Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment

Pollution control performance of solidified nickel-cobalt tailings on site: Bioavailability of heavy metals and microbial response

There has been increasing attention given to nickel-cobalt tailings (NCT), which pose a risk of heavy metal pollution in the field. In this study, on site tests and sampling analysis were conducted to assess the physical and chemical characteristics, heavy metal toxicity, and microbial diversity of the original NCT, solidified NCT, and the surrounding soil. The research results show that the potential heavy metal pollution species in NCT are mainly Ni, Co, Mn, and Cu. Simultaneous solidification and passivation of heavy metals in NCT were achieved, resulting in a reduction in biological toxicity and a fivefold increase in seed germination rate. The compressive strength of the original tailings was increased by 20 times after solidification. The microbial diversity test showed that the abundance of microbial community in the original NCT was low and the population was monotonous. This study demonstrates, for the first time, that the use of NCT for solidification in ponds can effectively solidification of heavy metals, reduce biological toxicity, and promote microorganism diversity in mining areas (tended to the microbial ecosystem in the surrounding soil). Indeed, this study provides a new perspective for the environmental remediation of metal tailings.

Compost-assisted revegetation of highly phytotoxic sulfidic tailings with Medicago sativa L. plants grown from the seed to seedpod stage under greenhouse experimental mesocosms conditions

The revegetation of highly phytotoxic sulfidic tailings is a challenging task which may often be successfully accomplished only following the addition of soil amendments. This study evaluated the use of green compost at increasing rates (10, 25 and 50% v/v) for the revegetation of extremely acidic sulfidic tailings of the North Mathiatis mine, Cyprus, with the use of alfalfa (Medicago sativa L.) plants, under greenhouse conditions. Alfalfa seeds were successfully germinated in tailings amended either with 25% or 50% (v/v) compost (52 and 85%, respectively). Plants managed to complete their life cycle and produce seeds only in the tailings amended with 50% (v/v) compost, since plants grown in tailings amended with lower rates of compost (i.e., 10 or 25% v/v) showed severe symptoms of phytotoxicity and eventually died. The amendment of tailings with 50% (v/v) green compost resulted in increased pH values, water holding capacity and organic content levels, soil respiration rates, as well as changes in soil elemental composition compared with tailings alone treatment, which in turn facilitated the growth and development of alfalfa plants during the whole experimental period (140 days). Plants managed to reach the late seedpod growth stage, indicating their potential regeneration and continual existence to the amended tailings, simultaneously uncovering the development of favorable conditions in the rhizosphere for the successful revegetation of studied tailings.

Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.

The effect of biogeochemical redox oscillations on arsenic release from legacy mine tailings

Exposed and un-remediated metal(loid)-bearing mine tailings are susceptible to wind and water erosion that disperses toxic elements into the surrounding environment. Compost-assisted phytostabilization has been successfully applied to legacy tailings as an inexpensive, eco-friendly, and sustainable landscape rehabilitation that provides vegetative cover and subsurface scaffolding to inhibit offsite transport of contaminant laden particles. The possibility of augmented metal(loid) mobility from subsurface redox reactions driven by irrigation and organic amendments is known and arsenic (As) is of particular concern because of its high affinity for adsorption to reducible ferric (oxyhydr)oxide surface sites. However, the biogeochemical transformation of As in mine tailings during multiple redox oscillations has not yet been addressed. In the present study, a redox-stat reactor was used to control oscillations between 7 d oxic and 7 d anoxic half-cycles over a three-month period in mine tailings with and without amendment of compost-derived organic matter (OM) solution. Aqueous and solid phase analyses during and after redox oscillations by mass spectrometry and synchrotron X-ray absorption spectroscopy revealed that soluble OM addition stimulated pyrite oxidation, which resulted in accelerated acidification and increased aqueous sulfate activity. Soluble OM in the reactor solution significantly increased mobilization of As under anoxic half-cycles primarily through reductive dissolution of ferrihydrite. Microbially-mediated As reduction was also observed in compost treatments, which increased partitioning to the aqueous phase due to the lower affinity of As(III) for complexation on ferric surface sites, e.g. ferrihydrite. Oxic half-cycles showed As repartitioned to the solid phase concurrent with precipitation of ferrihydrite and jarosite. Multiple redox oscillations increased the crystallinity of Fe minerals in the Treatment reactors with compost solution due to the reductive dissolution of ferrihydrite and precipitation of jarosite. The release of As from tailings gradually decreased after repeated redox oscillations. The high sulfate, ferrous iron, and hydronium activity promoted the precipitation of jarosite, which sequestered arsenic. Our results indicated that redox oscillations under compost-assisted phytostabilization can promote As release that diminishes over time, which should inform remediation assessment and environmental risk assessment of mine site compost-assisted phytostabilization.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Past, present and future trends in the remediation of heavy-metal contaminated soil - Remediation techniques applied in real soil-contamination events

Most worldwide policy frameworks, including the United Nations Sustainable Development Goals, highlight soil as a key non-renewable natural resource which should be rigorously preserved to achieve long-term global sustainability. Although some soil is naturally enriched with heavy metals (HMs), a series of anthropogenic activities are known to contribute to their redistribution, which may entail potentially harmful environmental and/or human health effects if certain concentrations are exceeded. If this occurs, the implementation of rehabilitation strategies is highly recommended. Although there are many publications dealing with the elimination of HMs using different methodologies, most of those works have been done in laboratories and there are not many comprehensive reviews about the results obtained under field conditions. Throughout this review, we examine the different methodologies that have been used in real scenarios and, based on representative case studies, we present the evolution and outcomes of the remediation strategies applied in real soil-contamination events where legacies of past metal mining activities or mine spills have posed a serious threat for soil conservation. So far, the best efficiencies at field-scale have been reported when using combined strategies such as physical containment and assisted-phytoremediation. We have also introduced the emerging problem of the heavy metal contamination of agricultural soils and the different strategies implemented to tackle this problem. Although remediation techniques used in real scenarios have not changed much in the last decades, there are also encouraging facts for the advances in this field. Thus, a growing number of mining companies publicise in their webpages their soil remediation strategies and efforts; moreover, the number of scientific publications about innovative highly-efficient and environmental-friendly methods is also increasing. In any case, better cooperation between scientists and other soil-related stakeholders is still required to improve remediation performance.

