Effects of heavy metals on microbial communities in sediments and establishment of bioindicators based on microbial taxa and function for environmental monitoring and management

Pesticide and methylmercury fluxes to a marine protected region of Australia influenced by agricultural expansion

Estuarine environments provide diverse ecological services, including carbon burial and the sequestration of pollutants. Yet, urban expansion and anthropogenic activities can impact the ability of estuarine systems to retain and store pollutants, with unknown consequences for marine communities. Here, we present dated sediment cores from within the Solitarily Island Marine Park, a marine life sanctuary in Australia subject to runoff from a highly impacted catchment. We reveal historical accumulation rates of trace metals and pesticides likely associated with specific types of agricultural activities, including banana and blueberry production. Propiconazole and tebuconazole, fungicides highly reactive in marine habitats, were recorded in the sediment profile located at the site nearest the freshwater source. Furthermore, mercury content revealed elevated levels in the most recent sediments, up to 0.13 mg kg-1 in 1999, while methylmercury (MeHg) was detected ranging from 0.1 mg kg-1 in 2017 to 0.2 mg kg-1 in more recent sediments. Additionally, arsenic accumulation rates are shown here to have significantly increased from 19.1 mg m-2 year-1 in 1930 to 259.6 mg m-2 year-1 in 2020. These substances were found to be related to organic matter which was determined to be mostly of terrestrially derived sources, probably related to historical catchment deforestation, as indicated through δ13C and C:N molar ratios. This study highlights the importance in monitoring and evaluating agriculture-derived pollutant discharge to protected coastal regions and provides an initial dataset that may be used to monitor pollutant runoff in catchments impacted by expanding agricultural activities throughout Australia, and around the globe.

Microbial taxonomic diversity and functional genes mirror soil ecosystem multifunctionality in nonferrous metal mining areas

The pollution of metal ions triggers great risks of damaging biodiversity and biodiversity-driven ecosystem multifunctioning, whether microbial functional gene can mirror ecosystem multifunctionality in nonferrous metal mining areas remains largely unknown. Macrogenome sequencing and statistical tools are used to decipher linkage between functional genes and ecosystem multifunctioning. Soil samples were collected from subdams in a copper tailings area at various stages of restoration. The results indicated that the diversity and composition of soil bacterial communities were more sensitive than those of the fungal and archaeal communities during the restoration process. The mean method revealed that nutrient, heavy metal, and soil carbon, nitrogen, and phosphorus multifunctionality decreased with increasing bacterial community richness, whereas highly significant positive correlations were detected between the species richness of the bacterial, fungal, and archaeal communities and the multifunctionality of the carbon, nitrogen, and phosphorus functional genes and of functional genes for metal resistance in the microbial communities. SEM revealed that soil SWC and pH were ecological factors that directly influenced abiotic factor-related EMF; microbial diversity was a major biotic factor influencing the functional gene multifunctionality of the microbiota; and different abiotic and biotic factors associated with EMF had differential effects on whole ecosystem multifunctionality. These findings will help clarify the contributions of soil microbial diversity and functional genes to multifunctionality in degraded ecosystems.

Centennial trends in human and climate influences on sediment-associated microorganisms in an oligotrophic lake

Microorganisms in lake ecosystems exhibit sensitive and dynamic changes in response to human activities and climate change. However, studies correlating microbial communities with anthropogenic changes over a century-long timescale are currently lacking. In this study, DNA extracted from sediments and lake sediment environmental proxy analyses were employed to reconstruct a centennial-scale time series of prokaryotic and microeukaryotic community changes, revealing distinct differences in their evolutionary patterns. The results indicated that the heterogeneity of the prokaryotic community was increasing, and the community assembly was consistently influenced by both deterministic and stochastic processes. Microeukaryotes showed significant fluctuations in the relative abundance of the dominant species, a continuous increase in alpha diversity, and stochastic processes as a key mechanism of community assembly. In addition, climate and human activities were identified as key factors influencing microbial communities. It was found that the dynamics of the prokaryotic community were influenced by both biotic and environmental factors, whereas microeukaryotic population dynamics were particularly influenced by external factors. In general, changes in the watershed environment significantly impacted microbial evolutionary patterns, providing new insights into the evolution of lake ecosystems and offering strong support for future lake management and conservation efforts.

Understanding the implicit effects of 16S rRNA gene databases on microbial bioindicator studies

Analysis of the presence and the abundance of microorganisms related to diseases can be used to monitor marine environmental health. Our study evaluated the interference of taxonomic databases (SILVA, Greengenes v13.8, Greengenes2, and RDP) to monitor the distribution of bacterial genera potentially related to diseases in marine organisms (BGPRDs) from low- (Dois Rios Beach-DR), medium- (Abraão Beach-AB) and high (Guanabara Bay-GB) impacted marine environments. The frequency, richness, diversity, and composition of BGPRDs present in DR, AB and GB were significantly influenced by the different databases (p < 0.05). Consequently, the analyses revealed that the use of different databases resulted in controversial results regarding the distribution of BGPRDs in the DR, AB and GB. While Greengenes v13.8 and RDP showed that GB had the highest frequency of BGPRDs (p < 0.05), analysis based on Greengenes2 and SILVA revealed a greater frequency of BGPRDs in AB (p < 0.05). Additionally, there was no congruence of BGPRDs detected by each taxonomic database in DR, AB and GB. In highly-impacted GB, Arcobacter was the main BGPRD obtained with the Greengenes2 and RDP databases, whereas Synechococcus and Alteromonas represented the main BGPRD according to the Greengenes v13.8 and SILVA databases, respectively. Our results showed we cannot determine the exact composition and abundance of BGPRDs in low-, medium- and highly-impacted marine environments. These findings emphasize the critical influence of database choice on microbial community characterization and its implications for effective environmental monitoring and management strategies. Interestingly, alpha diversity indices of BGPRDs obtained from DR, AB and GB were consistent among the different databases and showed greater congruence than did the frequency, richness, distribution and abundance of BGPRDs. The use of diversity indices of BGPRDs can be an alternative to overcome the limitations caused by the bias of taxonomic annotations for biomonitoring marine environments.

Characterisation of Heavy Metals and Microbial Communities in Urban River Sediments: Interactions and Pollution Origin Analysis

Urbanisation has significantly impacted urban rivers, by introducing substantial amounts of heavy metals and altering microbial communities in the river sediments. This study investigated the characteristics, interactions, and pollution sources of heavy metals and microbial communities in the sediments of two typical urban rivers in Xi'an, China. The analytical results showed significant differences in heavy metal concentrations between the two rivers, with higher levels of copper, zinc, and antimony in the Chan River, and higher levels of cadmium, lead and arsenic in the Ba River. The geoaccumulation index indicated that selenium reached moderate-to-heavy pollution levels in the sediments. The microbial communities in the sediments were dominated by Proteobacteria, Firmicutes, and Actinobacteria, with similar compositions in both rivers. However, the Ba River exhibited more abundant indicator taxa. Correlation analysis revealed complex interactions between the heavy metals and the microbial communities, with copper having the most significant effect on the microbial diversity, and arsenic the least. Principal component analysis and Pearson correlation analyses identified the pollution sources of heavy metals, which were mainly influenced by agricultural activities, whereas the Chan River was primarily affected by industrial activities. This study provides scientific evidence for the environmental management and pollution control of urban rivers.

