Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

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.

Altering environmental conditions induce shifts in simulated deep terrestrial subsurface bacterial communities-Secretion of primary and secondary metabolites

The deep terrestrial subsurface (DTS) harbours a striking diversity of microorganisms. However, systematic research on microbial metabolism, and how varying groundwater composition affects the bacterial communities and metabolites in these environments is lacking. In this study, DTS groundwater bacterial consortia from two Fennoscandian Shield sites were enriched and studied. We found that the enriched communities from the two sites consisted of distinct bacterial taxa, and alterations in the growth medium composition induced changes in cell counts. The lack of an exogenous organic carbon source (ECS) caused a notable increase in lipid metabolism in one community, while in the other, carbon starvation resulted in low overall metabolism, suggesting a dormant state. ECS supplementation increased CO2 production and SO4 2- utilisation, suggesting activation of a dissimilatory sulphate reduction pathway and sulphate-reducer-dominated total metabolism. However, both communities shared common universal metabolic features, most probably involving pathways needed for the maintenance of cell homeostasis (e.g., mevalonic acid pathway). Collectively, our findings indicate that the most important metabolites related to microbial reactions under varying growth conditions in enriched DTS communities include, but are not limited to, those linked to cell homeostasis, osmoregulation, lipid biosynthesis and degradation, dissimilatory sulphate reduction and isoprenoid production.

Tracking Initial Fe(II)-Driven Ferrihydrite Transformations: A Mössbauer Spectroscopy and Isotope Investigation

Transformation of nanocrystalline ferrihydrite to more stable microcrystalline Fe(III) oxides is rapidly accelerated under reducing conditions with aqueous Fe(II) present. While the major steps of Fe(II)-catalyzed ferrihydrite transformation are known, processes in the initial phase that lead to nucleation and the growth of product minerals remain unclear. To track ferrihydrite-Fe(II) interactions during this initial phase, we used Fe isotopes, Mössbauer spectroscopy, and extractions to monitor the structural, magnetic, and isotope composition changes of ferrihydrite within ∼30 min of Fe(II) exposure. We observed rapid isotope mixing between aqueous Fe(II) and ferrihydrite during this initial lag phase. Our findings from Mössbauer spectroscopy indicate that a more magnetically ordered Fe(III) phase initially forms that is distinct from ferrihydrite and bulk crystalline transformation products. The signature of this phase is consistent with the early stage emergence of lepidocrocite-like lamellae observed in previous transmission electron microscopy studies. Its signature is furthermore removed by xylenol extraction of Fe(III), the same approach used to identify a chemically labile form of Fe(III) resulting from Fe(II) contact that is correlated to the ultimate emergence of crystalline product phases detectable by X-ray diffraction. Our work indicates that the mineralogical changes in the initial lag phase of Fh transformation initiated by Fe(II)-Fh electron transfer are critical to understanding ferrihydrite behavior in soils and sediments, particularly with regard to metal uptake and release.

Mobility of antimony in contrasting surface environments of a mine site: influence of redox conditions and microbial communities

Microbial processes can influence the complex geochemical behaviour of the toxic metalloid antimony (Sb) in mining environments. The present study is aimed to evaluate the influence of microbial communities on the mobility of Sb from solid phases to water in different compartments and redox conditions of a mining site in southwest (SW) Spain. Samples of surface materials presenting high Sb concentrations, from two weathered mining waste dumps, and an aquatic sediment were incubated in slurries comparing oxic and anoxic conditions. The initial microbial communities of the three materials strongly differed. Incubations induced an increase of microbial biomass and an evolution of the microbial communities' structures and compositions, which diverged in different redox conditions. The presence of active bacteria always influenced the mobility of Sb, except in the neutral pH waste incubated in oxic conditions. The effect of active microbial activities in oxic conditions was dependent on the material: Sb oxic release was biologically amplified with the acidic waste, but attenuated with the sediment. Different bacterial genera involved in Sb, Fe and S oxidation or reduction were present and/or grew during incubation of each material. The results highlighted the wide diversity of microbial communities and metabolisms at the small geographic scale of a mining site and their strong implication in Sb mobility.