Molecular speciation controls arsenic and lead bioaccessibility in fugitive dusts from sulfidic mine tailings

Communities nearby mine wastes in arid and semi-arid regions are potentially exposed to high concentrations of toxic metal(loid)s from fugitive dusts deriving from impoundments. To assess the relation between potentially lofted particles and human health risk, we studied the relationship between pharmacokinetic bioaccessibility and metal(loid) molecular speciation for mine tailings dust particulate matter (PM), with elevated levels of arsenic and lead (up to 59 and 34 mmol kg-1, respectively), by coupling in vitro bioassay (IVBA) with X-ray absorption spectroscopy (XAS). Mine tailing efflorescent salts (PMES) and PM from the surface crust (0-1 cm, PMSC) and near surface (0-25 cm) were isolated to <10 μm and <150 μm effective spherical diameter (PM10 and PM150) and reacted with synthetic gastric and lung fluid for 30 s to 100 h to investigate toxic metal(loid) release kinetics. Bioaccessible (BAc) fractions of arsenic and lead were about 10 and 100 times greater in gastric than in lung fluid simulant, respectively, and 10-100% of the maximum gastric BAc from PM10 and PM150 occurred within 30 s, with parabolic dissolution of fine, highly-reactive particles followed by slower release from less soluble sources. Evaporite salts were almost completely solubilized in gastric-fluid simulants. Arsenate within jarosite and sorbed to ferrihydrite, and lead from anglesite, were identified by XAS as the principal contaminant sources in the near surface tailings. In the synthetic lung fluid, arsenic was released continuously to 100 h, suggesting that residence time in vivo must be considered for risk determination. Analysis of pre- and post-IVBA PM indicated the release of arsenic in lung fluid was principally from arsenic-substituted jarosite, whereas in synthetic gastric fluid arsenic complexed on ferrihydrite surfaces was preferentially released and subsequently repartitioned to jarosite-like coordination at extended exposures. Lead dissolved at 30 s was subsequently repartitioned back to the solid phase as pyromorphite in phosphate rich lung fluid. The bioaccessibility of lead in surface tailings PM was limited due to robust sequestration in plumbojarosite. Kinetic release of toxic elements in both synthetic biofluids indicated that a single IVBA interval may not adequately describe release dynamics.

Effect of composite amendments on physicochemical properties of copper tailings repaired by herbaceous plants

Phytoremediation is considered to be the most environmentally friendly green restoration technology for dealing with mine waste. Adding amendments can improve the substrate environment for plant growth and enhance remediation efficiency. Herbaceous plants have become the preferred species for vegetation restoration in abandoned mines because of their fast greening and simple management. After 8 weeks of pot experiments in the early stage, it was shown that the plant height and fresh weight of the plants treated with 5% conditioner and 0.5% straw (C₂S₂) were significantly higher than those of other treatments. Considering that, in this paper, to explore the effect of composite amendments on physicochemical properties of copper tailings repaired by herbaceous plants, the untreated copper tailings were employed as the control group, whereas copper tailings repaired by ryegrass (Lolium perenne L.), vetiver grass (Chrysopogon zizanioides L.), and tall fescue (Festuca arundinacea) with or without conditioners and straw combination into the compound amendments were taken separately as the test group. After 6 months of planting, the pH, electrical conductivity, water content, available potassium, organic matter, total nitrogen, and available phosphorus in the main physical and chemical properties of copper tailings in each experimental area were analyzed. The results showed that the electrical conductivity, organic matter, and total nitrogen content of copper tailings were improved to a certain extent by planting plants without treatment. Meanwhile, compared with the control group, all indexes of planting plants showed an upward trend after adding composite amendments. Among them, pH, water content, and available potassium content of copper tailings were enhanced more obviously. Furthermore, as discovered from the gray correlation analysis results, vetiver grass planted with composite amendments has the best comprehensive effect of improving the physicochemical properties of copper tailings, followed by tall fescue and ryegrass.

New approach strategy for heavy metals immobilization and microbiome structure long-term industrially contaminated soils

The progress of engineering technologies highly influences the development of methods that lead to the condition improvement of areas contaminated with heavy metals (HMs). The aided phytostabilization fits into this trend, and was used to evaluate HM-immobilization effectiveness in phytostabilized soils under variable temperatures by applying 16 freezing-thawing cycles (FTC). Diatomite amendment and Lolium perenne L., also were applied. Cd/Ni/Cu/Pb/Zn each total content in phytostabilized soils were determined, along with the verification for each metal of its distribution in four extracted fractions (F1 ÷ F4) from soils. Based on changes in HM distribution, each metal's stability was estimated. Moreover, HM accumulation in plant roots and stems and soil microbial composition were investigated. Independently of the experimental variant (no-FTC-exposure or FTC-exposure), the above-ground biomass yields in the diatomite-amended series were higher as compared to the corresponding control series. The evident changes in Pb/Zn-bioavailability were observed. The metal stability increase was mainly attributed to metal concentration decreasing in the F1 fraction and increasing in the F4 fraction, respectively. Diatomite increased Cd/Zn-stability in not-FTC-exposed-phytostabilized soils. FTC-exposure favorably influenced Pb/Zn stability. Diatomite increased soil pH values and Cd/Ni/Cu/Zn-bioaccumulation (except Pb) in roots than in stems (in both experimental variants). FTC-exposure influenced soil microbial composition, increasing bacteria abundance belonging to Actinobacteria, Gammaproteobacteria, and Sphingobacteria. At the genus level, FTC exposure significantly increased the abundances of Limnobacter sp., Tetrasphaera sp., Flavobacterium sp., and Dyella sp. Independently of the experimental variant, Sphingomonas sp. and Mycobacterium sp., which have a tolerance to HM contamination, were core bacterial groups, comprising about 6 ÷ 7% of all soil bacteria.