Dynamics of nitrogen-transforming microbial populations in wastewater treatment during recirculation of hydrothermal liquefaction process-water

The global reliance on non-renewable fossil fuels highlights the urgent need for sustainable alternative energy sources. Hydrothermal liquefaction (HTL) offers a promising solution by converting biomass, such as sewage sludge, into biocrude oil. However, the integration of excess HTL-process water (HTL-PW), a by-product of this process, into conventional wastewater treatment requires careful evaluation. This study investigates the effects of recirculating HTL-PW in sequencing batch reactors (SBRs) using synthetic wastewater. Two SBRs were operated in parallel: one fed 0.15 % (v/v) HTL-PW and the other with only synthetic feed. The reactor receiving HTL-PW demonstrated superior stability, effective nitrification, and consistent denitrification with no adverse effects on nitrogen species turnover. A comprehensive approach combining 16S rRNA gene amplicon sequencing for relative abundance and metagenomic analysis, for enhanced resolution of nitrogen-transforming populations, revealed the genetic repertoire and potential of 58±4 % and 65±4 % of the genus-level annotations from the HTL-PW and control reactors, respectively. The HTL-PW-fed reactor maintained robust performance, with microbial community analysis revealing a strong association between nitrogen transformations and specific microbial taxa, thereby explaining the observed reactor stability and efficiency in nitrogen conversion. These findings demonstrate the feasibility of integrating HTL-PW into wastewater treatment systems, showing that recirculating HTL-PW at the tested concentrations does not adversely affect nitrogen transformations, supports stable nitrification and denitrification, ensures complete ammonium utilisation, and promotes diverse and dynamic microbial communities similar to those in full-scale wastewater treatment plants.

Integrated rice-fish farming dynamically altered the metal resistances and microbial-mediated iron, arsenic, and mercury biotransformation in paddy soil

Given the global concern over heavy metal contamination in agricultural soil, comprehensive and in-depth investigations into the microbial ecological impacts of different agricultural practices on soil heavy metals and their biotransformation processes are both urgent and necessary. We employed metagenomic sequencing to investigate the impacts of integrated rice-fish farming on metal concentrations, metal resistance genes (MRGs), and microbial-mediated Fe, As, and Hg biotransformation processes within rice field. Our findings revealed that integrated rice-fish farming significantly reduced both the diversity and total abundance of MRGs. It also reduced the soil Al, Cd, Cu, Fe, Hg, Ni, Se, V, and Zn levels, with a marked correlation observed between metal concentration and MRGs profiles. Furthermore, integrated rice-fish farming markedly altered the microbial-mediated biotransformation processes for Fe, As, and Hg. It notably upregulated the abundance of Fe biotransformation genes, particularly those involved in the Fe gene regulation, oxidation, reduction, and storage. Biotransformation genes responsible for the As (III) oxidation and As methylation also exhibited increased abundances, along with mercury methylation and demethylation genes. Through metagenome assembled genomes (MAGs), we identified the Mycobacterium aubagnese from paddy soil which contained As oxidation genes and other multiple MRGs, exhibiting strong As remediation potential. Our findings demonstrated the potential of integrated rice-fish farming to reduce soil metal concentrations and mitigate soil metal pollution.

Microbial community structure and causal analysis in sediments of shallow eutrophic freshwater lakes under heavy metal compound pollution

Heavy metals, due to their toxicity, persistence, and non-biodegradability, have become some of the most severe environmental pollutants globally. Their accumulation in lake sediments can significantly impact aquatic ecosystems' biogeochemical cycles by altering the ecological dynamics of microbial communities. To further elucidate the mechanisms underlying microbial responses to complex heavy metal pollution in lake sediments, sediment samples were collected from Nan Yi Lake, and their physicochemical properties and microbial composition were systematically analyzed. The results demonstrated that the sediments of Nan Yi Lake were significantly contaminated with heavy metals, which were identified as the predominant factors shaping microbial community structure. Heavy metals influenced microbial richness and distribution patterns along sediment depth gradients, driving the establishment of optimal ecological niches. Meanwhile, other physicochemical factors indirectly affected microbial communities by modulating the concentration of heavy metals. Furthermore, the microbial co-occurrence network was closely associated with the concentrations of Fe and As, with sediment particle size also playing a contributing role. This study highlights the intricate interactions between physicochemical factors and microorganisms, offering critical insights into the multifaceted impacts of heavy metal compound pollution on lake ecosystems. It provides a scientific foundation for effective management of lake environmental pollution and ecological restoration efforts.

Profiling heavy metals distribution in surface sediments from the perspective of coastal industrial structure and their impacts on bacterial communities

Heavy metal pollution of marine sediments along the coastal industrial parks have always received extensive attention due to their persistent hazard to local marine ecosystem. Despite this, our knowledge about the influence of geography and coastal industrial structures on heavy metal distributions remains little. In this study, surface sediment samples were collected from the coastal zone of the industrial park in Ningbo. The physicochemical properties, heavy metals with ecological risk levels and bacterial structures as well as their relationships in these sediments were comprehensively analyzed. We found that: heavy metal concentrations of surface sediment revealed wide variation between this study sea area and other coastal economic areas; increasing attention should be paid to the Cu, Hg, Cd and As pollution due to their high contamination degree and environment risk; the distribution of heavy metals is closely related to the geographic location and nearshore industrial structures; the physicochemical features (e.g., TN, PHCs and pH) of sediments could better explain the occurrence characteristics of heavy metals present; individual metals (Cu and Cr) significantly affected the bacterial α-diversity; Cr inhibits multiple functional pathways associated with energy metabolism and pollutant degradation; RDA analysis and co-occurrence network confirmed that several heavy metals (especially Zn, Cr, Cu and Cd) exhibited large effects on bacterial community structure; moreover, genera Idiomarina Sulfurovum and Sulfurimonas could be used as biological indicators for specific heavy metals contamination in our study. Our findings provide a novel insight to understand the heavy metal distribution and bacterial variation associated with industrial activities.

Repercussions of anthropogenic activities on soil contamination: sources, distribution, and health risks of arsenic and other non-radioactive metals in urban Bangladesh

In recent decades, non-radioactive metals (n-RMs) and metalloids, notably arsenic (As), have become widespread in surface soil due to human-induced activities such as industrial operations, mining, agriculture, and untreated waste disposal. To determine the accumulation of such n-RMs in the soil content, samples were collected from an industrial area in Bangladesh and analyzed using Inductively Coupled Plasma-mass Spectrometry (ICP-MS). Results indicated that the mean concentrations (mg/kg) of n-RMs followed the order of Mn (428.84 ± 61.30 mg/kg) > Zn (119.03 ± 70.04 mg/kg) > Cr (36.80 ± 8.50 mg/kg) > Ni (34.86 ± 8.05 mg/kg) > Cu (30.56 ± 4.85 kg/kg) > Co (12.12 ± 3.31 mg/kg) > Pb (9.26 ± 3.29 mg/kg) > As (7.36 ± 5.98 mg/kg) > Hg (0.22 ± 0.19 mg/kg) > Cd (0.21 ± 0.15 mg/kg). Analysis of environmental risk assessment indices yielded low to moderate contamination throughout the study area. Enrichment factor (EF) analysis for As and Zn revealed significant levels of enrichment for these two, reflecting their heightened concentrations compared to guideline values. Results from health risk analysis indices, that is hazard quotient (HQ) and hazard index (HI), demonstrated adults to be on the safer side whereas children were prone to developing cancer from long-term exposure to As. Correlation matrix, principal component analysis (PCA), and cluster analysis (CA) suggested geogenic sources for Zn, and Mn and synthetic sources for other metals. These findings attributed the presence and accumulation of n-RMs in soil to icreased human activities in the area, which in turn facilitate their uptake by plants exposing the residents of the study site to grave health impacts. The accumulation of n-RMs poses significant risks to ecosystems, including aquatic life, crops, agricultural fields, and water reservoirs.

Interactions between riverine sediment organic matter molecular structure and microbial community as regulated by heavy metals

Heavy metals (HMs) exert a profound influence on soil carbon storage potential. The microbially-mediated association between HM content and carbon structure in riverine sediments remains unclear in lotic ecosystems. We investigated the spatiotemporal variations of HMs content, carbon content and microbial communities in riverine surface sediments, and further explored the chemical structure of sediment organic carbon (OCsed), the molecular composition of dissolved organic matter (DOM), and their interactions with microorganisms. The spatial-temporal variations in the chemical structure of OCsed, excluding O-alkyl C, were minimal, whereas the molecular composition of DOM underwent substantial fluctuations with seasons and sites. Significantly positive correlations were observed between Cu, Zn, Pb, and OCsed content. However, within a certain content range, HMs can promote the mineralization risk of OCsed, as reflected in their ability to increase the proportion of unstable O-alkyl C and decrease the proportion of stable carbon fractions (aromatic C, alkyl C, and phenolic C). Additionally, appropriate contents of HMs also improved the abundance and diversity of bacteria and fungi. Bacteria consumed more stable OC under HMs enrichment, whereas fungi increased the consumption of DOM fractions (condensed aromatic hydrocarbons and amino sugars). Our findings contribute to the understanding of the molecular mechanisms of carbon storage in HM-rich riverine sediments.

