Dark Reduction of Mercury by Microalgae-Associated Aerobic Bacteria in Marine Environments

Simultaneous Reduction and Methylation of Nanoparticulate Mercury: The Critical Role of Extracellular Electron Transfer

Mercury nanoparticles are abundant in natural environments. Yet, understanding their contribution to global biogeochemical cycling of mercury remains elusive. Here, we show that microbial transformation of nanoparticulate divalent mercury can be an important source of elemental and methylmercury.Geobacter sulfurreducensPCA, a model bacterium predominant in anoxic environments (e.g., paddy soils), simultaneously reduces and methylates nanoparticulate Hg(II). Moreover, the relative prevalence of these two competing processes and the dominant transformation pathways differ markedly between nanoparticulate Hg(II) and its dissolved and bulk-sized counterparts. Notably, even when intracellular reduction of Hg(II) nanoparticles is constrained by cross-membrane transport (a rate-limiting step that also regulates methylation), the overall Hg(0) formation remains substantial due to extracellular electron transfer. With multiple lines of evidence based on microscopic and electrochemical analyses, gene knockout experiments, and theoretical calculations, we show that nanoparticulate Hg(II) is preferentially associated with c-type cytochromes on cell membranes and has a higher propensity for accepting electrons from the heme groups than adsorbed ionic Hg(II), which explains the surprisingly larger extent of reduction of nanoparticles than dissolved Hg(II) at relatively high mercury loadings. These findings have important implications for the assessment of global mercury budgets as well as the bioavailability of nanominerals and mineral nanoparticles.

The coupling effect promotes superoxide radical production in the microalgal-fungal symbiosis systems: Production, mechanisms and implication for Hg(II) reduction

Redox transformation of mercury (Hg) is critical for Hg exchange at the air-water interface. However, the superoxide radicals (O2•─) contribution of microalgal-fungal symbiotic systems in lake water to Hg(II) reduction is mainly unknown. Here, we studied the enhanced potential for O2•─ production by the coupling effect between microalgae and fungi. The relationships between microenvironment, microorganisms, and O2•─ production were also investigated. Furthermore, the implication of O2•─ for Hg(II) reduction was explored. The results showed that the coupling effect of microalgae and fungi enhanced O2•─ generation in the symbiotic systems, and the O2•─ generation peaked on day 4 in the lake water at 160.51 ± 13.06-173.28 ± 18.21 μmol/kg FW (fresh weight). In addition, O2•- exhibited circadian fluctuations that correlated with changes in dissolved oxygen content and redox potential on the inter-spherical interface of microalgal-fungal consortia. Partial least squares path modeling (PLS-PM) indicates that O2•─ formation was primarily associated with microenvironmental factors and microbial metabolic processes. The experimental results suggest that O2•─ in the microalgal-fungal systems could mediate Hg(II) reduction, promoting Hg conversion and cycling. The findings highlight the importance of microalgae and fungal symbiotic systems in Hg transformation in aquatic environments.

The different effects of molybdate on Hg(II) bio-methylation in aerobic and anaerobic bacteria

In nature, methylmercury (MeHg) is primarily generated through microbial metabolism, and the ability of bacteria to methylate Hg(II) depends on both bacterial properties and environmental factors. It is widely known that, as a metabolic analog, molybdate can inhibit the sulfate reduction process and affect the growth and methylation of sulfate-reducing bacteria (SRB). However, after it enters the cell, molybdate can be involved in various intracellular metabolic pathways as a molybdenum cofactor; whether fluctuations in its concentration affect the growth and methylation of aerobic mercury methylating strains remains unknown. To address this gap, aerobic γ-Proteobacteria strains Raoultella terrigena TGRB3 (B3) and Pseudomonas putida TGRB4 (B4), as well as an obligate anaerobic δ-Proteobacteria strain of the SRB Desulfomicrobium escambiense CGMCC 1.3481 (DE), were used as experimental strains. The growth and methylation ability of each strain were analyzed under conditions of 500 ng·L-1 Hg(II), 0 and 21% of oxygen, and 0, 0.25, 0.50, and 1 mM of MoO4 2-. In addition, in order to explore the metabolic specificity of aerobic strains, transcriptomic data of the facultative mercury-methylated strain B3 were further analyzed in an aerobic mercuric environment. The results indicated that: (a) molybdate significantly inhibited the growth of DE, while B3 and B4 exhibited normal growth. (b) Under anaerobic conditions, in DE, the MeHg content decreased significantly with increasing molybdate concentration, while in B3, MeHg production was unaffected. Furthermore, under aerobic conditions, the MeHg productions of B3 and B4 were not influenced by the molybdate concentration. (c) The transcriptomic analysis showed several genes that were annotated as members of the molybdenum oxidoreductase family of B3 and that exhibited significant differential expression. These findings suggest that the differential expression of molybdenum-binding proteins might be related to their involvement in energy metabolism pathways that utilize nitrate and dimethyl sulfoxide as electron acceptors. Aerobic bacteria, such as B3 and B4, might possess distinct Hg(II) biotransformation pathways from anaerobic SRB, rendering their growth and biomethylation abilities unaffected by molybdate.

