Adaptation of soil fungi to heavy metal contamination in paddy fields-a case study in eastern China

Eco-resilience of China's mangrove wetlands: The impact of heavy metal pollution and dynamics

Mangrove forests in China have significantly degraded over the past several decades primarily due to rapid economic growth and land reclamation for aquaculture and infrastructure development. Among various threats, heavy metal pollution, primarily from urbanization, agricultural runoff, and industrial runoff, poses a substantial risk to mangroves in China. It impairs their ecological functions, limiting biodiversity and reducing their natural ability to sequester carbon and detoxify coastal areas. Despite these challenges, the mangrove ecosystem's resilience in China has not been completely compromised. Natural adaptations and phytoremediation mechanisms, such as limiting metal uptake, excreting metal binding proteins, upregulating antioxidants, forming Fe plague, excreting metals through salt glands, and tolerance to specific metal concentrations, help mitigate heavy metal toxicity. However, these adaptive strategies are limited by the extent of pollutants and the speed at which these pollution factors arise. This review highlights a need to shift restoration efforts from expanding mangrove areas to enhancing ecosystem integrity, with a specific focus on reducing heavy metal pollution through phytoremediation. It also examines how heavy metal interactions at the sediment-water interface impact microbial communities and local fauna, contributing to climate change. Addressing these challenges is critical to improving mangrove conservation in China and ensuring the long-term health and resilience of these critical ecosystems for future generations.

Rice endophytic fungal community and its potential role on rice grains Cd accumulation

Rice is a cadmium (Cd) high-accumulator, therefore, the soils Cd contamination may cause food security problems. Endophytes played a crucial role on host plants' heavy metal accumulation. However, the endophytic fungal community of rice and its role on rice grains Cd accumulation is still unclear. In this study, the endophytic fungal community of rice at different growth stages from different Cd-contaminated sites (LC and HC, contains lower and higher concentration of Cd, respectively) were investigated by high-throughput sequencing method. In addition, the culturable fungal endophytes were isolated and Cd tolerance assessments were also conducted for some of the isolates. The results showed that the soils Cd concentration and rice tissue showed greater effect on the endophytic fungal community than that of the rice growth stage. The dominant endophytic fungi changed with the soils Cd concentration, and higher Cd concentration reduced the species diversity (Shannon index) and evenness (Evenness index) of endophytic fungi, especially in the roots. In addition, the correlation analysis of dominant endophytic fungi with environmental factors showed that Alternaria, Fusarium and Saccharomyces had a significant positive correlation with Cd concentration. While, the linear discriminant analysis effect size (LEfSe) analysis showed that Stellatospora, Westerdykella, Sarocladium, Spencerozyma and Penicillium were the biomarkers (the relative abundance significantly increased) in multiple tissues from higher Cd-contaminated site. The endophytic fungi from site HC possessed higher ration of Cd tolerant isolates, and the tolerant isolates belong to Sarocladium, Alternaria, Fusarium, etc. Notably, the co-occurrence networks showed that higher Cd concentration increased modularity and number of communities of rice endophytes, especially in the roots, while decreased the positive correlation among different endophytic groups (genus level) in different tissues. These results suggested that rice may respond to higher Cd stress through enriching Cd tolerant endophytic fungi. While, the endophytic fungal community affected rice Cd tolerance by improving its microbiome stability, diversifying microbial survival strategies and maintaining the ecological balance.

Interactive impact of biochar, selenium and water management on rice plants and soil microbial diversity in a cadmium-contaminated soil and assessment of health risk