The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks’ excrement contamination in plateau, China

The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (&gt;3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.

Indigenous microbial populations of abandoned mining sites and their role in natural attenuation

Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.

Long-Term Amelioration Practices Reshape the Soil Microbiome in a Coastal Saline Soil and Alter the Richness and Vertical Distribution Differently Among Bacterial, Archaeal, and Fungal Communities

Globally soil salinity is one of the most devastating environmental stresses affecting agricultural systems and causes huge economic losses each year. High soil salinity causes osmotic stress, nutritional imbalance and ion toxicity to plants and severely affects crop productivity in farming systems. Freezing saline water irrigation and plastic mulching techniques were successfully developed in our previous study to desalinize costal saline soil. Understanding how microbial communities respond during saline soil amelioration is crucial, given the key roles soil microbes play in ecosystem succession. In the present study, the community composition, diversity, assembly and potential ecological functions of archaea, bacteria and fungi in coastal saline soil under amelioration practices of freezing saline water irrigation, plastic mulching and the combination of freezing saline water irrigation and plastic mulching were assessed through high-throughput sequencing. These amelioration practices decreased archaeal and increased bacterial richness while leaving fungal richness little changed in the surface soil. Functional prediction revealed that the amelioration practices, especially winter irrigation with saline water and film mulched in spring, promoted a community harboring heterotrophic features. β-null deviation analysis illustrated that amelioration practices weakened the deterministic processes in structuring coastal saline soil microbial communities. These results advanced our understanding of the responses of the soil microbiome to amelioration practices and provided useful information for developing microbe-based remediation approaches in coastal saline soils.

Responses of fungal communities along a chronosequence succession in soils of a tailing dam with reclamation by Heteropogon contortus

Phytoremediation can obviously change the fungal communities in the soils, which will significantly impact carbon (C) and nitrogen (N) cycling in ecological system. So far, the relationship between soil fungal communities and environmental factors is still poorly understood along a long chronosequence. In this study, fungal communities in the surface and rhizosphere soils of a tailing dam with Heteropogon contortus phytoremediation were investigated to explore the evolution of fungal community in a span of 50 years. The results showed that microbial community diversity increases along with time series of Heteropogon contortus phytoremediation. The dominant Dothideomycetes (20.86%), Agaricomycetes (18.09%), and Arthoniomycetes (1.69%) in rhizosphere soils were relatively higher than those in topsoil (13.9%, 2.65%, and 0.20%) at class level. Spearman correction analysis by phylum level was conducted to detect whether microflora was related to soil Physico-chemical properties, which affecting the composition of fungal communities along with the Heteropogon contortus phytoremediation. The nitrogen cycle indicators represented good linear correlations as chronosequence goes on, the indexes in the rhizosphere soil were much higher than those in the surface soils and the highest level has occurred in the 47-year-old Heteropogon contortus phytoremediation. The relative abundance of plant pathogen, wood saprotroph, dung saprotroph, and Arbuscular Mycorrhizal showed an upward tendency in rhizosphere soils along with the Heteropogon contortus phytoremediation. The highest soil fungal communities abundance and diversity were possibly attributed to the high-quality Heteropogon contortus litter returning to the ground and artificial disturbance treatments. Such changes in soil fungal communities might demonstrate a significant step forward and provided theoretical support for the biological governance of Heteropogon contortus phytoremediation in 50 years. Our study provides an insight on microbial communities connecting with soil C, N, P and S cycles and community functions in a complex plant-fungal-soil system along a long chronosequence in mine micro-ecology.

Barriers for plant establishment in the abandoned tailings of Nacozari, Sonora, Mexico: the influence of compost addition on seedling performance and tailing properties

Past mining activities have left a legacy of abandoned mine tailing deposits whose metal contaminants poses serious risks to ecosystems and human health. While the development of a vegetated cover in mine tailings can help in mitigating these risks, the local factors limiting plant establishment in these sites are not well understood, restricting phytostabilization efforts. Here, we explore some of the barriers that limit seedling establishment of two species (Vachellia farnesiana and Prosopis velutina) in a mine tailing deposit located in Nacozari, Sonora, Mexico, and assess whether compost addition can help in overcoming these barriers in pot and field experiments. Our field observations found 20 times more carbon and at least 4 times more nitrogen concentration in areas under vegetated patches than in non-vegetated areas, while a previous study found no difference in metal concentrations and other physicochemical parameters. This suggests that organic matter and nutrients are a major limitation for plant establishment. In agreement with this, species failed to establish without compost addition in the field experiment. Compost addition also had a positive effect on biomass accumulation, pH and microbial activity, but increased the substrate soluble concentration of As, Cu, and Zn. Nonetheless, only Cu, K, and Mo in P. velutina accumulated in tissues at levels considered toxic for animal consumption. Our study documents that compost addition facilitated plant establishment for the phytostabilization of mine tailings and help to prevent the dispersion of most metal contaminants via animal consumption. We encourage the use of complementary strategies to minimize the risk of dispersion of metal contaminants.

