Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil

Effect of Soil Aggregate Separation Methods on the Occurrence Characteristics of Typical Pollutants

To study the distribution characteristics of typical pollutants in soil aggregates using different sieving methods, urban and arable soils were collected from Beijing and separated to different sizes by dry and wet sieving methods, to analyze present concentrations of inorganic chlorine and nine typical heavy metals (Cr, Mn, Co, Ni, Cu, Zn, Cd, As, and Pb). Results revealed that the distribution of wet-sieved aggregates was biased towards microaggregates (<250 μm), while the contrary result was found for the dry sieving method. Inorganic chlorine was more likely to be enriched in <53 μm fractions attained by both sieving methods. However, the content of inorganic chlorine in wet-sieved aggregates was significantly lower than in those that were dry sieved, which means the water’s effect on soluble ions was more pronounced. Heavy metals in urban soils were preferentially enriched in microaggregates no matter what kind of sieving method was applied. As for Mn and As found in agricultural soils using the dry sieving method, they were preferentially enriched in the fractions of 1000–2000 μm and 250–1000 μm, while the other seven heavy metals were preferentially enriched in <53 μm fractions, indicating that Mn and As in agricultural soils were easily transferred in aggregates with different particle sizes. Samples with particle sizes <53 μm showed the highest distribution factors for all heavy metals when the wet sieving method was applied. The dry sieving method resulted in a higher mass loading of heavy metals in coarser fractions and lower proportions in finer fractions. Results of a potential ecological risk analysis showed that the ecological risk (Eri) value of Cd found in aggregates by the different sieving methods was significantly different (p < 0.05). The findings suggest that different sieving methods could result in different occurrence patterns of pollutants in the soil aggregates of different land use types.

Responses of Bacterial Taxonomical Diversity Indicators to Pollutant Loadings in Experimental Wetland Microcosms

Urbanization results in higher stormwater loadings of pollutants such as metals and nutrients into surface waters. This directly impacts organisms in aquatic ecosystems, including microbes. Sediment microbes are known for pollution reduction in the face of contamination, making bacterial communities an important area for bioindicator research. This study explores the pattern of bacterial responses to metal and nutrient pollution loading and seeks to evaluate whether bacterial indicators can be effective as a biomonitoring risk assessment tool for wetland ecosystems. Microcosms were built containing sediments collected from wetlands in the urbanizing Pike River watershed in southeastern Wisconsin, USA, with metals and nutrients added at 7 day intervals. Bacterial DNA was extracted from the microcosm sediments, and taxonomical profiles of bacterial communities were identified up to the genera level by sequencing 16S bacterial rRNA gene (V3–V4 region). Reduction of metals (example: 90% for Pb) and nutrients (example: 98% for NO3−) added in water were observed. The study found correlations between diversity indices of genera with metal and nutrient pollution as well as identified specific genera (including Fusibacter, Aeromonas, Arthrobacter, Bacillus, Bdellovibrio, and Chlorobium) as predictive bioindicators for ecological risk assessment for metal pollution.

Heavy metals uptake and translocation of typical wetland plants and their ecological effects on the coastal soil of a contaminated bay in Northeast China

Heavy metal pollution in coastal zone is a global environment problem concerning the international society. As an eco-friendly and economical method, phytoremediation is a promising strategy for improving heavy metal pollution in coastal soil. In order to alleviate the ecological risk of heavy metal pollution in Jinzhou Bay, a typical and important heavy industrial area in China, three local wetland plants (Scirpus validus, Typha orientalis and Phragmites australis) were selected and planted in the field. The plants showed strong tolerance of high concentrations of heavy metals. Stressed by the heavy metals, the root weight of S. validus and P. australis increased 114.74% and 49.91%, respectively. The concentrations of heavy metals (Cd, Cr, Cu, Ni, Pb, Zn, As, Hg) accumulated in the plant roots were 4-60 times higher than that in plant shoots. The SEM analysis found that abundant heavy metals were adhered to the root surface closely. Bioconcentration factor of heavy metals on the plant roots were 0.08-0.89 (except Cr, Ni), while the translocation factor from roots to above ground of plants were 0.02-0.27. Furthermore, the wetland plants improved the regional ecological environment quality. The concentrations of heavy metals in the rhizosphere soil decreased significantly. Compared with the bulk soil, the potential ecological risk index in the rhizosphere soil reduced 26.51%-69.14%. Moreover, the microbial diversity in rhizosphere soil increased significantly, and the abundances of Proteobacteria and Bacteroidetes also increased in rhizosphere soil. Pearson correlations indicated that Hg, As, Ni and Cr were negatively correlated with Proteobacteria (p < 0.05), and Cu was significantly negative correlated with Bacteroidetes (p < 0.05). The results support that using suitable local plants is a promising approach for repairing heavy metal contaminated costal soil, not only because it can improve the regional ecological environment quality, but also because it can enhance the landscape value of coastal zone.

Can moderate heavy metal soil contaminations due to cement production influence the surrounding soil bacterial communities?

Events of soil contamination by heavy metals are mostly related to human activities that release these metals into the environment as emissions or effluents. Among the industrial activities related to heavy metal pollution, cement production plants are considered one of the most common sources. In this work we applied the High-throughput sequencing approach called 16 S rDNA metabarcoding to perform the taxonomic characterization of the prokaryotic communities of the soil surrounding three cement plants as well as two areas outside the influence of the cement plants that represented agricultural production environments free of heavy metal contamination (control areas). We applied the environmental genomics approaches known as "structural community metrics" (α- and β-diversity metrics) and "functional community metrics" (PICRUSt2 approach) to verify whether or not the effects of heavy metal contamination in the study area generated impacts on soil bacterial communities. We found that the impact related to the elevation of heavy metal concentration due to the operation of cement plants in the surrounding soil can be considered smooth according to globally recognized indices such as Igeo. However, we identified that both the taxonomic and functional structures of the communities surrounding cement plants were different from those found in the control areas. We consider that our findings contribute significantly to the general understanding of the effects of heavy metals on the soil ecosystem by showing that light contamination can disturb the dynamics of ecosystem services provided by soil, specifically those associated with microbial metabolism.