Global soil cadmium (Cd) contamination demands practical, low-cost solutions to ensure safe food production. This study presents findings from a pot experiment designed to examine the interactive effects of biochar (BC) (B1: 0 %, B2: 1 %, B3: 2 % w/w), foliar selenium (Se) (S1: 0, S2: 0.25 mM, S3: 0.50 mM), and water management (WM) (W1: 70 % water holding capacity, W2: continuous flooding) on Cd effects on rice plants and microbial communities in a Cd-contaminated soil (0.92 mg/kg total Cd) and the associated health risk. The results indicated that the main effects of BC and WM significantly influenced pH and SPAD during the tillering and milk stage, with B2 and B3, and W2 increasing these values compared to B1 and W1. At the milk stage, the B3W2 interaction was significant for SPAD, increasing by 7.40 % compared to B1W1. The measured yield parameters were significantly affected by the main effects of BC, Se, and WM, with B2 and B3, S2 and S3, and W2 showing increased values over B1, S1, and W1. Similar results were observed for bioavailable Cd content; however, Se showed no significant effect. The B3S3W2 interaction significantly increased SOD by 91.56 %, while the B2S3W2 interaction exhibited the highest reductions in MDA (28.35 %) and H₂O₂ (57.61 %) relative to B1S1W1. Furthermore, the B2S3W2 interaction resulted in a 95.32 % reduction in grain Cd content compared to B1S1W1 and enhanced the bacterial ACE, Chao1, and Shannon indices, and the fungal ACE and Chao1 indices. Lastly, the B1S1W1 interaction had the highest daily intake (DI) (1.66E-04) and health risk index (HRI) (0.166), while the B2S3W2 interaction had the lowest DI (8.10E-06) and HRI (0.008). Our results suggest that the application of B2S3W2 can significantly inhibit Cd absorption and concentration in rice, mitigate the resulting health consequences, and enhance the soil microbial environment.

Metal pollution-induced alterations in soil fungal community structure and functional adaptations across regional scales

Soil contamination with heavy metal(loid)s (HMs) threatens soil ecosystem health and function. However, how cross-regional HM contamination influences the structure and function of soil fungal communities remains understudied. We conducted a large-scale soil survey in southern China, using the Nemerow synthetic Pollution Index to assess contamination levels of seven metals (copper, lead, cadmium, arsenic, nickel, zinc and chromium). Soils were classified as low, medium, and high contamination (LC/MC/HC) to examine HM biogeographic patterns and their ecological impacts on soil fungi along the gradient. Cd was the most prevalent contaminant, followed by As in all the studied soils. The combined soil pollution significantly altered fungal community structure, with Cd and Pb identified as key drivers of structural and evenness changes, respectively. Fungal diversity and evenness declined with pollution, accompanied by reduced Staphylotrichum (-0.45 %) and Saitozyma (-1.5 %). Homogeneous selection dominated the assembly processes of soil fungal communities across all contamination levels (contributing 55.8-64.9 %). The most enriched characteristic species included Eurotiomycetes (LC), Sordariales (MC), and Coniochaeta (HC). Pollution-induced habitat heterogeneity enhanced the complexity and stability of fungal symbiotic networks, with 10.0 % more synergistic interactions in highly contaminated soils. The abundance of potential pathogenic fungi increased by 3.0-5.8 % in highly polluted soils compared to low- and moderately polluted soils, indicating possible negative implications for ecosystem health. Our findings provide novel and comprehensive insights into the ecological response of soil fungal communities to HM contamination.

Whispers in the mangroves: Unveiling the silent impact of potential toxic metals (PTMs) on Indian Sundarbans fungi

This study investigates sediment samples from the Indian Sundarbans' mangrove habitat, where most samples were alkaline and hypersaline, except for one acidic sample. Elemental analysis revealed poor sediment quality, with elevated Enrichment Factors (2.20-9.7), Geo-accumulation indices (-2.19-1.19), Contamination Factors (0.61-3.18), and Pollution Load Indices (1.04-1.32). Toxic metal ions, including Pb, Cu, Ni, Cd, Zn, and Cr, were identified as key contributors to compromised sediment quality. These metals inhibit crucial sediment enzymes, such as CMC-cellulase, β-glucosidase, aryl sulfatase, urease, and phosphatases, essential for nutrient cycling and organic matter decomposition. A negative correlation was found between heavy metals and biodiversity, as indicated by the Shannon index, and a similar trend was observed with fungal load. The study highlights the adverse effects of persistent trace metals on the fungal community, potentially disrupting the mangrove ecosystem and suggests using manglicolous fungi as biological indicators of environmental health.

