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

Integrated analysis of transcriptomics and metabolomics and high-throughput amplicon sequencing reveals the synergistic effects of secondary metabolites and rhizosphere microbiota on root rot resistance in Psammosilene tunicoides

Psammosilene tunicoides is a plant with significant medicinal and ecological value, exhibiting remarkable medicinal properties, particularly in anti-inflammatory, antioxidant, and immune-regulatory effects. Root rot is one of the primary diseases affecting Psammosilene tunicoides, leading to a significant decline in its quality. In this study, we utilized an integrated analysis of transcriptomics, metabolomics, high-throughput amplicon sequencing, and culturomics for revealing the difference of healthy samples (CH) and diseased samples (CD) and studying the defense mechanism of P. tunicoides in resisting root rot. Transcriptome revealed distinct patterns of gene expression between healthy root samples (HR) and diseased root samples (DR) of P. tunicoides. The Key enzyme genes involved in triterpene (e.g., HMGS, DXS, SQS, CYP450) and flavonoid (e.g., PAL, CHS, CHI) biosynthesis pathways were significantly upregulated in DR. Consistent results were observed in the metabolomic analysis, where triterpene saponins and flavonoids were more highly accumulated in DR than in HR. Microbiome data indicated a significant enrichment of Actinobacteria at the genus level in the rhizosphere soil of diseased samples (DS) compared to healthy samples (HS) while the mostly beneficial growth-promoting bacterial groups were found in DR root endophytes, including Enterobacter, Pseudomonas, Klebsiella, Stenotrophomonas, and Bacillus. Through culturomics, we successfully isolated and identified over 220 bacterial strains from the rhizosphere soil of diseased samples, including genera including Bacillus, Streptomyces, Cupriavidus, Pseudomonas, and Paenarthrobacter. Notably, the strain Pseudomonas sp., which was significantly enriched in DR, exhibited a clear antagonistic effect against Fusarium oxysporum. Co-occurrence network analysis of multi-omics data revealed that many Actinomycetes positively correlated with triterpenoid and flavonoid compounds and their key genes. Therefore, we conclude that these secondary metabolites may could resist pathogen invasion directly or serve as an "intermediate medium" to recruit growth-promoting microorganisms to resistant the root rot. This study investigates the "Plant-Microbe" interaction network associated with root rot resistance in P. tunicoides, revealing its significant implications for the ecological cultivation and management of this species.

The trigger mechanisms and the gene regulatory pathways of organic acid secretion during the vanadium-titanium magnetite tailing bioleaching

The long-term mining of vanadium-titanium (V-Ti) magnetite has generated a large accumulation of tailings, which can lead to metal pollution via microbial bioleaching. Current research has focused on the bioleaching of minerals, and a few studies have explored microbial responses to metals only through limited metabolite concentrations. However, the trigger mechanisms of metal release during the V-Ti magnetite tailing bioleaching and key gene regulatory pathways for organic acid metabolism are still unclear. This study screened a bioleaching fungus from the V-Ti magnetite tailing pond groundwater. The fungus promoted tailing dissolution by secreting more organic acids (808.99 mg L-1) than without tailings (671.11 mg L-1). The released metals were responsible for the difference in organic acid metabolism. The tailing-released Fe, Zn, and V were the triggers for the organic acid secretion via up-regulating the functional genes of citric, formic, and succinic acids in the TCA cycle, Methane metabolism, and D-arginine and D-ornithine metabolisms. Fe and V also led to the accumulation of malic acid through up-regulating functional genes during the conversion of phenylalanine, tyrosine, and glycine. Ni and Cu were the inhibitors by up-regulating related functional genes and promoting the conversion of acetyl-CoA to acetoacetyl-CoA, resulting in a decrease in organic acid concentrations. This study demonstrated the triggering metals of bioleaching and fungal gene regulation pathways, which provide a novel strategy for fungi domestication by considering the up-regulating metals to improve the bioleaching efficiency.