Streptomyces pactum and Bacillus consortium influenced the bioavailability of toxic metals, soil health, and growth attributes of Symphytum officinale in smelter/mining polluted soil

Soil microbes influence the uptake of toxic metals (TMs) by changing soil characteristics, bioavailability and translocation of TMs, and soil health indicators in polluted environment. The potential effect of Streptomyces pactum (Act12) and Bacillus consortium (B. subtilis and B. licheniformis; 1:1) on soil enzymes and bacterial abundance, bioavailability and translocation of Zn and Cd by Symphytum officinale, and physiological indicators in soil acquired from Fengxian (FX) mining site. Act12 and Bacillus consortium were applied at 0 (CK), 0.50 (T1), 1.50 (T2), and 2.50 (T3) g kg^-1 in a split plot design and three times harvested (H). Results showed that soil pH significantly dropped, whereas, electrical conductivity increased at higher Act12 and Bacillus doses. The extractable Zn lowered and Cd increased at each harvest compared to their controls. Soil β-glucosidase, alkaline phosphatase, urease and sucrase improved, whereas, dehydrogenase reduced in harvest 2 and 3 (H2 and H3) as compared to harvest 1 (H1) after Act12 and Bacillus treatments. The main soil phyla individually contributed ∼5-55.6%. Soil bacterial communities' distribution was also altered by Act12 and Bacillus amendments. Proteobacteria, Acidobacteria, and Bacteroidetes increased, whereas, the Actinobacteria, Chloroflexi, and Gemmatimonadetes decreased during the one-year trial. The Zn and Cd concentration significantly decreased in shoots at each harvest, whereas, the roots concentration was far higher than the shoots, implicating the rhizoremediation by S. officinale. Accumulation factor (AF) and bioconcentration ratio (BCR) of Zn and Cd in shoots were lower and remained higher in case of roots than the standard level (≥1). BCR values of roots indicated that S. officinale can be used for rhizoremediation of TMs in smelter/mines-polluted soils. Thus, field trials in smelter/mines contaminated soils and the potential role of saponin and tannin exudation in metal translocation by plant will broaden our understanding about the mechanism of rhizoremediation of TMs by S. officinale.

Effects of virgin microplastics on the transport of Cd (II) in Xiangjiang River sediment

River sediments are considered as sinks of microplastics (MPs). Although numerous studies have been conducted on MPs pollution in river sediments, the impact of MPs on the environmental behavior of Cd (II) in river sediments is still unknown. In this work, the effects of six MPs (polyethylene, polypropylene, polystyrene, polyvinyl chloride, polymethyl methacrylate and polylactic acid) on the adsorption of Cd (II) by Xiangjiang River sediment and the transport of Cd (II) in sediment were studied. The results showed that the adsorption ability of sediment to Cd (II) decreased with the increase of the content of MPs in sediment. When the content of MPs in sediment increased to 10%, polypropylene had the greatest effect on the adsorption affinity of sediments to Cd (II). Moreover, the addition of MPs accelerated transport of Cd (II) in sediment, and the transport of Cd (II) in sediment increased with the increase of the content of MPs. The reason may be that after adding MPs, the adsorption capacity of sediment to Cd (II) decreases, and the mass transfer resistance of Cd (II) to sediment reduces, which leads to faster transport of Cd (II) in sediment. Especially, when the content of MPs in sediment increased to 10% (w/w), the saturation point of the breakthrough curve decreased by about 70 pore volumes. This work hopes to provide helpful views on the environmental behavior and risk assessment of Cd (II) in the presence of MPs.

Sheltering Role of Well-Decayed Conifer Logs for Forest Floor Fungi in Long-Term Polluted Boreal Forests

Coarse woody debris (CWD) provides food and shelter to a large proportion of forest biota and is considered vital for biodiversity during periods of harsh weather. However, its importance in long-term stressed ecosystems remains largely unknown. In this work, we explored the contribution of CWD to fungal diversity along the gradient of boreal forest degradation caused by 77 years of heavy industrial emissions. We analyzed the diversity and composition of fungi in 270 samples of well-decayed Picea abies and Abies sibirica logs, as well as forest litter both adjacent to and distant from the logs. Compared with forest litter, the wood had higher water content and possessed substantially lower concentrations of heavy metals, which suggests its potential favorability for biota in polluted areas. The pollution-induced loss of fungal diversity in forest litter reached 34% and was stronger in the microhabitats not influenced by CWD. Meanwhile, wood fungal communities lost less than 10% of their total richness and even increased in alpha diversity. These processes led to the diversity and compositional convergence of fungal communities from different microhabitats and substrates in polluted areas. Despite this, the importance of wood and CWD-influenced microhabitats for fungal diversity maintenance was low. Apart from wood-associated fungi, the taxa whose diversity increased in the wood of polluted areas were ectomycorrhizal fungi and eurytopic soil saprotrophs (Mucoromycota, Mortierellomycota, Eurotiomycetes, and Helotiales) that easily tolerate highly toxic litter. Within the majority of pollution-sensitive soil saprotrophic groups, only terricolous Tricholomataceae benefit from CWD as microrefugia. Upon considering the ecological variability within low-rank taxa, the importance of decayed logs as safe sites can be high for certain soil-inhabiting fungal groups in polluted areas.

Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China

The mining, smelting, manufacturing, and disposal of vanadium (V) and associated products have caused serious environmental problems. Although the microbial ecology in V-contaminated soils has been intensively studied, the impacted watershed ecosystems have not been systematically investigated. In this study, geochemistry and microbial structure were analyzed along ~30 km of the Jinsha River and its two tributaries across the industrial areas in Panzhihua, one of the primary V mining and production cities in China. Geochemical analyses showed different levels of contamination by metals and metalloids in the sediments, with high degrees of contamination observed in one of the tributaries close to the industrial park. Analyses of the V4 hypervariable region of 16S rRNA genes of the microbial communities in the sediments showed significant decrease in microbial diversity and microbial structure in response to the environmental gradient (e.g., heavy metals, total sulfur, and total nitrogen). Strong association of the taxa (e.g., Thauera, Algoriphagus, Denitromonas, and Fontibacter species) with the metals suggested selection for these potential metal-resistant and/or metabolizing populations. Further co-occurrence network analysis showed that many identified potential metal-mediating species were among the keystone taxa that were closely associated in the same module, suggesting their strong inter-species interactions but relative independence from other microorganisms in the hydrodynamic ecosystems. This study provided new insight into the microbe-environment interactions in watershed ecosystems differently impacted by the V industries. Some of the phylotypes identified in the highly contaminated samples exhibited potential for bioremediation of toxic metals (e.g., V and Cr).

Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States

The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know. To fill this knowledge gap, we present a comprehensive analysis of gut bacteria associated with wild cotton mice (Peromyscus gossypinus) trapped from several areas affected by legacies of HM and radionuclide contamination. We explore how these contaminants affect gut microbial community (GMC) composition and diversity and the enrichment of antibiotic, biocide, and metal resistance genes. Although we were able to identify that a myriad of co-occurring antimicrobial and HM resistance genes appear in mice from all areas, including those without a history of contamination, the proportions of co-occurring ARGs and metal resistance genes (MRGs) are higher in sites with radionuclide contamination. These results support those from several previous studies and enhance our understanding of the coselection process, while providing new insights into the ubiquity of antimicrobial resistance in the resistome of wild animals. IMPORTANCE Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics. However, previous studies have demonstrated that the spread of antibiotic resistance genes can also be influenced by heavy metal contamination. This coselection phenomenon, whereby different resistance determinants are genetically linked on the same genetic element (coresistance) or a single genetic element provides resistance to multiple antimicrobial agents (cross-resistance), has profound clinical and environmental implications. In contrast to antibiotics, heavy metals can persist in the environment as a selection pressure for long periods of time. Thus, it is important to understand how antibiotic resistance genes are distributed in the environment and to what extent heavy metal contaminants may be driving their selection, which we have done in one environmental setting.

Identification of Cd-resistant microorganisms from heavy metal-contaminated soil and its potential in promoting the growth and Cd accumulation of bermudagrass

Phytoremediation has been increasingly used as a green technology for the remediation of heavy metal contaminated soils. Microorganisms could enhance phytoremediation efficiency by solubilizing heavy metal and improve plant growth by producing phytohormones in the heavy metal contaminated soils. In this study, we investigated the abundance and composition of soil microbial communities in heavy metal contaminated soils. Furthermore, we identified a Cd-resistant fungal strain Penicillium janthinellum ZZ-2 and assessed its potential in improving plant growth, Cd accumulation and Cd tolerance in bermudagrass. The results indicated that long-term heavy metal pollution decreased microbial biomass and activity by inhibiting microbial community diversity, but did not significantly affect community composition. Mainly, the relative abundance of some specific bacterial and fungal taxa, such as Actinobacteria, Chloroflexi, Bacteroidetes, Ascomycota and Basidiomycota, changes under metal pollution. Furthermore, at genus level, certain microbial taxa, such as Pseudonocardiaceae, AD3, Latescibacteria, Apiotrichum and Paraboeremia, only exist in polluted soil. One Cd-resistant fungus ZZ-2 was isolated and identified as Penicillium janthinellum. Further characterization revealed that ZZ-2 had a greater capacity for Cd²⁺ absorption, produced indole-3-acid (IAA), and facilitated plant growth in the presence of Cd. Interestingly, ZZ-2 inoculation significantly increased Cd uptake in the stem and root of bermudagrass. Thus, ZZ-2 could improve plant growth under Cd stress by reducing Cd-toxicity, increasing Cd uptake and producing IAA. This study suggests a novel fungus-assisted phytoremediation approach to alleviate Cd toxicity in heavy metals contaminated soils.

Stress causes interspecific facilitation within a compost community

Ecological theory predicts interactions between species to become more positive under abiotic stress, while competition should prevail in more benign environments. However, experimental tests of this stress gradient hypothesis in natural microbial communities are lacking. We test this hypothesis by measuring interactions between 10 different members of a bacterial community inhabiting potting compost in the presence or absence of toxic copper stress. We found that copper stress caused significant net changes in species interaction signs, shifting the net balance towards more positive interactions. This pattern was at least in part driven by copper-sensitive isolates - that produced relatively small amounts of metal-detoxifying siderophores - benefitting from the presence of other species that produce extracellular detoxifying agents. As well as providing support for the stress gradient hypothesis, our results highlight the importance of community-wide public goods in shaping microbial community composition.

Study on the spatial distribution of ureolytic microorganisms in farmland soil around tailings with different heavy metal pollution

Ureolytic microorganisms, a kind of microorganism which can secrete urease and decompose urea, have great potential in remediation of soil heavy metals based on microbial induced carbonate precipitation. However, the horizontal and vertical distribution of ureolytic microbial community in heavy metals contaminated soils is poorly understood. In this study, urease genes in agricultural soils surrounding tailings were first investigated using metagenomic in two dimensions: heavy metal pollution (Low-L, Middle-M, High-H) and soil depth (0-20 cm, 20-40 cm, 40-60 cm, 60-80 cm, 80-100 cm). Results showed that the effect of heavy metal concentration on ureolytic microorganisms was indeed significant, while the changes of ureolytic microorganisms with increasing soil depth varied in the vertical direction at the same level of heavy metal contamination. H site had the highest diversity of ureolytic microorganisms except for the topsoil. And at the same heavy metal contamination level, the ureolytic microbial diversity was lower in deeper soils. Proteobacteria, Actinobacteria and Thaumarchaeota (Archaea) were the dominant phyla of ureolytic microorganisms in all three sites, accounting for more than 80% of the total. However, the respond to the heavy metal concentrations of three phyla were different, which were increasing, decreasing and essentially unchanged, respectively. Besides, other environmental factors such as SOM and pH had different effects on ureolytic microorganisms, with Proteobacteria being positively correlated and Actinobacteria being the opposite. Another phenomenon was that Actinobacteria and Verrucomicrobia were biomarkers of group L, which could significantly explain the difference with the other two sites. These results provided valuable information for further research on the response mechanism and remediation of heavy metal pollution by ureolytic microbial system.

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

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

Bradyrhizobium sp. sv. retamae nodulates Retama monosperma grown in a lead and zinc mine tailings in Eastern Morocco

The aim of this work was to characterize and identify some bacteria isolated from the root nodules of Retama monosperma grown in Sidi Boubker lead and zinc mine tailings. Very few root nodules were obtained on the root nodules of R. monosperma grown in these soils. The three bacteria isolated from the root nodules were tolerant in vitro to different concentrations of heavy metals, including lead and zinc. The rep-PCR experiments showed that the three isolates have different molecular fingerprints and were considered as three different strains. The analysis of their 16S rRNA gene sequences proved their affiliation to the genus Bradyrhizobium. The analysis and phylogeny of the housekeeping genes atpD, glnII, gyrB, recA, and rpoB confirmed that the closest species was B. valentinum with similarity percentages of 95.61 to 95.82%. The three isolates recovered from the root nodules were slow-growing rhizobia capable to renodulate their original host plant in the presence of Pb-acetate. They were able to nodulate R. sphaerocarpa and Lupinus luteus also but not Glycine max or Phaseolus vulgaris. The phylogeny of the nodA and nodC nodulation genes as well as the nifH gene of the three strains showed that they belong to the symbiovar retamae of the genus Bradyrhizobium. The three strains isolated could be considered for use as inoculum for Retama plants before use in phytoremediation experiments.