Diversity of soil fungi and entomopathogenic fungi in subtropical mountain forest in southwest China

Till now, the diversity of entomopathogenic fungi in subtropical mountain forest was less studied. Here, the vertical distribution of forest soil fungi, entomopathogenic fungi, and their environmental influencing factors in a subtropical mountain in western China were investigated. Soil samples were collected from four elevations in a subtropical forest in Shaanxi. The results indicated a greater richness of soil fungi at middle elevations and soil fungi were more even at low elevation. Soil pH, available iron, available potassium, total potassium, and available zinc were the most important influencing factors affecting this vertical distribution of fungi. Interestingly, the Isaria genus was predominant while Metarhizium and Beauveria showed decreasing abundance. The presence of Isaria showed a significant positive correlation with both total phosphorus and available iron, while, available zinc was negatively correlated. Metarhizium was influenced by elevation, pH, available phosphorus, and available copper and Beauveria was influenced by soil organic carbon, total nitrogen, total potassium, available potassium, and available zinc. Overall, as environmental factors affecting soil fungi, elevation, and plant species diversity were less important than soil physical and chemical properties. The virulence of isolated entomopathogenic fungi were tested against larvae of Tenebrio molitor, with mortality ranging from 31.11% to 100%. The above findings provide valuable data to deepen our understanding of the diversity of entomopathogenic fungi in subtropical mountain forests.

Enhancing phytoremediation of cadmium and arsenic in alkaline soil by Miscanthus sinensis: A study on the synergistic effect of endophytic fungi and biochar

Endophytic fungi (Trichoderma harzianum (TH) and Paecilomyces lilacinus (PL)) showed potential in phytoremediation for soils contaminated with potentially toxic elements (PTEs (Cd and As)). However, their efficiency is limited, which can be enhanced with the assistance of biochar. This study sought to investigate the effects of TH at two application rates (T1: 4.5 g m-2; T2: 9 g m-2), PL at two application rates (P1: 4.5 g m-2; P2: 9 g m-2), in conjunction with biochar (BC) at 750 g m-2 on the phytoremediation of PTEs by Miscanthus sinensis (M. sinensis). The results showed that the integration of endophytic fungi with biochar notably enhanced the accumulation of Cd and As in M. sinensis by 59.60 %-114.38 % and 49.91 %-134.60 %, respectively. The treatments T2BC and P2BC emerged as the most effective. Specifically, the P2BC treatment significantly enhanced the soil quality index (SQI > 0.55) across all examined soil layers, markedly improving the overall soil condition. It was observed that T2BC treatment could elevate the SQI to 0.56 at the 0-15 cm depth. The combined amendment shifted the primary influences on plant PTEs accumulation from fungal diversity and soil nutrients to bacterial diversity and the availability of soil PTEs. Characteristic microorganisms identified under the combined treatments were RB41 and Pezizaceae, indicating an increase in both bacterial and fungal diversity. This combination altered the soil microbial community, influencing key metabolic pathways. The combined application of PL and biochar was superior to the TH and biochar combination for the phytoremediation of M. sinensis. This approach not only enhanced the phytoremediation potential but also positively impacted soil health and microbial community, suggesting that the synergistic use of endophytic fungi and biochar is an effective strategy for improving the condition of alkaline soils contaminated with PTEs.

Combination of Biochar and Trichoderma harzianum Can Improve the Phytoremediation Efficiency of Brassica juncea and the Rhizosphere Micro-Ecology in Cadmium and Arsenic Contaminated Soil

Phytoremediation is an environment-friendly method for toxic elements remediation. The aim of this study was to improve the phytoremediation efficiency of Brassica juncea and the rhizosphere soil micro-ecology in cadmium (Cd) and arsenic (As) contaminated soil. A field experiment was conducted with six treatments, including a control treatment (CK), two treatments with two contents of Trichoderma harzianum (T1: 4.5 g m-2; T2: 9 g m-2), one biochar treatment (B: 750 g m-2), and two combined treatments of T1B and T2B. The results showed Trichoderma harzianum promoted the total chlorophyll and translocation factor of Brassica juncea, while biochar promoted plant biomass compared to CK. T2B treatment showed the best results, which significantly increased Cd accumulation by 187.49-308.92%, and As accumulation by 125.74-221.43%. As a result, the soil's total Cd content was reduced by 19.04% to 49.64% and total As contents by 38.76% to 53.77%. The combined amendment increased the contents of soil available potassium, phosphorus, nitrogen, and organic matter. Meanwhile, both the activity of glutathione and peroxidase enzymes in plants, together with urease and sucrase enzymes in soil, were increased. Firmicutes (dominant bacterial phylum) and Ascomycota (dominant fungal phylum) showed positive and close correlation with soil nutrients and plant potentially toxic elements contents. This study demonstrated that phytoremediation assisted by biochar and Trichoderma harzianum is an effective method of soil remediation and provides a new strategy for enhancing plant remediation efficiency.

