during anoxygenic photosynthesis that is in between the values reported for anaerobic respiratory microbial Hg reduction and abiotic photoreduction. Isotope enrichment during fermentation is closer to what has been observed in aerobic bacteria that reduce Hg through dedicated detoxification pathways. Our work suggests that similar controls likely underpin diverse microbe-mediated Hg transformations that affect Hg's fate in oxic and anoxic habitats. IMPORTANCE Anaerobic and photosynthetic bacteria that reduce mercury affect mercury delivery to microbes in methylation sites that drive bioaccumulation in food webs. Anaerobic mercury reduction pathways remain underappreciated in the current view of the global mercury cycle because they are challenging to study, bearing no dedicated genetic targets to establish physiological mechanisms. In this study, we used stable isotopes to characterize the physiological processes that control mercury reduction during photosynthesis and fermentation in the model anaerobe Heliobacterium modesticaldum Ice1. The sensitivity of isotope analyses highlighted the subtle contribution of mercury uptake to the isotope signature associated with anaerobic mercury reduction. When considered alongside the isotope signatures associated with microbial pathways for which genetic determinants have been identified, our findings underscore the narrow range of isotope enrichment that is characteristic of microbial mercury transformations. This suggests that there are common atomic-level controls for biological mercury transformations across a broad range of geochemical conditions.

Microbial methane cycling in a landfill on a decadal time scale.

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.

Reduced sulphur sources favour HgII reduction during anoxygenic photosynthesis by Heliobacteria.

The consumption of rice has become a global food safety issue because rice paddies support the production of high levels of the potent neurotoxin, methylmercury. The production of methylmercury is carried out by chemotrophic anaerobes that rely on a diversity of terminal electron acceptors, namely sulphate. Sulphur can be a limiting nutrient in rice paddies, and sulphate amendments are often used to stimulate crop production, which can increase methylmercury production. Mercury (Hg) redox cycling can affect Hg methylation by controlling the delivery of inorganic Hg substrates to methylators in anoxic habitats. Whereas sulphur is recognized as a key substrate controlling methylmercury production, the controls sulphur exerts on other microbe-mediated Hg transformations remain poorly understood. To explore the potential coupling between sulphur assimilation and anaerobic HgII reduction to Hg0 , we studied Heliobacillus mobilis, a mesophilic anoxygenic phototroph representative from the Heliobacteriacea family originally isolated from a rice paddy. Here, we tested whether the redox state of the sulphur sources available to H. mobilis would affect its ability to reduce HgII . By comparing Hg0 production over a redox gradient of sulphur sources, we demonstrate that phototrophic HgII reduction is favoured in the presence of reduced sulphur sources such as thiosulphate and cysteine. We also show that cysteine exerts dynamic control on Hg cycling by affecting not only Hg's bioavailability but also its abiotic photoreduction under low light conditions. Specifically, in the absence of cells we show that organic matter (as yeast extract) and cysteine are both required for photoreduction to occur. This study offers insights into how one of the most primitive forms of photosynthesis affects Hg redox transformations and frames Heliobacteria as key players in Hg cycling within paddy soils, forming a basis for management strategies to mitigate Hg accumulation in rice.

A little bit of light goes a long way: the role of phototrophs on mercury cycling.

Among toxic metals, mercury (Hg) is a global priority contaminant due to the biomagnification of the most toxic form methylmercury (MeHg) in food webs, even in remote regions, such as the high Arctic. The importance of Hg as a chemical of major concern to human health was underscored by the recent adoption of the Minamata Convention on Mercury, a legally binding treaty that requires government agencies be equipped to monitor processes affecting global mercury transport and cycling. For several decades now, field and laboratory experiments have shown that phototrophs can directly interact with Hg and affect its speciation and fate. While an important body of work on the role of chemotrophic microbes on Hg cycling has been undertaken, the role of phototrophs is too often overlooked. Strikingly, what is known about phototroph-Hg interactions pertains mostly to oxygenic phototrophs with relatively little being known about anoxygenic phototrophs. Ongoing environmental change will no doubt affect the physical and chemical properties of aquatic ecosystems, which in turn will alter all phototrophic community dynamics. How these changes will affect the Hg cycle represent an important knowledge gap. After synthesizing what is currently known about chemotrophic Hg transformations, we describe the current state of knowledge on what is known about how phototrophs (bacteria and algae) affect Hg cycling (i.e., alteration of Hg redox state, Hg scavenging, potential for methylation) as well as describe the cellular and molecular targets of Hg toxicity in phototrophs. We discuss these interactions in an evolutionary context and provide recommendations for future research directions.