An integrated multidisciplinary-based framework for characterizing environmental risks of heavy metals and their effects on antibiotic resistomes in agricultural soils

Distribution and relationship of heavy metals, microbial communities and antibiotic resistance genes in the riparian soils of Daye Lake, China

Heavy metals pose ecological and resistome risks to aquatic systems. To comprehensively assess the health status of aquatic ecosystems, it is necessary to quantify the ecological risks of heavy metals in riparian soils and their associations with microbial communities and antibiotic resistance genes (ARGs), yet related evidence was scarce. This study evaluated the potential ecological risk of heavy metal-contaminated riparian soils of Daye Lake, revealed the distribution of bacterial communities and ARGs by high-throughput sequencing techniques, and explored the association between heavy metals and bacterial communities and ARGs. The results showed that As, Cd, Cu, Pb, and Se were the primary polluting metals in the riparian soils of Daye Lake. Microbial community analysis presented that Proteobacteria (31.5%), Actinobacteria (30.3%), and Acidobacteria (14.1%) appeared to be the top three prevalent phylums, and seven pathogenic genera were identified based on VFDB. Correlation analysis showed that 17 bacterial communities among the top 50 bacterial genera had significant negative associations with heavy metals (r < -0.5; P < 0.05), and 10 bacterial communities had significant positive associations with heavy metals (r > 0.5; P < 0.05), indicating that heavy metals could exert co-selection forces on the microbial community. ARGs analysis presented that vancomycin, multidrug, and aminoglycoside resistance genes were the dominant ARGs. The co-occurrence of ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs) (r > 0.8; P < 0.05) suggested high transmission risk of ARGs in environments. The significant correlations of heavy metals and ARGs (P < 0.05), co-occurrence of the resistance genes (MRGs) and ARGs (r > 0.8; P < 0.05), and significant associations between the geochemical enrichment of heavy metals and ARGs (P < 0.05) consistently indicated important impacts of heavy metals on environmental resistome risks. This research firstly revealed the associations between heavy metals and microbial communities and ARGs in riparian soils, which offers valuable insights into risk prevention and pollution control of heavy metals in the environment.

Effects and mechanisms of reclaimed water irrigation and tillage treatment on the propagation of antibiotic resistome in soil

Reclaimed water irrigation can alleviate water resource pressure, while soil tillage is a common agricultural practice to increase crop yield. However, both of these practices may lead to the propagation of antibiotic resistance genes (ARGs). To date, there has been little research that has systematically investigated this issue. To fill this gap, this study has conducted microcosmic experiments to reveal the effect and mechanisms of using reclaimed water for irrigation and tillage treatment on the propagation of ARGs in soil, by utilizing high-throughput sequencing-based metagenomic assembly analysis approaches. The results showed irrigation significantly enhanced the abundance and diversity of ARGs in the soil. Compared to the initial soil, the total coverage of ARGs in the irrigated soil increased by 14.0 % (without tillage) to 22.7 % (with tillage). In particular, tillage treatment facilitated the enhancement of antibiotic resistome in the environment. The analysis with null model suggested soil tillage enabled ecological drift (52.4 %-66.7 %) to dominate the ARGs. Quantitative source apportionment using a machine learning-based microbial source tracking tool showed the irrigation exhibited considerable effect on the ARGs in the soil, with an average contribution of about 13.3 %-17.0 %. Network analysis revealed a close association of ARGs with mobile genetic elements (MGEs) and virulence factors, indicating potential dissemination risk of ARGs in the soil. Microbial communities, MGEs, and environmental factors collectively shaped the ARGs in the environment. Relatively, soil tillage enhanced the complex and stability of network structure and led to the colonization of ARGs in modular manner, resulting in higher contribution of ecological drift to soil resistome. Findings of this study will contribute to the management of resistome risks in reclaimed water utilization and agricultural activities for protecting soil ecosystem safety and public health.