The microbiome of a brownfield highly polluted with mercury and arsenic

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Effects of microwave and plastic content on the sulfur migration during co-pyrolysis of biomass and plastic

In order to reduce the risks of sulfur-containing contaminants present in biofuels, the effects of microwave and content of hydrogen donor on the cracking of C-S bonds and the migration of sulfur were studied by co-pyrolysis of biomass and plastic. The synergistic mechanism of microwave and hydrogen donor was explored from the perspective of deducing the evolution of sulfur-containing compounds based on microwave thermogravimetric analysis. By combining temperature-weight curves, it was found that microwaves and hydrogen radicals promoted the cracking of sulfur-containing compounds and increased the mass loss of biomass during pyrolysis. The mixing ratio of hydrogen donor (plastic) was the key parameter resulting in the removal of sulfur from oil. By adjusting the mixing ratio, the yield of co-pyrolyzed oil was three times higher than that of cow dung pyrolysis alone and the relative removal rate of sulfur reached 73.67%. The relative content of sulfur in the oil was reduced by 73.77% due to the escape of sulfur-containing gases (H₂S, COS and C₂H₅SH) and the formation of sulfate crystals in the char. Microwave selectively heated sulfur-containing organics and hydrogen radicals stimulated the breaking of C-S bonds, which improved the cracking efficiency of the oil. This breaking will provide a theoretical and technological reference for the environmentally friendly treatment of biomass and biofuels.

Fungal assisted bio-treatment of environmental pollutants with comprehensive emphasis on noxious heavy metals: Recent updates

In the present time of speedy developments and industrialization, heavy metals are being uncovered in aquatic environment and soil via refining, electroplating, processing, mining, metallurgical activities, dyeing and other several metallic and metal based industrial and synthetic activities. Heavy metals like lead (Pb), mercury (Hg), cadmium (Cd), arsenic (As), Zinc (Zn), Cobalt (Co), Iron (Fe), and many other are considered as seriously noxious and toxic for the aquatic environment, human, and other aquatic lives and have damaging influences. Such heavy metals, which are very tough to be degraded, can be managed by reducing their potential through various processes like removal, precipitation, oxidation-reduction, bio-sorption, recovery, bioaccumulation, bio-mineralization etc. Microbes are known as talented bio-agents for the heavy metals detoxification process and fungi are one of the cherished bio-sources that show noteworthy aptitude of heavy metal sorption and metal tolerance. Thus, the main objective of the authors was to come with a comprehensive review having methodological insights on the novel and recent results in the field of mycoremediation of heavy metals. This review significantly assesses the potential talent of fungi in heavy metal detoxification and thus, in environmental restoration. Many reported works, methodologies and mechanistic sights have been evaluated to explore the fungal-assisted heavy metal remediation. Herein, a compact and effectual discussion on the recent mycoremediation studies of organic pollutants like dyes, petroleum, pesticides, insecticides, herbicides, and pharmaceutical wastes have also been presented.

Responses of soil fungal taxonomic attributes and enzyme activities to copper and cadmium co-contamination in paddy soils

Excess heavy metals, especially copper (Cu) and cadmium (Cd), are common in paddy soils in the red soil hilly areas of southern China. Microorganisms are regulators of soil organic matter accumulation and pollutant transformation. Clarifying the effects of Cu and Cd accumulation on microbial community composition and function is a prerequisite for bioremediation of paddy soil contamination. However, it remains unclear how Cu and Cd contamination affects soil fungal taxonomic attributes and microbial-mediated biogeochemical processes in paddy soils. Here, soil heavy metals, fungal community composition, and soil enzyme activities were determined in paddy fields downstream of a typical mining area in southern China, and the effects of Cu and Cd co-contamination on fungal community diversity and co-occurrence networks, as well as the associations between them were assessed. The concentrations of Cu and Cd in paddy soils decreased from upstream to downstream of the river, and were positively correlated with the Shannon index of fungal communities. Soil Cu and Cd concentrations exhibited a greater impact on the structure and assembly of fungal communities than soil general properties. Increases in soil Cu and Cd concentrations were correlated with drastic changes in the cumulative relative abundance of ecological clusters in fungal co-occurrence networks. Soil Cu and Cd concentrations were positively correlated with the relative abundances of Eurotiomycetes, Pezizomycetes, Ustilaginomycetes, and Kickxellomycetes, respectively, whereas negatively correlated with hydrolase activities related to carbon, nitrogen, and phosphorus cycles. These results confirmed in the field that long-term Cu and Cd enrichment significantly altered the structure and diversity of fungal communities in the subtropical paddy soils, thereby affecting soil nutrient transformation and organic matter accumulation. This can also provide a basis for the bioremediation of heavy metal pollution in paddy soils.