Landfill: An eclectic review on structure, reactions and remediation approach

Since the enactment of the Clean Water Act (1972), which was supplemented by increased accountability under Resource Conservation and Recovery Act (RCRA) Subtitle D (1991) and the Clean Air Act Amendments (1996), landfills have indeed been widely used all around the world for treating various wastes. The landfill's biological and biogeochemical processes are believed to be originated about 2 to 4 decades ago. Scopus and web of Science based bibliometric study reveals that there are few papers available in scientific domain. Further, till today not a single paper demonstrated the detailed landfills heterogenicity, chemistry and microbiological processes and their associated dynamics in a combined approach. Accordingly, the paper addresses the recent applications of cutting-edge biogeochemical and biological methods adopted by different countries to sketch an emerging perspective of landfill biological and biogeochemical reactions and dynamics. Additionally, the significance of several regulatory factors controlling the landfill's biogeochemical and biological processes is highlighted. Finally, this article emphasizes the future opportunities for integrating advanced techniques to explain landfill chemistry explicitly. In conclusion, this paper will provide a comprehensive vision of the diverse dimensions of landfill biological and biogeochemical reactions and dynamics to the scientific world and policymakers.

Upside down sulphate dynamics in a saline inland lake

The sulphur cycle has a key role on the fate of nutrients through its several interconnected reactions. Although sulphur cycling in aquatic ecosystems has been thoroughly studied since the early 70's, its characterisation in saline endorheic lakes still deserves further exploration. Gallocanta Lake (NE Spain) is an ephemeral saline inland lake whose main sulphate source is found on the lake bed minerals and leads to dissolved sulphate concentrations higher than those of seawater. An integrative study including geochemical and isotopic characterization of surface water, porewater and sediment has been performed to address how sulphur cycling is constrained by the geological background. In freshwater and marine environments, sulphate concentration decreases with depth are commonly associated with bacterial sulphate reduction (BSR). However, in Gallocanta Lake sulphate concentrations in porewater increase from 60 mM at the water-sediment interface to 230 mM at 25 cm depth. This extreme increase could be caused by dissolution of the sulphate rich mineral epsomite (MgSO₄·7H₂O). Sulphur isotopic data was used to validate this hypothesis and demonstrate the occurrence of BSR near the water-sediment interface. This dynamic prevents methane production and release from the anoxic sediment, which is advantageous in the current context of global warming. These results underline that geological context should be considered in future biogeochemical studies of inland lakes with higher potential availability of electron acceptors in the lake bed compared to the water column.

Dynamic processes in conjunction with microbial response to unveil the attenuation mechanisms of tris (2-chloroethyl) phosphate (TCEP) in non-sanitary landfill soils

Although the environmental and health risks of chlorinated organophosphate esters (OPEs-Cl) have drawn much attention, its environmental behaviors have been insufficiently characterized. As a notable sink of this emerging contaminant, non-sanitary landfills, which may decompose/accumulate OPEs-Cl, is of particular concern. In the present study, the dynamic processes of the typical OPEs-Cl, tris(2-chloroethyl) phosphate (TCEP), in non-sanitary landfill soils were analyzed under anaerobic condition, and the microbial taxa involved in these processes were explored. Our results showed that TCEP could be simultaneously reduced by abiotic and biotic processes, as it was reduced by 73.9% and 65.5% over the 120-day experiment in landfill humus and subsoil, respectively. Notably, the degradation of TCEP was significantly (p < 0.05) enhanced under the stress of a high TCEP concentration (10 μg g^-1), while its ecological consequences were found insignificant regarding the microbial diversity and community structure and the typical soil redox processes, including Fe(III)/SO₄^2- reduction and methanogenesis, in both soils. The microbial diversity of subsoil was significantly lower, and acetate was an important factor in changing microbial communities in landfill soils. The microbes in the family Nocardioidaceae and genus Pseudomonas might contribute to in the degradation of TCEP in landfill humus and subsoil, respectively. The metabolism related to sulfur and sulfate respiration were significantly (p < 0.05) correlated with TCEP reduction, and Desulfosporosinus were found as a potentially functional microbial taxon in TCEP degradation in both soils. The results could advance our understanding of the environmental behavior of OPEs-Cl in landfill-like complex environments.

