Anaerobic microbial metabolism in soil columns affected by highly alkaline pH: Implication for biogeochemistry near construction and demolition waste disposal sites.

Construction and demolition wastes (CDWs) have become a significant environmental concern due to urbanization. CDWs in landfill sites can generate high-pH leachate and various constituents (e.g., acetate and sulfate) following the dissolution of cement material, which may affect subsurface biogeochemical properties. However, the impact of CDW leachate on microbial reactions and community compositions in subsurface environments remains unclear. Therefore, we created columns composed of layers of concrete debris containing-soil (CDS) and underlying CDW-free soil, and fed them artificial groundwater with or without acetate and/or sulfate. In all columns, the initial pH 5.6 of the underlying soil layer rapidly increased to 10.8 (without acetate and sulfate), 10.1 (with sulfate), 10.1 (with acetate), and 8.3 (with acetate and sulfate) within 35 days. Alkaliphilic or alkaline-resistant microbes including Hydrogenophaga, Silanimonas, Algoriphagus, and/or Dethiobacter were dominant throughout the incubation in all columns, and their relative abundance was highest in the column without acetate and sulfate (50.7-86.6%). Fe(III) and sulfate reduction did not occur in the underlying soil layer without acetate. However, in the column with acetate alone, pH was decreased to 9.9 after day 85 and Fe(II) was produced with an increase in the relative abundance of Fe(III)-reducing bacteria up to 9.1%, followed by an increase in the methanogenic archaea Methanosarcina, suggestive of methanogenesis. In the column with both acetate and sulfate, Fe(III) and sulfate reduction occurred along with an increase in both Fe(III)- and sulfate-reducing bacteria (19.1 and 17.7%, respectively), while Methanosarcina appeared later. The results demonstrate that microbial Fe(III)- and sulfate-reduction and acetoclastic methanogenesis can occur even in soils with highly alkaline pH resulting from the dissolution of concrete debris.

Delineation of LNAPL plumes in a clay-rich site in Gyeongsangnam-do Province, South Korea: integration of geophysical survey data with borehole data and soil sampling information.

To effectively delineate the spatial distribution of oil contaminant plumes, geophysical methods indirectly measure the physical properties of the subsurface and can provide spatial information and images on a large scale, as opposed to traditional direct methods such as borehole drilling, sampling, and chemical analysis, which are time-consuming and costly. However, interpreting geophysical responses over non-aqueous phase liquid (NAPL)-contaminated sites is not straightforward due to inconsistent responses from biodegraded oil contaminants. In this study, we performed multi-geophysical surveys including seismic refraction, ground-penetrating radar, electrical resistivity tomography (ERT), and induced polarization (IP) surveys, to locate NAPL-contaminated zones in a clay-rich site. To reduce ambiguity in discriminating between oil contaminants and clay layers, we first figure out the geological structure of the site by interpreting geophysical data incorporating with borehole data. The ERT data highlighted the heavily contaminated regions in the unsaturated zone but were less distinctive below groundwater levels. Conversely, IP responses revealed potential hotspots within the clay layers, extending beneath the groundwater. Considering the 3D geological model, NAPL-contaminated zones are properly delineated through interpretation of ERT and IP data together with borehole data, and the contaminant source zone was properly estimated within the site.

Impact of organic acids and sulfate on the biogeochemical properties of soil from urban subsurface environments.