Arsenic and iron speciation and mobilization during phytostabilization of pyritic mine tailings

Particulate and dissolved metal(loid) release from mine tailings is of concern in (semi-) arid environments where tailings can remain barren of vegetation for decades and, therefore, become highly susceptible to dispersion by wind and water. Erosive weathering of metalliferous tailings can lead to arsenic contamination of adjacent ecosystems and increased risk to public health. Management via phytostabilization with the establishment of a vegetative cap using organic amendments to enhance plant growth has been employed to reduce both physical erosion and leaching. However, prior research suggests that addition of organic matter into the oxic weathering zone of sulfide tailings has the potential to promote the mobilization of arsenate. Therefore, the objective of the current work was to assess the impacts of phytostabilization on the molecular-scale mechanisms controlling arsenic speciation and lability. These impacts, which remain poorly understood, limit our ability to mitigate environmental and human health risks. Here we report on subsurface biogeochemical transformations of arsenic and iron from a three-year phytostabilization field study conducted at a Superfund site in Arizona, USA. Legacy pyritic tailings at this site contain up to 3 g kg^-1 arsenic originating from arsenopyrite that has undergone oxidation to form arsenate-ferrihydrite complexes in the top 1 m. Tailings were amended in the top 20 cm with 100, 150, or 200 g kg^-1 (300-600 T ha^-1) of composted organic matter and seeded with native halotolerant plant species. Treatments and an unamended control received irrigation of 360 ± 30 mm y^-1 in addition to 250 ± 160 mm y^-1 of precipitation. Cores to 1 m depth were collected annually for three years and sectioned into 20 cm increments for analysis by synchrotron iron and arsenic X-ray absorption spectroscopy (XAS) coupled with quantitative wet chemical and mass balance methods. Results revealed that > 80% of arsenic exists in ammonium oxalate-extractable and non-extractable phases, including dominantly ferrihydrite and jarosite. Arsenic release during arsenopyrite oxidation resulted in both downward translocation and As^(V) attenuation by stable Fe^(III)(oxyhydr)oxide and Fe^(III) (hydroxy)sulfate minerals over time, highlighting the need for sampling at multiple depths and time points for accurate interpretation of arsenic speciation, lability, and translocation in weathering profiles. Less than 1% of total arsenic was highly-labile, i.e. water-extractable, from all treatments, depths, and years, and more than 99% of arsenate released by arsenopyrite weathering was attenuated by association with secondary minerals. Although downward translocation of both arsenic and iron was detected during phytostabilization by temporal enrichment analysis, a similar trend was measured for the uncomposted control, indicating that organic amendment associated with phytostabilization practices did not significantly increase arsenic mobilization over non-amended controls.

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure - A mesocosm study

Bauxite residues (BR), commonly named red muds, are the saline-sodic waste produced during the extraction of alumina from bauxite. In this study, four kinds of BR were mixed at increasing concentrations with two soils in a mesososm experiment. Unamended BR from Provence (PRO) and Guinea (GUI) bauxite were selected, and Modified Bauxite Residues from PRO and GUI (MBR-PRO and MBR-GUI) were obtained by gypsum application and repeated leaching, in order to reduce their pH, electrical conductivity (EC) and exchangeable sodium percentage (ESP). Several indicators of microbial community functions and structure (growth of culturable bacteria; enzymatic activities; C-sourced substrates degradation (Biolog®); bacteria and fungi PCR-RFLP fingerprints) were measured after 35 days of incubation. Results showed that PRO residue had stronger negative effects than GUI on all the tested indicators. Residues modified by gypsum addition (MBR-PRO, MBR-GUI) were equally or sometimes less harmful compared to unamended residues. Microbial activities (bacterial growth and enzyme activities) were more inhibited than the diversity of microbial functions (Biolog®), and the structure of bacterial and fungal communities was not affected by increasing concentrations of bauxite residues. EC and ESP were the main factors explaining the inhibition of microbial activities, although the origin of bauxite residue is of great importance too.

Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings

Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.

Differences of the microbial community structures and predicted metabolic potentials in the lake, river, and wetland sediments in Dongping Lake Basin

In freshwater ecosystems, wetlands are generally distinguished from deep-water ecosystems by 2-m water level as boundary. However, the difference of sediment microbial communities between wetlands and deep-water ecosystems is still unclear. We combined 16S rRNA gene sequencing and community metabolic prediction to compare sediment microbial communities and predicted metabolic genes of wetlands (natural and constructed wetlands) and deep-water ecosystems (river and lake) along with environmental factors in summer and autumn in Dongping Lake Basin. Results showed that the deep-water ecosystems had significantly higher community richness than the wetlands in autumn in the freshwater basin, which was mostly related to the pH of sediments. However, no significant difference in community richness was found in summer. Besides, the composition of both predicted metabolic genes and microbial communities was significantly affected by dissolved organic carbon (DOC) and dissolved oxygen (DO). The wetlands exhibited high predicted gene abundances related to xenobiotic biodegradation possibly due to the high DOC or DO level. Compared with the wetlands, most of the deep-water ecosystems exhibited high predicted gene abundances related to element (carbon, nitrogen, and sulfur) metabolism possibly due to the low DOC and DO levels in the freshwater basin. This study can expand the knowledge of ecological function distribution and detoxification mechanism of microbial communities in freshwater ecosystems.

