Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles

Comparison of microbial communities in unleached and leached ionic rare earth mines

The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species

The oil sands mining operations in Alberta have produced billions of m³ of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored. This study aimed to monitor the structural and functional responses of microbial communities in tailings subjected to different capping and vegetation strategies over two growing seasons (GS). To achieve this, a column-based greenhouse experiment was conducted to investigate microbial communities in tailings that were capped with a layer (10 or 30 cm) of peat-mineral mix (PMM) and planted with either upland or wetland communities. DNA metabarcoding analysis of the bacterial 16S rRNA gene and fungal ITS2 region as well as shotgun metagenomics were used to asses the impact of treatments on microbial taxonomy and functions, respectively. Results showed that tailings microbial diversity and community composition changed considerably after two GS compared to baseline samples, while communities in the PMM capping layer were much more stable. Likewise, several microbial functions were significantly enriched in tailings after two GS. Interestingly, the impact of capping on bacterial communities in tailings varied depending on the plant community, leading to a higher number of differentially abundant taxa and to a decrease in Shannon diversity and evenness in the upland treatment but not in the wetland treatment. Moreover, while capping in the presence of wetland vegetation increased the energy-related metabolic functions (carbon, nitrogen, and sulfur), these functions were depleted by capping in the upland treatment. Fungi represented a small proportion of the microbial community in tailings, but the relative abundance of several taxa changed over time, while the capping treatments favored the growth of some beneficial taxa, notably the root endophyte Serendipita, in both upland and wetland columns. The results suggest that selecting the right combination of capping material and vegetation type may contribute to improve below-ground microbial processes and sustain plant growth in harsh environments such as oil sands tailings.

Influence mechanism of plant litter mediated reduction of iron and sulfur on migration of potentially toxic elements from mercury-thallium mine waste

The decomposition of plant litter in soil changes soil nutrient content and plays an important role in regulating soil pH and availability of potentially toxic elements (PTEs). However, there remains limited studies on the mechanism under which litter influences the transport of PTEs in the process of ecological restoration. This study examined the effect of plant litter decomposition mediated reduction of iron and sulfur components on migration of PTEs from mercury-thallium mine waste. The results showed that the four kinds of litter alleviated the acidity of the waste, especially the Bpa and Tre litter. The nitro and nitroso groups produced by the decomposition of the litter were adsorbed onto the waste, thereby providing an electron transfer medium for iron reducing microorganisms, such as Geobacter. This promoted the reduction and release of Fe³⁺ to Fe²⁺ and reduced the electronegativity (El) value of waste. The reduced El promoted the adsorption of metal cations such as Hg and Tl to maintain electrical neutrality. However, it was not conducive to the adsorption of oxygen containing anions of As and Sb. An increase in litter resulted in an increase in reductivity of mercury-thallium mine waste. This maintained the reduction of Fe³⁺ to Fe²⁺ and changed or destroyed the structure of silicate minerals. PTEs, such as Tl, Hg, As, and Sb, were released, resulting in reductions in their residual fraction. However, the strong reduction conditions, especially the decomposition of Bpa, caused part of the released Hg(II) combining with S^2- produced by the reduction of SO₄^2- to form insoluble HgS, thereby reducing its migration. The findings could provide a theoretical basis to guide the situ-control and ecological restoration of PTEs in waste slag site.

Soil covering measure mitigates vanadium loss during short-term simulated rainfall in the vanadium titano-magnetite tailings reservoir