A Matter of Metals: Copper but Not Cadmium Affects the Microbial Alpha-Diversity of Soils and Sediments - a Meta-analysis

Heavy metal (HM) accumulation in soil affects plants and soil fauna, yet the effect on microbial alpha-diversity remains unclear, mainly due to the absence of dedicated research synthesis (e.g. meta-analysis). Here, we report the first meta-analysis of the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered studies conducted between 2013 and 2022 using DNA metabarcoding of bacterial and fungal communities to overcome limitations of other cultivation- and electrophoresis-based techniques. Fungi were discarded due to the limited study number (i.e. 6 studies). Bacterial studies resulted in 66 independent experiments reported in 32 primary papers from four continents. We found a negative dose-dependent response for Cu but not for Cd for bacterial alpha-diversity in the environments, only for Cu additions exceeding 29.6 mg kg^-1 (first loss of - 0.06% at 30 mg kg^-1). The maximal loss of bacterial alpha-diversity registered was 13.89% at 3837 mg kg^-1. Our results first highlight that bacterial communities behave differently to soil pollution depending on the metal. Secondly, our study suggests that even extreme doses of Cu do not cause a dramatic loss in alpha-diversity, highlighting how the behaviour of bacterial communities diverges from soil macro-organisms.

Significance of Arbuscular Mycorrhizal Fungi in Mitigating Abiotic Environmental Stress in Medicinal and Aromatic Plants: A Review

Medicinal and aromatic plants (MAPs) have been used worldwide for thousands of years and play a critical role in traditional medicines, cosmetics, and food industries. In recent years, the cultivation of MAPs has become of great interest worldwide due to the increased demand for natural products, in particular essential oils (EOs). Climate change has exacerbated the effects of abiotic stresses on the growth, productivity, and quality of MAPs. Hence, there is a need for eco-friendly agricultural strategies to enhance plant growth and productivity. Among the adaptive strategies used by MAPs to cope with the adverse effects of abiotic stresses including water stress, salinity, pollution, etc., their association with beneficial microorganisms such as arbuscular mycorrhizal fungi (AMF) can improve MAPs' tolerance to these stresses. The current review (1) summarizes the effect of major abiotic stresses on MAPs' growth and yield, and the composition of EOs distilled from MAP species; (2) reports the mechanisms through which AMF root colonization can trigger the response of MAPs to abiotic stresses at morphological, physiological, and molecular levels; (3) discusses the contribution and synergistic effects of AMF and other amendments (e.g., plant growth-promoting bacteria, organic or inorganic amendments) on MAPs' growth and yield, and the composition of distilled EOs in stressed environments. In conclusion, several perspectives are suggested to promote future investigations.

The Impact of Bio-Based Fertilizer Integration Into Conventional Grassland Fertilization Programmes on Soil Bacterial, Fungal, and Nematode Communities