Degradation of organic mercury in high salt environments by a marine aerobic bacterium Alteromonas macleodii KD01

Mercury (Hg), particularly organic mercury, poses a global concern due to its pronounced toxicity and bioaccumulation. Bioremediation of organic mercury in high-salt wastewater faces challenges due to the growth limitations imposed by elevated Cl- and Na+ concentrations on microorganisms. In this study, an isolated marine bacterium Alteromonas macleodii KD01 was demonstrated to degrade methylmercury (MeHg) efficiently in seawater and then was applied to degrade organic mercury (MeHg, ethylmercury, and thimerosal) in simulated high-salt wastewater. Results showed that A. macleodii KD01 can rapidly degrade organic mercury (within 20 min) even at high concentrations (>10 ng/mL), volatilizing a portion of Hg from the wastewater. Further analysis revealed an increased transcription of organomercury lyase (merB) with rising organic mercury concentrations during the exposure process, suggesting the involvement of mer operon (merA and merB). These findings highlight A. macleodii KD01 as a promising candidate for addressing organic mercury pollution in high-salt wastewater.

Elemental mercury production from contaminated riparian soil suspensions under air and nitrogen bubbling conditions

The dynamic change of redox conditions is a key factor in emission of elemental mercury (Hg0) from riparian soils. The objective of this study was to elucidate the influences of redox conditions on Hg0 emission from riparian soils. Soil suspension experiments were conducted to measure Hg0 emission from five Hg-contaminated soil samples in two redox conditions (i.e., treated with air or with N2). In four of the five samples, Hg0 emission was higher in air treatment than on N2 treatment. Remaining one soil, which has higher organic matter than other soils, showed no distinct difference in Hg0 production between air and N2 treatment. In soil suspensions subject to N2 treatment, the dissolved organic carbon (DOC) and Fe2+ concentrations were 3.38- to 1.34-fold and 1.44- to 2.28-fold higher than those in air treatment, respectively. Positive correlations were also found between the DOC and Fe2+ (r = 0.911, p < 0.01) and Hg2+ (r = 0.815, p < 0.01) concentrations in soil solutions, suggesting Fe2+ formation led to the release of DOC, which bound to Hg2+ in the soil and, in turn, limited the availability of Hg2+ for reduction to Hg0 in N2 treatment. On the other hand, for remaining one soil, more Hg2+ might be adsorbed onto the DOM in the air treatment, resulted in the inhibition of Hg0 production in air treatment. These results imply that the organic matter is important to prevent Hg0 production by changing redox condition. Further study is needed to prove the role of organic matter in the production of Hg0.

Bidirectional Enhancement of Nitrogen Removal by Indigenous Synergetic Microalgal-Bacterial Consortia in Harsh Low-C/N Wastewater