Unveiling the critical role of overlooked consumer protist-bacteria interactions in antibiotic resistance gene dissemination in urban sewage systems

Antibiotic resistance genes (ARGs) are emerging contaminants of significant concern due to their role in facilitating the spread of antibiotic resistance, especially high-risk ARGs, which are characterized by high human accessibility, gene mobility, pathogenicity, and clinical availability. Studies have shown that cross-domain interactions, such as those between consumer protists (consumers) and bacteria, can influence bacterial diversity, distribution, and function through top-down control. The consumers-bacteria interactions may also affect the occurrence and distribution of ARGs, yet this has been scarcely explored in field investigations. We conducted a city-scale investigation of ARGs, protists, and bacterial communities across each unit of the urban sewage system (USS), including 49 sewage pumping stations (SW), as well as influent (IF), activated sludge (AS), and effluent (EF) from seven wastewater treatment plants. Interestingly, consumers-bacteria interactions, as indicated by indices of bipartite relevance networks (i.e., connectedness and cohesion), increased from SW and IF to AS and EF. Structural equation modelling (SEM) revealed that consumers-bacteria interactions had a greater influence on the abundance of total ARGs and high-risk ARGs than seasonal or environmental factors. Notably, the total effects of consumers-bacteria interactions in SEM were significant (P < 0.05) and comparable in both IF and EF, even with the decrease in ARG abundance from IF to EF. This suggests a potential risk of ARG spread to the environment, facilitated by consumer protists in the EF. Additionally, the relevance network also demonstrated an increasing trend in the relationships between consumer protists and potential hosts of high-risk ARGs from raw sewage (SW and IF) to AS and EF. Overall, this study emphasizes the importance of integrating multitrophic microbial interactions to better understand and mitigate the dissemination of ARGs in sewage systems.

Source-oriented risks of heavy metals and their effects on resistance genes in natural biofilms

Heavy metal (HM) introduction from various land-use patterns can be a major source of metal resistance genes (MRGs) entering river environments. This influx can trigger the occurrence of other resistomes, such as antibiotic resistance genes (ARGs), by improving co-resistant conjugative transfer. Biofilms, which form at water-solid interfaces, could serve as potential hotspots for HMs and resistance genes. However, the enrichment of HMs from various sources within biofilms and their effect on resistomes remain undocumented. This study aims to investigate the physicochemical properties of biofilm samples collected from the Heihui River, a tributary of the Lancang River, and to analyze the concentrations of nine HMs (As, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) within these biofilms. The 16S rRNA gene and metagenomic high-throughput sequencing techniques were integrated to uncover the association between HM accumulation levels in biofilms and ecological and health risks, considering the presence of two resistance genes. Natural sources (Co, Cr), industrial (As, Cu, V), agricultural (Cd, Ni), and transportation activities (Pb, Zn) markedly contributed to HM presence within biofilms, with industrial activities posing higher noncarcinogenic and carcinogenic risks than other sources. The network-correlation analyses revealed higher levels of ARG-MRG coexistence in biofilms, with the ecological and health risk index of HMs in biofilms closely associated with the abundance of both resistance genes. Furthermore, the biofilm As concentration markedly affected the abundance and expression of ARGs and MRGs, with elevated As levels within biofilms significantly and positively influencing all four functional categories of MRGs. Water pH also indirectly impacted these functional types by modulating the ionic form of HMs within the biofilm matrix. Our findings underscore the significance of integrating biofilms into environmental management practices and standards for assessing environmental quality.

Deciphering the pollution risks, sources and their links of heavy metals in soils

Heavy metals in soils pose serious ecological and health risks. To make efficient strategies for mitigating the underlying hazards, it is critical to reveal the pollution sources and their links with the risks. Researchers have investigated source identification and risk evaluation of heavy metals in soils, yet few have systematically deciphered the source-sink relationship of soil metals and the links between source apportionment and risk assessment. In the study, an integrated technological framework has been proposed to address the gaps, and applied to characterize the pollution risks, sources and their links of soil metals in a typical coal resource city in China. The assessment using geochemical tool and ecological risk index shows the soils in study area are polluted by Cd, Hg, Cr, As and Pb in varied degrees, and particularly, Cd and Hg present significant ecological risk. Two advanced receptor models (multivariate curve resolution-weighted alternating least-squares and multilinear engine 2) are comparatively applied for apportioning the potential sources of soil metals, and the results suggest the two models have identified similar sources (r2 > 0.90), including agricultural activities, atmospheric depositions and industrial discharges with contributions of 35.5 %-38.3 %, 30.3 %-35.1 %, and 26.6 %-34.1 %, respectively. Then, apportionment results of the two models are jointly employed for evaluating the source-specific health risks of metals in the environment using a probabilistic risk assessment model. The risk levels within the area are overall acceptable or tolerable, and relatively, the industrial discharges present higher contribution on the non-carcinogenic and carcinogenic risks of soil metals to public. Findings will help the managers to design targeted policies for reducing the risks of soil metals, and the framework proposed provides a useful guideline to better understand the source-risk relationship of soil metals in other environments worldwide.

