Heavy metal pollution triggers a shift from bacteria-based to fungi-based soil micro-food web: Evidence from an abandoned mining-smelting area

A global meta-analysis reveals effects of heavy metals on soil microorganisms

Heavy metal (HM) contamination disrupts soil ecosystem functions. Microorganisms are pivotal for sustaining soil health, but accurately assessing the ecological risks of HM contamination to microorganisms remains challenging. Here, we conducted a meta-analysis synthesizing 914 datasets from 72 studies to quantify and evaluate the impacts of HMs on microorganisms. The overall effect value results indicate that HM negatively impacts most microbiological indicators, with bacterial abundance (-38 %), fungal abundance (-18 %), microbial biomass carbon (-42 %), microbial biomass nitrogen (-44 %), arylsulfatase (-45 %) and dehydrogenase activity (-66 %) were significantly reduced (p < 0.01), suggesting they can act as sensitivity indicators for assessing ecological risk of microorganisms. Compared to bacteria, fungal indicators (e.g., fungal community structure and Shannon index) are less responsive to HM contamination. At low potential ecological risk index (RI < 150), HM contamination positively impacted certain microbial indicators, such as fungal abundance, fungal Shannon index, and β-glucosidase activity. With increasing RI levels, the negative effects of HMs on microorganisms became more pronounced. Microbiological indicators in acidic soils (pH < 6.5), coarse textured soils, and mining soils were more negatively affected by HMs. Random forest and structural equation modeling analysis also identified RI levels and pH as crucial factors in determining the microbial response to HMs. Adjusted RI (adRI) were calculated using adjusted toxicity factors (adTF). The adRI demonstrated stronger correlations with microbial indicators and lower root-mean-square error (RMSE) in the random forest model than the RI, indicating that adTF is a more effective method for evaluating the effects of HMs on microorganisms. This study enhances the accuracy of quantifying and assessing HM impacts on microorganisms, offering crucial scientific basis for environmental protection and soil remediation.

Cadmium inhibits carbon and nitrogen cycling through soil microbial biomass and reduces soil nitrogen availability

Microbial mediated carbon and nitrogen cycling response to cadmium are often observed in soil; however, a unified framework of this response has not yet been established. By analyzing 1232 observations from 166 publications, we found that cadmium decreased microbial biomass carbon (-16 %) and nitrogen (-21 %), dissolved organic nitrogen (-27 %), nitrification rate (-17 %), microbial respiration rate (-12 %), and β-1,4-glucosidase (-21 %) and urease (-16 %) activities, but increased microbial metabolic quotient (+11 %) and fungal-to-bacterial ratio (+39 %). The cadmium impact was concentration-dependent, becoming more pronounced at higher concentrations. Increasing cadmium concentration reduced soil N mineralization rate and total N content, but increased microbial biomass carbon-to-nitrogen ratio. These results indicate that cadmium reduced carbon and nitrogen assimilation into microbial biomass and limited soil inorganic nitrogen production. Soil bulk density drove soil microbial biomass and nitrogen availability response to cadmium. Lower soil bulk density and higher initial carbon and clay contents and soil pH reduced the negative impact of cadmium on microbial biomass and nitrogen availability, suggesting that anthropogenic activities that enhance soil quality may mitigate the inhibitory effect of cadmium on soil carbon and nitrogen cycling. Our analysis provides critical implications for improving our understanding of the ecological consequences of cadmium on soil carbon and nitrogen cycling.

Soil resource availability regulates the response of micro-food web multitrophic interactions to heavy metal contamination

The effects of heavy metal contamination on soil biomes have been of considerable interest. However, the effects of heavy metal pollution on the interactions between soil multi-trophic biota in soil food webs and the regulatory mechanisms still need more research, especially in different soil situations. This study examined the impact of heavy metal contamination on soil micro-food web in two distinct soil resource availability situations. Under low soil resources availability situation, heavy metals mainly affected the community structure of soil bacteria and nematodes, with the number of edges of the bacterial network and network complexity reduced by 60.5% and 187%, respectively. In addition, the presence of heavy metals led to a significant reduction in the energy flow from soil resources to bacterivores in the nematode food web. For micro-food webs, heavy metal contamination increased the network average degree by 18.8% and 11.56% in the low and high resource availability situations, respectively. However, in high soil resource availability, heavy metal contamination decreased micro-food web stability and eased competitive relationships among multitrophic organisms and increased microbial carbon limitation and mitigates nitrogen limitation. In low soil resource availability, it increased network stability and shifted relationships among micro-food web organisms from cooperative to competitive and decreased microbial carbon limitation and aggravated nitrogen limitation. This study offers new research insights into the feedback discrepancy between resource availability and pollution stress from the perspective of multitrophic level interactions and further deepens the understanding of the environmental impacts of heavy metal pollution at the ecosystem level.