Soil covering is an operative measure to decline pollutant release in tailings reservoirs and promote vegetation restoration, yet urgent research still needs to probe into pollutant leaching and migration in the artifact technology under extreme precipitation. Here, a soil column leaching experiment was designed to explore the migration and behaviors of vanadium (V) in the system of vanadium titano-magnetite tailings (VTMTs) covered by soils with different depths (5 cm, 10 cm, and 15 cm). Chemical fractions of V in the VTMTs and covered soils were analyzed to decipher the mechanisms underlying the V migration. We found a limited V leaching (0.26-0.52 μg/L, <0.01% of total V) in the columns during the experiments, and V in the VTMTs was not apt to be leached or migrate upward to the overlying soils. The soil volumes overlaid had nonsignificant effect on the V behaviors in the VTMTs (P > 0.05), because of the dominant and stable residual V (96.4% of total V) in the tailings. Although acid soluble V might be transformed to oxidizable V, it was resupplied by the fractions of weak-bound V in the solid phases during the leaching experiments. The mineral metal (hydr)oxides (e.g., aluminum, iron) determined the V behaviors in the VTMTs via absorption effect, and the high affinity of V to organic matters probably prevented its migration throughout the overlying soils. The results indicate that soil covering measure in the VTMTs reservoirs effectively reduces V migration or release from the tailings through leaching or upward migration, which provides a significant guidance for vegetation restoration in V-rich tailings reservoirs.

Temporal evolution of surface and sub-surface geochemistry and microbial communities of Pb-rich mine tailings during phytostabilization: A one-year pilot-scale study

Old mine waste repositories can present health and/or environmental issues linked to their erosion, inducing dissemination of metals and metalloids in air and water that can be attenuated through phytostabilization. Here, the effect of this widespread phytomanagement option on the biogeochemistry of a Pb-rich mine waste was evaluated with a laboratory pilot-scale experiment giving access to the non-saturated and saturated zones below the rhizosphere compartment. Amendment of the tailings surface with biochar, manure and iron-oxide-rich ochre promoted growth of the seeded Agrostis capillaris plants. These events were accompanied by an increase of pH and a decrease of Pb concentration in pore water of the surface layer, and by a transient increase of Pb, Zn, and Ba concentrations in the deeper saturated levels. Macroscopic and microscopic observations (SEM) suggest that Pb was immobilized in A. capillaris rhizosphere through mechanical entrapment of tailing particles. Microbial taxonomic and metabolic diversities increased in the amended phytostabilized surface levels, with a rise of the proportion of heterotrophic micro-organisms. Below the surface, a transient modification of microbial communities was observed in the non-saturated and saturated levels, however 11 months after seeding, the prokaryotic community of the deepest saturated zone was close to that of the initial tailings. pH and water saturation seemed to be the main parameters driving prokaryotic communities' structures. Results obtained at pilot-scale will help to precisely evaluate the impacts of phytostabilization on the temporal evolution of reactions driving the fate of pollutants inside the tailings dumps.

Insight into functional microorganisms in wet–dry conversion to alleviate the toxicity of chromium fractions in red soil

Soil contamination with potentially toxic element such as chromium (Cr) poses a threat to the environment and human health. The environmental toxicity of Cr is related not only to the total Cr content but also to the distribution of Cr fractions. In this study, laboratory simulation experiments were conducted to explore the characteristics of Cr fractions and responses of the functional microbial community during dynamic leaching and static drying processes. The results showed that acid-soluble Cr and reducible Cr transformed into other relatively stable fractions under dry conditions, and ammonium nitrogen promoted the transformation. Nitrate-nitrogen was significantly positively correlated with Cr fractions in the wet stage (p < 0.05), while ammonium nitrogen showed the same relation in the dry process. Analysis of the microbial community showed that the bacterial and fungal genera Flavihumibacter, Altererythrobacter, Methylobacillus, Flavisolibacter, Lysobacter, and Cladosporium were related to the Cr fractions (acid-soluble Cr, reducible Cr, and oxidizable Cr) under wet conditions, while the microbial genera Ellin6067, MND1, and Ramlibacter were related to Cr fractions under dry conditions. Moreover, the proliferation of the functional microbial genera Methylobacillus, Ellin6067, and MND1 related to Cr fractions in the wet–dry conversion process alleviated the environmental toxicity of Cr. These findings provide useful information for the remediation of Cr-contaminated soils by monitoring the distribution fractions of Cr and the functional microbial community under wet–dry conditions.

Rapid elimination of foodborne and environmental fungal contaminants by benzo analogs

BACKGROUND

Contamination of food or the environment by fungi, especially those resistant to conventional fungicides or drugs, represents a hazard to human health. The objective of this study is to identify safe, natural antifungal agents that can remove fungal pathogens or contaminants rapidly from food and / or environmental sources.