Development of an integrated framework for dissecting source-oriented ecological and health risks of heavy metals in soils

Heavy metals (HMs) in soils pose significant risks on ecosystem and human health. To design targeted regulatory measures for mitigating and controlling the risk, it is necessary to accurately identify the pollution sources and environmental risks of soil HMs, as well as to reveal the linkages between them. To date, yet systematic investigation aimed at deciphering the links between source apportionment of soil HMs and their associated environmental risks is still lacking. To fill the gap, an integrated framework has been developed in this study and applied for dissecting the source-sink relationship and source-oriented ecological and health risks of soil HMs in Shanxi, a province with rich coal resource, in which long-term coal mining activities in history has resulted in soil HMs pollution and unavoidably posed environmental risks. Two advanced receptor models, multivariate curve resolution alternating least squares based on maximum likelihood principal component analysis (MCR-ALS/MLPCA) and multilinear engine 2 (ME2), have been employed for apportioning the potential sources, and their apportionment results are jointly incorporated into a modified ecological risk index and a probabilistic health risk assessment model for identifying the source-oriented ecological and health risks posed by soil metals. The results show that the soils in study area have been polluted by HMs (i.e., Cd, Cr, Hg and As) to varying degrees. Industrial activities (35%-35.8%), agricultural activities (11.1%-20.5%), atmospheric deposition (10.5%-13%) and mix source (31.5%-42.6%) are apportioned as the main contributors of soil HMs in the area. The source-oriented ecological risk assessment suggests Hg has presented significant ecological risk and largely contributed by the sources from atmospheric deposition and industrial activities. The source-oriented health risk assessment shows the non-carcinogenic hazard level and carcinogenic risk posed by soil HMs in the study area are acceptable. Relatively, industrial activities and mix source have contributed more on the health risks.

Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals

Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.

A critical review on the migration and transformation processes of heavy metal contamination in lead-zinc tailings of China

The health risks of lead-zinc (Pb-Zn) tailings from heavy metal (HMs) contamination have been gaining increasing public concern. The dispersal of HMs from tailings poses a substantial threat to ecosystems. Therefore, studying the mechanisms of migration and transformation of HMs in Pb-Zn tailings has significant ecological and environmental significance. Initially, this study encapsulated the distribution and contamination status of Pb-Zn tailings in China. Subsequently, we comprehensively scrutinized the mechanisms governing the migration and transformation of HMs in the Pb-Zn tailings from a geochemical perspective. This examination reveals the intricate interplay between various biotic and abiotic constituents, including environmental factors (EFs), characteristic minerals, organic flotation reagents (OFRs), and microorganisms within Pb-Zn tailings interact through a series of physical, chemical, and biological processes, leading to the formation of complexes, chelates, and aggregates involving HMs and OFRs. These interactions ultimately influence the migration and transformation of HMs. Finally, we provide an overview of contaminant migration prediction and ecological remediation in Pb-Zn tailings. In this systematic review, we identify several forthcoming research imperatives and methodologies. Specifically, understanding the dynamic mechanisms underlying the migration and transformation of HMs is challenging. These challenges encompass an exploration of the weathering processes of characteristic minerals and their interactions with HMs, the complex interplay between HMs and OFRs in Pb-Zn tailings, the effects of microbial community succession during the storage and remediation of Pb-Zn tailings, and the importance of utilizing process-based models in predicting the fate of HMs, and the potential for microbial remediation of tailings.

Source-oriented ecological and resistome risks associated with geochemical enrichment of heavy metals in river sediments