Intimate microbe-water-mineral interactions mediate alkalization in the pyroxene-rich iron ore mines in Panxi area, Southwest China

In contrast to acid mine drainage, the microbial assembly and (bio)geochemical processes in alkaline mine conditions remain under-investigated. Here, microbe-water-mineral interactions were systematically investigated in two representative iron mines with alkaline conditions in the Panxi mining area, Southwest China. Compared to reference riverine samples less interfered by mining activities, the iron ore samples, composed of vanadium-titanium magnetite and pyroxene-rich bedrocks, exhibited elevated levels of Fe, HCl-extractable Fe(II), total sulfur, nitrate and sulfate, but lower total carbon (TC). Meanwhile, the mine drainage showed significantly higher sulfate, but lower TC concentrations than the riverine samples. Intriguingly, the Serpentinimonas spp., typically reported in serpentinites, prevailed in the microbial communities from the mine samples exhibiting higher pH. This suggests that the alkaline environments in Panxi mines result from serpentinization-like reactions. Enrichment of Thiobacillus spp. was observed in the mine-dwelling microbial communities, positively correlated with total sulfur, sulfate, nitrate, and Fe(II). Genome-resolved metagenomics suggested a chemoautotrophic lifestyle for the Thiobacillus species (e.g., carbon fixation, sulfur oxidation, and oxygen respiration), which may generate H+ and mitigate alkalization. This study provides valuable insights into progressive development of alkaline mine ecosystems and offers guidance for developing appropriate engineering strategies to restore the abandoned alkaline mines.

Effects of coal-fired power plants on soil microbial diversity and community structures

Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. Here, we collected the samples of power plant soils (PS), coal-stacking soils (CSS) and agricultural soils (AS) around three coal-fired power plants and background control soils (BG) in Huainan, a typical mineral resource-based city in East China, and investigated the microbial diversity and community structures through a high-throughput sequencing technique. Coal-stacking significantly increased (p < 0.05) the contents of total carbon, total nitrogen, total sulfur and Mo in the soils, whereas the deposition of atmospheric pollutants enhanced the levels of V, Cu, Zn and Pb. Proteobacteria, Actinobacteria, Thaumarchaeota, Thermoplasmata, Ascomycota and Basidiomycota were the dominant taxa in all soils. The bacterial community showed significant differences (p < 0.05) among PS, CSS, AS and BG, whereas archaeal and fungal communities showed significant differences (p < 0.01) according to soil samples around three coal-fired power plants. The predominant environmental variables affecting soil bacterial, archaeal and fungal communities were Mo-TN-TS, Cu-V-Mo, and organic matter (OM)-Mo, respectively. Certain soil microbial genera were closely related to multiple key factors associated with stacking coal and heavy metal deposition from power plants. This study provided useful insight into better understanding of the relationships between soil microbial communities and long-term disturbances from coal-fired power plants.

DNA-SIP delineates unique microbial communities in the rhizosphere of the hyperaccumulator Sedum alfredii which are beneficial to Cd phytoextraction

Rhizo-microbe recruited by hyperaccumulating plants are crucial for the extraction of metals from contaminated soils. It is important, but difficult, to identify the specific rhizosphere microbes of hyperaccumulators shaped by root exudation. Continuous 13CO2 labeling, microbial DNA-based stable isotope probing (DNA-SIP), and high throughput sequencing were applied to identify those rhizosphere microorganisms using exudates from the Cd hyperaccumulator Sedum alfredii. In contrast to its non-hyperaccumulating ecotype (NAE), the hyperaccumulating ecotype (HAE) of S. alfredii strongly changed the rhizosphere environment and extracted a 5-fold higher concentration of Cd from contaminated soil. Although both HAE and NAE harbored Streptomyces, Massilia, Bacillus, and WPS-2 Uncultured Bacteria with relative abundance of more than 1% in the rhizosphere associated with plant growth and immunity, the HAE rhizosphere specifically recruited Rhodanobacter (2.66%), Nocardioides (1.16%), and Burkholderia (1.01%) through exudates to benefit the extraction of Cd from soil. Different from the bacterial network with weak cooperation in the NAE rhizosphere, a closed-loop bacterial network shaped by exudates was established in the HAE rhizosphere to synergistically resist Cd. This research reveals a specific rhizosphere bacterial community induced by exudates assisted in the extraction of Cd by S. alfredii and provides a new perspective for plant regulation of the rhizo-microbe community beneficial for optimizing phytoremediation.

Geochemical properties, heavy metals and soil microbial community during revegetation process in a production Pb-Zn tailings

Lead-zinc (Pb-Zn) tailings pose a significant environmental threat from heavy metals (HMs) contamination. Revegetation is considered as a green path for HM remediation. However, the interplay between HM transport processes and soil microbial community in Pb-Zn tailings (especially those in production) remain unclear. This study investigated the spatial distribution of HMs as well as the crucial roles of the soil microbial community (i.e., structure, richness, and diversity) during a three-year revegetation of production Pb-Zn tailings in northern Guangdong province, China. Prolonged tailings stockpiling exacerbated Pb contamination, elevating concentrations (from 10.11 to 11.53 g/kg) in long-term weathering. However, revegetation effectively alleviated Pb, reducing its concentrations of 9.81 g/kg. Through 16 S rRNA gene amplicon sequencing, the dominant genera shifted from Weissella (44%) to Thiobacillus (17%) and then to Pseudomonas (comprising 44% of the sequences) during the revegetation process. The structural equation model suggested that Pseudomonas, with its potential to transform bioavailable Pb into a more stable form, emerged as a potential Pb remediator. This study provides essential evidence of HMs contamination and microbial community dynamics during Pb-Zn tailings revegetation, contributing to the development of sustainable microbial technologies for tailings management.

Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.

New insights on the effect of non-ferrous metal mining and smelting activities on microbial activity characteristics and bacterial community structure

Mining and smelting activities have brought potentially serious heavy metal(loid)s pollution to their surrounding locale. However, studies on microbial metabolic activities, community structure, and adaptation in soils proximal to non-ferrous metal mining and smelting areas are still lacking. Here the effects of biotic and abiotic characteristics of soil taken from sites surrounding inactive and active non-ferrous metal mine smelting facilities on microbial enzyme activity, microcalorimetry, and high-throughput sequencing of 16S rRNA gene barcoding were studied. Data indicated that the soils were heavily polluted by toxic metal(loid)s, of which As and Cd were the main contaminants. Microbial acid phosphatase activity and microcalorimetric total heat value were sensitive metabolic indicators in the studied areas. Actinobacteriota had the highest relative abundance, followed by Proteobacteria, Chloroflexi, and Acidobacteria. Microbial metabolic activity, bacterial community structure and phenotype varied between inactive and active sites (p < 0.05). Such analyses indicated that electrical conductivity, total As, Cu, and Mn contents, and bioavailable As, Cu, Cd, and Mn concentrations were key factors determining microbial activities, bacterial community structure, and phenotypes. Knowledge of microbial adaptation to heavy metal stressors is important for better understanding the aerial transfer of fugitive heavy metal(loid)s (and possibly microbes) and for designing future strategies for improved soil bioremediation.

Evaluation of the potential of recovering various valuable elements from a vanadiferous titanomagnetite tailing based on chemical and process mineralogical characterization

In order to evaluate the potential of recovering various valuable elements from vanadiferous titanomagnetite tailing (VTMT), the chemical and process mineralogical characterization of VTMT were investigated in this study by various analytical techniques such as XRF, XRD, optical microscopy, SEM, EDS, and AMICS. It was found that VTMT is a coarser powder in general; about 50% of the particle size is greater than 54.30 μm. The total iron content of the VTMT was 22.40 wt.%, and its TiO2 grade is 14.45 wt.%, even higher than those found in natural ilmenite ores. The majority of iron and titanium were located in ilmenite and hematite; 62.84% of hematite and 90.27% of ilmenite were present in monomeric form. However, there is still a portion of ilmenite and hematite embedded in gangue such as anorthite, diopside, and serpentite. For the recovery of valuable fractions such as Fe and TiO2 from VTMT, a treatment process including ball milling-high-intensity magnetic separation-one roughing and three refining flotation was proposed. Finally, a concentrate with TiO2 grade of 47.31% and total Fe (TFe) grade of 35.44% was produced; TiO2 and TFe had recovery rates of 57.71% and 28.23%, respectively. The recovered product is adequate as a raw material for the production of rutile. This study provides a reference and a new research direction for the recycling and comprehensive utilization of VTMT.

Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field

Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.

Multiple heavy metal distribution and microbial community characteristics of vanadium-titanium magnetite tailing profiles under different management modes

Vanadium-titanium (V-Ti) magnetite tailings have caused great concern due to their safety hazards and environmental risks. However, the microbial community structure and the key geochemical factors of V-Ti magnetite tailing profiles under different management modes remain unclear. Therefore, we investigated the heavy metal distribution and the microbial community structure of the soils and tailings at varied depths of V-Ti magnetite tailing profiles with and without soil coverage. The results indicated that the topsoil covering measures retarded the acidification of tailings during stockpiling. However, As, Mn, and V in tailings have the ability to migrate to the overlying soil. Based on 16S rRNA gene amplicon sequencing, Proteobacteria was the dominant genus in the topsoil-covered tailings, whereas the most abundant genus in the exposed tailings was Betaproteobacteria. Furthermore, Rhodobacter, Hydrogenophaga, Novosphingobium, and Geobacter enriched in tailings may potentially contribute to V(V) biotransformation and the development of mine bioreremediation technologies. RDA and Spearman correlation analysis showed that pH, EC, Cd, Mn, Pb, and V were the main influencing factors regulating microbial community composition. Overall, this study provides insights for evaluating the soil covering management mode and the engineering applications of microbial technologies to manage V-Ti magnetite tailings.

