Biology subjects

Gregoire, D. S.

Publications and source records attributed to Gregoire, D. S..

10 recordsLinked to original sources

bioRxiv2026

Raman Spectroscopy Enables Real-Time Identification and Monitoring of Plastic Biodegradation Metabolites

Managing plastic pollution is challenging because current physical and chemical recycling methods are inefficient and environmentally intensive. Biological recycling approaches have been framed as sustainable alternatives but are challenging to optimize due to a lack of process analytical technologies that provide real time data on microbial plastic metabolism. In this study we used Piscinibacter sakaiensis 201-F6, a model bacterium with a well-studied polyethylene terephthalate (PET) metabolism, to validate non-destructive Raman spectroscopy methods to monitor plastic biodegradation by tracking metabolite production. Cells were grown on PET and known metabolites stemming from PET metabolism. Raman spectroscopy was used alongside destructive mass spectrometry techniques to monitor PET metabolite production and uptake under different growth conditions. Although cells grew effectively using PET, Raman spectroscopy did not detect the known PET metabolite terephthalic acid during growth assays. Instead, Raman detected isophthalic acid (IPA), a metabolite not previously associated with PET metabolism whose identity was confirmed with LC-HRMS. Raman spectroscopy was also used alongside thermoanalytical techniques to predict the biodegradability of PET at different crystallinities through the release of IPA. This study frames Raman spectroscopy as a promising tool to study metabolic pathways for plastic recycling and optimize their application in situ.

microbiology↗

bioRxiv2026

Diverse microbial metal resistance and novel metal cycling organisms in copper/nickel mine tailings

Mine tailings contribute to environmental heavy metal contamination through the formation of acid mine drainage (AMD). Microbially-mediated processes such as iron and sulfur redox cycling influence metal mobility. Here, we applied an integrated metagenomic and metaproteomic approach to profile microbial communities across vertical geochemical gradients in legacy copper/nickel tailings in Sudbury, Ontario, Canada. From 43 samples, we recovered 454 non-redundant metagenome-assembled genomes (MAGs), revealing diverse populations within the Actinobacteriota, Desulfobacterota, and uncultured lineages such as Candidatus Eremiobacterota and SZUA-79. Functional profiling identified 301 putative iron- and sulfur-cycling MAGs, including those within the Ca. Eremiobacterota and SZUA-79 phyla. Metal resistance genes were widespread and diverse, with abundances that did not correlate with measured metal concentrations. Proteomic data confirmed in situ expression of selected metal resistance genes and iron/sulfur metabolism genes, despite limited protein recovery from this challenging matrix. Our findings highlight both the depth of microbial diversity in metal resistance and metal biogeochemical cycling in mining waste, as well as the technical challenges that currently limit genomic and proteomic sequencing coverage in low-biomass, metal-rich matrices. This work also presents new protocols for multi-omics data capture and analysis from metal contaminated environments, including new protein extraction and bioinformatic gene annotation tools. HighlightsO_LIMetagenomics recovered 454 non-redundant MAGs from copper/nickel mine tailings, revealing high taxonomic novelty including uncultured Ca. Eremiobacterota and SZUA-79 lineages. C_LIO_LIA custom HMM-based pipeline targeting metal resistance genes uncovered a widespread and diverse set of metal resistance genes across MAGs in tailings, which did not correlate with metal concentrations. C_LIO_LIMetaproteomics validated in situ expression of both iron/sulfur cycling genes and metal resistance proteins, although low biomass and contamination limited proteomic sequencing coverage. C_LI

microbiology↗

bioRxiv2026

Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste

Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership and metal cycling across a landfills lifespan have not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing between Older (aged 31 - 39 years) and Newer (aged 3 - 20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals - all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemistry data from time of filling to present and microbial membership across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual framework for understanding this critical, final stage in a landfills life cycle. ImportanceAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond [~]20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension - a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer-term.

microbiology↗

bioRxiv2025

Methane Cycling Microbes are Important Predictors of Methylmercury Accumulation in Rice Paddies

Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice growing season to identify microbial and environmental factors influencing methylmercury dynamics. We show that hgcA gene abundance, the key gene required for methylation, was not a significant predictor of methylmercury concentration in paddy soils. We also show that merB gene abundance correlated with methylmercury in mercury-polluted rhizosphere samples. Methane cycling genes were actively expressed, and their beta-diversity was significantly associated with methylmercury levels. Methanogen abundance correlated with higher methylmercury under elevated total mercury concentrations. Analysis of the methanotroph-associated mbnT gene, implicated in demethylation, revealed an unexpected positive correlation with methylmercury. Multiple regression and machine learning models converged on mercury bioavailability and methanogen/methanotroph abundances as key predictors of methylmercury, with methanogen-associated hgcA gene abundance and methanogen-methanotroph interactions highlighted under flooded, low-redox conditions. These findings suggest that methane-cycling microbes play key roles in methylmercury cycling dynamics and point to management strategies that could simultaneously mitigate mercury pollution and greenhouse gas emissions. ImportanceMethylmercury is a microbially-derived neurotoxin that accumulates in rice, which is a global food staple. Predicting mercurys fate in rice paddies is challenging because of the interplay between microbes responsible for methylmercury cycling and variables that control mercury availability. Our study coupled genomic and geochemical measurements with machine learning to identify the key predictors of methylmercury accumulation in paddy soils. We demonstrate that methanogen and methanotroph abundance, and mercury bioavailability, are major predictors of methylmercury variability in paddies. We show that considering interactions between methane cycling guilds improves our capacity to predict methylmercury accumulation in soils compared to approaches that rely solely on mercury cycling genes. This work can inform remediation strategies for mercury in rice paddies but also wetlands and permafrost where methane and mercury cycling are tightly coupled. Such strategies could provide a solution to simultaneously mitigate methylmercury exposure and reduce greenhouse gas emissions amid global environmental change.

microbiology↗

bioRxiv2025

Investigating Cobalt Corrosion Mechanisms in a Phenazine Producing Bacterium

Microbially-induced corrosion (MIC) has been well-studied in the context of damage to iron-bearing infrastructure, where microbes can solubilize solid elemental iron using redox-active metabolites such as phenazines. Whether such pathways can solubilize economically-critical cobalt remains poorly understood. We hypothesized that secondary metabolites produced by the model bacterium Pseudomonas chlororaphis subspecies aureofaciens associated with MIC of iron could corrode cobalt by oxidation (i.e., phenazines) or by acting as a ligand (i.e., cyanide). One-week incubations using live cells supplied with Co(0) wires led to 20-30% cobalt mass losses and [~]2200 {micro}M Co(2+) recovered in solution, which was at least 3-fold higher than filtered cultures and sterile medium controls. Removing the capacity for cells to produce phenazines and cyanide showed similar corrosion compared to wild type cells and phenazine standards did not corrode cobalt, ruling these metabolites out as contributors to MIC. Further experiments testing whether metabolite mixtures devoid of phenazines could corrode Co(0) in the presence and absence of oxygen confirmed that atmospheric oxygen initiates Co(0) oxidation, and that unidentified cell-derived metabolites drive MIC forward by keeping Co(2+) from precipitating as oxides that form a passivation layer on the wire surface. This revised mechanistic explanation underscores the importance of considering how abiotic redox cycling and cellular metabolites that solubilize metals interact in the MIC of non-ferrous metals. Identifying the biosynthetic pathways involved in solubilizing cobalt will be key to reframing MIC as more than an environmental concern and optimizing sustainable cobalt recovery strategies for solid waste that rely on naturally-occurring microbial metabolites. ImportanceCharacterizing microbially-induced corrosion mechanisms for cobalt is important for predicting the fate of critical metals in the environment and optimizing sustainable strategies for cobalt reclamation from electronic waste. This study uses the model bacterium Pseudomonas chlororaphis subspecies aureofaciens to test if redox-active phenazines and the metal-binding metabolite cyanide can corrode elemental cobalt. We repeatedly observed that live cells corroded cobalt, but that corrosion did not rely on phenazines or cyanide. Instead, our results show that oxygen oxidized elemental cobalt and unidentified metabolites keep cobalt ions in solution to limit cobalt oxide precipitation and drive the corrosion reaction forward. Our study reinforces the need to consider connections between abiotic and biotic reactions in the corrosion of metals other than iron. Understanding these mechanisms is critical to reframing microbial corrosion as a sustainable approach for metal recovery and our study makes the case that it is possible for the critical metal cobalt.

microbiology↗

bioRxiv2025

Multi-omics highlights challenges in assessing the composition and performance of microbial consortia for commercial applications