Heavy metals (HMs) pose ecological and resistome risks to aquatic systems. To efficiently develop targeted risk mitigation strategies, apportioning HM sources and assessing their source-oriented risks are essential. Although many studies have reported risk assessment and source apportionment of HMs, yet few have explored source-specific ecological and resistome risks associated with geochemical enrichment of HMs in aquatic environments. Therefore, this study proposes an integrated technological framework to characterize source-oriented ecological and resistome risks in the sediments of a plain river in China. Several geochemical tools quantitatively showed Cd and Hg had the highest pollution levels in the environment, with 19.7 and 7.5 times higher than their background values, respectively. Positive matrix factorization (PMF) and Unmix were comparatively used to apportion sources of HMs. Essentially, the two models were complementary and identified similar sources including industrial discharges, agricultural activities, atmospheric deposition and natural background, with contributions of 32.3-37.0%, 8.0-9.0%, 12.1-15.9% and 42.8-43.0%, respectively. To analyze source-specific ecological risks, the apportionment results were integratively incorporated into a modified ecological risk index. The results showed anthropogenic sources were the most significant contributors to the ecological risks. Particularly, industrial discharges majorly contributed high- (44%) and extremely high (52%) ecological risk for Cd, while agricultural activities posed a greater percentage of considerable-(36%) and high- (46%) ecological risk for Hg. Furthermore, the high-throughput sequencing metagenomic analysis identified abundant and diverse antibiotic resistance genes (ARGs), including some carbapenem-resistance genes and emerging genes such as mcr-type in the river sediments. Network and statistical analyses displayed significant correlations between ARGs and geochemical enrichment of HMs (ρ > 0.8; P-value <0.01), indicating their important impacts on resistome risks in the environment. This study provides useful insights into risk prevention and pollution control of HMs, and the framework can be made applicable to other rivers facing environmental challenges worldwide.

Soil heavy metal(loid) pollution and health risk assessment of farmlands developed on two different terrains on the Tibetan Plateau, China

The quality of farmland soils on the Tibetan Plateau is important because of the region's ecological vulnerability and their close link with local food security. Investigation on the pollution status of heavy metal (loid)s (HMs) in the farmlands of Lhasa and Nyingchi on the Tibetan Plateau, China revealed that Cu, As, Cd, Tl, and Pb were apparently enriched, with the soil parent materials being the primary sources of the soil HMs. Overall, the farmlands in Lhasa had higher contents of HMs compared to those in the farmlands of Nyingchi, which could be attributed to the fact that the former were mainly developed on river terraces while the latter were mainly developed on the alluvial fans in mountainous areas. As displayed the most apparent enrichment, with the average concentrations in the vegetable field soils and grain field soils of Lhasa being 2.5 and 2.2 times higher compared to those of Nyingchi. The soils of vegetable fields were more heavily polluted than those of grain fields, probably due to the more intensive input of agrochemicals, particularly the use of commercial organic fertilizers. The overall ecological risk of the HMs in the Tibetan farmlands was low, while Cd posed medium ecological risk. Results of health risk assessment show that ingestion of the vegetable field soils could pose elevated health risk, with children facing greater risk than adults. Among all the HMs targeted, Cd had relatively high bioavailability of up to 36.2% and 24.9% in the vegetable field soils of Lhasa and Nyingchi, respectively. Cd also showed the most significant ecological and human health risk. Thus, attention should be paid to minimize further anthropogenic input of Cd to the farmland soils on the Tibetan Plateau.

Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels

Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.

Metal-mining-induced sediment pollution presents a potential ecological risk and threat to human health across China: A meta-analysis

Aquatic sediment polluted by potentially toxic elements (PTEs) from mining activities represents a potential health "time bomb" for humans and the local ecology, but the integrated analysis of pollution and hazards of PTEs in sediment around typical metal mines in China is limited. Presently, the associated pollution status, spatial distribution, and ecological and health hazards of Cd, Cu, Zn, Pb, Cr, and As were investigated through index evaluation, spatial analysis, health risk assessment models, and Monte Carlo simulation. Overall, the sediment exhibited varying degrees of PTE contamination; notably, the level of Cd was 104.85 times higher than its background value, and it became the most enriched element in the surveyed sediment, followed in descending order by Cu, As, Zn, Pb, and Cr. Nationally, over 64.5% of metal-mining-affected sediment presented a very high ecological risk, contributed mostly by Cd (43.2%-98.7%) followed by As, Pb, and Cu; the risk contributed by both Cr and Zn was found to be negligible. The adverse health risk posed to children by most sediment was 1.72 and 6.46 times higher than that posed to adults for cancerous and noncancerous risks, respectively. The potential noncarcinogenic risks were mainly caused by As, which contributed over 78.9% of the Hazard Index values, then followed by Pb (>9.3%). For both children and adults, the carcinogenic risk of PTEs decreased in the following order: As > Cd > Cr > Pb. The investigated sediment was found seriously affected by nearby metal mines, especially those in regions with long-term and large-scale nonferrous-metal-mining activities. This study could provide a reference for policymakers to develop control strategies for PTE pollution in sediment around mining areas.

Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria

Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 10⁶ cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.