Urban subsurface environments are often different from undisturbed subsurface environments due to the impacts of human activities. For example, deterioration of underground infrastructure can introduce elevated levels of Ca, Fe, and heavy metals into subsurface soils and groundwater. Likewise, leakage from sewer systems can lead to contamination by organic C, N, S, and P. However, the impact of these organic and inorganic compounds on biogeochemical processes including microbial redox reactions, mineral transformations, and microbial community transitions in urban subsurface environments is poorly understood. Here we conducted a microcosm experiment with soil samples from an urban construction site to investigate the possible biotic and abiotic processes impacted when sulfate and acetate or lactate were introduced into an urban subsurface environment. In the top-layer soil (0-0.3 m) microcosms, which were highly alkaline (pH > 10), the major impact was on abiotic processes such as secondary mineral precipitation. In the mid-layer (2-3 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were greatly impacted by the specific organic acid added, and sulfate-reduction was not observed until after Fe(III)-reduction was complete. Near the end of the incubation, some genera related to syntrophic acetate oxidation and methanogenesis were observed in the lactate-amended microcosms. In the bottom-layer (7-8 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were affected by the concentration of amended sulfate. Sulfate-reduction was concurrent with Fe(III)-reduction, suggesting that Fe(II) production was likely due to abiotic reduction of Fe(III) by sulfide produced by microbial sulfate reduction. The slightly acidic initial pH (~5.8) of the mid-soil system was a major factor controlling sequential microbial Fe(III) and sulfate reduction versus parallel Fe(III) and sulfate reduction in the bottom soil system, which had a neutral initial pH (~7.2). 16S rRNA gene-based community analysis revealed a variety of indigenous microbial groups including alkaliphiles, dissimilatory iron and sulfate reducers, syntrophes, and methanogens tightly coupled with, and impacted by, these complex abiotic and biogeochemical processes occurring in urban subsurface environments.

Waste nutrient solutions from full-scale open hydroponic cultivation: Dynamics of effluent quality and removal of nitrogen and phosphorus using a pilot-scale sequencing batch reactor.

Hydroponic cultivation is revolutionizing agricultural crop production techniques all over the world owing to its minimal environmental footprint, enhanced pest control, and high crop yield. However, waste nutrient solutions (WNS) generated from hydroponic systems contain high concentrations of N and P; moreover, they are discharged into surface and subsurface environments, leading to eutrophication and subsequent ecosystem degradation. In this study, the nutrient concentrations in WNS from 10 hydroponic indoor tomato, capsicum, and strawberry farms (greenhouses) were monitored for up to six months. The concentrations of N and P in WNS discharged from these farms were 48.0-494.0 mg L-1 and 12.7-96.9 mg L-1, respectively, which exceeded the Korean water quality guidelines (40.0 mg L-1 N and 4.0 mg L-1 P) for effluents. These concentrations were varied and dependent on the supplied nutrient concentrations, crop types, and growth stages. In general, the concentrations of N and P were in the following order: tomato > capsicum > strawberry. High N as NO3- and P as PO43- but low organic C in WNS warrant subsequent treatment before discharge. Therefore, this study tested a pilot-scale sequencing batch reactor (SBR) system as a potential technology for WNS treatment. The SBR system had BOD, COD, nitrate, and phosphate removal efficiency of 100, 100, 89.5, and 99.8%, respectively. In addition, the SBR system removed other cations such as Ca2+, dissolved Fe, K+, Mg2+, and Na+ and the removal efficiencies of those ions were 48, 67, 18, 14 and 15%, respectively. Lower methanol addition (0.63 mg L-1) and extended aeration (~30 min) improved SBR performance efficiency of C, N, and P removal. Thus, SBR showed significant promise as a treatment alternative to WNS pollutants originating from hydroponic systems.

Geochemical and microbial characteristics of seepage water and mineral precipitates in a radwaste disposal facility impacted by seawater intrusion and high alkalinity.

