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.

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.

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⁻.

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.

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.

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.

Potential natural attenuation of petroleum hydrocarbons in fuel contaminated soils: Focusing on anaerobic fuel biodegradation involving microbial Fe(III) reduction.

Liquid fossil fuels, collectively known as total petroleum hydrocarbons (TPHs), are highly toxic and frequently leak into subsurface environments due to anthropogenic activities. As an in-situ biological remedial option for TPH contamination, aerobic TPH biodegradation is limited due to oxygen's low solubility in water, and because it is consumed quickly by aerobic bacteria. Thus, we investigated the potential of anaerobic TPH degradation by indigenous fermenting bacteria and Fe(III)-reducing bacteria. Twenty 6-10 m soil cores were collected from a closed military base subject to ongoing TPH contamination since the 1980s. Physicochemical and microbial properties were determined at 0.5-m intervals in each core. To assess the relationship between TPH degradation and microbial Fe(III) reduction, soil samples were grouped into high-TPH (>500 mg kg-1) and high-Fe(II) (>450 mg kg-1), high-TPH and low-Fe(II), low-TPH and high-Fe(II), and low-TPH and low-Fe(II) groups. Alpha diversity was significantly lower in high-TPH groups than in low-TPH groups, suggesting that high TPH concentrations exerted a strong selective pressure on bacterial communities. In the high-TPH and low-Fe(II) group, fermenting bacteria, including Microgenomatia and Chlamydiae, were more abundant, suggesting that TPH biodegradation occurred via fermentation. In the high-TPH and high-Fe(II) group, Fe(III)-reducing bacteria, including Geobacter and Zoogloea, were more abundant, suggesting that microbial Fe(III) reduction enhances TPH biodegradation. In contrast, the fermenting and/or Fe(III)-reducing bacteria were not statistically abundant in the low-TPH groups.

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.

Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures.

Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (Cu) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing Cu. However, oxygen diffusion into the system was controlled by SD rather than Cu. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.

Zn speciation and fate in soils and sediments along the ground transportation route of Zn ore to a smelter.

Assessment of Zn toxicity/mobility based on its speciation and transformations in soils is critical for maintaining human and ecosystem health. Zn-concentrate (56 % Zn as ZnS, sphalerite) has been imported through a seaport and transported to a Zn-smelter for several decades, and smelting processes resulted in aerial deposition of Zn and sulfuric acids in two geochemically distinct territories around the smelter (mountain-slope and riverside). XAFS analysis showed that the mountain-slope soils contained franklinite (ZnFe2O4) and amorphous (e.g., sorbed) species of Zn(II), whereas the riverside sediments contained predominantly hydrozincite [Zn5(OH)6(CO3)2], sphalerite, and franklinite. The mountain-slope soils had low pH and moderate levels of total Zn (~ 1514 ppm), whereas the riverside sediments had neutral pH and higher total Zn (12,363 ppm). The absence of sphalerite and the predominance of franklinite in the mountain-slope soils are attributed to the susceptibility of sphalerite and the resistance of franklinite to dissolution at acidic pH. These results are compared to previous Zn analyses along the transportation routes, which showed that Zn-concentrate spilled along the roadside in dust and soils underwent transformation to various O-coordinated Zn species. Overall, Zn-concentrate dispersed in soils and sediments during transportation and smelting transforms into Zn phases of diverse stability and bioavailability during long-term weathering.

Antimony redox processes in the environment: A critical review of associated oxidants and reductants.

The environmental behavior of antimony (Sb) has recently received greater attention due to the increasing global use of Sb in a range of industrial applications. Although present at trace levels in most natural systems, elevated Sb concentrations in aquatic and terrestrial environments may result from anthropogenic activities. The mobility and toxicity of Sb largely depend on its speciation, which is dependent to a large extent on its oxidation state. To a certain extent, our understanding of the environmental behavior of Sb has been informed by studies of the environmental behavior of arsenic (As), as Sb and As have somewhat similar chemical properties. However, recently it has become evident that the speciation of Sb and As, especially in the context of redox reactions, may be fundamentally different. Therefore, it is crucial to study the biogeochemical processes impacting Sb redox transformations to understand the behavior of Sb in natural and engineered environments. Currently, there is a growing body of literature involving the speciation, mobility, toxicity, and remediation of Sb, and several reviews on these general topics are available; however, a comprehensive review focused on Sb environmental redox chemistry is lacking. This paper provides a review of research conducted within the past two decades examining the redox chemistry of Sb in aquatic and terrestrial environments and identifies knowledge gaps that need to be addressed to develop a better understanding of Sb biogeochemistry for improved management of Sb in natural and engineered systems.

Bacterial distribution on the ocular surface of patients with primary Sjögren's syndrome.

Many studies have shown that gut microbial dysbiosis is a major factor in the etiology of autoimmune diseases but none have suggested that the ocular surface (OS) microbiome is associated with Sjögren's syndrome (SS). In this prospective study, we analyzed bacterial distribution on the OS in patients with primary SS. Among the 120 subjects included in this study, 48 patients (group A) had primary SS, whereas 72 subjects (group B) had dry eye symptoms that were unrelated to SS. We evaluated clinical dry eye parameters such as the OS disease index, ocular staining score (OSS), Schirmer's I test, and tear break-up time (TBUT). Conjunctival swabs were used to analyze the microbial communities from the two groups. Bacterial 16S rRNA genes were sequenced using the Illumina MiSeq platform, and the data were analyzed using the QIIME 1.9.1 program. The Shannon index was significantly lower in group A than in group B microbiota (p < 0.05). An analysis of similarity using the Bray-Curtis distance method found no difference in beta-diversity between the two groups (p > 0.05). In group A, Actinobacteria at the phylum level and Corynebacteria at the genus level exhibited low abundance than group B, but the differences were not statistically significant (p > 0.05). SS apparently decreases the diversity of the OS microbial community. These observations may be related to the pathophysiology of SS and should be investigated in future studies.