Conventional microalgal-bacterial consortia have limited capacity to treat low-C/N wastewater due to carbon limitation and single nitrogen (N) removal mode. In this work, indigenous synergetic microalgal-bacterial consortia with high N removal performance and bidirectional interaction were successful in treating rare earth tailing wastewaters with low-C/N. Ammonia removal reached 0.89 mg N L-1 h-1, 1.84-fold more efficient than a common microalgal-bacterial system. Metagenomics-based metabolic reconstruction revealed bidirectional microalgal-bacterial interactions. The presence of microalgae increased the abundance of bacterial N-related genes by 1.5- to 57-fold. Similarly, the presence of bacteria increased the abundance of microalgal N assimilation by 2.5- to 15.8-fold. Furthermore, nine bacterial species were isolated, and the bidirectional promotion of N removal by the microalgal-bacterial system was verified. The mechanism of microalgal N assimilation enhanced by indole-3-acetic acid was revealed. In addition, the bidirectional mode of the system ensured the scavenging of toxic byproducts from nitrate metabolism to maintain the stability of the system. Collectively, the bidirectional enhancement system of synergetic microalgae-bacteria was established as an effective N removal strategy to broaden the stable application of this system for the effective treatment of low C/N ratio wastewater.

A marine bacteria-inspired electrochemical regulation for continuous uranium extraction from seawater and salt lake brine

Oceans and salt lakes contain vast amounts of uranium. Uranium recovery from natural water not only copes with radioactive pollution in water but also can sustain the fuel supply for nuclear power. The adsorption-assisted electrochemical processes offer a promising route for efficient uranium extraction. However, competitive hydrogen evolution greatly reduces the extraction capacity and the stability of electrode materials with electrocatalytic activity. In this study, we got inspiration from the biomineralisation of marine bacteria under high salinity and biomimetically regulated the electrochemical process to avoid the undesired deposition of metal hydroxides. The uranium uptake capacity can be increased by more than 20% without extra energy input. In natural seawater, the designed membrane electrode exhibits an impressive extraction capacity of 48.04 mg-U per g-COF within 21 days (2.29 mg-U per g-COF per day). Furthermore, in salt lake brine with much higher salinity, the membrane can extract as much uranium as 75.72 mg-U per g-COF after 32 days (2.37 mg-U per g-COF per day). This study provides a general basis for the performance optimisation of uranium capture electrodes, which is beneficial for sustainable access to nuclear energy sources from natural water systems.

Development and optimization of a triple quadrupole ICP-MS-based system for the quantification of pre-concentrated gaseous elementary mercury

Understanding the redox reactions and transformation rates of mercury (Hg) species in the environment is important for predicting future gaseous elemental Hg (Hg0) levels and assessing the impacts of anthropogenic Hg0 emissions on human health. Stable Hg isotope tracers are a promising tool for estimating Hg0 production rates; however, traditional analytical approaches for quantifying Hg0, such as atomic fluorescence spectroscopy or atomic absorption spectrometry, cannot differentiate between Hg isotopes, and alternative approaches, such as inductively coupled plasma mass spectrometry (ICP-MS) with a typical aqueous sample introductory system, have relatively higher detection limit of Hg. Here, we developed and evaluated a custom-made thermal desorption unit coupled directly to a triple quadrupole ICP-MS (ICP-QQQ) for the quantification of Hg0 pre-concentrated on Au traps. The performance of the system was validated with measurements of a Hg standard gas and of Hg0 generated from aqueous Hg standards. Using our system, we were able to detect ultra-trace amounts of Hg0 and obtain precise Hg isotope measurements with an analytical error of ≤ 3.5%. Calibration curves with superb linearity (r2 > 0.999) were obtained for the Hg concentration range of 0-300 pg. The method detection limit was approximately 0.01-0.03 pg of Hg. Using the latest ICP-QQQ instrument (Agilent 8900; Agilent Technologies Ltd.) was far superior to using a previous model (Agilent 8800), with the Agilent 8900 showing approximately five times higher sensitivity than the Agilent 8800 as well as the ability to precisely and simultaneously analyze up to five Hg isotopes by time-resolved analysis.

Mercury transformations in algae, plants, and animals: The occurrence, mechanisms, and gaps