The construction of an underground facility can dramatically change the quality, flow direction, and level of groundwater. It may also impact subsurface microbial composition and activity. Groundwater quality was monitored over eight years in two observational wells near an underground disposal facility on the east coast of South Korea. The results showed dramatic increases in dissolved ions such as O2, Na, Ca, Mg, and SO4 during facility construction. Seepage water samples downgradient from the silos and tunnels, and precipitates deposited along the seepage water flow path were collected to determine the impact inside the disposal facility. X-ray analysis (powder X-ray diffraction (pXRD) and X-ray absorption fine structure (XAFS)) were used to characterize the mineral precipitates. Microbial community composition was determined by 16S rRNA gene sequencing. The seepage water composition was of two types: Ca-Cl and Ca-Na-HCO3. The ratio of Cl and δ18O showed that the Ca-Cl type seepage water was influenced by groundwater mixed with seawater ranging from 2.7% to 15.1%. Various sulfate-reducing bacteria were identified in the Ca-Cl type seepage water, exhibiting relatively high sulfate content from seawater intrusion. Samples from the Ca-Na-HCO3 type seepage water had an extremely high pH (>10) and abundance of Hydrogenophaga. The precipitates observed along the flow path of the seepage water included calcite, ferrihydrite, green rust, and siderite, depending on seepage water chemistry and microbial activity. This study suggests that the construction of underground structures creates distinct, localized geochemical conditions (e.g., high alkalinity, high salinity, and oxic conditions), which may impact microbial communities. These biogeochemical changes may have undesirable large-scale impacts such as water pump clogging. An understanding of the process and long-term monitoring are essential to assess the safety of underground facilities.

Inhibitory Effects of Pterocarpus santalinus Extract against IgE/Antigen-Sensitized Mast Cells and Atopic Dermatitis-Like Skin Lesions.

Pterocarpus santalinus has been traditionally used as a medicinal plant owing to its anti-inflammatory, anthelmintic, tonic, antihyperglycemic, and diaphoretic properties. We hypothesized that P. santalinus might have therapeutic potential in alleviating allergy and atopic dermatitis. Thus, we investigated the inhibitory effects of P. santalinus extract against allergic responses and 2,4-dinitrochlorobenzene-induced atopic dermatitis-like dorsal skin lesions using immunoglobulin E-sensitized rat basophilic leukemia-2H3 mast cells and NC/Nga mice. Degranulation and enzyme-linked immunosorbent assays were conducted to measure degranulation, proinflammatory cytokine levels, and prostaglandin E2 concentrations in immunoglobulin E/antigen-sensitized RBL-2H3 mast cells. The therapeutic efficacy of P. santalinus extract in 2,4-dinitrochlorobenzene-induced atopic dermatitis was evaluated through morphological, physiological, and immunological analysis. P. santalinus extract inhibited ß-hexosaminidase and histamine release and reduced tumor necrosis factor-α, interleukin-4, and prostaglandin E2 secretion. Furthermore, P. santalinus extract suppressed atopic dermatitis-like skin lesions by regulating the serum levels of immunoglobulin E and immunoglobulin G2a, and messenger ribonucleic acid expression of T helper cell 1- and T helper cell 2-related mediators in the skin lesions. Histopathological analyses showed a decrease in epidermal thickness and intradermal inflammatory cell infiltration. These results suggested that P. santalinus extract might have beneficial effects in treating allergic and atopic dermatitis-like skin disorders.

Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations.

Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into two size fractions (<0.063- and <2-mm) was utilized in two monitoring wells: DH1 (located close to the injection and extraction wells for in-situ soil flushing) and DH2 (located beyond sheet piles placed to block the transport of leaked diesel). Total petroleum hydrocarbon (TPH) concentrations and biogeochemical properties were monitored both in soil and groundwater for six months. A shift occurred in the groundwater type from Ca-HCO3 to Na-Cl due to seawater intrusion during intense pumping, while the concentrations of Ni, Cu, Co, V, Cr, and Se increased substantially following surfactant (TWEEN 80) injection. The in-situ sampler with fine particles was more sensitive to variations in conditions during the remedial soil flushing process. In both wells, soil TPH concentrations in the <0.063-mm fraction were much higher than those in the <2-mm fraction. Increases in soil TPH in DH1 were consistent with the expected outcomes following well pumping and surfactant injection used to enhance TPH extraction. However, the number of diesel-degrading microorganisms decreased after surfactant injection. 16S-rRNA gene-based analysis also showed that the community composition and diversity depended on both particle size and diesel contamination. The multidisciplinary approach to the contaminated site assessments showed that soil flushing with surfactant enhanced diesel extraction, but negatively impacted in-situ diesel biodegradation as well as groundwater quality. The results also suggest that the in-situ sampler can be an effective monitoring tool for subsurface biogeochemistry as well as contaminant dynamics.