New Soil, Old Plants, and Ubiquitous Microbes: Evaluating the Potential of Incipient Basaltic Soil to Support Native Plant Growth and Influence Belowground Soil Microbial Community Composition

The plant–microbe–soil nexus is critical in maintaining biogeochemical balance of the biosphere. However, soil loss and land degradation are occurring at alarmingly high rates, with soil loss exceeding soil formation rates. This necessitates evaluating marginal soils for their capacity to support and sustain plant growth. In a greenhouse study, we evaluated the capacity of marginal incipient basaltic parent material to support native plant growth and the associated variation in soil microbial community dynamics. Three plant species, native to the Southwestern Arizona-Sonora region, were tested with three soil treatments, including basaltic parent material, parent material amended with 20% compost, and potting soil. The parent material with and without compost supported 15%, 40%, and 70% germination of Common Bean (Phaseolus vulgaris L. ‘Tarahumara Norteño’), Mesquite (Prosopis pubescens Benth), and Panic Grass (Panicum Sonorum Beal), respectively, though germination was lower than in the potting soil. Plant growth was also sustained over the 30 day period, with plants in parent material (with and without amendment) reaching 50% height compared to those in the potting soil. A 16S rRNA gene amplicon sequencing approach showed Proteobacteria to be the most abundant phyla in both parent material and potting soil, followed by Actinobacteria. The potting soil showed Gammaproteobacteria (19.6%) to be the second most abundant class, but its abundance was reduced in the soil + plants treatment (5.6%–9.6%). Within the basalt soil type, Alphaproteobacteria (42.7%) and Actinobacteria (16.3%) had a higher abundance in the evaluated bean plant species. Microbial community composition had strong correlations with soil characteristics, but not plant attributes within a given soil material. Predictive functional potential capacity of the communities revealed chemoheterotrophy as the most abundant metabolism within the parent material, while photoheterotrophy and anoxygenic photoautotrophy were prevalent in the potting soil. These results show that marginal incipient basaltic soil, both with and without compost amendments, can support native plant species growth, and non-linear associations may exist between plant–marginal soil–microbial interactions.

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.

Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings

Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N2-fixing) versus acid-generating bacteria (AGB; including Fe-cycling/S-oxidizing). Results indicated that a shift in microbial diversity and community composition occurred at around pH 4. At higher pH (>4) the species richness and community composition of the rhizosphere and bulk compartments were similar, and PGPB, such as Pseudomonas, Arthrobacter, Devosia, Phyllobacterium, Sinorhizobium, and Hyphomicrobium, were present and active in both compartments with minimal presence of AGB. In comparison, at lower pH (<4) the rhizosphere had a significantly higher number of species than the bulk (p < 0.05) and the compartments had significantly different community composition (unweighted UniFrac; PERMANOVA, p < 0.05). Whereas some PGPB persisted in the rhizosphere at lower pH, including Arthrobacter and Devosia, they were absent from the bulk. Meanwhile, AGB dominated in both compartments; the most abundant were the Fe-oxidizer Leptospirillum and Fe-reducers Acidibacter and Acidiphilium, and the most active was the Fe-reducer Aciditerrimonas. This predominance of AGB at lower pH, and even their minimal presence at higher pH, contributes to acidifying conditions and poses a significant threat to sustainable plant establishment. These findings have implications for phytostabilization field site management and suggest re-application of compost or an alternate buffering material may be required in regions susceptible to re-acidification to maintain a beneficial bacterial community conducive to long-term plant establishment.

Emerging strategies for engineering microbial communities

From biosynthesis to bioremediation, microbes have been engineered to address a variety of biotechnological applications. A promising direction in these endeavors is harnessing the power of designer microbial consortia that consist of multiple populations with well-defined interactions. Consortia can accomplish tasks that are difficult or potentially impossible to achieve using monocultures. Despite their potential, the rules underlying microbial community maintenance and function (i.e. the task the consortium is engineered to carry out) are not well defined, though rapid progress is being made. This limited understanding is in part due to the greater challenges associated with increased complexity when dealing with multi-population interactions. Here, we review key features and design strategies that emerge from the analysis of both natural and engineered microbial communities. These strategies can provide new insights into natural consortia and expand the toolbox available to engineers working to develop novel synthetic consortia.

Integrated Management of Pig Residues and Copper Mine Tailings for Aided Phytostabilization

There is high demand for identifying socio-environmentally sound ways to dispose of large quantities of offensive odor-generating organic residues produced by intensive livestock farming. The use of these residues as amendments at large-scale mine tailings storage facilities for in situ plant-based reclamation may be a useful alternative. We performed a greenhouse assay to evaluate effectiveness of pig slurries and the solid organic fraction of aerobic-aerated pig slurries, both treated and not treated for odor emission, as amendments for copper tailings. Different doses of slurries or the solid organic fraction of the slurries, untreated and treated with either ozone or a commercial product used to manage strong odors (Just a Drop), were incorporated into tailings and stabilized (15 d) under greenhouse conditions. L. (ryegrass) was used as bioindicator for Cu and Zn toxicity. Plant performance (shoot and root dry biomass, Cu and Zn content in leaves) and general physicochemical characteristics of substrates were evaluated. Our results showed that odor management of pig residues was possible with commercial products, and their incorporation into tailings rapidly and effectively reduced odor emission. The solid organic fraction of the slurries neutralized acidic tailings, and both pig residues increased organic matter and nutrient content in tailings while reducing extractable Cu. As a result, ryegrass productivity was significantly improved by incorporation of either slurries or their solid organic fraction into tailings in a dose-dependent form. Foliar Cu content in ryegrass was not affected but foliar Zn content increased; however, Zn remained within acceptable ranges. Both the pig slurries and their soil organic fractions proved to be valuable residues for tailings reclamation.