The use of commercial microbial consortia in bioremediation is a promising method for addressing environmental pollution. These consortia are comprised of complex communities that include unculturable species that make it challenging to optimize consortia performance and carry out risk assessments for regulatory purposes. In this study, we provide a framework for using multi-omics to monitor the composition and performance of an aerobic ammonia oxidizing consortium in development for wastewater treatment. Long-read sequencing showed the consortium was dominated by an unclassified Nitrosospira species with the capacity for ammonia oxidation with many lower abundance taxa displaying the potential for denitrification. Considerable shifts in community composition and nitrogen cycling occurred when the consortium was grown along a redox gradient representative of wastewater for eight weeks. All aerobic and anaerobic cultures produced ammonia during the first four weeks and only aerobic cultures decreased ammonia concentrations after that time. Shotgun metagenomic sequencing showed the key ammonia oxidizing Nitrosospira sp. population decreased in abundance in aerobic cultures yet remained dominant in anaerobic cultures. Shotgun metatranscriptomic sequencing revealed that aerobic cultures decreased ammonia oxidation activity during the incubation and taxa that precluded detection in the starting material likely contributed to denitrification in anaerobic cultures. Metatranscriptomics showed that deamination of amino acids was an unexpected contributor to ammonia production that could negatively affect consortium performance. This study highlights how multi-omics provides insights that can be used to optimize performance and carry out risks assessments for consortia applied in different environmental settings. ImportanceThe use of microbial consortia from diverse environments is gaining traction in terms of advancing a more sustainable bioeconomy. Optimizing consortia for different applications and ensuring they are compliant with environmental regulations is difficult because current practices rely on growing microbes with unknown physiological requirements. In this study we apply leading-edge sequencing approaches to develop a framework that addresses these challenges using a consortium in development for ammonia removal from wastewater. We demonstrate that long-read DNA sequencing provides complete genome assemblies and functional insights into key populations involved in ammonia removal that are poorly represented in taxonomic databases. We show that coupling DNA to RNA sequencing provides valuable information on changes in composition and metabolic activity that can occur under environmentally representative conditions for wastewater. Ultimately, our approach serves as an example of cutting-edge genomics applications for stakeholders to consider in developing microbial consortia for safe and effective use across diverse applications.

microbiology↗

bioRxiv2024

Aquifer microbial communities are highly variable in response to thermal arsenic mobilization

Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic resistance, including efflux and methylation. Microorganisms may also perform reduction/oxidation of As(V)/As(III) as part of their detoxification and/or metabolic pathways. We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread amongst community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high-arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.

microbiology↗

bioRxiv2024

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

The oxidation of sulfide-bearing mine tailings catalysed 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 endogenous microbes living in 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.

microbiology↗

bioRxiv2023

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 69% by the year 2050, there is a pressing need to better understand the biogeochemical processes that control microbial methane cycling in landfills. In this study, we had the rare opportunity to characterize the microbial community responsible for methane cycling in landfill waste covering a 39-year timeframe. We coupled long term geochemical analyses to whole-community DNA (i.e., metagenomic) sequencing and identified key features that shape methane cycling communities over the course of a landfills lifecycle. Anaerobic methanogenic microbes are more abundant, diverse, and metabolically versatile in newer waste, fueling rapid methane production early in a landfills lifecycle. Aerobic methanotrophs were repeatedly found in leachate where low levels of oxygen were present and exhibited adaptations that aid survival under steep redox gradients in landfills. The potential for anaerobic methane oxidation, which has historically been overlooked despite anoxic habitats dominating landfills, was prevalent in a 26-year-old landfill cell which was in a state of slow methanogenesis. Finally, we identified the metabolic potential for methane oxidation in lineages that are widespread in aquatic and terrestrial habitats, whose capacity to metabolize methane remains poorly characterized. Ultimately, this work expands the diversity of methane cycling guilds in landfills and outlines how these communities can curb methane emissions from municipal solid waste. SignificanceMicrobes are major contributors to methane emissions from solid waste however the temporal dynamics of methane cycling communities in landfills remain poorly understood. We addressed this gap by using whole-community DNA (i.e., metagenomic) approaches to characterize microbial methane cycling in waste covering a 39-year timeframe. We show that methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. We highlight that methane oxidation in the absence of oxygen is overlooked in landfill biogeochemical models and that novel lineages can potentially contribute to methane sinks across a broad range of habitats. These findings can strengthen predictive models for methane cycling in landfills and inform sustainable waste management strategies to curb methane emissions from solid waste.

microbiology↗

bioRxiv2020

Common physiological processes control mercury reduction during photosynthesis and fermentation

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 hotspots, 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. We show that isotope 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. These results demonstrate that common controls exist at the atomic level for Hg reduction during photosynthesis and fermentation in H. modesticaldum. Our work suggests that similar controls likely underpin diverse microbe-mediated Hg transformations that affect Hgs fate in oxic and anoxic habitats. IMPORTANCEAnaerobic 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 show that common physiological processes 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 towards 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 exist common atomic-level controls for biological mercury transformations across a broad range of geochemical conditions.

microbiology↗