Cr(OH)3(s) oxidation induced by surface catalyzed Mn(II) oxidation.

We examined the feasibility of Cr(OH)3(s) oxidation mediated by surface catalyzed Mn(II) oxidation under common groundwater pH conditions as a potential pathway of natural Cr(VI) contaminations. Dissolved Mn(II) (50 µM) was reacted with or without synthesized Cr(OH)3(s) (1.0 g/L) at pH 7.0-9.0 under oxic or anoxic conditions. Homogeneous Mn(II) oxidation by dissolved O2 was not observed at pH ≤ 8.0 for 50 days. At pH 9.0, by contrast, dissolved Mn(II) was completely removed within 8 days and precipitated as hausmannite. When Cr(OH)3(s) was present, this solid was oxidized and released substantial amounts of Cr(VI) as dissolved Mn(II) was added into the suspension at pH ≥ 8.0 under oxic conditions. Production of Cr(VI) was attributed to Cr(OH)3(s) oxidation by a newly formed Mn oxide via Mn(II) oxidation catalyzed on Cr(OH)3(s) surface. XANES results indicated that this surface-catalyzed Mn(II) oxidation produced a mixed valence Mn(III/IV) solid phase. Our results suggest that toxic Cr(VI) can be naturally produced via Cr(OH)3(s) oxidation coupled with the oxidation of dissolved Mn(II). In addition, this study evokes the potential environmental hazard of sparingly soluble Cr(OH)3(s), which has been considered the most common and a stable remediation product of Cr(VI) contamination.

Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

A fermentative, non-spore forming, motile, rod-shaped bacterium, designated strain MJ1(T), was isolated from an RDX contaminated aquifer at a live-fire training site in Northwest NJ, United States. On the basis of 16S rRNA gene sequencing and DNA base composition, strain MJ1(T) was assigned to the Firmicutes. The DNA G+C content was 42.8 mol%. Fermentative growth was supported by glucose and citrate in a defined basal medium. The bacterium is a strict anaerobe that grows between at pH 6.0 and pH 8.0 and 18 and 37 °C. The culture did not grow with hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) as the electron acceptor or mineralize RDX under these conditions. However, MJ1(T) transformed RDX into MNX, methylenedinitramine, formaldehyde, formate, ammonium, nitrous oxide, and nitrate. The nearest phylogenetic relative with a validly published name was Desulfotomaculum guttoideum (95 % similarity). However, MJ1(T) was also related to Clostridium celerecrescens DSM 5628 (95 %), Clostridium indolis DSM 755 (94 %), and Clostridium sphenoides DSM 632 (94 %). DNA:DNA hybridization with these strains was between 6.7 and 58.7 percent. The dominant cellular fatty acids (greater than 5 % of the total, which was 99.0 % recovery) were 16:0 fatty acid methyl ester (FAME) (32.12 %), 18:1cis 11 dimethyl acetal (DMA) (16.47 %), 16:1cis 9 DMA (10.28 %), 16:1cis 9 FAME (8.10 %), and 18:1cis 9 DMA (5.36 %). On the basis of morphological, physiological, and phylogenetic data, Clostridium geopurificans is proposed as a new species in genus Clostridium, with strain MJ1(T) as the type strain.

Hydrogenophaga carboriunda sp. nov., a tertiary butyl alcohol-oxidizing, psychrotolerant aerobe derived from granular-activated carbon (GAC).