Phosphorus adsorption on iron-coated sand under reducing conditions

Mitigation measures are needed to prevent large loads of phosphate originating in agriculture from reaching surface waters. Iron-coated sand (ICS) is a residual product from drinking water production. It has a high phosphate adsorption capacity and can be placed around tile drains, taking no extra space, which increases the farmers' acceptance. The main concern regarding the use of ICS filters below groundwater level is that limited oxygen supply and high organic matter concentrations may lead to the reduction and dissolution of iron (hydr)oxides present and the release of previously adsorbed phosphate. This study aimed to investigate phosphate adsorption on ICS at the onset of iron reduction. First, we investigated whether simultaneous metal reduction and phosphate adsorption were relevant at two field sites in the Netherlands that use ICS filters around tile drains. Second, the onset of microbially mediated reduction of ICS in drainage water was mimicked in complementary laboratory microcosm experiments by varying the intensity of reduction through controlling the oxygen availability and the concentration of degradable organic matter. After 3 yr, ICS filters in the field removed phosphorus under low redox conditions. Over 45 d, the microbial reduction of manganese and iron oxides did not lead to phosphate release, confirming field observations. Electron microscopy and X-ray absorption spectroscopy did not evince systematic structural or compositional changes; only under strongly reducing conditions did iron sulfides form in small percentages in the outer layer of the iron coating. Our results suggest that detrimental effects only become relevant after long periods of operation.

Iron reducing sludge as a source of electroactive bacteria: assessing iron reduction in biofilm bacteria, planktonic cells and isolates from a microbial fuel cell

In this study, bacteria from a microbial fuel cell (MFC) and isolates were evaluated on their Fe³⁺ reduction capability at different concentrations of iron using acetate as the sole source of carbon. The results demonstrated that the planktonic cells can reach an iron reduction up to 60% at 27 mmol Fe³⁺. Azospira oryzae (µ 0.89 ± 0.27 d^-1) and Cupriavidus metallidurans CH34 (µ 2.34 ± 0.81 d^-1) presented 55 and 62% of Fe³⁺ reduction, respectively, at 16 mmol l^-1. Enterobacter bugandensis (µ 0.4 ± 0.01 d^-1) 40% Fe³⁺ at 27 mmol l^-1, Citrobacter freundii ATCC 8090 (µ 0.23 ± 0.05 d^-1) and Citrobacter murliniae CDC2970-59 (µ 0.34 ± 0.02 d^-1) reduced Fe³⁺ in ~ 50%, at 55 mmol l^-1. This is the first report on these bacteria on a percentage of iron reduction. These results may be useful for anode design to contribute to a higher energy generation in MFCs.

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO₄. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.

Influence of Fe2+ and Fe3+ on the Performance and Microbial Community Composition of a MFC Inoculated with Sulfate-Reducing Sludge and Acetate as Electron Donor