Phosphorus (P) is an essential plant macro-nutrient applied to soil in agriculture, mainly sourced from non-renewable mined phosphate-rock, of which readily accessible reserves are currently under pressure, while global food demand continues to grow. Meanwhile, an abundance of P is lost in waste-streams. Hence, bio-based fertilizers are increasingly produced using nutrient-recovery technologies and evaluated as a sustainable fertilizer alternative. However, there is little knowledge of how these products affect soil microorganisms. In this study, four new phosphate bio-based fertilizers (two struvite and two incinerator ashes) were assessed in permanent grassland-plots to understand their impact on soil bacterial, fungal, and nematode community responses. The experiment consisted of 40 plots (each 6 × 2 m2) of 8 treatments (2 struvite, 2 ash, cattle slurry, 100% mineral fertilizer, zero P fertilizer, and a control without fertilization) with 5 replications arranged in a randomized complete block design. Community data were obtained by amplicon sequencing of DNA extracted from soil samples and subsequent analysis of community composition, diversity, structure and influencing environmental variables. Diversity of the soil microorganisms was maintained by all bio-based fertilizer treatments. Results showed that soil bacterial, fungal, and nematode communities of the struvite-treatments were similar to those in 100% mineral treatment. Communities in ash-treatments were more disturbed in their compositions, abundances and structures, possibly due to their high pH and heavy metal content. From canonical correspondence analysis, available P, K, and Mg, as well as plant P uptake and biomass yield, were identified as factors significantly influencing bacterial and nematode communities across different treatment groups. In particular, the abundance of environmental disturbance sensitive nematodes (e.g., Dorylaimida) was significantly reduced by one of the ash products. Overall, results indicate that both struvites are benign to soil bacterial, fungal, and nematode communities and can be safely applied as a source of renewable P to meet crop nutrition requirement. The ash products require further investigations before recommending their regular application as fertilizer. As the application of novel bio-based fertilizers will increase in the foreseeable future, the findings of this study would be valuable to feed into developing environmental risk assessment protocols.

Structure and diversity of fungal communities in long-term copper-contaminated agricultural soil

Copper (Cu) contamination threatens the stability of soil ecosystems. As important moderators of biochemical processes and soil remediation, the fungal community in contaminated soils has attracted much research interest. In this study, soil fungal diversity and community composition under long-term Cu contamination were investigated based on high-throughput sequencing. The co-occurrence networks were also constructed to display the co-occurrence patterns of the soil fungal community. The results showed that the richness and Chao1 index both significantly increased at 50 mg kg^-1 Cu and then significantly decreased at 1600 and 3200 mg kg^-1 Cu. Soil fungal diversity was significantly and positively correlated with plant dry weight. Specific tolerant taxa under different Cu contamination gradients were illustrated by linear discriminant analysis effect size (LEfSe). Soil Cu concentration and shoot dry weight were the strongest driving factors influencing fungal composition. The relative abundance of arbuscular mycorrhizal fungi increased first and then declined along with elevating Cu concentrations via FUNGuild analysis. The interactions among fungi were enhanced under light and moderate Cu contamination but weakened under heavy Cu contamination by random matrix theory (RMT)-based molecular ecological network analysis. Penicillium, identified as a keystone taxon in Cu-contaminated soils, had the function of removing heavy metals and detoxification, which might be vital to trigger the resistance of the fungal community to Cu contamination. The results may facilitate the identification of Cu pollution indicators and the development of in situ bioremediation technology for contaminated cultivated fields.

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.

Iron stress response and bioaccumulation potential of three fungal strains isolated from sewage-irrigated soil

AIMS

Contamination with heavy metal (HM) is a severe environmental issue. Therefore, there is a pressing need to create environmentally safe and cost-effective HM bioremediation approaches.

METHODS AND RESULTS

Three iron-tolerant fungal strains were isolated from sewage-irrigated soils, molecularly identified and deposited in the GenBank as Aspergillus flavus MT639638, A. terreus MT605370 and Fusarium oxysporum MT605399. The fungal growth, minimum inhibitory concentration (MIC), tolerance index (TI), removal efficiency, bioaccumulation, and enzymatic and non-enzymatic antioxidants were determined. Based on MIC values, A. flavus MT639638 was the most resistant strain. F. oxysporum displayed the highest percent removal efficiency (93.65% at 4000 mg L^-1 ) followed by A. flavus (92.92%, at 11,000 mg L^-1 ), and A. terreus (91.18% at 3000 mg L^-1 ). F. oxysporum was selected based on its highly sensitivity for further characterization of its response to Fe(II) stress using TEM, SEM and EDX, in addition to HPLC analysis of organic acids. These analyses demonstrated the localization of bioaccumulated Fe(II) and ultrastructural changes induced by iron and indicated induction release of organic acids.

CONCLUSIONS

Our fungal strains showed an effective capacity for removal of Fe(II) via bioaccumulation and biosorption mechanisms which were supported by instrumental analyses. The iron tolerance potentiality was mediated by induction of selected antioxidative enzymes and biomolecules.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study depicts a potential utilization of the three fungal strains for the bioremediation of iron-contaminated soils.

Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea

Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.