Extreme Geochemical Conditions and Dispersal Limitation Retard Primary Succession of Microbial Communities in Gold Tailings

Microbial community succession in tailings materials is poorly understood at present, and likely to be substantially different from similar processes in natural primary successional environments due to the unusual geochemical properties of tailings and the isolated design of tailings storage facilities. This is the first study to evaluate processes of primary succession in microbial communities colonizing unamended tailings, and compare the relative importance of stochastic (predominantly dust-borne dispersal) and deterministic (strong selection pressures from extreme geochemical properties) processes in governing community assembly rates and trajectories to those observed in natural environments. Dispersal-based recruitment required > 6 months to shift microbial community composition in unamended, field-weathered gold tailings; and in the absence of targeted inoculants, recruitment was dominated by salt- and alkali-tolerant species. In addition, cell numbers were less than 10⁶ cells/g tailings until > 6 months after deposition. Laboratory experiments simulating microbial cell addition via dust revealed that high (>6 months' equivalent) dust addition rates were required to effect stabilization of microbial cell counts in tailings. In field-weathered tailings, topsoil addition during rehabilitation works exerted a double effect, acting as a microbial inoculant and correcting geochemical properties of tailings. However, microbial communities in rehabilitated tailings remained compositionally distinct from those of reference soils in surrounding environments. pH, water extractable Mg, and water extractable Fe emerged as major controls on microbial community composition in the field-weathered gold tailings. Overall, this study highlights the need for application of targeted microbial inoculants to accelerate rates of microbial community succession in tailings, which are limited primarily by slow dispersal due to physical and spatial isolation of tailings facilities from inoculant sources; and for geochemical properties of tailings to be amended to moderate values to encourage microbial community diversification and succession.

Glucose-induced changes in the bacterial communities of mine tailings at different acidification stages

Ecological restoration technologies applied to tailings can influence the associated bacterial communities. However, it is unknown if the shifts in these bacterial communities are caused by increased organic carbon. Glucose-induced respiration and high-throughput sequencing were used to assess the microbial activity and bacterial communities, respectively. Glucose addition increased the microbial activity, and glucose + ammonium nitrate addition resulted in slightly higher CO₂ emission than did glucose addition alone, suggesting that carbon and nitrogen limited microbial community growth. In neutral pH tailings, the bacterial taxa that increased by glucose addition were assigned to the phyla Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Planctomycetes. However, the bacterial taxa that increased by glucose addition in acidic tailings only belonged to the phylum Actinobacteria (maximum increase of 43.78%). In addition, the abundances of the total nitrogen-fixing genera and of the genus Arthrobacter (representing approximately 97.89% of the total nitrogen-fixing genera) increased by glucose addition in acidic tailings (maximum increase of 46.98%). In contrast, the relative abundances of the total iron- and (or) sulfur-oxidizing bacteria decreased (maximum decrease of 10.41%) in response to the addition of glucose. These findings indicate that the addition of organic carbon is beneficial to the development of bacterial communities in mine tailings.

Sulfate-Reducing Bacteria as an Effective Tool for Sustainable Acid Mine Bioremediation

Mining industries produce vast waste streams that pose severe environmental pollution challenge. Conventional techniques of treatment are usually inefficient and unsustainable. Biological technique employing the use of microorganisms is a competitive alternative to treat mine wastes and recover toxic heavy metals. Microorganisms are used to detoxify, extract or sequester pollutants from mine waste. Sulfate-reducing microorganisms play a vital role in the control and treatment of mine waste, generating alkalinity and neutralizing the acidic waste. The design of engineered sulfate-reducing bacteria (SRB) consortia will be an effective tool in optimizing degradation of acid mine tailings waste in industrial processes. The understanding of the complex functions of SRB consortia vis-à-vis the metabolic and physiological properties in industrial applications and their roles in interspecies interactions are discussed.

Unrevealing variation of microbial communities and correlation with environmental variables in a full culture-cycle of Undaria pinnatifida

Bacteria are the most abundant organisms in natural environment and dominant drivers of multiple geochemical functions. Drawing a global picture of microbial community structure and understanding their ecological status remain a grand challenge. As a typical artificial process, aquaculture provides a large amount of foods and creates great economic benefits for human beings. However, few studies are aimed at the microbial community in the aquaculture environment of aquatic plants. We analyzed microbial communities from 21 water samples in a coastal aquaculture area during the whole cultural process of Undaria pinnatifida by using high-throughout sequencing of 16S rRNA gene. The progression of U. pinnatifida aquaculture can be divided into three stages, named Seeding, Growth, and Maturity, respectively. Microbial community structures in water of the aquaculture area were significantly changed during the progression of U. pinnatifida aquaculture. The relative abundance of Flavobacteriia and Thaumarchaeota classes increased in Growth stage, and β-proteobacteria and Acidimirobiia classes decreased with the growth of U. pinnatifida. Meanwhile, environmental factors shaping the microbial community structures were uncovered during the U. pinnatifida aquaculture by using canonical correspondence analysis and Mantel test, in which temperature, dissolved oxygen, pH and nitrogen could be the major influencing factors. In addition, the microbial functions based on KEGG pathways were predicted from the microbial community compositions by PICRUSt. The comparison of predicted functions suggested that Environmental Information Processing and Genetic Information Processing were the functional categories with the most obvious shift in abundance among different stages of U. pinnatifida aquaculture. The findings of this study allowed us to better understand the microbial community in coastal aquaculture systems and the impact of seaweed cultivation on coastal ecosystems.