Long-term exposure to fly ash leachate enhances the bioavailability of potentially toxic metals and decreases bacterial community diversity in sediments

The interaction between microorganisms and the physicochemical properties of sediments is the key to maintaining the stability of the ecological environment. However, the effect of fly ash stockpiling on the relationship between sediment bacterial communities and their physicochemical properties remains unclear. In this study, the interactions between geophysical and chemical factors, morphological distribution of potentially toxic metals (PTMs), and bacterial community diversity in sediments affected by long-term ash water seepage were examined. The results showed that (1) Ash water seepage markedly lowered the pH and elevated the electrical conductance; available potassium, available phosphorus, organic carbon contents; small particle size (<0.25 mm), and concentrations of eight PTMs, including nickel (P < 0.05); (2) Ash water seepage considerably raised the relative abundance of Proteobacteria in the sediments, reduced bacterial community α-diversity, and altered the community structure; (3) Bacterial communities in sediments were strongly correlated with the contents of available potassium organic carbon, selenium, arsenic (oxidizable and reducible), antimony (extractable with weak acids), and chromium (extractable with weak acids); and (4) Fly ash perturbation reduced the connectivity and cohesion in the molecular ecological network of sediment bacteria and increased the abundance of pollution-degrading metabolic pathways, such as low-toxicity and organic classes, as well as coupled stimulus-response and chemotaxis-avoidance defense mechanisms. In summary, the results of this study reveal the changes in bacterial communities, major physicochemical factors, and the morphological distribution of PTMs in sediments affected by long-term ash water leakage of fly ash landfills and provides a theoretical basis for ecological environmental management.

Typical heavy metals in wastewater treatment plants in Nanjing, China: perspective of abundance, removal, and microbial response

Heavy metals (HMs) are hazardous contaminants with persistence and bioaccumulation, attracting widespread attention. Wastewater treatment plants (WWTPs) play vital roles in the pollution control of sewage, closely related to human health and the biological environment. Therefore, eight HMs in three typical WWTPs of Nanjing were determined in this study. The results revealed that Cr, Ni, Cu, and Zn were high-level HMs in all WWTPs. Notably, the highest contents of high-level HMs were found in electroplating WWTP (EWWTP) influent among three WWTPs, probably causing their higher removal (19.34-55.32%) during their primary treatment. In contrast, most HMs could be removed in the secondary treatment stage of municipal WWTP (MWWTP) and industrial WWTP (IWWTP) with the highest removal of As (72.00-85.81%). Analogously, nutrients were mainly removed during the secondary stage, with superior performance in MWWTP. A decrease in HMs removal was observed in the tertiary treatment of MWWTP and IWWTP compared to the secondary stage, while higher HMs removal (0.51-29.15%) was found in EWWTP except Hg. The highest content of HMs in sludge was Zn and Cr, which was more abundant in EWWTP than other WWTPs. The results of Illumina Miseq sequencing demonstrated the inhibition of microbial richness and diversity of EWWTP and IWWTP by industrial wastewater. Besides, alterations of microbial community structure and components were also observed owing to various influent sources. More similarity was found between EWWTP and MWWTP, in which the abundance of dominant genera, including Saccharimonadales (7.60-9.56%), Raineyella (5.06-7.38%), and Thauera (2.48-4.45%) was much higher than IWWTP.

The effects of polycyclic aromatic hydrocarbons on ecological assembly processes and co-occurrence patterns differ between soil bacterial and fungal communities

Polycyclic aromatic hydrocarbons (PAHs) are hazardous organic pollutants prevalent in soil ecosystems. Bacteria and fungi play important roles in the degradation of PAHs in the soils. However, little is known about the differences between the bacterial and fungal community assemblies in PAH-contaminated soils. In this study, soil bacterial and fungal community distributions were investigated in maize farmlands and roadside barelands around nine coking plants in Shanxi, China. Most of the soil samples were severely polluted with PAHs. A clear microbial biogeographic pattern was observed. Bacterial communities are primarily affected by environmental factors, whereas fungal communities are primarily affected by spatial factors. Null modeling showed that homogeneous selection (deterministic processes) and dispersal limitation (stochastic processes) dominated the bacterial and fungal community assemblages, respectively. PAH concentrations were closely linked to community assembly processes, and influenced microbial co-occurrence by mediating specific network modules. Overall, the effects of PAHs on bacterial community assembly and co-occurrence relationships were greater than those on fungal communities. Some microbial taxa associated with PAH degradation can be considered potential biomarkers that reflect the degree of PAH pollution. These results expand the understanding of the mechanisms underlying the assembly and maintenance of soil microbial communities in response to PAH contamination.

Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions

Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.

The responses of root exudates and microbiome in the rhizosphere of main plant and aromatic intercrops to soil Cr stress

Soil chromium (Cr) stress has a well-recognized negative impact on plant growth, and intercropping is a commonly used method to mitigate heavy metal toxicity to main plants. However, the responses of root exudates-microbial and their interactions among soil zones to soil Cr stress are always in need of clarification in intercropping system. In this study, three intercropping patterns (CT, Malus only; TM, Malus × Mentha and TA, Malus × Ageratum) with different soil Cr addition levels (NCR, LCR, HCR) were applied, and the rhizosphere ecological traits in the main plant (FRS) and intercrop (ARS) were investigated. The results indicate that intercropping with either Mentha or Ageratum has a positive effect on main plants response to soil Cr stress, and intercropping with Ageratum showing a more significant effect. Importantly, we found that the rhizosphere of main plant tends to alleviate stress by accumulating organic acids and amino acids, while aromatic plants exhibit a broader accumulation of metabolites. Additionally, we identified five core differential microbial genera. Our findings provide novel insights into intercrop Cr detoxification in the main plant.

Integrated assessment of heavy metal pollution in the great bačka canal: Comparing active and passive sampling methods

This study investigates the environmental risks posed by heavy metals in sediment from the Great Bačka Canal using both active and passive sampling methods. The necessity of this research lies in the critical need to address sediment contamination in ecological hotspots and enhance sediment management practices. Active sampling revealed total heavy metal concentrations, while sequential extraction showed bioavailability varied across metal fractions. Passive sampling with SPeeper™ quantified freely dissolved metal concentrations in sediment pore water, identifying zinc (41 μg/L) as the most bioavailable metal. Risk indices, including Igeo (geo-accumulation index) and IWCTU (interstitial water criteria toxic units), revealed low to moderate contamination levels. Although copper content classified the sediment as extremely polluted (195.7 mg/kg), its low bioavailability (16 μg/L in pore water) mitigates immediate ecological risks. These findings emphasize the importance of integrating passive sampling in regulatory frameworks for a realistic environmental risk assessment of sediments.

Key drivers of heavy metal bioavailability in river sediments and microbial community responses under long-term high-concentration pollution

Given the urgent need for effective environmental management of metal-polluted ecosystems, understanding the drivers of heavy metal bioavailability and microbial adaptation is crucial. The Dongdagou River, a major pollution source to the upper Yellow River, presents significant risks to regional water quality and biodiversity. This study investigates heavy metal bioavailability and its drivers, alongside microbial community responses, in 39 surface sediment samples from the river. The results revealed severe contamination, particularly with cadmium (Cd). Statistical analysis revealed that effective sulfur (ES) plays a crucial role in driving bioavailability. High-throughput sequencing indicated that bacterial communities were primarily dominated by Proteobacteria, with increased microbial diversity observed downstream. Functional predictions highlighted the prevalence of chemoheterotrophy and nitrogen cycling processes, alongside a significant presence of metal-resistance genes and enzymes, such as Cu-Zn superoxide dismutase and metal-efflux transporters. These adaptations imply that microbial communities are developing mechanisms of resilience in response to prolonged heavy metal exposure. These findings offer valuable insights for formulating targeted remediation strategies in environments affected by heavy metal pollution.

Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives

The mining industry in the copper belt region of Africa was initiated in the early 1900s, with copper being the main ore extracted to date. The main objectives of the present study are (1) to characterize the microbial structure, abundance, and diversity in different ecological conditions in the cupriferous city of Lubumbashi and (2) to assess the metal phytoextraction potential of Leucaena leucocephala, a main plant species used in tailing. Four ecologically different sites were selected. They include a residential area (site 1), an agricultural dry field (site 2), and an agricultural wetland (site 3), all located within the vicinity of a copper/cobalt mining plant. A remediated tailing was also added as a highly stressed area (site 4). As expected, the highest levels of copper and cobalt among the sites studied were found at the remediated tailing, with 9447 mg/kg and 2228 mg/kg for copper and cobalt, respectively. The levels of these metals at the other sites were low, varying from 41 mg/kg to 579 mg/kg for copper and from 4 mg/kg to 110 mg/kg for cobalt. Interestingly, this study revealed that the Leucaena leucocephala grown on the remediated sites is a copper/cobalt excluder species as it accumulates soil bioavailable metals from the rhizosphere in its roots. Amplicon sequence analysis showed significant differences among the sites in bacterial and fungal composition and abundance. Site-specific genera were identified. Acidibacter was the most abundant bacterial genus in the residential and remediated tailing sites, with 11.1% and 4.4%, respectively. Bacillus was predominant in both dry (19.3%) and wet agricultural lands (4.8%). For fungi, Fusarium exhibited the highest proportion of the fungal genera at all the sites, with a relative abundance ranging from 15.6% to 20.3%. Shannon diversity entropy indices were high and similar, ranging from 8.3 to 9 for bacteria and 7.0 and 7.4 for fungi. Β diversity analysis confirmed the closeness of the four sites regardless of the environmental conditions. This lack of differences in the microbial community diversity and structures among the sites suggests microbial resilience and physiological adaptations.

Mechanisms of heavy metal-induced rhizosphere changes and crop metabolic evolution: The role of carbon materials

To investigate the effects of modified carbon-based materials on soil environmental remediation and crop physiological regulation, this research relied on rice pots with lead (Pb) and cadmium (Cd) composite contamination. Dolomite, montmorillonite, attapulgite and sepiolite modified biochar with different doses have been developed to explore the mechanisms on heavy metal passivation, nutrient improvement, microbial activation, and crop growth. The results indicated that the modified materials effectively reduced heavy metal bioavailability and accumulation in plant tissues through adsorption complexation. Specifically, under montmorillonite and sepiolite modified treatments, the Grains-Pb content significantly decreased by 29.23-30.31% and 27.49-30.58%, compared to the control group (CK). Meantime, carbon-based materials increased available nutrient levels, providing a biological substrate for soil microorganisms metabolism. The content of ammonium nitrogen (NH4+-N) and available phosphorus (AP) in different proportions of montmorillonite modified biochar increased by 10.99-13.98% and 55.76-77.86%, respectively, compared to CK. Furthermore, sepiolite modified biochar enhanced bacterial community diversity, significantly improving the tolerance and resistance of bacterial communities such as Proteobacteria and Acidobacteria to heavy metals. Meanwhile, carbon-based materials enhanced community stability and network complexity, improving microbial stress resistance to adverse environments. In summary, montmorillonite and sepiolite modified biochar regulated microbial community interaction mechanisms by mitigating the physiological toxicity of heavy metals. This process enhanced soil available nutrients and ecological function stability, which had significant implications for improving crop growth and quality.

Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins

Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.

Optimized extraction methodology for phenolic compounds in soil and plant tissues: Their implications in plant growth and gall formation

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. Phenolic in soil microorganisms have the potential to impact a wide range of activities in plant-soil interactions. However, the existing methods for measuring microbial activity are typically time-consuming, intricate, and expensive. In this study, we propose modifications to the method used for the extraction and quantification of various types of phenolics in soil and plant tissues. There have been substantial advancements in research aimed at extracting, identifying, and quantifying phenolic compounds in the plant and soil samples. This study discusses the use of different methodologies in the analysis of phenolic compounds. In addition, we investigated the effect of phenolics on plant growth and cues in gall-forming under environmental disturbances.•This method is the optimum way to extract phenolic from soil and microbial activity in bulk and rhizosphere soil.•It can be used on any soil type and plant tissue, metabolites extracted from living organisms.

Multifaceted roles of zinc nanoparticles in alleviating heavy metal toxicity in plants: a comprehensive review and future perspectives

Heavy metal (HM) toxicity is a serious concern across the globe owing to their harmful impacts on plants, animals, and humans. Zinc oxide nanoparticles (ZnO-NPs) have gained appreciable attention in mitigating the adverse effects of abiotic stresses. The exogenous application of ZnO-NPs induces tolerance against HMs by improving plant physiological, metabolic, and molecular responses. They also interact with potential osmolytes and phyto-hormones to regulate the plant performance under HM stress. Moreover, ZnO-NPs also work synergistically with microbes and gene expression which helps to withstand HM toxicity. Additionally, ZnO-NPs also restrict the uptake and accumulation of HMs in plants which improves the plant performance. This review highlights the promising role of ZnO-NPs in mitigating the adverse impacts of HMs in plants. In this review, we explained the different mechanisms mediated by ZnO-NPs to counter the toxic effects of HMs. We also discussed the interactions of ZnO-NPs with osmolytes, phytohormones, and microbes in mitigating the toxic effects of HMs in plants. This review will help to learn more about the role of ZnO-NPs to mitigate HM toxicity in plants. Therefore, it will provide new insights to ensure sustainable and safer production with ZnO-NPs in HM-polluted soils.

Long-term landfill leachate pollution suppresses soil health indicators in natural ecosystems of a semi-arid environment

Landfills pose a global issue for soil functionality and health, especially in underdeveloped nations where limited resources impede the adoption of comprehensive waste management policies, such as waste processing and sorting techniques. Leachate emissions from waste landfills are a cause for concern, primarily due to their toxic effect if left uncontrolled in the environment, and the potential for waste storage sites to produce leachate for hundreds of years after closure. Few efforts have been made to improve waste collection and disposal facilities in the world, especially in developing countries. This research aims to investigate the influence of waste leachate on soil health indicators in natural woodland and rangeland ecological systems in a semi-arid mountainous region in the north of Iran. Based on results, forest unpolluted sites (2008) exhibited the highest values of nutrient elements in litter and root components. Landfills led to a rise in soil bulk density and a simultaneous decrease in soil organic matter (SOM), porosity, aggregate stability, particulate organic carbon and nitrogen (POC and PON), as well as available nutrients, ammonium (NH4+) and nitrate (NO3-) levels. Additionally, microbial parameters (respiration and biomass) and enzymes (urease, acid phosphatase, arylsulfatase and invertase) experienced a decrease in areas affected by the landfill sites over time of 2008-2023. Forest and rangeland landfill sites (2023) sites had lower density and biomass of the three earthworm groups. Acari, Collembola, nematodes, protozoans, fungi and bacteria were also reduced in landfill sites (nearly 1-2 times more in uncontaminated forest and rangeland sites). Lumbricus terrestris earthworms exhibited a clear presence in all the studied sites, and this demonstrates the ability of this earthworm species to be active in severe pollution conditions. The spatial pattern of soil cadmium and lead changes indicates the high variance of these characteristics under the influence of landfills in the study sites. Finally, the soil health indicators (according to soil physical, chemical, and biological parameters) decreased from forest unpolluted sites in 2008 to rangeland landfill sites in 2023, which is linked to the release of landfill leachate. These results are noteworthy for all countries and governments that rely on natural ecosystems for waste management without engineering operations or technical intervention. Furthermore, both governments and stakeholders must implement effective waste management systems. The research offers valuable information that can assist decision-makers engaged in sustainable solid waste management in Iran and comparable areas. Besides that, it is highly recommended to prioritize recycling and phytoremediation processes. Ultimately, worldwide efforts to achieve environmental sustainability need a significant focus on the effective management of hazardous waste. Consequently, investigations covering this topic should be continued, as they allow the evaluation of the environmental effects of the gradual accumulation of pollution in soils surrounding uncontrolled municipal solid waste landfills.