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.

Edaphic and climatic factors control the response of nutrient-cycling enzyme activity to common heavy metals in soils

Soil enzymes, which are crucial catalysts in soil nutrient cycling, are sensitive to heavy metals and metalloids (HMMs). Yet, the mechanistic understanding of soil enzyme activities (EAs) response to HMMs is still only rudimentarily known. By analyzing 1989 paired observations from 145 studies investigating HMMs effect on 14 enzymes, we found that HMMs decreased the activity of β-D-glucosidase (-25.3 %), cellulase (-10.3 %), urease (-26.8 %), protease (-22.5 %), phosphatase (-21.0 %), arylsulphatase (-37.0 %), catalase (-19.2 %) and dehydrogenase (-33.1 %), with natural ecosystems being more severely affected than croplands. This decrease in EAs was mainly due to decreased microbial biomass content and abundance and increased microbial metabolic quotient. However, HMMs increased polyphenol oxidase activity (82.2 %), possibly because HMMs can serve as cofactors or activators for polyphenol oxidase and/or because microbes produced it as a defense mechanism under stress. The response ratio of EAs is driven by cation exchange capacity (CEC) and dominantly influenced by soil organic carbon (SOC), clay, and bulk density (BD). Increased CEC, SOC and clay content and decreased BD reduced the negative effect of HMMs on EAs. Climate impact on the response ratio of EAs was mediated through soil properties. Our analysis provides a more holistic representation of EAs response to HMMs, offering comprehensive insights into the ecological consequences of HMMs on ecosystem functioning.

The influences of heavy metals on soil microbial C, N, P cycling and heavy metal resistance under different fertilization regimes

Heavy metal pollution changes microbial heavy metal resistance and ecological functions of carbon (C), nitrogen (N), phosphorus (P), sulfur (S) cycling, although the connections between these changes have been insufficiently explored. The study investigated the effects of varying levels of heavy metal pollution and nutrient on microbial heavy metal resistance and C, N, P, S cycling in soils. The results indicated that heavy metal pollution significantly enhanced microbial metabolic potentials, such as denitrification, Dissimilatory nitrate reduction (DNRA), P uptake and transport, as well as resistance to Cu, Cd, Pb, and As. Heavy metals and pH were identified as major factors affecting these microbial functions. The diversity and evenness of host microorganisms carrying functional genes and heavy metal resistance genes (MRGs) were significantly affected by heavy metal pollution, but this effect was alleviated with the nutrient increased. In low-nutrient soils, a strong correlation between nitrogen degradation and Zn resistance was observed due to heavy metal pollution. As nutrients increased, the close correlations between hemicellulose, P uptake and transport, nitrogen degradation and Zn resistance were also observed. Bradyrhizobium, Nitrospira, Steroidobacter, and Luteitalea might play important roles in regulating C, N, P cycling and heavy metal resistance. This study revealed the adjustment mechanisms of microbial heavy metals resistance and ecological functions under heavy metal pollution and identified the primary host microorganisms.

Effects of heavy metals on variation in bacterial communities in farmland soil of tailing dam collapse area

Heavy metals are commonly present in polluted soil in mining areas. In this study, we investigated 10 sites of farmland soil in the heavy metal tailing dam collapse area (TDCA) with the dominant phyla Acidobacteriota, Proteobacteria, Bacteroidetes, and Planctomycetes. The heavy metal dam collapse area is a composite contamination area of multiple heavy metals, with Cd, Pb and Zn being the most severely contaminated, and the levels of Hg and Cu exceeding the screening values at some of the sites. The Shannon, Chao1 and ACE indices revealed high microbial diversity but low relative abundance of microorganisms at the severely polluted TDCA1 and TDCA3 sites. The results of redundancy analysis (RDA) showed that Hg (Max = 4.31 mg/kg) and Cu (Max = 100 mg/kg) were important factors affecting soil microbial community in the TDCA compared to other heavy metals. Correlation analysis of heavy metals with microbial communities showed that RB41 (Acidobacteria) was more resistant to high concentrations of Cd, Pb, and Zn pollution. The genera of UTCFX1 (Chloroflxi) and norank_TRA3-20 had strong tolerance to the heavy metal Hg. Cu was significantly negatively correlated with norank_WD2101_soil_group (P < 0.05). Therefore these can be used as indicators for monitoring potential heavy metal contamination. The results can be used to predict the changes in the ecosystem of the mining area to maintain its ecological balance and health.