Endophyte Pseudomonas putida enhanced Trifolium repens L. growth and heavy metal uptake: A promising in-situ non-soil cover phytoremediation method of nonferrous metallic tailing

Non-soil cover phytoremediation is the most promising method for high heavy metal contaminated, pH imbalanced and oligotrophic tailing remediation. In this study, a promising method of tailing non-soil cover phytoremediation by endophyte assisting Trifolium repens L. was established. Endophytic Pseudomonas putida strain RE02, with great heavy metal detoxification ability, could colonize in both rhizosphere and endosphere of roots. With RE02 inoculation, the germination percentage of Trifolium repens L. seeds was improved form 40.33%, 45.33% and 56.67%-60.00%, 57.00% and 73.33% in 20 mg/kg Cd, 20 mg/kg Cr and 100 mg/kg Pb contained tailing. The LC50 (concentrations causing 50% mortality of seedlings) and IC50 (concentrations inhibiting the dry biomass by 50%) of Cd, Cr and Pb increased by 6.62, 4.87, 6.27, 4.28, 22.18 and 22.63 mg/kg respectively. Moreover, RE02 inoculation improved soil fertility that the available P and available K was dramatically enhanced in endophyte inoculated groups. Thus, plant NPK concentration was significantly enhanced by 16.72%, 30.55% and 3.81% respectively, and the total heavy metal uptake by 30.03-574.58%. Taken together, Trifolium repens L. successfully grew and developed in heavy metal contaminated, oligotrophic and pH imbalanced tailing, realizing non-soil cover phytoremediation by RE02 inoculation. Overall, this study provided a feasible and promising method for in-situ non-soil cover phytoremediation of tailing, laying a foundation for ecological restoration of tailing.

Application of enzymes as a diagnostic tool for soils as affected by municipal solid wastes

Assessing the relationship between soil enzyme activities (SEAs) and heavy metals (HMs) without any amendment has rarely been conducted in soils contaminated with municipal solid wastes (MSW). Five soil enzymes [dehydrogenase (DHA), alkaline phosphatase (ALP), acid phosphatase (ACP), urease (UR), and nitrate reductase (NR)] have been assessed for HMs bioremediation using Zea mays L. grown in unamended soils that were contaminated with different types of MSW. Pot experiment was conducted for two seasons with soils collected from seven different locations within the MSW site. Experimental soil samples included a control (CA), contaminated by brick kiln wastes (SA1), kitchen and household wastes (SA2), medical wastes (SA3), mixed wastes (SA4), glass wastes (SA5), and metal scrap wastes (SA6). Rhizospheric soils were collected after the harvest of each season to investigate the impact of HMs on SEAs and physicochemical properties of soil. The results revealed an increase in DHA, ALP, and NR activities by 89.30%, 58.03% and 21.98% in SA1. Likewise, enhanced activities for UR (28.26%) and ACP (19.6%) were observed in SA3 and SA5 respectively. Insignificant increase in the macronutrients and organic carbon (OC) were also noted. The increased microbial count and the relatively higher amount of organic matter (OM) in the rhizosphere indicated the role of OM in HMs immobilization. Principal component analysis (PCA) indicated that DHA and NR are the important soil enzymes, underscored by their active involvement in the C and N turnover in the soil. Likewise, correlation analysis showed that DHA and NR activities were positively correlated with copper (Cu) (0.90, p < 0.01; 0.88, p < 0.01), suggesting its participation as a cofactor in enzymatic activities. In contrast, DHA was negatively correlated with cadmium (Cd) (-0.48, p < 0 0.05). Finally, these results indicated that in the absence of exogenous nutrient amendment, the SEAs were governed by OC, available nitrogen (Avl. N), Cu and Cd respectively. The study also highlighted the need for extensive research on SEAs for its utilization as a bioindicator in various soil bioremediation and quality management practices.

The effects of vehicular emissions on the activity and diversity of the roadside soil microbial community

Motor vehicles emit a variety of pollutants including metals, petroleum hydrocarbons and polycyclic aromatic hydrocarbons (PAHs). The relationships between metals, petroleum hydrocarbons and PAHs, soil respiration and microbial diversity (fungi and bacteria) were studied using control (n = 3) and roadside soils (n = 27) with different exposure periods to vehicle emissions (2-63 years). Bacterial diversity was found to be higher than control sites (P = 0.002) but was the same across different categories of road age (P = 0.328). Significant (r = -0.49, P = 0.007) contrasting behaviour of fungal and bacterial diversity was reported, with diversity increasing across all road types for bacteria and decreasing across all road types for fungi compared to control soils. Analysis of the bacterial community identified three distinct clusters, separated on age of contamination, suggesting that roadside bacterial communities change over time with pollution from vehicles with the potential development of metal resistant bacteria in roadside soils. In contrast, for fungal communities, a reduction in diversity with time of exposure to roadside vehicle emissions was observed suggesting the potential for reduced ecosystem functionality and soil health in roadside soils. This is the first study in the published literature to include both bacterial and fungal responses from aged roadside soils. The results from this study suggest that normal functionality of soil ecosystem services is being affected in roadside soils, potentially globally.

Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

Response of carbon and microbial properties to risk elements pollution in arctic soils

A 180-day incubation study was conducted to evaluate the effects of risk elements (REs) on organic carbon use and microbial activities in organic soils in the Arctic during the summer snowmelt period. Soils were artificially spiked with Cd, Pb, Cr, Ni, Cu, As, and a combination of these REs according to the levels measured in Arctic soils from REs-polluted industrial sites. During the incubation period, microbial activities and microbial biomass carbon (MBC) formation were inhibited, and microbial quotient (qCO2) values were relatively high in the spiked soils indicating that more energy was used by microbes for maintenance under REs stress. Meanwhile, microbial metabolism was significantly restrained. Microbial Specific phospholipid fatty acids (PLFAs) were reduced in RE spiked soils relative to the control, especially in the As- and multi-RE-spiked soils. The abundance of both fungi and bacteria was reduced in response to RE amendments by 14-24% and 1-55%, respectively. PLFA biomarkers indicated a shift in soil microbial community structure and activities influenced by REs, consequently having a negative effect on soil organic carbon degradation. This study addresses the knowledge gap regarding the alternation of biochemical reactions in Arctic soils under anthropogenic REs with relevant contamination levels.

Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area

Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.

Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China

BACKGROUND

The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils.

METHODS

In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively.

RESULTS

The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potassium (K) significantly affected fungal community composition in park soils in Shanghai. Soil available Zn was also the most important factor affecting the bacterial community composition in this study.

CONCLUSION

There were significant differences in the soil molecular biomass, fungal abundance, and the community composition and co-occurrence relations of both soil bacterial and fungal communities between urban and suburban park soils. Soil available Zn played an important part in shaping the structures of both the bacterial and fungal communities in park soils in Shanghai.