Co-pollution risk of petroleum hydrocarbons and heavy metals in typically polluted estuarine wetlands: Insights from the Xiaoqing River

Excessive accumulation of total petroleum hydrocarbons (TPH) and heavy metals (HMs) in sediments poses a significant threat to the estuarine ecosystem. In this study, the spatial and temporal distribution, ecological risks, sources, and their impacts on the microbial communities of TPH and nine HMs in the estuarine sediments of the Xiaoqing River were determined. Results showed that the spatial distribution of TPH and HMs were similar but opposite in temporal. Ni, Cr, Pb, and Co concentrations were similar to the reference values (RVs). However, the other five HMs (Cu, Zn, Cd, As, and Hg) and TPH concentrations were 2.00-763.44 times higher than RVs; hence, this deserves attention, particularly for Hg. Owing to the water content of the sediments, Hg was mainly concentrated on the surface during the wet season and on the bottom during the dry season. Moreover, because of weak hydrodynamics and upstream pollutant sinks, TPH-HMs in the river were higher than those in the estuary. TPH and HM concentrations were negatively correlated with microbial diversity. Structural equation modeling showed that HMs (path coefficient = -0.50, p < 0.001) had a negative direct effect on microbial community structure and a positive indirect effect on TPH. The microbial community (path coefficient = 0.31, 0.01 < p < 0.05) was significantly correlated with TPH. In summary, this study explores both the chemical analysis of pollutants and their interaction with microbial communities, providing a better understanding of the co-pollution of TPH and HMs in estuarine sediments.

The effect of different amendments on Cd availability and bacterial community after three-year consecutive application in Cd-contaminated paddy soils

In situ immobilization is a widely used measure for passivating Cd-contaminated soils. Amendments need to be continuously applied to achieve stable remediation effects. However, few studies have evaluated the impact of consecutive application of amendments on soil health and the microecological environment. A field experiment was conducted in a Cd-contaminated paddy (available Cd concentration 0.40 mg kg-1) on the Chengdu Plain to investigate the changes in soil Cd availability and response characteristics of soil bacterial communities after consecutive application of rice straw biochar (SW), fly ash (FM) and marble powder (YH) amendments from 2018 to 2020. Compared with control treatment without amendments (CK), soil pH increased by 0.6, 0.5 and 1.5 under SW, FM and YH amendments, respectively, and the soil available Cd concentration decreased by 10.71%, 21.42% and 25.00%, respectively. The Cd concentration in rice grain was less than 0.2 mg kg-1 under YH amendment, which was within the Chinese Contaminant Limit in Food of National Food Safety Standards (GB2762-2022) in the second and third years. The three amendments had different effects on the transformation of Cd fractions in soil, which may be relevant to the specific bacterial communities shaped under different treatments. The proportion of Fe-Mn oxide-bound fraction Cd (OX-Cd) increased by 11% under YH treatment, which may be due to the promotion of Fe(III) and Cd binding by some enriched iron-oxidizing bacteria, such as Lysobacter, uncultured_Pelobacter sp. and Sulfurifusis. Candidatus_Tenderia and Sideroxydans were enriched under SW and FM amendments, respectively, and were likely beneficial for reducing Cd availability in soil through Cd immobilization. These results revealed the significance of the bacterial community in soil Cd immobilization after consecutive application of amendments and highlighted the potential of applying YH amendment to ensure the safe production of rice in Cd-contaminated soil.

Greenhouse gas emission potential of tropical coastal sediments in densely urbanized area inferred from metabarcoding microbial community data

Although benthic microbial community offers crucial insights into ecosystem services, they are underestimated for coastal sediment monitoring. Sepetiba Bay (SB) in Rio de Janeiro, Brazil, holds long-term metal pollution. Currently, SB pollution is majorly driven by domestic effluents discharge. Here, functional prediction analysis inferred from 16S rRNA gene metabarcoding data reveals the energy metabolism profiles of benthic microbial assemblages along the metal pollution gradient. Methanogenesis, denitrification, and N2 fixation emerge as dominant pathways in the eutrophic/polluted internal sector (Spearman; p < 0.05). These metabolisms act in the natural attenuation of sedimentary pollutants. The methane (CH4) emission (mcr genes) potential was found more abundant in the internal sector, while the external sector exhibited higher CH4 consumption (pmo + mmo genes) potential. Methanofastidiosales and Exiguobacterium, possibly involved in CH4 emission and associated with CH4 consumers respectively, are the main taxa detected in SB. Furthermore, SB exhibits higher nitrous oxide (N2O) emission potential since the norB/C gene proportions surpass nosZ up to 4 times. Blastopirellula was identified as the main responsible for N2O emissions. This study reveals fundamental contributions of the prokaryotic community to functions involved in greenhouse gas emissions, unveiling their possible use as sentinels for ecosystem monitoring.

Isolation of biocrust cyanobacteria and evaluation of Cu, Pb, and Zn immobilisation potential for soil restoration and sustainable agriculture

Soil contamination by heavy metals represents an important environmental and public health problem of global concern. Biocrust-forming cyanobacteria offer promise for heavy metal immobilisation in contaminated soils due to their unique characteristics, including their ability to grow in contaminated soils and produce exopolysaccharides (EPS). However, limited research has analysed the representativeness of cyanobacteria in metal-contaminated soils. Additionally, there is a lack of studies examining how cyanobacteria adaptation to specific environments can impact their metal-binding capacity. To address this research gap, we conducted a study analysing the bacterial communities of cyanobacteria-dominated biocrusts in a contaminated area from South Sardinia (Italy). Additionally, by using two distinct approaches, we isolated three Nostoc commune strains from cyanobacteria-dominated biocrust and we also evaluated their potential to immobilise heavy metals. The first isolation method involved acclimatizing biocrust samples in liquid medium while, in the second method, biocrust samples were directly seeded onto agar plates. The microbial community analysis revealed Cyanobacteria, Bacteroidota, Proteobacteria, and Actinobacteria as the predominant groups, with cyanobacteria representing between 13.3 % and 26.0 % of the total community. Despite belonging to the same species, these strains exhibited different growth rates (1.1-2.2 g L-1 of biomass) and capacities for EPS production (400-1786 mg L-1). The three strains demonstrated a notable ability for metal immobilisation, removing up to 88.9 % of Cu, 86.2 % of Pb, and 45.3 % of Zn from liquid medium. Cyanobacteria EPS production showed a strong correlation with the removal of Cu, indicating its role in facilitating metal immobilisation. Furthermore, differences in Pb immobilisation (40-86.2 %) suggest possible environmental adaptation mechanisms of the strains. This study highlights the promising application of N. commune strains for metal immobilisation in soils, offering a potential bioremediation tool to combat the adverse effects of soil contamination and promote environmental sustainability.