A sulfidogenic sludge supplemented with acetate was evaluated in the anodic chamber of microbial fuel cells (MFCs) in the presence of sulfate (SO4-2)/Fe3+ and sulfate (SO4-2)/Fe2+ to investigate the MFC performance and the effect of the iron ions on the composition of the microbial community since sulfate and iron ions are frequently present in wastewater derived from several anthropogenic activities. The current densities were up to 0.025 mA/cm2 and 0.017 mA/cm2 for MFCs with Fe2+ and Fe3+, respectively. Accordingly, the redox activity was slightly higher in the presence of Fe2+ than Fe3+. In general, the metabolic activity of the MFC supplemented with Fe2+ was higher than the system with Fe3+ reaching a percentage of sulfate reduction (% SR), sulfide concentration (mg/L HS-), and removal of chemical oxygen demand (% COD removal) of $35.2\pm 0.75$ , $450.3\pm 3.6$ , and $50.05\pm 0.24$ for % SR, HS-, and % COD, respectively, whereas in the MFC with Fe3+, the percentages were of $30.1\pm 1.076$ , $220.6\pm 2.0$ , and $11.78\pm 10.81$ for % SR, HS-, and % COD, respectively. The microbial population determined in each system was also correlated to the metabolic activity. Rhodospirillales, Caulobacterales, and Burkholderiales were the most abundant orders of bacteria in the MFC with Fe3+, whereas with Fe2+, Rhodobacterales, Sphingomonadales, and Rhizobiales. Desulfohalobiaceae and Desulfovibrionaceae were identified in the presence of Fe2+. Unexpected interactions and combinations of microorganisms were observed in a relatively short culturing time, demonstrating the importance of characterizing the anode biofilm prior to shifts in iron ion concentrations on a long-term basis.

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 Fe^III 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 Fe^III-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.

Microbially mediated mobilization of arsenic from aquifer sediments under bacterial sulfate reduction

Understanding the biogeochemical processes controlling arsenic (As) mobilization under bacterial sulfate reduction (BSR) in aquifer sediments is essential for the remediation of high As groundwater. Here, we conducted microcosm experiments with shallow aquifer sediments from the Jianghan Plain (central Yangtze River Basin) under the stimulation of exogenous sulfate. Initially, co-increases of As(III) (from 0.0 to 88.5 μg/L), Fe(II) (from 0.5 to 6.0 mg/L), and S(-II) (from 0.0 to 90.0 μg/L) indicated the concurrent occurrence of sulfate, Fe(III), and arsenate reduction. The corresponding increase of the relative abundance of OTUs classified as sulfate-reducing bacteria, Desulfomicrobium (from 0.5 to 30.6%), and dsrB gene abundance indicated the strong occurrence of BSR during the incubation. The underlying mechanisms of As mobilization could be attributed to the biotic and abiotic reduction of As-bearing iron (hydro)oxides either through the iron-reducing bacteria or the bacterially generated sulfide, which were supported by the variations in solid speciation of Fe, S, and As. As the incubation progressed, we observed a transient attenuation followed by a re-increase of aqueous As, due to the limited abundance of newly-formed Fe-sulfide minerals with a weak ability of As sequestration. Moreover, the formation of thioarsenate (H₂AsS₄^-) during the mobilization of As from the sediments was observed, highlighting that BSR could facilitate As mobilization through multiple pathways. The present results provided new insights for the biogeochemical processes accounting for As mobilization from sediments under BSR conditions.

Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.

Reduction of Sb(V) by coupled biotic-abiotic processes under sulfidogenic conditions

Increasing use and mining of antimony (Sb) has resulted in greater concern involving its fate and transport in the environment. Antimony(V) and (III) are the two most environmentally relevant oxidation states, but little is known about the redox transitions between the two in natural systems. To better understand the behavior of antimony in anoxic environments, the redox transformations of Sb(V) were studied in biotic and abiotic reactors. The biotic reactors contained Sb(V) (2 mM as KSb(OH)₆), ferrihydrite (50 mM Fe(III)), sulfate (10 mM), and lactate (10 mM), that were inoculated with sediment from a wetland. In the abiotic reactors, The interaction of Sb(V) with green rust, magnetite, siderite, vivianite or mackinawite was examined under abiotic conditions. Changes in the concentrations of Sb, Fe(II), sulfate, and lactate, as well as the microbial community composition were monitored over time. Lactate was rapidly fermented to acetate and propionate in the bioreactors, with the latter serving as the primary electron donor for dissimilatory sulfate reduction (DSR). The reduction of ferrihydrite was primarily abiotic, being driven by biogenic sulfide. Sb and Fe K-edge X-ray absorption near edge structure (XANES) analysis showed reduction of Sb(V) to Sb(III) within 4 weeks, concurrent with DSR and the formation of FeS. Sb K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy analysis indicated that the reduced phase was a mixture of S- and O-coordinated Sb(III). Reduction of Sb(V) was not observed in the presence of magnetite, siderite, or green rust, and limited reduction occurred with vivianite. However, reduction of Sb(V) to amorphous Sb(III) sulfide occurred with mackinawite. These results are consistent with abiotic reduction of Sb(V) by biogenic sulfide and reveal a substantial influence of Fe oxides on the speciation of Sb(III), which illustrates the tight coupling of Sb speciation with the biogeochemical cycling of S and Fe.