A Gram-negative, rod-shaped bacterium was isolated from a mixed culture that degraded tert-butyl alcohol (TBA) in a granular-activated carbon (GAC) sample from a Biological-GAC reactor. Strain YZ2(T) was assigned to the Betaproteobacteria within the family Comamonadaceae based on 16S rRNA gene similarities. The nearest phylogenetic relative (95.0 % similarity) with a valid name was Hydrogenophaga taeniospiralis. The DNA G+C content was 66.4 mol%. DNA:DNA hybridization indicated that the level of relatedness to members of the genus Hydrogenophaga ranged from 1.1 to 10.8 %. The dominant cellular fatty acids were: 18:1 w7c (75 %), 16:0 (4.9 %), 17:0 (3.85 %), 18:0 (2.93 %), 11 methyl 18:1 w7c (2.69 %), Summed Feature 2 (2.27 %), and 18:0 3OH (1.35 %). The primary substrate used was TBA, which is a fuel oxygenate and groundwater contaminant. YZ2(T) was non-motile, without apparent flagella. It is a psychrotolerant, facultative aerobe that grew between pH 6.5 and 9.5, and 4 and 30 °C. The culture grew on and mineralized TBA at 4 °C, which is the first report of psychrotolerant TBA degradation. Hydrogen was used as an alternative electron donor. The culture also grew well in defined freshwater medium with ethanol, butanol, hydroxy isobutyric acid, acetate, pyruvate, citrate, lactate, isopropanol, and benzoic acid as electron donors. Nitrate was reduced with hydrogen as the sole electron donor. On the basis of morphological, physiological, and chemotaxonomic data, a new species, Hydrogenophaga carboriunda is proposed, with YZ2(T) as the type strain.

Multi-approach assessment of groundwater biogeochemistry: Implications for the site characterization of prospective spent nuclear fuel repository sites.

The disposal of spent nuclear fuel in deep subsurface repositories using multi-barrier systems is considered to be the most promising method for preventing radionuclide leakage. However, the stability of the barriers can be affected by the activities of diverse microbes in subsurface environments. Therefore, this study investigated groundwater geochemistry and microbial populations, activities, and community structures at three potential spent nuclear fuel repository construction sites. The microbial analysis involved a multi-approach including both culture-dependent, culture-independent, and sequence-based methods for a comprehensive understanding of groundwater biogeochemistry. The results from all three sites showed that geochemical properties were closely related to microbial population and activities. Total number of cells estimates were strongly correlated to high dissolved organic carbon; while the ratio of adenosine-triphosphate:total number of cells indicated substantial activities of sulfate reducing bacteria. The 16S rRNA gene sequencing revealed that the microbial communities differed across the three sites, with each featuring microbes performing distinctive functions. In addition, our multi-approach provided some intriguing findings: a site with a low relative abundance of sulfate reducing bacteria based on the 16S rRNA gene sequencing showed high populations during most probable number incubation, implying that despite their low abundance, sulfate reducing bacteria still played an important role in sulfate reduction within the groundwater. Moreover, a redundancy analysis indicated a significant correlation between uranium concentrations and microbial community compositions, which suggests a potential impact of uranium on microbial community. These findings together highlight the importance of multi-methodological assessments in better characterizing groundwater biogeochemical properties for the selection of potential spent nuclear fuel disposal sites.

Prediction of arsenic retention in vadose zone based on empirical relationship between soil properties and segmented retardation factors.

Arsenic (As) is a widespread environmental contaminant that poses a significant threat to ecosystems and human health. Although previous studies have qualitatively revealed the effects of individual soil properties on the transport and fate of As in the vadose zone, their integrated impacts remain obscure. Moreover, studies investigating the retardation factor therein, which is a key parameter for comprehending As transport in the vadose zone, are extremely limited. In this study, we investigated the interplay of soil properties with As transport and retention within the vadose zone, while focusing on the retardation factor of As. We employed steady-state unsaturated water-flow soil column experiments coupled with a mobile-immobile model and multiple linear regression analysis to elucidate the dependence of As retardation factors on the soil properties. In the mobile water zone, iron and organic matter contents emerged as the two most influential properties that impedes As mobility. Whereas, in the immobile water zone, the coefficient of uniformity and bulk density were the most influential factors that enhanced As retention. Finally, we derived an empirical equation for calculating the As retardation factors in each zone, offering a valuable tool for describing and predicting As behavior to protect the groundwater resources underneath.