Investigating the interaction of uranium(VI) with diatoms and their bacterial community: A microscopic and spectroscopic study

Diatoms and bacteria play a vital role in investigating the ecological effects of heavy metals in the environment. Despite separate studies on metal interactions with diatoms and bacteria, there is a significant gap in research regarding heavy metal interactions within a diatom-bacterium system, which closely mirrors natural conditions. In this study, we aim to address this gap by examining the interaction of uranium(VI) (U(VI)) with Achnanthidium saprophilum freshwater diatoms and their natural bacterial community, primarily consisting of four successfully isolated bacterial strains (Acidovorax facilis, Agrobacterium fabrum, Brevundimonas mediterranea, and Pseudomonas peli) from the diatom culture. Uranium (U) bio-association experiments were performed both on the xenic A. saprophilum culture and on the four bacterial isolates. Scanning electron microscopy and transmission electron microscopy coupled with spectrum imaging analysis based on energy-dispersive X-ray spectroscopy revealed a clear co-localization of U and phosphorus both on the surface and inside A. saprophilum diatoms and the associated bacterial cells. Time-resolved laser-induced fluorescence spectroscopy with parallel factor analysis identified similar U(VI) binding motifs both on A. saprophilum diatoms and the four bacterial isolates. This is the first work providing valuable microscopic and spectroscopic data on U localization and speciation within a diatom-bacterium system, demonstrating the contribution of the co-occurring bacteria to the overall interaction with U, a factor non-negligible for future modeling and assessment of radiological effects on living microorganisms.

Potential applications of microbial genomics in nuclear non-proliferation

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

Microbial mediated remediation of heavy metals toxicity: mechanisms and future prospects

Heavy metal pollution has become a serious concern across the globe due to their persistent nature, higher toxicity, and recalcitrance. These toxic metals threaten the stability of the environment and the health of all living beings. Heavy metals also enter the human food chain by eating contaminated foods and cause toxic effects on human health. Thus, remediation of HMs polluted soils is mandatory and it needs to be addressed at higher priority. The use of microbes is considered as a promising approach to combat the adverse impacts of HMs. Microbes aided in the restoration of deteriorated environments to their natural condition, with long-term environmental effects. Microbial remediation prevents the leaching and mobilization of HMs and they also make the extraction of HMs simple. Therefore, in this context recent technological advancement allowed to use of bioremediation as an imperative approach to remediate polluted soils. Microbes use different mechanisms including bio-sorption, bioaccumulation, bioleaching, bio-transformation, bio-volatilization and bio-mineralization to mitigate toxic the effects of HMs. Thus, keeping in the view toxic HMs here in this review explores the role of bacteria, fungi and algae in bioremediation of polluted soils. This review also discusses the various approaches that can be used to improve the efficiency of microbes to remediate HMs polluted soils. It also highlights different research gaps that must be solved in future study programs to improve bioremediation efficency.

Impact of soil physicochemical factors and heavy metals on co-occurrence pattern of bacterial in rural simple garbage dumping site

Rural waste accumulation leads to heavy metal soil pollution, impacting microbial communities. However, knowledge gaps exist regarding the distribution and occurrence patterns of bacterial communities in multi-metal contaminated soil profiles. In this study, high-throughput 16 S rRNA gene sequencing technology was used to explore the response of soil bacterial communities to various heavy metal pollution in rural simple waste dumps in karst areas of Southwest China. The study selected three habitats in the center, edge, and uncontaminated areas of the waste dump to evaluate the main factors driving the change in bacterial community composition. Pollution indices reveal severe contamination across all elements, except for moderately polluted lead (Pb); contamination severity ranks as follows: Mn > Cd > Zn > Cr > Sb > V > Cu > As > Pb. Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota predominate, collectively constituting over 60% of the relative abundance. Analysis of Chao and Shannon indices demonstrated that the waste dump center boasted the greatest bacterial richness and diversity. Correlation data indicated a predominant synergistic interaction among the landfill's bacterial community, with a higher number of positive associations (76.4%) compared to negative ones (26.3%). Network complexity was minimal at the dump's edge. RDA analysis showed that Pb(explained:46%) and Mn(explained:21%) were the key factors causing the difference in bacterial community composition in the edge area of the waste dump, and AK(explained:42.1%) and Cd(explained:35.2%) were the key factors in the center of the waste dump. This study provides important information for understanding the distribution patterns, co-occurrence networks, and environmental response mechanisms of bacterial communities in landfill soils under heavy metal stress, which helps guide the formulation of rural waste treatment and soil remediation strategies.

Assessment of growth, reproduction, and vermi-remediation potentials of Eisenia fetida on heavy metal exposure

Heavy metal pollution is a significant environmental concern with detrimental effects on ecosystems and human health, and traditional remediation methods may be costly, energy-intensive, or have limited effectiveness. The current study aims were to investigate the impact of heavy metal toxicity in Eisenia fetida, the growth, reproductive outcomes, and their role in soil remediation. Various concentrations (ranging from 0 to 640 mg per kg of soil) of each heavy metal were incorporated into artificially prepared soil, and vermi-remediation was conducted over a period of 60 days. The study examined the effects of heavy metals on the growth and reproductive capabilities of E. fetida, as well as their impact on the organism through techniques such as FTIR, histology, and comet assay. Atomic absorption spectrometry demonstrated a significant (P < 0.000) reduction in heavy metal concentrations in the soil as a result of E. fetida activity. The order of heavy metal accumulation by E. fetida was found to be Cr > Cd > Pb. Histological analysis revealed a consistent decline in the organism's body condition with increasing concentrations of heavy metals. However, comet assay results indicated that the tested levels of heavy metals did not induce DNA damage in E. fetida. FTIR analysis revealed various functional group peaks, including N-H and O-H groups, CH2 asymmetric stretching, amide I and amide II, C-H bend, carboxylate group, C-H stretch, C-O stretching of sulfoxides, carbohydrates/polysaccharides, disulfide groups, and nitro compounds, with minor shifts indicating the binding or accumulation of heavy metals within E. fetida. Despite heavy metal exposure, no significant detrimental effects were observed, highlighting the potential of E. fetida for sustainable soil remediation. Vermi-remediation with E. fetida represents a novel, sustainable, and cutting-edge technology in environmental cleanup. This study found that E. fetida can serve as a natural and sustainable method for remediating heavy metal-contaminated soils, promising a healthier future for soil.

Interactions between microbial communities and polymers in hydraulic fracturing water cycle: A review

Hydraulic fracturing (HF) has substantially boosted global unconventional hydrocarbon production but has also introduced various environmental and operational challenges. Understanding the interactions between abundant and diverse microbial communities and chemicals, particularly polymers used for proppant delivery, thickening, and friction reduction, in HF water cycles is crucial for addressing these challenges. This review primarily examined the recent studies conducted in China, an emerging area for HF activities, and comparatively examined studies from other regions. In China, polyacrylamide (PAM) and its derivatives products became key components in hydraulic fracturing fluid (HFF) for unconventional hydrocarbon development. The microbial diversity of unconventional HF water cycles in China was higher compared to North America, with frequent detection of taxa such as Shewanella, Marinobacter, and Desulfobacter. While biodegradation, biocorrosion, and biofouling were common issues across regions, the mechanisms underlying these microbe-polymer interactions differed substantially. Notably, in HF sites in the Sichuan Basin, the use of biocides gradually decreased its efficiency to mitigate adverse microbial activities. High-throughput sequencing proved to be a robust tool that could identify key bioindicators and biodegradation pathways, and help select optimal polymers and biocides, leading to more efficient HFF systems. The primary aim of this study is to raise awareness about the interactions between microorganisms and polymers, providing fresh insights that can inform decisions related to enhanced chemical use and biological control measures at HF sites.

Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China

The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.