Isolation and molecular identification of microorganisms isolated from soils contaminated with heavy metals in Mosul city

This research is concerned with organisms isolated from soils contaminated with heavy metals in industrial and residential areas in Mosul, the center of Nineveh Governorate, and the diagnosis of these organisms using molecular biology techniques. Samples were collected from four locations in the city between the industrial area and residential neighborhoods. Soil samples were analyzed, and dilutions were prepared, then the dilutions were grown on potato extract and dextrose (PDA) medium for the development of fungi and Nutrient agar for bacterial development. The dilutions were planted by the casting method by three replications, then the process of purifying the fungal and bacterial colonies was carried out using the traditional methods. To diagnose these pure colonies using PCR technique, colonies of fungi were grown on the medium of PDA, and bacteria were grown on the medium of nutritious broth. As a result, nine fungal species were diagnosed; two of them are new undiagnosed genera that have been registered in the gene bank, four of them contain genetic mutations, and three of them are known and previously diagnosed fungi. As for bacteria, two new strains were isolated and registered in the gene bank among the four diagnosed types. And some of these genera exhibited severe resistance to antibiotics, while others showed moderate resistance, in contrast to the control, which was very sensitive to antibiotics.

Effects of heavy metals and organic matter fractions on the fungal communities in mangrove sediments from Techeng Isle, South China

Heavy metal pollution has become a serious environmental problem in mangrove ecosystems and has attracted more attention. Most of previous studies have mainly focused on the effects of heavy metals on bacterial communities in mangrove sediments. This study was the first to investigate the effects of heavy metals (e.g., As, Co, Cr, Cu, Mn, Ni, Pb, V and Zn) and organic matter fractions (including total organic carbon (TOC), total nitrogen (TN), and total sulfur (TS)) on the fungal communities in mangrove sediments from Techeng Isle, South China. The results of this study indicated that the average contents of Mn, Pb and V of 8.30-161.80 μg/g presented relatively higher pollution levels, while the concentrations of Zn, Cr, Cu and Ni of 0.80-21.93 μg/g were lower than those recorded in other mangrove ecosystems. Furthermore, the sediment fungal community structures responded differently to the nine heavy metals and three organic matter fractions. Heavy metals Cr, Pb and V displayed significant positive correlations with Eutypella (P < 0.05), whereas significant negative correlations with Cystobasidium, Lulworthia, Cladosporium, Lulwoana and Cephalotheca (P < 0.05). In addition, the effects of heavy metals and TS on many fungal genera were opposite to those of TOC and TN. Fungal genera that decreased with high TOC and TN contents may be increased with high heavy metal contents and TS, and vice versa, and the genera that increased with high TOC and TN contents may be decreased with high heavy metals and TS. Our results suggested that many heavy metals, such as Cr, Pb and V, were sensitive to several fungal genera in mangrove sediments, and heavy metals together with organic matter fractions may participate and shape the fungal communities in mangrove sediments.

Metal-Fungus interaction: Review on cellular processes underlying heavy metal detoxification and synthesis of metal nanoparticles

The most adverse outcome of increasing industrialization is contamination of the ecosystem with heavy metals. Toxic heavy metals possess a deleterious effect on all forms of biota; however, they affect the microbial system directly. These heavy metals form complexes with the microbial system by forming covalent and ionic bonds and affecting them at the cellular level and biochemical and molecular levels, ultimately leading to mutation affecting the microbial population. Microbes, in turn, have developed efficient resistance mechanisms to cope with metal toxicity. This review focuses on the vital tolerance mechanisms employed by the fungus to resist the toxicity caused by heavy metals. The tolerance mechanisms have been basically categorized into biosorption, bioaccumulation, biotransformation, and efflux of metal ions. The mechanisms of tolerance to some toxic metals as copper, arsenic, zinc, cadmium, and nickel have been discussed. The article summarizes and provides a detailed illustration of the tolerance means with specific examples in each case. Exposure of metals to fungal cells leads to a response that may lead to the formation of metal nanoparticles to overcome the toxicity by immobilization in less toxic forms. Therefore, fungal-mediated green synthesis of metal nanoparticles, their mechanism of synthesis, and applications have also been discussed. An understanding of how fungus resists metal toxicity can provide insights into the development of adaption techniques and methodologies for detoxification and removal of metals from the environment.

Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil

Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.