Mercury (Hg) is a global pollutant showing potent toxicity to living organisms. The transformations of Hg are critical to global Hg cycling and Hg exposure risks, considering Hg mobilities and toxicities vary depending on Hg speciation. Though currently well understood in ambient environments, Hg transformations are inadequately explored in non-microbial organisms. The primary drivers of in vivo Hg transformations are far from clear, and the impacts of these processes on global Hg cycling and Hg associated health risks are not well understood. This hinders a comprehensive understanding of global Hg cycling and the effective mitigation of Hg exposure risks. Here, we focused on Hg transformations in non-microbial organisms, particularly algae, plants, and animals. The process of Hg oxidation/reduction and methylation/demethylation in organisms were reviewed since these processes are the key transformations between the dominant Hg species, i.e., elemental Hg (Hg0), divalent inorganic Hg (IHgII), and methylmercury (MeHg). By summarizing the current knowledge of Hg transformations in organisms, we proposed the potential yet overlooked drivers of these processes, along with potential challenges that hinder a full understanding of in vivo Hg transformations. Knowledge summarized in this review would help achieve a comprehensive understanding of the fate and toxicity of Hg in organisms, providing a basis for predicting Hg cycles and mitigating human exposure.

Superoxide-Mediated Extracellular Mercury Reduction by Aerobic Marine Bacterium Alteromonas sp. KD01

Microbial reduction plays a crucial role in Hg redox and the global cycle. Although intracellular Hg(II) reduction mediated by MerA protein is well documented, it is still unclear whether or how bacteria reduce Hg(II) extracellularly without its internalization. Herein, for the first time, we discovered the extracellular reduction of Hg(II) by a widely distributed aerobic marine bacterium Alteromonas sp. KD01 through a superoxide-dependent mechanism. The generation of superoxide by Alteromonas sp. KD01 was determined using 3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide and methyl cypridina luciferin analogue as probes via UV-vis and chemiluminescence detection, respectively. The results demonstrated that Hg(II) reduction was inhibited by superoxide scavengers (superoxide dismutase (SOD) and Cu(NO3)2) or inhibitors of reduced nicotinamide adenine dinucleotide (NADH) oxidoreductases. In contrast, the addition of NADH significantly improved superoxide generation and, in turn, Hg(II) reduction. Direct evidence of superoxide-mediated Hg(II) reduction was provided by the addition of superoxide using KO2 in deionized water and seawater. Moreover, we observed that even superoxide at an environmental concentration of 9.6 ± 0.5 nM from Alteromonas sp. KD01 (5.4 × 106 cells mL-1) was capable of significantly reducing Hg(II). Our findings provide a greater understanding of Hg(II) reduction by superoxide from heterotrophic bacteria and eukaryotic phytoplankton in diverse aerobic environments, including surface water, sediment, and soil.

Gaseous mercury exchange between air and highly dynamic tidal flats: A laboratory incubation experiment

Gaseous mercury (mainly elemental mercury, Hg(0)) exchange between air and Earth's surfaces is one of the most critical fluxes governing global Hg cycle. As an important and unique part of intertidal ecosystem, tidal flat is characterized by periodic inundation and exposure due to tidal cycle, generating varying hydrological, photochemical and biogeochemical processes. However, quantitative and mechanistic understanding of Hg(0) dynamics between air and exceptionally dynamic tide flats has remained limited to date. In this study, we select five representative tidal flat sediments from typical coastal habits of Chinese coastlines to perform laboratory incubation experiments for deciphering the effect of the interaction of tidal cycle and solar radiation on Hg(0) dynamics over tidal flats with different sediment compositions. We show that sediment Hg concentration, tidal cycle and solar radiation collectively modulate the air-surface Hg(0) exchange over tidal flats and highlight that the photochemistry dominates the Hg(0) production and emission over tidal flats. We find that the daytime inundation presents highest Hg(0) emission fluxes for Hg-poor sediment, but the daytime exposure is the hot moment of Hg(0) emission from Hg-rich sediments and substantially contributes to daily Hg(0) emission fluxes. In the treatment to mimic semidiurnal tide, the daily Hg(0) fluxes are positively correlated to sediment Hg concentrations. Combining our mechanistic insights on air-surface Hg(0) exchange over tidal flats and related data and knowledge reported by other studies, we discuss the implications of our study for field measurement and model development of Hg(0) dynamics over highly dynamic tidal flats. We conclude that the air-surface Hg(0) dynamics over tidal flats are extremely complex and highly variable, and a greater understanding the interactions between natural processes, human impacts and climate forcings will better constrain current and future Hg biogeochemical cycle in global tidal flats.