Cadmium stress causes differential effects on growth and the secretion of carbon-degrading enzymes in four mycorrhizal basidiomycetes

We hypothesised that cadmium exposure would hinder growth and secretion of carbon-degrading enzymes by mycorrhizal fungi, and that this would vary according to their tolerance to cadmium stress. The enzymes measured were β-Glucosidase, β-Xylosidase, β-D-cellubiosidase, N-acetyl-β-Glucosaminidase in three strains of ectomycorrhizal fungi Hebeloma subsaponaceum, Scleroderma sp., Hebeloma sp. and a feremycorrhizal fungus Austroboletus occidentalis. Fungi were subjected to cadmium stress for 28 d (in modified Melin-Norkrans liquid medium). The results showed unanticipated differential response of enzyme activities among the fungal species, including potential hormesis effects. Austroboletus occidentalis showed an increase in enzyme activity under cadmium stress.

Altered fungal communities in contaminated soils from French industrial brownfields

Polycyclic aromatic hydrocarbons (PAHs) and metals are contaminants of industrial brownfield soils. Pollutants can have harmful effects on fungi, which are major actors of soil functioning. Our objective was to highlight fungal selection following long-term contamination of soils. Fungal diversity was assessed on 30 top-soil samples from ten sites gathered in three groups with different contamination levels and physico-chemical characteristics: 1) uncontaminated controls, 2) slag heaps displaying high PAH and moderate metal contaminations, and 3) settling ponds displaying high metal and intermediate PAH contaminations. Although fungal abundance and richness were similar among the soil groups, the diversity and evenness indices were lower for the slag heap group. Fungal diversity differed among soil groups at the phylum and OTU levels, and indicator species were identified. The relative abundance of Agaricomycetes, Saccharomycetes, Leotiomycetes and Chytridiomycota was higher in the control soils than in the two groups of contaminated soils. Cryptomycota LKM11 representatives were favoured in the slag heap and settling pond groups, and their relative abundance was correlated to the zinc and lead contamination levels. Dothideomycetes - positively linked to PAH contamination - and Eurotiomycetes were specific to the slag heap group. Pucciniomycetes and especially Gymnosporangium members were favoured in the settling pond soils.

Recent Advances in the Chemistry of Bioactive Compounds from Plants and Soil Microbes: a Review

Bioactive compounds derived from plants and microbial sources are required for the survival of the human race and groundbreaking research must continue in this line. Plants and microbes are the major sources of naturally occurring bioactive compounds for numerous biotechnological applications. Recent progress in the fields of bioactive compounds and soil chemistry in agriculture has since given man a lead to the discovery of potent drugs that combat both human and plant diseases. The soil provides the medium for the growth of medicinal plants, but its contamination greatly affects the quality of drugs, food crops, and other essential elements present in the plants which give strength to the body. This area has attracted the attention of scientists and the drug industry toward developing more potent drugs from medicinal plants grown in different soil. The studies of the effect of various parameters and the properties of soil such as; effect of heavy metals, pH, soil organic matter, and phytoremediation process have given a measure of some quality dependence of the soil producing secondary metabolites and soil containing microbes. The information provided will be useful in determine the action of microbes and their interaction with the soil and all true plants producing drugs. Some active compounds in plants and microbes, their properties, and applications have been described in this review. The soil microbes, activities and their interactions, effects of soil particle size, dispersibility and stability of microbes in the soil, and the future outlook for the development of novel active compounds have been reported.

Trifolium repens L. regulated phytoremediation of heavy metal contaminated soil by promoting soil enzyme activities and beneficial rhizosphere associated microorganisms

Rhizosphere soil physiochemical properties, enzyme activities and rhizosphere associated microbial communities are of the central importance for modulating phytoremediation in heavy metal contaminated soil. In this study, the rhizosphere micro-ecological characteristics of phytoremediation in seven groups of contaminated soil with different heavy metal species and concentrations were examined. The results showed that heavy metal-enrichment inhibited plant growth, but enhanced both anions (Cr₂O₇^2-) and cations (Cd²⁺ and Pb²⁺) uptake with corresponding mean values ranging from 19.37 to 168.74 mg/kg in roots and 10.89-86.53 mg/kg in shoots. Trifolium repens L. planting was able to compensate the lost caused by the heavy metal on the soil organic matter, available N, available P, available K and enzyme activities as well. According to the cluster, some species like Lysobacter, Kaistobacter and Pontibacter, was significantly related to heavy metal accumulation while others such as Flavisolibacter, Adhaeribacter and Bacillus promoted plant growth. The importance of root-associated microbial community could relatively regulate plant growth and heavy metal uptake. Our study not only illustrated the correlation among rhizosphere micro-ecological parameters, and the possible mechanisms of phytoremediation regulation, but also provide clear strategy for improving the phytoremediation efficiency.

On-line monitoring of repeated copper pollutions using sediment microbial fuel cell based sensors in the field environment

Most microbial fuel cells (MFCs) based sensors rely on exoelectrogenic bacteria to sense contaminants. However, these sensors cannot monitor repeated pollutions unless the exoelectrogenic bacteria are recovered or re-inoculated. To overcome this drawback, a novel sediment microbial fuel cell (SMFC) based sensor was developed for online and in situ monitoring of repeated Cu²⁺ shocks to the overlaying water of paddy soil. The SMFC sensor was operated for a period of eight months in the field environment and a group of CuCl₂ solutions ranging from 12.5 to 400 mg L^-1 Cu²⁺ were repeatedly applied on sunny and rainy days in different seasons. Results show that the SMFC sensor generates one voltage peak in less than 20 s after each Cu²⁺ shock, regardless of the seasons and weather conditions, and the voltage increments from baseline to peak exhibit linear correlation (R² > 0.92) with the logarithm of Cu²⁺ concentrations. Repeated Cu²⁺ pollutions do not decrease the baseline voltage, indicating that the activity of exoelectrogenic bacteria was not significantly inhibited. Soil adsorbed and inactivated approximately 99% of total Cu²⁺. Only 1% of total Cu²⁺ was the toxic exchangeable fraction, of which the concentrations were 0.73, 0.23, and 0.22 mg kg^-1 in the surface (0-3 cm), middle (3-6 cm), and bottom (6-11 cm) layers, respectively. The abundance of 16S rRNA gene transcripts of exoelectrogenic bacteria-associated genera is the lowest in the surface layer (2.86 × 10¹¹ copies g^-1) and the highest in the bottom layer (7.99 × 10¹¹ copies g^-1). Geobacter, Clostridium, Anaeromyxobacter, and Bacillus are the most active exoelectrogenic bacteria-associated genera in the soil. This study suggests that the SMFC sensor could be applied in wetlands to monitor the repeated discharge of Cu²⁺ and other heavy metals.