RESULTS

Fifteen antifungal compounds (nine benzo derivatives as candidates; six conventional fungicides as references) were investigated. Three benzo analogs, namely octyl gallate (OG), trans-cinnamaldehyde (CA), and 2-hydroxy-5-methoxybenzaldehyde (2H5M), at 1 g L^-1 (3.54 mmol), 1 mL L^-1 (7.21 mmol), 1 mL L^-1 (5.39 mmol), respectively, achieved ≥99.9% fungal death after 0.5, 2.5 or 24 h of treatments, respectively, in in vitro phosphate-buffered saline (PBS) bioassay. However, when OG, CA, and 2H5M were examined in commercial food matrices, organic apple, or grape juices, only CA maintained a similar level of antifungal activity, compared with a PBS bioassay. trans-Cinnamaldehyde showed higher antifungal activity at pH 3.5, equivalent to that of commercial fruit juices, than at pH 5.6. In soil sample tests, the application of 1 mL L^-1 (7.21 mmol) CA to conventional maize / tomato soil samples (pH 6.8) for 2.5 h resulted in ≥99.9% fungal death, indicating CA could also eliminate fungal contaminants in soil. While the conventional fungicide thiabendazole exerted antifungal activity comparable to CA, thiabendazole enhanced the production of carcinogenic aflatoxins by Aspergillus flavus, an undesirable side effect.

CONCLUSION

trans-Cinnamaldehyde could be developed as a potent antifungal agent in food processing or soil sanitation by reducing the time / cost necessary for fungal removal. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.

Implications of spatial heterogeneity of tailing material and time scale of vegetation growth processes for the design of phytostabilisation

Phytostabilisation projects for tailing dams depend on processes occurring at spatial scales of 10⁶ m² and at decadal time scales. Most experiments supporting the design and monitoring of such projects have much smaller spatial and time scales. Usually, they are only designed for one single scale. Here, we report the results of three coupled experiments performed at pot, lysimeter and field plot scales using six sampling periodstimes from 3 to 20 months. The work explicitly accounts for the sampling times when evaluating the effects of amendments on the performance of plants grown in tailing substrates. Two treatments with potentially complementary roles were applied: zeolites to decrease availability of Cd, Cu, Pb and Zn and green fertilizer to increase the availability of nutrients. Zeolites have a positive influence on plant development, especially in the early stages. Analyses of the pooled datasets for all sampling times revealed the possibility of predicting plant physiological variables, such as protein concentrations, pigments and oxidative stress enzyme activities, as a function of the factors extracted by principal component analysis from the metal concentrations in plants, phosphorus concentrations in plants, and sampling times. Two potentially general methodological rules were extracted: account for the spatial geochemical variability of tailings, and cover the broadest possible range of time scales by experiments. The proposed experimental methodology can be of general use for the design of tailing dam remediation technologies with improvements involving the set of measured variables and sampling frequency and by carefully relating the costs to the institutional aspects of tailing dam management.

Effects of Amendments on Soil Microbial Diversity, Enzyme Activity and Nutrient Accumulation after Assisted Phytostabilization of an Extremely Acidic Metalliferous Mine Soil

Current criteria for successful phytostabilization of metalliferous mine wastelands have paid much attention to soil physico-chemical properties and vegetation characteristics. However, it remains poorly understood as to how the soil microbial community responds to phytostabilization practices. To explore the effects of amendments on the microbial community after assisted phytostabilization of an extremely acidic metalliferous mine soil (pH < 3), a pot experiment was performed in which different amendments and/or combinations including lime, nitrogen-phosphorus-potassium (NPK) compound fertilizer, phosphate fertilizer and river sediment were applied. Our results showed the following: (1) The amendments significantly increased soil microbial activity and biomass C, being 2.6–4.9 and 1.9–4.1 times higher than those in the controls, respectively. (2) The activities of dehydrogenase, cellulase and urease increased by 0.9–7.5, 2.2–6.8 and 6.7–17.9 times while acid phosphatase activity decreased by 58.6%–75.1% after the application of the amendments by comparison with the controls. (3) All the amendments enhanced the nutrient status of the mine soil, with organic matter, total nitrogen and total phosphorus increased by 5.7–7.8, 3.1–6.8 and 1.1–1.9 times, relative to the mine soil. In addition, there were strong positive correlations between soil microbial community parameters and nutrient factors, suggesting that they were likely to be synergistic. From an economic view, the combination of lime (25 t ha−1) and sediment from the Pearl River (30%) was optimal for functional rehabilitation of the microbial community in the extremely acidic metalliferous mine soil studied.