Influence of iron (hydr)oxide mineralogy and contents in aquifer sediments on dissolved organic carbon attenuations during aquifer storage and recovery.

Aquifer storage and recovery (ASR) is a promising approach for managing water resources that enhances water quality through biogeochemical reactions occurring within aquifers. Iron (hydr)oxides, which are the predominant metallic oxides in soil, play a crucial role in degrading dissolved organic carbon (DOC), primarily through a process known as dissimilatory iron reduction (DIR). However, the efficiency of this reaction varies depending on the mineralogy and composition of the aquifer, and this understanding is essential for adequate water quality in ASR. The objective of this study is to investigate the impact of iron (hydr)oxide on acetate, as an organic carbon source, attenuation during the ASR. To achieve this, three sets of laboratory sediment columns were prepared, each containing a different type of iron (hydr)oxide minerals: ferrihydrite, goethite, and hematite. Following an acclimation period of 28 days to simulate the microcosm within an aquifer, the columns were continuously supplied with the simulated river water spiked with acetate (DOC 40-60 mg L-1), and the acetate concentration in the effluent was monitored. The result revealed that the column containing ferrihydrite achieved 97% acetate attenuation through DIR with anoxic conditions (DO < 0.1 mg L-1), while the goethite and hematite columns exhibited limited attenuation rates of 40 and 50%, respectively. Furthermore, the efficiency of acetate attenuation in the ferrihydrite columns increased with the content of ferrihydrite but experienced a rapidly declined at higher contents (3-4%), possibly due to the partial conversion of ferrihydrite to goethite as a result of the interaction between ferrihydrite and the Fe(II) produced during DIR. Additionally, an analysis of the microbial community demonstrated that microorganisms known to possess the ability to reduce iron (hydr)oxides under anaerobic conditions were abundant in the ferrihydrite columns.

Synergetic effect of nitrate on dissolved organic carbon attenuation through dissimilatory iron reduction during aquifer storage and recovery.

Aquifer storage and recovery (ASR) is a promising water management technique in terms of quantity and quality. During ASR, iron (Fe) (hydr)oxides contained in the aquifer play a crucial role as electron acceptors in attenuating dissolved organic carbon (DOC) in recharging water through dissimilatory iron reduction (DIR). Considering the preference of electron acceptors, nitrate (NO3⁻), possibly coexisting with DOC as the prior electron acceptor to Fe (hydr)oxides, might influence DIR by interrupting electron transfer. However, this phenomenon is yet to be clarified. In this study, we systematically investigated the potential effect of NO3⁻ on DOC attenuation during ASR using a series of sediment columns representing typical aquifer conditions. The results suggest that DOC attenuation could be enhanced by the presence of NO3⁻. Specifically, total DOC attenuation was notably higher than that from the stoichiometric calculation simply employing NO3⁻ as the additional electron acceptor to Fe (hydr)oxides, implying a synergetic effect of NO3⁻ in the overall reactions. X-ray photoelectron spectroscopy analyzes revealed that the Fe(II) ions released from DIR transformed the Fe (hydr)oxides into a less bioavailable form, inhibiting further DIR. In the presence of NO3⁻, however, no aqueous Fe(II) was detected, and another form of Fe (hydr)oxide appeared on the sediment surface. This may be attributed to nitrate-dependent Fe(II) oxidation (NDFO), in which Fe(II) is (re)oxidized into Fe (hydr)oxide, which is available for the subsequent DOC attenuation. These mechanisms were supported by the dominance of DIR-relevant bacteria and the growth of NDFO-related bacteria in the presence of NO3⁻.

Reaction pathways and Sb(III) minerals formation during the reduction of Sb(V) by Rhodoferax ferrireducens strain YZ-1.