Bioavailable metal(loid)s and physicochemical features co-mediating microbial communities at combined metal(loid) pollution sites

Heavy metal contamination poses considerable threats to various ecosystems, yet little is known about the assembly and adaptation of microbial communities at sites with combined heavy metal(loid) pollution. Here, we examined metal(loid) pollutants and bacterial communities in three zones (Zones Ⅰ, Ⅱ, and Ⅲ) of an abandoned sewage reservoir with different usage years. The contamination level of multiple metal(loid)s was higher in Zone Ⅰ than in the other zones, and arsenic (As), zinc (Zn), selenium (Se), copper (Cu), tin (Sn), molybdenum (Mo), antimony (Sb), cadmium (Cd), lead (Pb), thallium (Tl), and nickel (Ni) were the major contaminants (pollution load index > 1). Bioavailable forms of titanium (Ti), chromium (Cr), Sn, and cobalt (Co) played essential roles in shaping the microbial structure, and physicochemical properties, especially organic matter (OM) and pH, also mediated the microbial diversity and composition in the metal(loid) contaminated zones. Metal-microbe interactions and heatmap analysis revealed that the bioavailability of metal(loid)s promoted the niche partitioning of microbial species. Metal-resistant species were abundant in Zone Ⅰ that had the highest metal-contaminated level, whereas metal-sensitive species prevailed in Zone Ⅲ that had the lowest pollution level. The bioavailable metal(loid)s rather than physicochemical and spatial variables explained a larger portion of the variance in the microbial community, and the homogeneous selection was the dominant ecological process driving the assembly of the microbial community. Overall, our study highlighted the importance of metal(loid) bioavailability in shaping microbial structure, future bioremediation, and environmental management of metal(loid) contaminated sites.

Use of Soil Enzymes as Indicators for Contaminated Soil Monitoring and Sustainable Management

Diagnosis of the risk of soil pollution and the performance of measures for the recovery of contaminated soil requires proper monitoring of the extent of soil function damage and its recovery process. Soil enzymes reveal ecosystem perturbations, are sensitive to management choices, and have been used as indicators of biogeochemical cycles, organic matter degradation, and soil remediation processes. Thus, enzymes can indicate, along with other physical or chemical properties, soil quality. In this paper, we review the effects of soil pollutants [toxic trace elements (TTE), and petroleum hydrocarbons (PHC)] on enzymatic activities and evaluate the usefulness of soil enzyme’s activity for monitoring recovery processes in contaminated soil. Soil enzymes can be said to be a powerful means of monitoring to properly indicate the degree of deterioration of soil quality caused by soil pollution and to diagnose the process of functional recovery of contaminated soil. Further research is needed to establish the quantitative relationships between the soil physico-chemical properties and enzyme activity and the effect of soil remediation on the functional recovery of soil-related to soil quality.

Mine Waste Rock: Insights for Sustainable Hydrogeochemical Management

Mismanagement of mine waste rock can mobilize acidity, metal (loid)s, and other contaminants, and thereby negatively affect downstream environments. Hence, strategic long-term planning is required to prevent and mitigate deleterious environmental impacts. Technical frameworks to support waste-rock management have existed for decades and typically combine static and kinetic testing, field-scale experiments, and sometimes reactive-transport models. Yet, the design and implementation of robust long-term solutions remains challenging to date, due to site-specificity in the generated waste rock and local weathering conditions, physicochemical heterogeneity in large-scale systems, and the intricate coupling between chemical kinetics and mass- and heat-transfer processes. This work reviews recent advances in our understanding of the hydrogeochemical behavior of mine waste rock, including improved laboratory testing procedures, innovative analytical techniques, multi-scale field investigations, and reactive-transport modeling. Remaining knowledge-gaps pertaining to the processes involved in mine waste weathering and their parameterization are identified. Practical and sustainable waste-rock management decisions can to a large extent be informed by evidence-based simplification of complex waste-rock systems and through targeted quantification of a limited number of physicochemical parameters. Future research on the key (bio)geochemical processes and transport dynamics in waste-rock piles is essential to further optimize management and minimize potential negative environmental impacts.

Effects of soil particle size on the adsorption, distribution, and migration behaviors of heavy metal(loid)s in soil: a review

In recent years, toxic pollution from heavy metal(loid)s in soil has become a severe environmental problem worldwide. The migration and transformation of heavy metal(loid)s in soil have become hot topics in the field of environmental research. Soil particle size plays an important role in influencing the environmental behavior of heavy metal(loid)s in soil. This review collates and synthesizes the research on the adsorption, distribution, and migration of heavy metal(loid)s in soil particles. There is no unified method for soil particle separation, since the purposes of different studies are different. Regardless of adsorption or distribution characteristics, fine soil particles generally exhibit a higher capacity to combine heavy metal(loid)s; however, certain studies have also observed a contrary phenomenon, according to which heavy metal(loid)s were more enriched in coarser particles. The adsorption and distribution of heavy metal(loid)s in soil particles were essentially determined by the physicochemical properties of the soil particles. Land use obviously affected the distribution of heavy metal(loid)s in the soil particles. Organic matter had an important influence on the distribution and availability of heavy metal(loid)s in agricultural and forest soils, while for urban soils and sediments, clay minerals or metal (hydr)oxides may play the dominant role. Preferential surface migration of fine particles during erosion processes did not always lead to the enrichment of heavy metal(loid)s in the lost soil. Further research should be conducted to explore the relationships among the soil aggregates, organic matter, heavy metal(loid)s, and soil microorganisms; the association between the distribution and availability of heavy metal(loid)s and the properties of soil particles; and the migration patterns of heavy metal(loid)s in soil particles at different scales.

The limits of lead (Pb) phytoextraction and possibilities of phytostabilization in contaminated soil: a critical review

This review article focuses on lead (Pb), one of the most ubiquitous and harmful toxicants found in soil. Our objective is to address misconceptions regarding the ability of plants to uptake Pb through their roots and translocate it to above-ground tissues, and their ability to act as hyperaccumulators and thereby phytoextract Pb. In accordance with a number of cited definitions, we suggest that species capable of Pb phytoextraction can be rated with the following three criteria: (1) root uptake above a nominal threshold of 1,000 mg Pb/kg, (2) bioconcentration factor (BCF or shoot/soil concentration) >1, and (3) translocation factor (TF or shoot/root concentration) > 1. We review the literature in the updated USDA Phytoremediation Database and conclude that without amendments: no plant has met all three criteria; no plant has been confirmed as a Pb hyperaccumulator. Our analysis suggests that Pb phytoextraction is not a viable remediation option. Pb phytostabilization, however, may be an effective remediation tool in a variety of settings. Planting some of the many species capable of tolerating soil Pb exposure and sequestering it in or around the root zone will limit Pb movement into other ecosystems, prevent resuspended dusts, and mitigate Pb exposure.

Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim's Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.

Fungal community composition change and heavy metal accumulation in response to the long-term application of anaerobically digested slurry in a paddy soil

Anaerobically digested slurry (ADS) has been widely used as a liquid fertilizer in agroecosystems. However, there is scant information on the effects of successive ADS applications on heavy metals (HMs) accumulation and fungal community composition in paddy soils. In this study, we conducted a field experiment over 10 years to assess the changes in soil HMs and fungal community composition under the long-term application of ADS in a paddy field. The four treatments were (1) no fertilizer (CK); (2) mineral fertilizer and 270 kg N ha^-1 from urea (MF); (3) 270 kg N ha^-1 from ADS (ADS1); and (4) 540 kg N ha^-1 from ADS (ADS2). The results revealed that ADS application improved paddy soil fertility compared to that under the MF treatment by increasing soil organic C (SOC), total N (TN) and available potassium (AK). Long-term application of ADS significantly increased soil total and available Zn (TZn and AZn) concentrations as compared to those under the MF treatment. However, there were no significant differences in the total and available Cu concentrations or the total Pb concentration between the ADS and MF treatments. Sequence analysis showed that application of ADS increased the fungal richness indexes (Chao1 and ACE) compared to MF treatment. Principal coordinate analysis (PCoA) showed that the soil fungal community compositions were significantly separated by high levels of ADS application. Long-term application of ADS increased the relative abundance of classes Sordariomycetes, Dothideomycetes and Agaricomycetes by 20.8-29.0%, 107.3-141.4% and 289.5-387.5%, respectively, but decreased that of Pezizomycetes by 14.0-33.0% compared to that under the MF treatment. At the genus level, compared to those under the MF treatment, the relative abundances of Pyrenochaetopsis and Myrothecium were significantly increased by the application of ADS, but those of Mrakia and Tetracladium were significantly decreased. Redundancy analysis (RDA) revealed that SOC, AZn and AP were the three most important factors affecting the fungal community composition of the paddy soil. Our findings suggested that fungal community composition could be affected by changes in the chemical properties and heavy metal contents of paddy soil under high application of ADS in the long term.

Use of a biostimulant obtained from okara in the bioremediation of a soil polluted by used motor car oil

In this manuscript we studied in the laboratory the bioremediation effects of a biostimulant obtained from okara by enzymatic hydrolysis processes in a soil polluted with used motor-car oil at a rate of 1 % (w/w) over an 89-day period. The biostimulant was added to the soil 6 times during the incubation period at a rate of 2 %. Dehydrogenase activity and the evolution of polycyclic aromatic hydrocarbons (PAHs) and pseudo total heavy metals in soil were studied. The successive applications of the biostimulant to the polluted soil gradually increased PAHs degradation during the experimental period. Thus, at the end of the experiment, the application of the biostimulant decreased the concentration of naphthalene in soil by 74 %, while PAHs with 3, 4, 5 and 6 aromatic rings had been reduced by around 58 %, 44 %, 30 % and 23 %, respectively. This degradation is possibly due to the high number of low molecular weight peptides (<300 Da) in the biostimulant which are readily available for PAHs-tolerant soil microorganisms that accelerate the degradation of the said toxins. The concentration of heavy metals in the oil used was not very high and consequently the dehydrogenase activity was not negatively affected.

Microbial inoculant and garbage enzyme reduced cadmium (Cd) uptake in Salvia miltiorrhiza (Bge.) under Cd stress

The uptake and accumulation of cadmium (Cd) in Salvia miltiorrhiza (Bge.) negatively affects the quality of its harvested roots, and seriously threatens human health. This study investigates the effect of a microbial inoculant (MI) and garbage enzyme (GE) on Cd uptake, the accumulation of bioactive compounds, and the community composition of microbes in the rhizosphere soil of S. miltiorrhiza under Cd stress. S. miltiorrhiza seedlings were transplanted to Cd-contaminated pots and irrigated with an MI, GE, a combination of an MI and GE (MIGE) or water (control). The results indicated that treatments with an MI, GE or MIGE can reduce Cd uptake in S. miltiorrhiza. The MIGE treatment had greater efficiency in reducing Cd uptake than the control (reduction by 37.90%), followed by the GE (25.31%) and MI (5.84%) treatments. Treatments with an MI, GE and MIGE had no significant impact on fresh and dry root biomass. Relative to the control, the MI treatment had the highest efficiency in increasing the accumulation of total tanshinones (an increase of 40.45%), followed by the GE treatment (40.08%), with the MIGE treatment (9.90%) treatment not having a more favorable effect than the separate application of an MI or GE. The salvianolic acid content for all groups was higher than the standard prescribed by Chinese pharmacopoeia, notwithstanding a slightly lower level in the treated groups relative to the control. In addition, metagenomic analysis indicated changes in the relative abundance of soil microbes associated with the bioremediation of heavy metals. The relative abundances of Brevundimonas, Microbacterium, Cupriavidus and Aspergillus were significantly greater in the treated groups than in the Control. These results suggest that using MI and GE, either separately or together, may not only improve the quality of S. miltiorrhiza but may also facilitate the microbial remediation of soil contaminated with Cd.

Root-induced changes in aggregation characteristics and potentially toxic elements (PTEs) speciation in a revegetated artificial zinc smelting waste slag site

Root-induced changes play a crucial role in influencing the fate and speciation of potentially toxic elements (PTEs) in contaminated soils, but their role in the phytostabilization of waste slag sites remain unclear. The aim of this study was to determine the effect of four phytostabilization plants, Broussonetia papyrifera, Arundo donax, Robinia pseudoacacia, and Cryptomeria fortunei, planted in a zinc smelting waste slag site for 5 years on PTEs speciation and the mineral and aggregation characteristics at the interface of the waste slag-plant system. The results showed that the presence of a higher content of oxalic acid in the rhizosphere slags of the four plant species than in the bare slag. Revegetation of the waste slag with the four plant species significantly changed the mineral composition and morphology of the waste slag. The mass percentage of large particles (1-5 mm) and small particles (0.5-1 mm, 0.25-0.5 mm, and <0.25 mm) in the rhizosphere slags decreased and increased, respectively. The PTEs (Cu, Pb, Zn, and Cd) in most of the rhizosphere slags were mainly distributed within the small particles, and the enrichment coefficients of PTEs in the large particles and small particles were less than and greater than 1, respectively. The bioavailability of the PTEs in the waste slag increased with decreasing particle size. Root-induced the transformation of acid-soluble PTEs into their reducible, oxidizable, and residual forms in the different waste slag particles weathered in the rhizosphere. These results suggested that there are root-induced changes in the aggregation characteristics and geochemical behaviours of PTEs in waste slag fractions during the phytoremediation of waste slag sites.