Ecotoxicity evaluation using the avoidance response of the oribatid mite Oppia nitens (Acari: Oribatida) in bioplastics, microplastics, and contaminated Superfund field sites

Bioplastics are considered sustainable alternatives to conventional microplastics which are recognized as a threat to terrestrial ecosystems. However, little is known about the potential ecotoxicological effects of bioplastics on soil fauna and ecosystems. The present study assessed the toxicity of microplastics [Polystyrene (PS), Polyethylene (PE)] and bioplastics [Polyvinyl alcohol (PVA), Sodium polyacrylate (NaPa) on a key soil fauna Oppia nitens, a soil oribatid mite, and investigated the ecological relevance of O. nitens avoidance response as a valuable tool for the risk assessment of contaminated soils such as the Superfund sites. Findings showed that the mites' net response indicated avoidance behavior such that in most cases as concentrations of micro- and bioplastics increased, so did the avoidance responses. The avoidance EC50 endpoints showed PS < PE < PVA < NaPa, indicating higher deleterious effects of microplastics. High toxicity of PS in soils to O. nitens at EC50 of 165 (±25) mg/kg compared to bioplastics and other known contaminants poses an enormous threat to soil. For bioplastics in this study, there were no significant avoidances at concentrations up to 16,200 mg/kg compared to PS and PE which showed avoidance responses at 300 and 9000 mg/kg respectively, implying that bioplastics might be relatively safer to soil mites compared to conventional microplastics. Also, results indicated that long-term heavy metal pollution such as in contaminated Superfund sites decreased microbial biomass; a useful bioindicator of soil pollution. Furthermore, O. nitens avoidance of heavy metals contaminated sites demonstrated the ecological relevance of avoidance response test when assessing the habitat integrity of contaminated soil. The present study further supports the inclusion of the oribatid mite, O. nitens in the ecological risk assessment of contaminants in soil.

Ions and nanoparticles of Ag and/or Cd metals in a model aquatic microcosm: Effects on the abundance, diversity and functionality of the sediment bacteriome

Metals can be adsorbed on particulate matter, settle in sediments and cause alterations in aquatic environments. This study assesses the effect of Ag and/or Cd, both in ionic and nanoparticle (NP) forms, on the microbiome of sediments. For that purpose, aquatic controlled-microcosm experiments were exposed to an environmentally relevant and at tenfold higher doses of each form of the metals. Changes in the bacteriome were inferred by 16S rDNA sequencing. Ionic Ag caused a significant decrease of several bacterial families, whereas the effect was opposite when mixed with Cd, e.g., Desulfuromonadaceae family; in both cases, the bacteriome functionalities were greatly affected, particularly the nitrogen and sulfur metabolism. Compared to ionic forms, metallic NPs produced hardly any change in the abundance of microbial families, although the α-biodiversity of the bacteriome was reduced, and the functionality altered, when exposed to the NPs´ mixture. Our goal is to understand how metals, in different forms and combinations, released into the environment may endanger the health of aquatic ecosystems. This work may help to understand how aquatic metal pollution alters the structure and functionality of the microbiome and biogeochemical cycles, and how these changes can be addressed.

Assessing long-term ecological impacts of PCE contamination in groundwater using a flow cytometric fingerprint approach

This study aims to develop and validate a comprehensive method for assessing ecological disturbances in groundwater ecosystems caused by tetrachloroethylene (PCE) contamination, utilizing flow cytometry (FCM) fingerprint approach. We hypothesized that the ecological disturbance resulting from PCE contamination would exhibit 'press disturbance', persisting over extended periods, and inducing notable phenotypic differences in the microbial community compared to undisturbed groundwater. We collected 40 groundwater samples from industrial district with a history of over twenty years of PCE contamination, along with 56 control groundwater from the national surveillance groundwater system. FCM revealed significant alterations in the phenotypic diversity of microbial communities in PCE-contaminated groundwater, particularly during the dry season. The presence of specific dechlorinating bacteria (Dehalococcoides, Dehalogenimonas, and Geobacter) and their syntrophic partners was identified as an indicator of contamination. Phenotypic diversity measures provided clearer and more direct reflections of contamination impact compared to taxonomic diversity measures. This study establishes FCM fingerprinting as a simple, robust, and accurate method for evaluating ecological disturbances, with potential applications in early warning systems and continuous monitoring of groundwater contamination. The findings not only underscore the sensitivity of FCM in detecting phenotypic variations induced by environmental stressors but also highlight its utility in understanding the complex dynamics of microbial communities in contaminated groundwater ecosystems.

Contrasting benthic bacterial and fungal communities in two temperate coastal areas affected by different levels of anthropogenic pressure

Benthic microbial communities play a crucial role in maintaining the stability and function of estuarine ecosystems. However, their organization and response to multiple stresses in severely disturbed coastal areas remains to be elucidated. In this study, we revealed the presence of contrasting benthic bacterial and fungal communities in the Liaohe (LH) and Yalujiang (YLJ) estuaries, which are located at similar latitudes and are characterized by similar climates but are subjected to different levels of anthropogenic pressure. The results showed that Firmicutes and Chloroflexi were more abundant in LH, which reflected the influence of anthropogenic pressure in this area. Functional analyses indicated that the functional genes involved in the generation of precursor metabolites and energy pathways were more enriched in the LH community, while genes regulating degradation/utilization/assimilation processes were more enriched in the YLJ community. Distance-dependent similarity analysis showed that the bacterial community in LH was more affected by environmental changes, while that in YLJ was more influenced by geographic dispersion. In contrast, no significant distance-dependent similarity was found for the fungal communities in the two areas. In addition, the network analysis showed that the bacterial-fungal network in YLJ was more complex and stable than that in the LH. Our results highlight the important roles of environmental heterogeneity in controlling microbial community composition, biogeographic patterns, and co-occurrence networks. These findings fill knowledge gaps in the understanding of the different response patterns of benthic communities under varying anthropogenic pressures.

Impacts of cadmium accumulation on the diversity, assembly processes, and co-occurrence patterns of archaeal communities in marine sediments

There is limited understanding regarding the changes in the ecological processes and the mechanisms of archaeal community in response to heavy metal contamination in the marine sediments. In this study, sediment samples were collected from 46 locations near harbors, and the concentration of heavy metals and the diversity of archaeal communities were investigated to understand the impact of Cd on archaeal communities. The results demonstrated a significant correlation between the diversity of archaeal community and Cd concentration, particularly showing a linear decrease in the species richness with rising Cd concentration. ANME-1b was identified as a significantly enriched archaeal taxon in the higher Cd environment. Null model and neutral community model indicated that the ecological assembly of archaeal communities in marine sediments was primarily governed by the stochastic processes, with dispersal limitation being the primary factor. The contribution of deterministic process to the assembly of archaeal communities in higher Cd environments increased clearly, accompanied by a notable reduction in species migration rates and widths of ecological niche of archaeal populations. Co-occurrence network analysis revealed an obvious increase in species interactions in higher Cd environments, with an apparent rise in the proportion of competitive relationships and an increase in the number of keystone species. Moreover, archaeal species formed a more complex and stable community to cope with Cd stress. This study provides new insights into the impacts of heavy metals on the ecological processes of marine microorganisms and the underlying mechanisms.

Flooding soil with biogas slurry suppresses root-knot nematodes and alters soil nematode communities

Root-knot nematodes (RKNs) pose a serious threat to crop production. Flooding soil with biogas slurry, combined with soil heating before crop planting, has the potential for RKN disease suppression. However, the actual effect of this method has not been verified under field conditions. Here, we present the results of a two-year field experiment in a greenhouse demonstrating the control effect on RKN disease and plant growth using this method, as well as its influence on the soil nematode community. Four treatments were set: untreated control (CK), local control method for RKN (CC), soil flooded with 70 % biogas slurry (BS70), and soil flooded with undiluted biogas slurry (BS100). In the first year, all three RKN control treatments significantly reduced the root-knot index (p < 0.05). In the next year, only BS70 and BS100 still presented significantly suppressed effects (p < 0.05), and it was more obvious under BS70 with a relative control effect of 74.6 %. In the first year, BS70 and BS100 significantly inhibited the plant height of watermelon (p < 0.05). In the next year, however, all three RKN control treatments promoted the growth of watermelon, and their stem diameter was significantly greater than that of CK. The application of biogas slurry (BS70 and BS100) significantly increased nematode richness and the Shannon index in the second year (p < 0.05). However, the structure index showed no significant difference among treatments (p > 0.05), indicating that biogas slurry application did not increase the soil food web complex. Principal component analysis showed that the application of biogas slurry changed the nematode community, especially under BS70, which presented a more lasting influence. The high-level input of biogas slurry also caused soil NH4+-N and heavy-metal and arsenic accumulation in the first year, but these soil-pollution risks disappeared in the second year.