Soil Plastisphere Reinforces the Adverse Effect of Combined Pollutant Exposure on the Microfood Web

Microbial interactions form microfood webs, crucial for ecological functions. The steady state of these webs, shaped by cooperation and competition among trophic levels, prevents pathogen proliferation and invasion, maintaining soil health. Combined pollutants pose a widespread environmental issue, exerting significant pressure on microfood webs. However, understanding how these webs respond to combined pollutants in soil plastispheres, an emerging niche, remains limited. This study explores trophic interactions among bacteria, fungi, and protists, examining their effects on potential pathogens in three soil types amended with Cu or disinfectant, along with their plastispheres, using a microcosm experiment. Pollutant exposure disrupts trophic-level interactions through bottom-up and top-down regulation in soils and plastispheres, respectively. Microfood web network topology parameters prove more sensitive to pollutant stress than indicators from a single trophic-level community composition. Combined exposure causes greater disruption to the microfood web than exposure to a single pollutant (Cu or didecyl dimethylammonium chloride (DDAC)). Plastisphere reinforces negative impacts of combined pollutant exposure on the microfood web network, escalating potential pathogenic bacteria. Overall, this study deepens our understanding of microfood web responses under pollutant pressure in soil plastispheres and provides valuable insights for health risk assessments of soil combined pollutants.

Environmental remediation potential of a pioneer plant (Miscanthus sp.) from abandoned mine into biochar: Heavy metal stabilization and environmental application

Pyrolysis stands out as an effective method for the disposal of phytoremediation residues in abandoned mines, yielding a valuable by-product, biochar. However, the environmental application of biochar derived from such residues is limited by the potential environmental risks of heavy metals. Herein, Miscanthus sp. residues from abandoned mines were pyrolyzed into biochars at varied pyrolysis temperatures (300-700 °C) to facilitate the safe reuse of phytoremediation residues. The results showed that pyrolysis significantly stabilizes heavy metals in biomass, with Cd exhibiting the most notable stabilization effect. Acid-soluble/exchangeable and reducible fractions of Cd decreased significantly from 69.91 % to 2.52 %, and oxidizable and residue fractions increased approximately 3.24 times at 700 °C. The environmental risk assessment indicated that biochar pyrolyzed over 500 °C pose lower environmental risk (RI < 30), making them optimal for the safe utilization of phytoremediation residues. Additionally, adsorption experiments suggested that biochars prepared at higher temperature (500-700 °C) exhibit superior adsorption capacity, attributed to alkalinity and precipitation effect. This study highlights that biochars produced by pyrolyzing Miscanthus sp. from abandoned mines above 500 °C hold promise for environmental remediation, offering novel insight into the reutilization of metal-rich biomass.

Heavy metals and nutrients mediate the distribution of soil microbial community in a typical contaminated farmland of South China

The effects of heavy metals on soil microbial communities have been extensively investigated, whereas the combined effects of heavy metals and nutrients on soil microbial communities and their interactions are rarely understood. In this study, we investigated the distribution patterns of heavy metals, nutrients and microbial communities in a typical contaminated farmland and explored their interaction mechanisms. The results showed that Cd and Pb were the main pollutants in this area, which mainly came from the smelter. Canonical correspondence analysis and variance decomposition analysis showed that the heavy metals played a more important role in restraining the microbial community structure of soils than other soil properties. Soil Cd, Pb, pH and available K content were the most important environmental factors affecting the microbial community structures in soil. Major Cd tolerant bacteria and fungi were detected including Actinobacteriota, Gemmatimonadota, Entorrhizomycota and Mortierellomycota. The analyses of molecular ecological networks showed that there were 84.1 % of negative correlations among microorganisms. Cd could regulate the abundance of key nodes in Cd-tolerant network modules, and these key nodes could improve the adaptability of the whole module to heavy metals through competition with other microorganisms. This study provides insights into the ecological effects of heavy metals and nutrients on soil microbial communities and will help to develop the bio-remediation technologies for contaminated soils.

Bioindicator responses to extreme conditions: Insights into pH and bioavailable metals under acidic metal environments