Mercury (Hg) in the "Skin" of the Ocean: Dissolved Gaseous Hg, Total Hg, and Hg Redox Chemistry in Sea Surface Microlayer and Implication for Air-Sea Hg Exchange

The sea surface microlayer (SML) is the uppermost ∼1000 μm of the surface of the ocean. With distinct physicochemical properties and position relative to the adjacent subsurface waters (SSWs), the ubiquitous distribution and high dynamics of the SML greatly regulate the global air-sea gas exchange and biogeochemistry. Mercury (Hg) redox chemistry in surface seawaters and air-sea exchange of gaseous Hg (mainly Hg(0)) fundamentally control the global oceanic Hg cycle. However, the occurrence and transformation of Hg in the SML have been poorly quantified. Here we optimize the traditional SML sampling system to make it more suitable for dissolved gaseous Hg (DGM, mainly Hg(0)) sampling. We then assess the temporal and spatial variability of DGM, total Hg, dissolved organic carbon (DOC), and Hg redox chemistry in the SML and SSWs of diverse marine environments. Our data suggest a general DGM, total Hg, and DOC enrichment in the SML relative to the SSWs but with complex variability in time and space. The incubation experiments further reveal the complex characteristics of Hg redox chemistry between the SML and SSWs. We discuss important implications of the SML Hg cycle on air-sea Hg exchange and suggest wider investigations of the SML Hg cycle in the global hydrosphere.

Coastal streams and sewage outfalls: Hot spots of mercury discharge, pollution and cycling in nearshore environments

The coastal streams (CSs) and sewage outfalls (SOs) are widely distributed and direct anthropogenic stress on global coastal ecosystems. However, the CS/SO-associated mercury (Hg) discharge, pollution and cycle in nearshore environment are less quantified. Here, we report that total Hg (THg) and methylmercury (MMHg) concentrations in waters of CSs (n = 8) and SOs (n = 15) of the northern China were ∼102 to 103 times of coastal surface waters and 10 to 102 times of major rivers in China and other regions. The CS/SO discharges resulted in the increase of total organic carbon (TOC) contents, THg and MMHg concentrations and TOC-normalized THg and MMHg concentrations in sediments of CS/SO-impacted coasts. The laboratory experiments further illustrated that the CS/SO-impacted sediments characterized with high potentials of dissolved THg and MMHg productions and releases. Our findings indicate that the layout optimization of SOs is able to reduce the Hg risk in coastal environment.

Dissolved organic matter mediated dark- and photo-aging processes of Hg(II): Critical impacts of binding sites and sulfidation on Hg(II) abiotic reduction and microbial methylation

Dissolved organic matter (DOM)-mediated divalent mercury (Hg(II)) aging kinetics play a crucial role in controlling Hg(II) transformation and bioavailability in natural aquatic environments. However, the differential environmental behaviors of new and aged Hg(II) in a same reaction system remains unknown. In this study, multi-isotope tracing was used to investigate the impacts of binding site and sulfidation during DOM-mediated Hg(II) aging processes on Hg(II) reduction and microbial methylation in the same reaction system. Stepwise reduction approach and liquid chromatography-inductively coupled plasma mass spectrometry (LC-ICP-MS) demonstrate that DOM-mediated dark aging processes are mainly driven by the rearrangement of DOM binding sites with Hg(II), but not the formation of mercury sulfide nanoparticles (HgSNP). The abundant but weaker RO/N (carboxyl and amino) Hg(II)-binding sites are replaced with stronger RSH (thiol) moieties towards Hg(II) binding with aging, resulting in a decrease in Hg(II) reduction. In contrast, besides reduction, DOM-mediated Hg(II) photoaging induces the formation of HgSNP, as revealed by LC-ICP-MS, which in turn decreases the microbial methylation potential of Hg(II). These findings help better understand and predict the kinetic characteristics of Hg(II) reactivity and its influence on Hg cycle within natural aquatic environments.