Plant-Soil Feedbacks for the Restoration of Degraded Mine Lands: A Review

Much effort has been made to remediate the degraded mine lands that bring severe impacts to the natural environments. However, it remains unclear what drives the recovery of biodiversity and ecosystem functions, making the restoration of these fragile ecosystems a big challenge. The interactions among plant species, soil communities, and abiotic conditions, i.e., plant-soil feedbacks (PSFs), significantly influence vegetation development, plant community structure, and ultimately regulate the recovery of ecosystem multi-functionality. Here, we present a conceptual framework concerning PSFs patterns and potential mechanisms in degraded mine lands. Different from healthy ecosystems, mine lands are generally featured with harsh physical and chemical properties, which may have different PSFs and should be considered during the restoration. Usually, pioneer plants colonized in the mine lands can adapt to the stressful environment by forming tolerant functional traits and gathering specific soil microbial communities. Understanding the mechanisms of PSFs would enhance our ability to predict and alter both the composition of above- and below-ground communities, and improve the recovery of ecosystem functions in degraded mine lands. Finally, we put forward some challenges of the current PSFs study and discuss avenues for further research in the ecological restoration of degraded mine lands.

Effect of the natural establishment of two plant species on microbial activity, on the composition of the fungal community, and on the mitigation of potentially toxic elements in an abandoned mine tailing

In Mexico, millions of tons of mining wastes are deposited in the open pit. Their content in potentially toxic elements (PTE) represents an environmental risk. In the tailings, pioneer plant communities are established, associated with a determined diversity of fungi; plants, and fungi are fundamental in the natural rehabilitation of mining wastes. The objective was to evaluate the impact of the natural establishment of two plant species on the microbial activity, on the composition of the fungal community, and on the mitigation of the effect of PTE in a contaminated mine tailing. In a tailing, we selected three sites: one non-vegetated; one vegetated by Reseda luteola, and one vegetated by Asphodelus fistulosus. In the substrates, we conducted a physical and chemical characterization; we evaluated the enzymatic activity, the mineralization of the carbon, and the concentration of PTE. We also determined the fungal diversity in the substrates and in the interior of the roots, and estimated the accumulation of carbon, nitrogen, phosphorus and PTE in plant tissues. The tailings had a high percentage of sand; the non-vegetated site presented the highest electric conductivity, and the plant cover reduced the concentration of PTE in the substrates. Plants increased the carbon content in tailings. The enzymatic activities of β-glucosidase and dehydrogenase, and the mineralization of carbon were highest at the site vegetated with A. fistulosus. Both plant species accumulated PTE in their tissues and exhibited potential in the phytoremediation of lead (Pb), cadmium (Cd), and copper (Cu). Fungal diversity was more elevated at the vegetated sites than in the bare substrate. Ascomycota prevailed in the substrates; the substrates and the plants shared some fungal taxa, but other taxa were specific. The plant coverage and the rhizosphere promoted the natural attenuation and a rehabilitation of the extreme conditions of the mining wastes, modulated by the plant species.

Microbial community profiles in soils adjacent to mining and smelting areas: Contrasting potentially toxic metals and co-occurrence patterns

Mining and smelting activities have introduced severe potentially toxic metals (PTMs) contamination into surrounding soil settings. Influences of PTMs on microbial diversity have been widely studied. However, variations of microbial communities, network structures and community functions in different levels of PTMs contaminated soils adjacent to mining and smelting aera are still poorly investigated. In this study, microbial communities of soils around different levels of PTMs contamination were comprehensively studied by 16S rRNA gene amplicons high-throughput sequencing. Microbial interactions and module functions were also exploited to ascertain the discrepancies of PTMs concentration levels on microbial ecological functions. Results indicated that the microbial community composition was significantly distinct attributed to the phylum Protebacteria (p = 0.002) dominating in soil with high level PTMs contents but Actinobacteria (p = 0.002) in low level of PTMs-contaminated soil. Microbial α diversity was not significantly influenced by different levels of PTMs contaminations. Microorganisms proactively responded to PTMs content levels by means of strengthening network complexities and modularities among microbe-microbe interactions. The functions of main network modules were predicted associating membrane transport, amino acid metabolism, energy metabolism and carbohydrate metabolism. The PTMs detoxification and anti-oxidation were significantly strengthened at the high level of PTMs contamination. The present study demonstrated that modification of microbial community by the adaptive adjustment of microbial compositions and strengthening their network complexity and modularity.

Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field

Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.