Variance in bacterial communities, potential bacterial carbon sequestration and nitrogen fixation between light and dark conditions under elevated CO2 in mine tailings

This study is the first to show the response of bacterial communities with primary carbon and nitrogen fixers to elevated CO₂ (eCO₂) in light and dark conditions based on 6 months of culture growth. Carbon sequestration and nitrogen fixation were analyzed by ¹³C and ¹⁵N isotope labeling using ¹³C-labeled CO₂ and ¹⁵N-labeled N₂, followed by pyrosequencing and DNA-based stable isotope probing (SIP) to identify carbon fixers and nitrogen fixers. The results indicated that eCO₂ decreased the Chao 1 richness, and the eCO₂-light treatment exhibited the highest Shannon diversity. In addition, eCO₂ (in either light or dark conditions) greatly increased the relative abundances of bacteria belonging to the classes Betaproteobacteria and Alphaproteobacteria. The ¹³C atom % in the mine tailings increased from 1.108 to 1.84 ± 0.11 under light conditions and 1.52 ± 0.17 under dark conditions after 6 months of culture growth. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I-coding gene (cbbL) copy numbers were 164.30-fold and 40.36-fold higher than RubisCO form II-coding gene (cbbM) copy numbers in the heavy fractions with a buoyant density of 1.7388 g·mL^-1 relative to the buoyant density gradients of DNA fractions obtained under eCO₂-light and eCO₂-dark treatment, respectively. The Proteobacteria-like cbbL genes were dominant in the carbon fixers. In addition, the ¹⁵N atom % in the mine tailings increased from 0.366 to 0.454 ± 0.021 in light conditions and 0.437 ± 0.018 in dark conditions. Furthermore, uncultured nitrogen-fixing bacteria were the dominant nitrogen fixers in light conditions, and bacteria harboring the Bradyrhizobium-like nifH and Leptospirillum-like nifH genes were the dominant nitrogen fixers in dark conditions. These first data for a mine tailing ecosystem are inconsistent with those obtained for a range of other ecosystems, in which the effects of CO₂ were limited to several nonphotoautotrophic communities and different nitrogen fixers.

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.

Challenges and Approaches in Microbiome Research: From Fundamental to Applied

We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).

Field comparison of the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China

To date, very few attempts have been made to systematically compare the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of mine tailings under field conditions. In this study, we performed a field trial to compare the effectiveness of three agricultural organic wastes: chicken manure (CM), crop straw (CS), and spent mushroom compost (SMC), with that of three nonagricultural organic wastes, municipal sludge (MS), medicinal herb residues (MHR), and sweet sorghum vinasse (SSV) for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China. Eight plant species naturally established in the vicinity of the mine were selected and seeded onto trial plots. It was found that the CM-amended plots had the highest (p < 0.05) vegetation cover (86%) and biomass production (881 g m^-2), compared to other treatments. CM was also one of the best amendments in terms of improving soil nutrient status, increasing activities of soil enzymes, and immobilizing soil Pb. In addition, CM-amended plots were characterized by their higher microbial diversity and distinct microbial community structure as compared to the control plots. MS was the second best amendment in promoting vegetation cover (71%) and biomass production (461 g m^-2), and it performed as well as CM for improving nutrient status, immobilizing heavy metals, and increasing the activities of enzymes in the mine tailings. Suggestions for further lines of research are made in order to develop future investigations.