Mercury reduction by black carbon under dark conditions

An accurate depiction of mercury (Hg) reduction is important to predict Hg biogeochemistry in both aquatic and soil systems. Although the photoreduction of Hg is well documented, reduction in the dark is poorly known and is thus the focus of this work. Black carbon (BC), an important constituent of organic matter in environments, can reduce Hg2+ in dark and oxygen-deficient conditions. Fast removal of Hg2+ in BC/Hg2+ solution was observed, with 4.99-86.88 L mg-1h-1 of the reaction rate constant, which could be ascribed to the combined actions of adsorption and reduction. Meanwhile, slow Hg reduction was obtained, compared to Hg removal, with 0.06-2.16 L mg-1h-1 of the reaction rate constant. Thus, in the initial stage, Hg2+ removal was mainly triggered by adsorption, rather than reduction. Afterward, the adsorbed Hg2+ on black carbon was converted into Hg0. Dissolved black carbon and aromatic CH on particulate black carbon were dominant triggers of Hg reduction for black carbon. During Hg reduction, the intastable intermediate, formed in the complex between aromatic CH and Hg2+, behaved as persistent free radicals, which could be detected by in situ electron paramagnetic resonance. Subsequently, the intastable intermediate was mainly converted into CO on black carbon and Hg0. Corresponding results of the present study highlight the important role of black carbon in the Hg biogeochemical cycle.

Photoreduction of Hg(II) by typical dissolved organic matter in paddy environments

The photochemical behavior of dissolved organic matter (DOM) in surface water and its effect on Hg(II) photoreduction has been extensively studied, but the contribution of DOM in paddy water to Hg(II) photoreduction is largely unknown. Herein, the effect of DOM from biochar (BC_DOM), rice straw (RS_DOM), and chicken manure (CM_DOM) on Hg(II) photoreduction were examined. The comparable reduction efficiency of Hg(II) suggested that DOM-like fraction (62.3-63.7%) contributes more than suspended particulate matter-like fraction (17.7-23.4%) and bacteria-like fraction (13.0-20.0%) in paddy water. Under irradiation, the typical DOM significantly promoted Hg(II) photoreduction, and the reduction efficiency of BC_DOM (65.5 ± 2.1%) was higher than that of CM_DOM (48.3 ± 2.6%) and RS_DOM (32.8 ± 2.4%) in 6 h. The quenching and kinetics experiments showed that superoxide anion (O₂^•-) was the main reactive species for Hg(II) photoreduction. Fluorescence spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry revealed that DOM with a higher degree of lignin/carboxy-rich acyclic molecules, condensed aromatics structures, and phenolic compounds could promote the formation of O₂^•-. These findings highlight the importance of DOM in Hg(II) photoreduction and provide new ideas for regulating Hg cycling and bioavailability in paddy environments.

Dissolved gaseous mercury production and sea-air gaseous exchange in impacted coastal environments of the northern Adriatic Sea

The northern Adriatic Sea is well known for mercury (Hg) contamination mainly due to historical Hg mining which took place in Idrija (Slovenia). The formation of dissolved gaseous mercury (DGM) and its subsequent volatilisation can reduce the amount of Hg available in the water column. In this work, the diurnal patterns of both DGM production and gaseous Hg fluxes at the water-air interface were seasonally evaluated in two selected environments within this area, a highly Hg-impacted, confined fish farm (VN: Val Noghera, Italy) and an open coastal zone less impacted by Hg inputs (PR: Bay of Piran, Slovenia). A floating flux chamber coupled with real-time Hg⁰ analyser was used for flux estimation in parallel with DGM concentrations determination through in-field incubations. Substantial DGM production was observed at VN (range = 126.0-711.3 pg L^-1) driven by both strong photoreduction and possibly dark biotic reduction, resulting in higher values in spring and summer and comparable concentrations throughout both day and night. Significantly lower DGM was observed at PR (range = 21.8-183.4 pg L^-1). Surprisingly, comparable Hg⁰ fluxes were found at the two sites (range VN = 7.43-41.17 ng m^-2 h^-1, PR = 0-81.49 ng m^-2 h^-1), likely due to enhanced gaseous exchanges at PR thanks to high water turbulence and to the strong limitation of evasion at VN by water stagnation and expected high DGM oxidation in saltwater. Slight differences between the temporal variation of DGM and fluxes indicate that Hg evasion is more controlled by factors such as water temperature and mixing conditions than DGM concentrations alone. The relative low Hg losses through volatilisation at VN (2.4-4.6% of total Hg) further confirm that static conditions in saltwater environments negatively affect the ability of this process in reducing the amount of Hg retained in the water column, therefore potentially leading to a greater availability for methylation and trophic transfer.

Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site

Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.