Antimony (Sb), a non-essential metalloid, can be released into the environment through various industrial activities. Sb(III) is considered more toxic than Sb(V), but Sb(III) can be immobilized through the precipitation of insoluble Sb2S3 or Sb2O3. In the subsurface, Sb redox chemistry is largely controlled by microorganisms; however, the exact mechanisms of Sb(V) reduction to Sb(III) are still unclear. In this study, a new strain of Sb(V)-reducing bacterium, designated as strain YZ-1, that can respire Sb(V) as a terminal electron acceptor was isolated from Sb-contaminated soils. 16S-rRNA gene sequencing of YZ-1 revealed high similarity to a known Fe(III)-reducer, Rhodoferax ferrireducens. XRD and XAFS analyses revealed that bioreduction of Sb(V) to Sb(III) proceed through a transition from amorphous valentinite to crystalline senarmontite (allotropes of Sb2O3). Genomic DNA sequencing found that YZ-1 possesses arsenic (As) metabolism genes, including As(V) reductase arsC. The qPCR analysis showed that arsC was highly expressed during Sb(V)-reduction by YZ-1, and thus is proposed as the potential Sb(V) reductase in YZ-1. This study provides new insight into the pathways and products of microbial Sb(V) reduction and demonstrates the potential of a newly isolated bacterium for Sb bioremediation.

Temperature-dependent microbial reactions by indigenous microbes in bentonite under Fe(III)- and sulfate-reducing conditions.

Bentonite is a promising buffer material for constructing spent nuclear fuel (SNF) repositories. However, indigenous microbes in bentonite can be introduced to the repository and subsequent sealing of the repository develops anoxic conditions over time which may stimulate fermentation and anaerobic respiration, possibly affecting bentonite structure and SNF repository stability. Moreover, the microbial activity in the bentonite can be impacted by the heat generated from radionuclides decay. Therefore, to investigate the temperature effect on microbial activities in bentonite, we created microcosms with WRK bentonil (a commercial bentonite) using lactate as the electron donor, and sulfate and/or ferrihydrite (Fe(III)) as electron acceptors with incubation at 18 â„ƒ and 50 â„ƒ. Indigenous WRK microbes reduced sulfate and Fe(III) at both temperatures but with different rates and extents. Lactate was metabolized to acetate at both temperatures, but only to propionate at 18 â„ƒ during early-stage microbial fermentation. More Fe(III)-reduction at 18 â„ƒ but more sulfate-reduction at 50 â„ƒ was observed. Thermophilic and/or metabolically flexible microbes were involved in both fermentation and Fe(III)/sulfate reduction. Our findings illustrate the necessity of considering the influence of temperature on microbial activities when employing bentonite as an engineered buffer material in construction of SNF repository barriers.

Bioreduction of hydrogen uranyl phosphate: mechanisms and U(IV) products.

The mobility of uranium (U) in subsurface environments is controlled by interrelated adsorption, redox, and precipitation reactions. Previous work demonstrated the formation of nanometer-sized hydrogen uranyl phosphate (abbreviated as HUP) crystals on the cell walls of Bacillus subtilis, a non-U(VI)-reducing, Gram-positive bacterium. The current study examined the reduction of this biogenic, cell-associated HUP mineral by three dissimilatory metal-reducing bacteria, Anaeromyxobacter dehalogenans strain K, Geobacter sulfurreducens strain PCA, and Shewanella putrefaciens strain CN-32, and compared it to the bioreduction of abiotically formed and freely suspended HUP of larger particle size. Uranium speciation in the solid phase was followed over a 10- to 20-day reaction period by X-ray absorption fine structure spectroscopy (XANES and EXAFS) and showed varying extents of U(VI) reduction to U(IV). The reduction extent of the same mass of HUP to U(IV) was consistently greater with the biogenic than with the abiotic material under the same experimental conditions. A greater extent of HUP reduction was observed in the presence of bicarbonate in solution, whereas a decreased extent of HUP reduction was observed with the addition of dissolved phosphate. These results indicate that the extent of U(VI) reduction is controlled by dissolution of the HUP phase, suggesting that the metal-reducing bacteria transfer electrons to the dissolved or bacterially adsorbed U(VI) species formed after HUP dissolution, rather than to solid-phase U(VI) in the HUP mineral. Interestingly, the bioreduced U(IV) atoms were not immediately coordinated to other U(IV) atoms (as in uraninite, UO2) but were similar in structure to the phosphate-complexed U(IV) species found in ningyoite [CaU(PO4)2·H2O]. This indicates a strong control by phosphate on the speciation of bioreduced U(IV), expressed as inhibition of the typical formation of uraninite under phosphate-free conditions.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols.