Oxidative weathering decreases bioaccessibility of toxic metal(loid)s in PM10 emissions from sulfide mine tailings

Environmental contamination from legacy mine-waste deposits is a persistent problem due to the long history of hard-rock mining. Sulfide ore deposits can contain elevated levels of toxic metal(loid)s that, when mobilized by weathering upon O₂ and H₂O infusion, can result in groundwater contamination. Dry-climate and lack of vegetative cover result in near-surface pedogenic processes that produce fine-particulate secondary minerals that can be translocated as geo-dusts leading to ingestion or inhalation exposure in nearby communities. In this study, in vitro bioassays were combined with synchrotron-based x-ray spectroscopy and diffraction to determine the potential risk for toxic element release from dust (PM₁₀) samples into biofluid simulants. PM₁₀ were isolated from across the oxidative reaction front in the top meter of tailings subjected to 50 years of weathering under semi-arid climate, and introduced to synthetic gastric- and alveolar-fluids. Aqueous concentrations were measured as a function of reaction time to determine release kinetics. X-ray diffraction and absorption spectroscopy analyses were performed to assess associated changes in mineralogy and elemental speciation. In vitro bioaccessibility of arsenic and lead was highest in less-weathered tailings samples (80-110 cm) and lowest in samples from the sub-oxic transition zone (40-52 cm). Conversely, zinc release to biofluids was greatest in the highly-weathered near-surface tailings. Results indicate that bioaccessibility of As and Pb was controlled by (i) the solubility of Fe²⁺-bearing solids, (ii) the prevalence of soluble SO₄ ^2-, and (iii) the presence of poorly-crystalline Fe(III) oxide sorbents, whereas Zn bioaccessibility was controlled by the pH-dependent solubility of the stable solid phase.

Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions

Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.

Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

Effects of root exudates on denitrifier gene abundance, community structure and activity in a micro-polluted constructed wetland

In micro-polluted constructed wetland (CW), the low pollutant concentrations and the low COD/N ratios (chemical oxygen demand: total nitrogen in influent), make the biological treatment more difficult. It is expected that root exudates drive microbial-based transformations within plant rhizosphere. In this research, the roles of root exudates of three aquatic plants (Phragmites australis, Typha angustifolia and Cyperus alternifolius) in improving the growth of heterotrophic denitrifying bacteria were determined in a micro-polluted CW. In studied root rhizospheres, the total organic carbon (TOC) released from the plant roots varied significantly among plant species and seasons; the average TOC ranged from 0.1715 to 0.9221mgg^-1rootDMd^-1, which could fuel a denitrification rate of approximately 156-841kgNO₃^--Nha^-1year^-1 if all were used by the denitrifying bacteria; the abundances of nirK- and nirS-encoding bacteria were significantly influenced by the concentration of sucrose and glucose (0.869≤r≤0.933, p<0.05), and microbial community richness and diversity had response to root exudates. The results revealed that root exudates can act as endogenous carbon sources for heterotrophic denitrifying bacteria and ultimately determine the microbe distribution patterns in micro-polluted CW.

Bacterial Rhizoplane Colonization Patterns of Buchloe dactyloides Growing in Metalliferous Mine Tailings Reflect Plant Status and Biogeochemical Conditions

Plant establishment during phytostabilization of legacy mine tailings in semiarid regions is challenging due to low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Plant-associated bacterial communities are particularly important under these harsh conditions because of their beneficial services to plants. We hypothesize that bacterial colonization profiles on rhizoplane surfaces reflect deterministic processes that are governed by plant health and the root environment. The aim of this study was to identify associations between bacterial colonization patterns on buffalo grass (Buchloe dactyloides) rhizoplanes and both plant status (leaf chlorophyll and plant cover) and substrate biogeochemistry (pH, electrical conductivity, total organic carbon, total nitrogen, and rhizosphere microbial community). Buffalo grass plants from mesocosm- and field-scale phytostabilization trials conducted with tailings from the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, Arizona, were analyzed. These tailings are extremely acidic and have arsenic and lead concentrations of 2-4 g kg^-1 substrate. Bacterial communities on rhizoplanes and in rhizosphere-associated substrate were characterized using fluorescence in situ hybridization and 16S rRNA gene amplicon sequencing, respectively. The results indicated that the metabolic status of rhizoplane bacterial colonizers is significantly related to plant health. Principal component analysis revealed that root-surface Alphaproteobacteria relative abundance was associated most strongly with substrate pH and Gammaproteobacteria relative abundance associated strongly with substrate pH and plant cover. These factors also affected the phylogenetic profiles of the associated rhizosphere communities. In summary, rhizoplane bacterial colonization patterns are plant specific and influenced by plant status and rhizosphere biogeochemical conditions.

A review on in situ phytoremediation of mine tailings

Mine tailings are detrimental to natural plant growth due to their physicochemical characteristics, such as high pH, high salinity, low water retention capacity, high heavy metal concentrations, and deficiencies in soil organic matter and fertility. Thus, the remediation of mine tailings has become a key issue in environmental science and engineering. Phytoremediation, an in situ cost-effective technology, is emerging as the most promising remediation method for mine tailings by introducing tolerant plant species. It is particularly effective in dealing with large-area mine tailings with shallow contamination of organic, nutrient and metal pollutants. In this review, the background, concepts and applications of phytoremediation are comprehensively discussed. Furthermore, proper amendments used to improve the physical, chemical and biological properties of mine tailings are systematically reviewed and compared. Emphasis is placed on the types and characteristics of tolerant plants and their role in phytoremediation. Moreover, the role of microorganisms and their mechanism in phytoremediation are also discussed in-depth.

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome

We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Global deserts occupy one-third of the Earth’s surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman’s rank correlation [r_s] = >0.81; false-discovery rate [q] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils.

IMPORTANCE We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome

Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman's rank correlation [r_s] = >0.81; false-discovery rate [q] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME μXRF)

Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME μXRF. The FISH and ME μXRF images were aligned using ImageJ software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49±0.19) than to bacteria (0.072±0.052) (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate.