Heavy Metal-Resistant Filamentous Fungi as Potential Mercury Bioremediators

Filamentous fungi native to heavy metals (HMs) contaminated sites have great potential for bioremediation, yet are still often underexploited. This research aimed to assess the HMs resistance and Hg remediation capacity of fungi isolated from the rhizosphere of plants resident on highly Hg-contaminated substrate. Analysis of Hg, Pb, Cu, Zn, and Cd concentrations by X-ray spectrometry generated the ecological risk of the rhizosphere soil. A total of 32 HM-resistant fungal isolates were molecularly identified. Their resistance spectrum for the investigated elements was characterized by tolerance indices (TIs) and minimum inhibitory concentrations (MICs). Clustering analysis of TIs was coupled with isolates’ phylogeny to evaluate HMs resistance patterns. The bioremediation potential of five isolates’ live biomasses, in 100 mg/L Hg²⁺ aqueous solution over 48 h at 120 r/min, was quantified by atomic absorption spectrometry. New species or genera that were previously unrelated to Hg-contaminated substrates were identified. Ascomycota representatives were common, diverse, and exhibited varied HMs resistance spectra, especially towards the elements with ecological risk, in contrast to Mucoromycota-recovered isolates. HMs resistance patterns were similar within phylogenetically related clades, although isolate specific resistance occurred. Cladosporium sp., Didymella glomerata, Fusarium oxysporum, Phoma costaricensis, and Sarocladium kiliense isolates displayed very high MIC (mg/L) for Hg (140–200), in addition to Pb (1568), Cu (381), Zn (2092–2353), or Cd (337). The Hg biosorption capacity of these highly Hg-resistant species ranged from 33.8 to 54.9 mg/g dry weight, with a removal capacity from 47% to 97%. Thus, the fungi identified herein showed great potential as bioremediators for highly Hg-contaminated aqueous substrates.

Fungal Community, Metabolic Diversity, and Glomalin-Related Soil Proteins (GRSP) Content in Soil Contaminated With Crude Oil After Long-Term Natural Bioremediation

Fungi have increased tolerance to environmental stress (also related to the access of pollutants, e.g., trace elements and polycyclic aromatic hydrocarbons PAHs). The aim of the study was to evaluate the mycobiome and functional diversity of fungi in long-term crude-oil contaminated soils as the potential bioremediators of oil contaminated sites. Samples were taken from three historical oil wells (over a century old) at two distances: within a 0.5 m radius of the oil wells (OWP1, OWP2, and OWP3) and within a 3 m radius from the oil wells as the controls (OW1, OW2, and OW3). Next generation sequencing (for the ITS region) was accompanied with determination of the functional fungal community based on Biolog FFPlates, glomalin related soil protein (GRSP) content, trace element and PAHs concentration. The research hypothesis assumed that long-term natural bioremediation of crude oil contaminated soils can contribute to intensive development of a unique fungal community adapted to the contamination conditions. The identification of such fungi can be of particular importance in soil bioremediation. There were significant differences in the fungal community and functional diversity between the soil samples. The soils collected directly from the oil wells were characterized by higher biological activity and higher diversity of PAH-degrading fungal candidates compared to the soils collected within 3 m of the oil wells. The total glomalin-related soil proteins (T-GRSP) and easily-extractable glomalin-related soil proteins (EE-GRSP) contents were lower in soil samples taken directly from the crude oil well. The control soil (OW) subjected to a long-term natural remediation may already have sufficient conditions for the growth and development of mycorrhizal fungi. The mycobiome of the soils collected directly from the oil wells (OWP1, OWP2, and OWP3) was characterized by a 35% share of PAH-degrading candidates, compared to the soil collected at the 3 m distance from the oil wells (OW1, OW2, and OW3) at < 5%. The main PAH-degrading fungal candidates belong to genera Ilyonectria, Chaetomium, Gibberella, Paraphoma, Schizothecium, Pseudorobillarda, Tetracladium, Ganoderma, Cadophora, Exophiala, Knufia, Mycoleptodiscus, Cyphellophora, Fusicolla, Devriesia, Didymella, Plenodomus, Pyrenochaetopsis, Symbiotaphrina, Phallus, Coprinellus, Plectosphaerella, Septoriella, and Hypholoma. The share of three- and four-ringed PAHs in soil was higher as the distance from the oil well increased. These results may indicate that more effective degradation processes occur closer to the oil wells.