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

Weathering extents and anthropogenic influences shape the soil bacterial community along a subsurface zonation.

Subsurface environments are composed of various active soil layers with dynamic biogeochemical interactions. We investigated soil bacterial community composition and geochemical properties along a vertical soil profile, which was categorized into surface, unsaturated, groundwater fluctuated, and saturated zones, in a testbed site formerly used as farmland for several decades. We hypothesized that weathering extent and anthropogenic inputs influence changes in the community structure and assembly processes and have distinct contributions along the subsurface zonation. Elemental distribution in each zone was strongly affected by the extent of chemical weathering. A 16S rRNA gene analysis indicated that bacterial richness (alpha diversity) was highest in the surface zone, and also higher in the fluctuated zone, than in unsaturated and saturated zones due to the effects of high organic matter, high nutrient levels, and/or aerobic conditions. Redundancy analysis showed that major elements (P, Na), a trace element (Pb), NO3, and the weathering extent were key driving forces shaping bacterial community composition along the subsurface zonation. Assembly processes were governed by specific ecological niches, such as homogeneous selection, in the unsaturated, fluctuated, and saturated zones, while in the surface zone, they were dominated by dispersal limitation. These findings together suggest that the vertical variation in soil bacterial community assembly is zone-specific and shaped by the relative influences of deterministic vs. stochastic processes. Our results provide novel insights into the relationships between bacterial communities, environmental factors, and anthropogenic influences (e.g., fertilization, groundwater, soil contamination), and into the roles of specific ecological niches and subsurface biogeochemical processes in these relationships.

Effects of natural non-volcanic CO2 leakage on soil microbial community composition and diversity.

Geological carbon capture and storage (CCS) can reduce anthropogenic CO2 emissions, but questions exist about impacts at the surface if CO2 leaks from deep storage reservoirs. To examine potential impacts on soils, previous studies have investigated the geochemistry and microbiology of volcanic soils hosting high fluxes of CO2 rich gas. This study builds on those previous investigations by considering impacts of CO2 leakage at a non-volcanic site, where deep geogenic CO2 leaks from a cracked well casing. At the site, we collected 26 soil cores adjacent to soil gas monitoring wells. Based on measured CO2 fluxes, the soil samples fall into two groups 1) high CO2 (flux = 304.6 ± 272.1 g m-2 d-1, conc. = 29.1 ± 34 %) and 2) low CO2 (flux = 15.8 ± 6.1 g m-2 d-1, conc. = 0.8 ± 0.9 %). Soil pH was significantly lower (p < 0.05) in high flux group samples (4.6 ± 0.3) than the low flux ones (5.3 ± 0.7). Beta diversity calculations using 16S rRNA gene sequences and redundancy analysis (RDA) revealed clear clustering of microbial communities relative to CO2 flux and significant correlations of community composition with pH and organic carbon content. In the high flux soils, abundant microbial groups included Acidobacteriota, Ktedonobacteria, and SC-I-84 in the phylum Proteobacteria, as well as Nitrososphaeria, a genus of ammonia oxidizing archaea. Compared to volcanic sites described previously, our non-volcanic site had slight differences in soil geochemical properties and gradual shifts in community compositions between CO2 hotspots and background locations. Moreover, the elevated abundance of SC-I-84 has not been reported in studies of volcanic sites. This study improves our ability to predict potential environmental impacts of geological CCS by expanding the range of conditions over which existing CO2 leakage has been observed.