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

Effect of phenolics on soil microbe distribution, plant growth, and gall formation

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. In this study, we explore the intricate relationships between phenolics, soil microbes, and gall formation in Ageratina adenophora (A. adenophora), an invasive plant species in China known for its allelopathic traits. Using metabolomic and microbial profiling, significant differences in soil microbial composition and metabolite profiles were observed between bulk and rhizosphere soil samples. Phenolics influenced bacterial communities, with distinct microbial populations enriched in each soil type. Additionally, phenolics impacted soil metabolic processes, with variations observed in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis between different soil treatments. Analysis of phenolic content in plant and soil samples revealed considerable variations, with higher concentrations observed in certain plant tissues and soil types. Bioactive phenols extracted from plant and soil samples were identified using gas chromatography/mass spectrometry (GC-MS), providing insights into the diverse chemical composition of these compounds. Furthermore, the effects of phenolics on plant growth and gall formation were investigated. Phenols exhibited both stimulatory and inhibitory effects on plant growth, with optimal concentrations promoting emergence but higher concentrations hindering growth. Gall formation was influenced by phenolic concentrations, leading to structural alterations in stem tissue and gall morphology. Histochemical analysis revealed starch and lipid accumulation in gall tissues, indicating metabolic changes induced by phenolics. The presence of phenolics disrupted tissue structures and influenced vascular bundle orientation in gall tissues. Overall, our study highlights the multifaceted roles of phenolic compounds in soil ecosystems, plant development, and gall formation, facilitating the utilization of secondary metabolites in agriculture.

Soil amendments alter cadmium distribution and bacterial community structure in paddy soils

Soil amendments play a pivotal role in ensuring the safety of food production by inhibiting the transfer of heavy metal ions from soils to crops. Nevertheless, their impact on soil characteristics and the microbial community and their role in reducing cadmium (Cd) accumulation in rice remain unclear. In this study, pot experiments were conducted to investigate the effects of three soil amendments (mineral, organic, and microbial) on the distribution of Cd speciation, organic components, iron oxides, and microbial community structure. The application of soil amendments resulted in significant reductions in the soil available Cd content (16 %-51 %) and brown rice Cd content (16 %-78 %), facilitating the transformation of Cd from unstable forms (decreasing 10 %-20 %) to stable forms (increasing 77 %-150 %) in the soil. The mineral and organic amendments increased the soil cation exchange capacity (CEC) and plant-derived organic carbon (OC), respectively, leading to reduced Cd accumulation in brown rice, while the microbial amendment enhanced OC complexity and the abundances of Firmicutes and Bacteroidota, contributing to the decreased rice Cd uptake. The synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectroscopy indicated that soil amendments regulated soil Cd species by promoting iron oxides and OC coupling. Moreover, both organic and microbial amendments significantly reduced the diversity and richness of the bacterial communities and altered their compositions and structures, by increasing the relative abundances of Bacteroidota and Firmicutes and decreasing those of Acidobacteria, Actinobacteria, and Myxococcota. Soil microbiome analysis revealed that the increase of Firmicutes and Bacteroidota associated with Cd adsorption and sequestration contributed to the suppression of soil Cd reactivity. These findings offer valuable insights into the potential mechanisms by which soil amendments regulate the speciation and bioavailability of Cd, and improve the bacterial communities, thereby providing guidance for agricultural management practices.

Bacterial-fungal interactions and response to heavy metal contamination of soil in agricultural areas

Introduction

Long-term heavy metal contamination of soil affects the structure and function of microbial communities. The aim of our study was to investigate the effect of soil heavy metal contamination on microorganisms and the impact of different heavy metal pollution levels on the microbial interactions.

Methods

We collected soil samples and determined soil properties. Microbial diversity was analyzed in two groups of samples using high-throughput sequencing technology. Additionally, we constructed microbial networks to analyze microbial interactions.

Results

The pollution load index (PLI) < 1 indicates that the area is not polluted. 1 < PLI < 2 represents moderate pollution. PLI was 1.05 and 0.14 for the heavy metal contaminated area and the uncontaminated area, respectively. Cd, Hg, Pb, Zn, and Cu were identified as the major contaminants in the contaminated area, with the contamination factors were 30.35, 11.26, 5.46, 5.19, and 2.46, respectively. The diversities and compositions of the bacterial community varied significantly between the two groups. Compared to the uncontaminated area, the co-occurrence network between bacterial and fungal species in the contaminated area was more complex. The keystone taxa of the co-occurrence network in the contaminated area were more than those in the uncontaminated area and were completely different from it.

Discussion

Heavy metal concentrations played a crucial role in shaping the difference in microbial community compositions. Microorganisms adapt to long-term and moderate levels of heavy metal contamination through enhanced interactions. Bacteria resistant to heavy metal concentrations may play an important role in soils contaminated with moderate levels of heavy metals over long periods of time.

Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations

Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.

Microbial strategies for copper pollution remediation: Mechanistic insights and recent advances

Environmental contamination is aninsistent concern affecting human health and the ecosystem. Wastewater, containing heavy metals from industrial activities, significantly contributes to escalating water pollution. These metals can bioaccumulate in food chains, posing health risks even at low concentrations. Copper (Cu), an essential micronutrient, becomes toxic at high levels. Activities like mining and fungicide use have led to Copper contamination in soil, water, and sediment beyond safe levels. Copper widely used in industries, demands restraint of heavy metal ion release into wastewater for ecosystem ultrafiltration, membrane filtration, nanofiltration, and reverse osmosis, combat heavy metal pollution, with emphasis on copper.Physical and chemical approaches are efficient, large-scale feasibility may have drawbackssuch as they are costly, result in the production of sludge. In contrast, bioremediation, microbial intervention offers eco-friendly solutions for copper-contaminated soil. Bacteria and fungi facilitate these bioremediation avenues as cost-effective alternatives. This review article emphasizes on physical, chemical, and biological methods for removal of copper from the wastewater as well asdetailing microorganism's mechanisms to mobilize or immobilize copper in wastewater and soil.

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.

Relationships between high-concentration toxic metals in sediment and evolution of microbial community structure and carbon-nitrogen metabolism functions under long-term stress perspective

Microorganisms are highly sensitive to toxic metal pollution and play an important role in the material cycling and energy flow of the water ecosystem. Herein, 13 sediment samples from Junchong Reservoir (Guangxi Province, China) were collected in December 2021. The spatial distribution of pollution levels for toxic metals and the effects of toxic metals on the composition, functional characteristics, and metabolism of microorganisms were investigated. The results demonstrated that the area is a proximate area to industrial zones with severity of toxic metal pollution. Their mean concentrations of As, Cu, Zn, and Pb were up to 128.79 mg/kg, 57.62 mg/kg, 594.77 mg/kg, and 97.12 mg/kg respectively. There was a strong correlation between As, Cu, Zn, and Pb, with the highest correlation coefficient reaching 0.94. As the level of toxic metal pollution increases, the diversity and abundance of microorganisms gradually decrease. Compared to those with lower pollution levels, the Shannon index in regions with higher pollution levels decreases by up to 0.373, and the Chao index decreases by up to 143.507. However, the relative abundance of Bacteroidota, Patescibacteria, and Chloroflexi increased by 23%, 20%, and 5%, respectively, indicating their higher adaptability to toxic metals. Furthermore, microbial carbon and nitrogen metabolism were also affected by the presence of toxic metals. FAPROTAX analysis demonstrated an abundant reduction of ecologically functional groups associated with carbon and nitrogen transformations under high toxic metal pollution levels. KEGG pathway analysis indicated that carbon fixation and nitrogen metabolism pathways were inhibited with increasing toxic metal concentrations. These findings would contribute to a better understanding of the effects of toxic metal pollution on sediment microbial communities and function, shedding light on the ecological consequences of toxic metal contamination.