Phytostabilization of mine tailings using compost-assisted direct planting: Translating greenhouse results to the field

Standard practice in reclamation of mine tailings is the emplacement of a 15 to 90cm soil/gravel/rock cap which is then hydro-seeded. In this study we investigate compost-assisted direct planting phytostabilization technology as an alternative to standard cap and plant practices. In phytostabilization the goal is to establish a vegetative cap using native plants that stabilize metals in the root zone with little to no shoot accumulation. The study site is a barren 62-hectare tailings pile characterized by extremely acidic pH as well as lead, arsenic, and zinc each exceeding 2000mgkg(-1). The study objective is to evaluate whether successful greenhouse phytostabilization results are scalable to the field. In May 2010, a 0.27ha study area was established on the Iron King Mine and Humboldt Smelter Superfund (IKMHSS) site with six irrigated treatments; tailings amended with 10, 15, or 20% (w/w) compost seeded with a mix of native plants (buffalo grass, arizona fescue, quailbush, mountain mahogany, mesquite, and catclaw acacia) and controls including composted (15 and 20%) unseeded treatments and an uncomposted unseeded treatment. Canopy cover ranging from 21 to 61% developed after 41 months in the compost-amended planted treatments, a canopy cover similar to that found in the surrounding region. No plants grew on unamended tailings. Neutrophilic heterotrophic bacterial counts were 1.5 to 4 orders of magnitude higher after 41months in planted versus unamended control plots. Shoot tissue accumulation of various metal(loids) was at or below Domestic Animal Toxicity Limits, with some plant specific exceptions in treatments receiving less compost. Parameters including % canopy cover, neutrophilic heterotrophic bacteria counts, and shoot uptake of metal(loids) are promising criteria to use in evaluating reclamation success. In summary, compost amendment and seeding, guided by preliminary greenhouse studies, allowed plant establishment and sustained growth over 4years demonstrating feasibility for this phytostabilization technology.

Arsenic and Environmental Health: State of the Science and Future Research Opportunities

BACKGROUND

Exposure to inorganic and organic arsenic compounds is a major public health problem that affects hundreds of millions of people worldwide. Exposure to arsenic is associated with cancer and noncancer effects in nearly every organ in the body, and evidence is mounting for health effects at lower levels of arsenic exposure than previously thought. Building from a tremendous knowledge base with > 1,000 scientific papers published annually with "arsenic" in the title, the question becomes, what questions would best drive future research directions?

OBJECTIVES

The objective is to discuss emerging issues in arsenic research and identify data gaps across disciplines.

METHODS

The National Institutes of Health's National Institute of Environmental Health Sciences Superfund Research Program convened a workshop to identify emerging issues and research needs to address the multi-faceted challenges related to arsenic and environmental health. This review summarizes information captured during the workshop.

DISCUSSION

More information about aggregate exposure to arsenic is needed, including the amount and forms of arsenic found in foods. New strategies for mitigating arsenic exposures and related health effects range from engineered filtering systems to phytogenetics and nutritional interventions. Furthermore, integration of omics data with mechanistic and epidemiological data is a key step toward the goal of linking biomarkers of exposure and susceptibility to disease mechanisms and outcomes.

CONCLUSIONS

Promising research strategies and technologies for arsenic exposure and adverse health effect mitigation are being pursued, and future research is moving toward deeper collaborations and integration of information across disciplines to address data gaps.

CITATION

Carlin DJ, Naujokas MF, Bradham KD, Cowden J, Heacock M, Henry HF, Lee JS, Thomas DJ, Thompson C, Tokar EJ, Waalkes MP, Birnbaum LS, Suk WA. 2016. Arsenic and environmental health: state of the science and future research opportunities. Environ Health Perspect 124:890-899; http://dx.doi.org/10.1289/ehp.1510209.

Ecological restoration alters microbial communities in mine tailings profiles

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

Arsenic remediation by formation of arsenic sulfide minerals in a continuous anaerobic bioreactor

Arsenic (As) is a highly toxic metalloid that has been identified at high concentrations in groundwater in certain locations around the world. Concurrent microbial reduction of arsenate (As(V) ) and sulfate (SO4 (2-) ) can result in the formation of poorly soluble arsenic sulfide minerals (ASM). The objective of this research was to study As biomineralization in a minimal iron environment for the bioremediation of As-contaminated groundwater using simultaneous As(V) and SO4 (2-) reduction. A continuous-flow anaerobic bioreactor was maintained at slightly acidic pH (6.25-6.50) and fed with As(V) and SO4 (2-) , utilizing ethanol as an electron donor for over 250 d. A second bioreactor running under the same conditions but lacking SO4 (2-) was operated as a control to study the fate of As (without S). The reactor fed with SO4 (2-) removed an average 91.2% of the total soluble As at volumetric rates up to 2.9 mg As/(L · h), while less than 5% removal was observed in the control bioreactor. Soluble S removal occurred with an S to As molar ratio of 1.2, suggesting the formation of a mixture of orpiment- (As2 S3 ) and realgar-like (AsS) solid phases. Solid phase characterization using K-edge X-ray absorption spectroscopy confirmed the formation of a mixture of As2 S3 and AsS. These results indicate that a bioremediation process relying on the addition of a simple, low-cost electron donor offers potential to promote the removal of As from groundwater with naturally occurring or added SO4 (2-) by precipitation of ASM.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.

Using Microorganisms to Facilitate Phytoremediation in Mine Tailings with Multi Heavy Metals

During mining activities, a large amount of wastes in the form of mine tailings were discharged, leading to a global problem in soil and water contamination. Phytoremediation was considered to be a potential method for remediation of mine wastes as vegetation can promote remediation for sustainable development of mine waste sites. Recently, studies were conducted to utilize microorganisms such as plant growth-promoting bacteria, or filamentous fungi to facilitate phytoremediation by increasing the plant biomass production, bioavailability of heavy metals (HMs), enhancing the plant uptake of HMs or reduce toxicity of HMs to plants. Some species of microorganisms can be beneficial to phytoremediation in the mine tailings contaminated with HMs.