Impact of Fe(III) (Oxyhydr)oxides Mineralogy on Iron Solubilization and Associated Microbial Communities

Iron-reducing bacteria (IRB) are strongly involved in Fe cycling in surface environments. Transformation of Fe and associated trace elements is strongly linked to the reactivity of various iron minerals. Mechanisms of Fe (oxyhydr)oxides bio-reduction have been mostly elucidated with pure bacterial strains belonging to Geobacter or Shewanella genera, whereas studies involving mixed IRB populations remain scarce. The present study aimed to evaluate the iron reducing rates of IRB enriched consortia originating from complex environmental samples, when grown in presence of Fe (oxyhydr)oxides of different mineralogy. The abundances of Geobacter and Shewanella were assessed in order to acquire knowledge about the abundance of these two genera in relation to the effects of mixed IRB populations on kinetic control of mineralogical Fe (oxyhydr)oxides reductive dissolution. Laboratory experiments were carried out with two freshly synthetized Fe (oxyhydr)oxides presenting contrasting specific surfaces, and two defined Fe-oxides, i.e., goethite and hematite. Three IRB consortia were enriched from environmental samples from a riverbank subjected to cyclic redox oscillations related to flooding periods (Decize, France): an unsaturated surface soil, a flooded surface soil and an aquatic sediment, with a mixture of organic compounds provided as electron donors. The consortia could all reduce iron-nitrilotriacetate acid (Fe(III)-NTA) in 1–2 days. When grown on Fe (oxyhydr)oxides, Fe solubilization rates decreased as follows: fresh Fe (oxyhydr)oxides > goethite > hematite. Based on a bacterial rrs gene fingerprinting approach (CE-SSCP), bacterial community structure in presence of Fe(III)-minerals was similar to those of the site sample communities from which they originated but differed from that of the Fe(III)-NTA enrichments. Shewanella was more abundant than Geobacter in all cultures. Its abundance was higher in presence of the most efficiently reduced Fe (oxyhydr)oxide than with other Fe(III)-minerals. Geobacter as a proportion of the total community was highest in the presence of the least easily solubilized Fe (oxyhydr)oxides. This study highlights the influence of Fe mineralogy on the abundance of Geobacter and Shewanella in relation to Fe bio-reduction kinetics in presence of a complex mixture of electron donors.

A Review of Landfill Microbiology and Ecology: A Call for Modernization With 'Next Generation' Technology

Engineered and monitored sanitary landfills have been widespread in the United States since the passage of the Clean Water Act (1972) with additional controls under RCRA Subtitle D (1991) and the Clean Air Act Amendments (1996). Concurrently, many common perceptions regarding landfill biogeochemical and microbiological processes and estimated rates of gas production also date from 2 to 4 decades ago. Herein, we summarize the recent application of modern microbiological tools as well as recent metadata analysis using California, USEPA and international data to outline an evolving view of landfill biogeochemical/microbiological processes and rates. We focus on United States landfills because these are uniformly subject to stringent national and state requirements for design, operations, monitoring, and reporting. From a microbiological perspective, because anoxic conditions and methanogenesis are rapidly established after daily burial of waste and application of cover soil, the >1000 United States landfills with thicknesses up to >100 m form a large ubiquitous group of dispersed 'dark' ecosystems dominated by anaerobic microbial decomposition pathways for food, garden waste, and paper substrates. We review past findings of landfill ecosystem processes, and reflect on the potential impact that application of modern sequencing technologies (e.g., high throughput platforms) could have on this area of research. Moreover, due to the ever evolving composition of landfilled waste reflecting transient societal practices, we also consider unusual microbial processes known or suspected to occur in landfill settings, and posit areas of research that will be needed in coming decades. With growing concerns about greenhouse gas emissions and controls, the increase of chemicals of emerging concern in the waste stream, and the potential resource that waste streams represent, application of modernized molecular and microbiological methods to landfill ecosystem research is of paramount importance.