Effect of CO2 on biogeochemical reactions and microbial community composition in bioreactors with deep groundwater and basalt.

Changes in subsurface microbiology following CO2 injection have the potential to impact carbon trapping in CO2 storage reservoirs. However, much remains to be learned about responses of natural microbial consortia to elevated CO2 in basaltic systems. This study asks: how will microbes from deep (700 m) groundwater change along a gradient in CO2 (0-20 psi) in batch reactor systems containing basalt chips and groundwater amended with lactate? Reactors incubated for 87 days at 23 °C. Results for reactors with low CO2 (0 and 3 psi) differed considerably from those with high CO2 (10 and 20 psi). In reactors with low CO2, pH was >6.5 and lactate started to be used within 24 days. By 40 days, lactate was completely consumed and acetate increased to ~4 mM. As lactate was consumed, sulfate decreased from 0.16 to 0 mM after 40 days. In contrast, in reactors with high CO2, pH was <6.5, lactate and sulfate concentrations varied little and acetate was not produced. Biogeochemical modeling and community analyses indicate that differences between reactors with low and high CO2 reflect tolerances of reactor microbes to CO2 exposure. Communities in the low CO2 reactors carried out syntrophic lactate oxidation coupled with methanogenesis and sulfate reduction. Bacteroidota and Firmicutes became dominant phyla after 24 days and groups capable of sulfate reduction and methanogenesis were detected. In reactors with high CO2, however, biogeochemical activity was insignificant, no groups capable of sulfate reducion or methanogenesis were observed, and the community became less diverse during the incubation. These findings show that the response of microbial consortia can vary sharply along a CO2 gradient, creating significant differences in community composition and biogeochemistry, and that the timescale of basalt weathering is likely not rapid enough to prevent significant stress following a rapid increase in CO2 abundance.

Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland.

The land-use change from natural to managed farmland ecosystems can undergo perturbations and significantly impact soil environment and communities. To understand how anthropogenic land-use alteration determines in-depth relationships among soil environmental factors and soil bacterial communities, high-resolution characterization was performed using soil samples (27 spots × 3 depths; top 10-20 cm, middle 90-100 cm, bottom 180-190 cm) from a natural forest and a 50 year-old farmland. The soil bacterial community abundance (number of OTU's per sample) and diversity (Faith's phylogenetic diversity) was significantly higher in the top layer of farmland soil than in forest soil. However, the differences in bacterial community abundance between farmland and forest decreased with depth, suggesting that the effect of fertilization was limited to top and middle layers. The phyla Acidobacteria and Proteobacteria were distributed distinctively during the land-use change. The subgroups Gp1-3 of Acidobacteria were more abundant in the forest samples (pH 3.5-5), while Gp4-7 and Gp10 were predominant in the farmland (pH 4.5-9.5). Members belonging to α-Proteobacteria and Xanthomonadales in γ-Proteobacteria were dominant in the forest, whereas ß-, δ-, and γ-Proteobacteria were relatively abundant in the farmland. Both multivariate and correlation network analyses revealed that Acidobacteria and Proteobacteria communities were significantly affected by soil pH, as well as toxic metals from pesticides (Zn, Cr, Ni, Cu, Cd, As) and terminal electron acceptors (NO3, bioavailable Fe(III), SO4). In line with the long history of anthropogenic fertilization, the farmland site showed high abundance of membrane and ATP-binding cassette transporter genes, suggesting the key for uptake of nutrients and for protection against toxic metals and environmental stresses. This study provides new insights into the use of both Acidobacteria and Proteobacteria community structures as a bacterial indicator for land-use change.

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.

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment.

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of FeIII reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory FeIII-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly "sulfate-reducing" phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.

Revisiting soil bacterial counting methods: Optimal soil storage and pretreatment methods and comparison of culture-dependent and -independent methods.

Although a number of different methods have been used to quantify soil bacteria, identifying the optimal method(s) for soil bacterial abundance is still in question. No single method exists for undertaking an absolute microbial count using culture-dependent methods (CDMs) or even culture-independent methods (CIMs). This study investigated soil storage and pretreatment methods for optimal bacterial counts. Appropriate storage temperature (4°C) and optimal pretreatment methods (sonication time for 3 min and centrifugation at 1400 g) were necessary to preserve bacterial cell viability and eliminate interference from soil particles. To better estimate soil bacterial numbers under various cellular state and respiration, this study also evaluated three CDMs (i.e., colony forming unit, spotting, and most probable number (MPN) and three CIMs (i.e., flow cytometry (FCM), epifluorescence microscopy (EM) count, and DNA quantitation). Each counting method was tested using 72 soil samples collected from a local arable farm site at three different depths (i.e., 10-20, 90-100, and 180-190 cm). Among all CDMs, MPN was found to be rapid, simple, and reliable. However, the number of bacteria quantified by MPN was 1-2 orders lower than that quantified by CIMs, likely due to the inability of MPN to count anaerobic bacteria. The DNA quantitation method appeared to overestimate soil bacterial numbers, which may be attributed to DNA from dead bacteria and free DNA in the soil matrix. FCM was found to be ineffective in counting soil bacteria as it was difficult to separate the bacterial cells from the soil particles. Dyes used in FCM stained the bacterial DNA and clay particles. The EM count was deemed a highly effective method as it provided information on soil mineral particles, live bacteria, and dead bacteria; however, it was a time-consuming and labor-intensive process. Combining both types of methods was considered the best approach to acquire better information on the characteristics of indigenous soil microorganisms (aerobic versus anaerobic, live versus dead).