Acid mine drainage (AMD) caused environmental risks from heavy metal pollution, requiring treatment methods such as chemical precipitation and biological treatment. Monitoring and adapting treatment processes was crucial for success, but cost-effective pollution monitoring methods were lacking. Using bioindicators measured through 16S rRNA was a promising method to assess environmental pollution. This study evaluated the effects of AMD on ecological health using the ecological risk index (RI) and the Risk Assessment Code (RAC) indices. Additionally, we also examined how acidic metal stress affected the diversity of bacteria and fungi, as well as their networks. Bioindicators were identified using linear discriminant analysis effect size (LEfSe), Partial least squares regression (PLS-R), and Spearman analyses. The study found that Cd, Cu, Pb, and As pose potential ecological risks in that order. Fungal diversity decreased by 44.88% in AMD-affected areas, more than the 33.61% decrease in bacterial diversity. Microbial diversity was positively correlated with pH (r = 0.88, p = 0.04) and negatively correlated with bioavailable metal concentrations (r = -0.59, p = 0.05). Similarly, microbial diversity was negatively correlated with bioavailable metal concentrations (bio_Cu, bio_Pb, bio_Cd) (r = 0.79, p = 0.03). Acidiferrobacter and Thermoplasmataceae were prevalent in acidic metal environments, while Puia and Chitinophagaceae were identified as biomarker species in the control area (LDA>4). Acidiferrobacter and Thermoplasmataceae were found to be pH-tolerant bioindicators with high reliability (r = 1, P < 0.05, BW > 0.1) through PLS-R and Spearman analysis. Conversely, Puia and Chitinophagaceae were pH-sensitive bioindicators, while Teratosphaeriaceae was a potential bioindicator for Cu-Zn-Cd metal pollution. This study identified bioindicator species for acid and metal pollution in AMD habitats. This study outlined the focus of biological monitoring in AMD acidic stress environments, including extreme pH, heavy metal pollutants, and indicator species. It also provided essential information for heavy metal bioremediation, such as the role of omics and the effects of organic matter on metal bioavailability.

Keystone taxa enhance the stability of soil bacterial communities and multifunctionality under steelworks disturbance

Continuous discharge of wastewater, emissions, and solid wastes from steelworks poses environmental risks to ecosystems. However, the role of keystone taxa in maintaining multifunctional stability during environmental disturbances remains poorly understood. To address this, we investigated the community diversity, assembly mechanisms, and soil multifunctionality of soils collected from within the steelworks (I), within 2.5 km radius from the steelworks (E), and from an undisturbed area (CK) in Jiangsu Province, China, via 16 S rRNA sequencing. Significant differences were found in the Chao1 and the richness indexes of the total taxa (p < 0.05), while the diversity of keystone taxa was not significant at each site (p > 0.05). The deterministic processes for total taxa were 42.9%, 61.9% and 47.7% in CK, E, and I, respectively. Steelworks stress increased the deterministicity of keystone taxa from 52.3% in CK to 61.9% in E and I soils. The average multifunctionality indices were 0.518, 0.506 and 0.513 for CK, E and I, respectively. Although the soil multifunctionality was positive correlated with α diversity of both the total and keystone taxa, the average degree of keystone taxa in functional network increased significantly (79.96 and 65.58, respectively), while the average degree of total taxa decreased (44.59 and 51.25, respectively) in the E and I. This suggests keystone taxa contribute to promoting the stability of ecosystems. With increasing disturbance, keystone taxa shift their function from basic metabolism (ribosome biogenesis) to detoxification (xenobiotics biodegradation, metabolism, and benzoate degradation). Here we show that keystone taxa are the most important factor in maintaining stable microbial communities and functions, providing new insights for mitigating pollution stress and soil health protection.

Assessing heavy metal contamination in Amomum villosum Lour. fruits from plantations in Southern China: Soil-fungi-plant interactions

Amomum villosum Lour. fruit is a common healthy food widely cultivated in southern China. Heavy metal contamination of farmland soils has becomes a serious environmental concern in China. Heavy metals in soil can be introduced into the food chain and pose health risks to humans. However, microbial communities may play beneficial roles in plants grown in metal-polluted soils. This study aimed to assess the potential health risks of heavy metals in soils and A. villosum fruits from different production areas and to explore the soil-microbe-plant regulation pattern for heavy metals in A. villosum fruits. Soil and A. villosum fruit samples were collected from nine planting fields in four provinces of southern China. The results showed that soils from seven areas were polluted with heavy metals to different degrees. Cr and Mn were the most serious contaminating elements. However, the accumulation of heavy metals in A. villosum fruit was negligible with no expected human health risks. Partial least squares path analysis of structural equation modeling showed that the accumulation of heavy metals in A. villosum fruits was influenced by multiple factors. More importantly, the PLS-SEM revealed that the heavy metal content in A. villosum fruits was indirectly affected by soil heavy metals through the regulation of the microbial community. Furthermore, some fungal phyla (e.g., Ascomycota and Chytridiomycota) and genera (e.g., Mucor) were related to the heavy metal content in the soil and in A. villosum fruits. The results of this study verified that soil fungal community play an important role in the accumulation of heavy metals in A. villosum fruits. Using fungi provides a potential biological strategy for reducing the health risk posed by heavy metals in food.