Electron Donor Utilization and Secondary Mineral Formation during the Bioreduction of Lepidocrocite by Shewanella putrefaciens CN32

The bioreduction of Fe(III) oxides by dissimilatory iron reducing bacteria (DIRB) may result in the production of a suite of Fe(II)-bearing secondary minerals, including magnetite, siderite, vivianite, green rusts, and chukanovite; the formation of specific phases controlled by the interaction of various physiological and geochemical factors. In an effort to better understand the effects of individual electron donors on the formation of specific Fe(II)-bearing secondary minerals, we examined the effects of a series of potential electron donors on the bioreduction of lepidocrocite (γ-FeOOH) by Shewanella putrefaciens CN32. Biomineralization products were identified by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. Acetate, citrate, ethanol, glucose, glutamate, glycerol, malate, and succinate were not effectively utilized for the bioreduction of lepidocrocite by S. putrefaciens CN32; however, substantial Fe(II) production was observed when formate, lactate, H2, pyruvate, serine, or N acetylglucosamine (NAG) was provided as an electron donor. Carbonate or sulfate green rust was the dominant Fe(II)-bearing secondary mineral when formate, H2, lactate, or NAG was provided, however, siderite formed with pyruvate or serine. Geochemical modeling indicated that pH and carbonate concentration are the key factors determining the prevalence of carbonate green rust verses siderite.

Phosphorous in the environment: characteristics with distribution and effects, removal mechanisms, treatment technologies, and factors affecting recovery as minerals in natural and engineered systems

Phosphorus (P), an essential element for living cells, is present in different soluble and adsorbed chemical forms found in soil, sediment, and water. Most species are generally immobile and easily adsorbed onto soil particles. However, P is a major concern owing to its serious environmental effects (e.g., eutrophication, scale formation) when found in excess in natural or engineered environments. Commercial chemicals, fertilizers, sewage effluent, animal manure, and agricultural waste are the major sources of P pollution. But there is limited P resources worldwide. Therefore, the fate, effects, and transport of P in association with its removal, treatment, and recycling in natural and engineered systems are important. P removal and recycling technologies utilize different types of physical, biological, and chemical processes. Moreover, P minerals (struvite, vivianite, etc.) can precipitate and form scales in drinking water and wastewater systems. Hence, P minerals (e.g., struvite, vivianite etc.) are problems when left uncontrolled and unmonitored although their recovery is beneficial (e.g., slow release fertilizers, sustainable P sources, soil enhancers). Sources like wastewater, human waste, waste nutrient solution, etc. can be used for P recycling. This review paper extensively summarizes the importance and distribution of P in different environmental compartments, the effects of P in natural and engineered systems, P removal mechanisms through treatment, and recycling technologies specially focusing on various types of phosphate mineral precipitation. In particular, the factors controlling mineral (e.g., struvite and vivianite) precipitation in natural and engineered systems are also discussed.

Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation

The delivery of fermentable substrate(s) to subsurface environments stimulates Fe(III)-bioreduction and achieves detoxification of organic/inorganic contaminants. Although, much research has been conducted on the microbiology of such engineered systems at lab and field scales, little attention has been given to the phage-host interactions and virus community dynamics in these environments. The objective was to determine the responses of soil bacterial communities and viral assemblages to stimulated anaerobic Fe(III)-bioreduction following electron donor (e.g. acetate) addition. Microbial communities, including viral assemblages, were investigated after 60 days of Fe(III)-bioreduction in laboratory-scale columns continuously fed with acetate-amended artificial groundwater. Viral abundances were greatest in the influent section and decreased along the flow path. Acetate availability was important in influencing bacterial diversity, microbial interactions and viral abundance and community composition. The impact of acetate addition was most evident in the influent section of the columns. The increased relative abundance of Fe(III)-reducing bacteria coincided with an increase in viral abundance in areas of the columns exhibiting the most Fe(III) reduction. The genetic composition of viruses in these column sections also differed from the control column and distal sections of acetate-treated columns suggesting viral communities responded to biostimulated Fe(III)-bioreduction.

Sulfur cycling in freshwater sediments: A cryptic driving force of iron deposition and phosphorus mobilization

Sulfur cycling in freshwater ecosystems has been previously considered minor, and the direct evidence of its impacts on iron and phosphorus cycles in freshwater sediments remains unclear. In this study, mesocosms with amended acetate and various sulfate concentrations (1.5-3.0 mmol L^-1) were set up to investigate sulfur cycling and its influences on iron-rich freshwater sediments. Acetate addition induced hypoxia and provided substrates, which stimulated the sulfur cycling with evidence of SO₄^2- decline, ΣS^2-, S⁰ increase and corresponding variations of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria. Meanwhile, the growth of iron-reducing bacteria (IRB) was suppressed, and lower Fe(II) release was correspondingly related to larger SRB abundance at higher sulfate level, indicating that microbial iron reduction might be blocked by SRB activities. However, continuous dissolution of Fe(III) oxides and generation of iron sulfides were observed, suggesting that sulfide-mediated chemical iron reduction (SCIR) became the dominant iron-reducing pathway, and Fe(II) was buried as iron sulfides instead of released to water column, which resulted in a transition of iron cycling into unidirectional SCIR. Consequently, continuous dissolution of Fe(III) oxides led to significant increase of PO₄^3- concentration in the water column and sediment pore-water, revealing the phosphorus mobility in sediments derived from the SCIR process. To note, sustained accumulation of iron sulfides was observed even without ΣS^2- presence, suggesting that ΣS^2- precipitation occurred prior to diffusion. Thus, ΣS^2--missing sulfur cycling seemed "cryptic" in this study. To highlight, the transition of the iron-reducing pathway and resulting PO₄^3- release can be induced even under current sulfate level of Lake Taihu, and elevated sulfate levels could significantly intensify SCIR and phosphorus mineralization. Thus, the stimulated iron deposition and the resulting phosphorus release derived from the sulfur cycling should be paid more attention to in the treatment of eutrophic freshwater ecosystems.

Low-Abundance Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic Mine Drainage From the Malanjkhand Copper Project, India

Sulfate- and iron-reducing heterotrophic bacteria represented minor proportion of the indigenous microbial community of highly acidic, oligotrophic acid mine drainage (AMD), but they can be successfully stimulated for in situ bioremediation of an AMD impacted soil (AIS). These anaerobic microorganisms although played central role in sulfate- and metal-removal, they remained inactive in the AIS due to the paucity of organic carbon and extreme acidity of the local environment. The present study investigated the scope for increasing the abundance and activity of inhabitant sulfate- and iron-reducing bacterial populations of an AIS from Malanjkhand Copper Project. An AIS of pH 3.5, high soluble SO4 2- (7838 mg/l) and Fe (179 mg/l) content was amended with nutrients (cysteine and lactate). Thorough geochemical analysis, 16S rRNA gene amplicon sequencing and qPCR highlighted the intrinsic metabolic abilities of native bacteria in AMD bioremediation. Following 180 days incubation, the nutrient amended AIS showed marked increase in pH (to 6.6) and reduction in soluble -SO4 2- (95%), -Fe (50%) and other heavy metals. Concomitant to physicochemical changes a vivid shift in microbial community composition was observed. Members of the Firmicutes present as a minor group (1.5% of total community) in AIS emerged as the single most abundant taxon (∼56%) following nutrient amendments. Organisms affiliated to Clostridiaceae, Peptococcaceae, Veillonellaceae, Christensenellaceae, Lachnospiraceae, Bacillaceae, etc. known for their fermentative, iron and sulfate reducing abilities were prevailed in the amended samples. qPCR data corroborated with this change and further revealed an increase in abundance of dissimilatory sulfite reductase gene (dsrB) and specific bacterial taxa. Involvement of these enhanced populations in reductive processes was validated by further enrichments and growth in sulfate- and iron-reducing media. Amplicon sequencing of these enrichments confirmed growth of Firmicutes members and proved their sulfate- and iron-reduction abilities. This study provided a better insight on ecological perspective of Firmicutes members within the AMD impacted sites, particularly their involvement in sulfate- and iron-reduction processes, in situ pH management and bioremediation.

Biofilm formation and potential for iron cycling in serpentinization-influenced groundwater of the Zambales and Coast Range ophiolites

Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential 'principal' microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities

Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from six different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 h, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g., Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g., Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure

We investigated the impacts of leachates from a swine carcass burial site and a cow manure heap on the geochemical and microbiological properties of agricultural water samples, including leachate, groundwater from monitoring wells and background wells, and stream water. The leachate from the livestock burial site showed extremely high electrical conductivity, turbidity, and major ion concentrations, but low redox potential and dissolved oxygen levels. The groundwater in the monitoring wells adjacent to both sites showed severe contamination from the leachate, as indicated by the increases in EC, turbidity, Cl^-, and SO₄^2-. Bacteria from the phylum Firmicutes and Bacteriodetes and Archaea from the phylum Euryarchaeota were the major phyla in both the leachates and manure heap. However, the class- or genus-level components of these phyla differed markedly between the leachate and manure heap samples. The relative abundance of Firmicutes decreased from 35% to 0.3~13.9% in the monitoring wells and background wells at both sites. The Firmicutes in these wells was unlikely to have originated from the transportation of leachate to the surrounding environment because Firmicutes genera differed drastically between the leachate and monitoring wells. Meanwhile, sulfate-reducing bacteria (SRB) from the livestock carcass burial site were detected in the monitoring wells close to the leachate. This was likely because the release of carcass decomposition products, such as organic acids, to adjacent areas improved the suitability of the local environments for SRB, which were not abundant in the leachate. This study highlights the need to better understand microbial community dynamics along groundwater flow paths to evaluate bacterial transport in subsurface environments and provides new insights into the effective management of groundwater quality at both farm and regional scales.

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer

To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H₂ oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO₄^-2, U(VI), NO₃^-, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4-31 days, whereas Desulfobacterium became dominant at 80-140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

To solve the competition problem of acidophilic bacteria and sulfate-reducing bacteria in the practical application of mine tailing bioremediation, research into the mechanisms of using different nutrients to adjust the microbial community was conducted. Competition experiments involving acidophilic bacteria and sulfate-reducing bacteria were performed by supplementing the media with yeast extract, tryptone, lactate, and glucose. The physiochemical properties were determined, and the microbial community structure and biomass were investigated using MiSeq sequencing and qRT-PCR, respectively. Four nutrients had different remediation mechanisms and yielded different remediation effects. Yeast extract and tryptone (more than 1.6 g/L) promoted sulfate-reducing bacteria and inhibited acidophilic bacteria. Lactate inhibited both sulfate-reducing and acidophilic bacteria. Glucose promoted acidophilic bacteria more than sulfate-reducing bacteria. Yeast extract was the best choice for adjusting the microbial community and bioremediation, followed by tryptone. Lactate kept the physiochemical properties stable or made slight improvements; however, glucose was not suitable for mine tailing remediation. Different nutrients had significant effects on the abundance of the second enzyme of the sulfate-reducing pathway (p < 0.05), which is the rate-limiting step of sulfate-reducing pathways. Nutrients changed the remediation effects effectively by adjusting the microbial community and the abundance of the sulfate-reducing rate-limiting enzyme.