Evaluation of nanoremediation strategy in a Pb, Zn and Cd contaminated soil

We addressed the efficiency of a nanoremediation strategy using zero-valent iron nanoparticles (nZVI), in a case of co-mingled heavy metals (HM) pollution (Pb, Cd and Zn). We applied a combined set of physical-chemical, toxicological and molecular analyses to assess the effectiveness and ecosafety of nZVI (5% w/w) for environmental restoration. After 120 days, nZVI showed immobilization capacity for Pb (20%), it was scarcely effective for Zn (8%) and negligibly effective for Cd. The HMs immobilization in the nZVI treated soils (compared to control soil), reaches its maximum after 15 days (T3) as reflected in the decrease of HM toxicity towards V. fischeri. The overall abundance of the microbial community was similar in both sets of samples during all experiment, although an increase in the number of metabolically active bacteria was recorded 15 days post treatment. We studied the induced impact of nanoremediation on the soil microbial community structure by Next Generation Sequencing (NGS). Even when higher HM immobilization was recorded, no significant recovery of the microbial community structure was found in nZVI-treated soil. The most marked nZVI-induced structural shifts were observed at T3 (increase in the Firmicutes population with a decrease in Gram-negative bacteria). Predictive metagenomic analysis using PICRUSt showed differences among the predicted metagenomes of nZVI-treated and control soils. At T3 we found decrease in detoxification-related proteins or over-representation of germination-related proteins; after 120 days of nZVI exposure, higher abundance of proteins involved in regulation of cellular processes or sporulation-related proteins was detected. This study highlights the partial effectiveness of nanoremediation in multiple-metal contaminated soil in the short term. The apparent lack of recovery of biodiversity after application of nZVI and the decreased effectiveness of nanoremediation over time must be carefully considered to validate this technology when assurance of medium- to long-term immobilization of HMs is required.

Effects of Elevated CO2 Concentration and Nitrogen Addition on Soil Respiration in a Cd-Contaminated Experimental Forest Microcosm

Forests near rapidly industrialized and urbanized regions are often exposed to elevated CO2, increased N deposition, and heavy metal pollution. To date, the effects of elevated CO2 and/or increased N deposition on soil respiration (Rs) under heavy metal contamination are unclear. In this study, we firstly investigated Rs in Cd-contaminated model forests with CO2 enrichment and N addition in subtropical China. Results showed that Rs in all treatments exhibited similar clear seasonal patterns, with soil temperature being a dominant control. Cadmium addition significantly decreased cumulative soil CO2 efflux by 19% compared to the control. The inhibition of Rs caused by Cd addition was increased by N addition (decreased by 34%) was partially offset by elevated CO2 (decreased by 15%), and was not significantly altered by the combined N addition and rising CO2. Soil pH, microbial biomass carbon, carbon-degrading hydrolytic enzymes, and fine root biomass were also significantly altered by the treatments. A structural equation model revealed that the responses of Rs to Cd stress, elevated CO2, and N addition were mainly mediated by soil carbon-degrading hydrolytic enzymes and fine root biomass. Overall, our findings indicate that N deposition may exacerbate the negative effect of Cd on Rs in Cd-contaminated forests and benefit soil carbon sequestration in the future at increasing atmospheric CO2 levels.

Soil organic matter prevails over heavy metal pollution and vegetation as a factor shaping soil microbial communities at historical Zn-Pb mining sites

This study examined the effects of soil heavy metals, macronutrients, texture and pH as well as plant species richness and composition on soil respiration, enzymatic activity, microbial biomass, metabolic quotient (qCO₂) and arbuscular mycorrhizal fungi (AMF) at sites of historical Zn-Pb mining. The study was conducted both on a large scale (65 heaps scattered over the area of 750 km²) and on a small scale (25 plots along two 48 m transects extending from heaps to adjacent fallow fields). Total concentrations of metals exceeded 400 (Cd), 20,000 (Pb) and 80,000 (Zn) mg kg^-1 at the most polluted sites. Although they decreased along the heap-fallow direction, they still remained above environmental standards in fallow soils. In contrast, some soluble metal forms increased with the increasing distance from heaps. Soil organic matter had the strongest positive effect on most microbial parameters. Total and/or available heavy metals exhibited significant negative effects on microbial biomass, enzymatic activity and AMF, and a positive effect on qCO₂. Organic matter alleviated negative effects of heavy metals on microorganisms; they were not observed where the increase in the contamination was accompanied by the increase in organic matter content. Plant species richness affected positively enzymatic activity and mycorrhization level. Plant species composition possibly contributed to the formation of soil microbial communities, but its effect was entangled in that of heavy metals as plant communities changed along pollution gradients (from metal-tolerant grasslands dominated by Festuca ovina to calcareous grasslands and ruderal communities at less polluted sites).

Physicochemical features, metal availability and enzyme activity in heavy metal-polluted soil remediated by biochar and compost

Biochar and compost have been widely used for pollution remediation of heavy metals in soil. However, little research was conducted to explore the efficiency of biochar, compost and their combination to reduce heavy metals availability, and the effects of their additive on soil biological properties are often neglected. Therefore, this study investigated the effects of biochar, compost and their combination on availability of heavy metals, physicochemical features and enzyme activities in soil. Results showed that adding amendments to polluted soil significantly altered soil properties. Compared to the separate addition of biochar or compost, their combined application was more effective to improve soil pH, organic matter (OM), organic carbon (TOC) and available potassium (AK). All amendments significantly decreased the availability of Cd and Zn, but slightly activated As and Cu. In addition, soil enzyme activities were activated by compost and inhibited by biochar, but exhibited highly variable responses to their combinations. Pearson correlation analysis indicated that electrical conductivity (EC) and AK were the most important environmental factors affecting metal availability and soil enzyme activities including dehydrogenase, catalase, β-glucosidase, urease, acid and alkaline phosphatase, arylsulfatase except for protease and invertase. Availability of As, Cu, Cd and Zn affected dehydrogenase, catalase and urease activities. These results indicated that biochar, compost and their combination have significant effects on physicochemical features, metals availability and enzyme activities in heavy metal-polluted soil.

The effects of ectomycorrhizal fungi on heavy metals' transport in Pinus massoniana and bacteria community in rhizosphere soil in mine tailing area

Pinus massoniana is one of the potential tree species of afforestation in barren mine tailing area, and ectomycorrhizal fungi contributes remarkably to its survival. However, how ectomycorrhizal fungi interacts with Pinus massoniana under heavy metals' stress is unknown. Two systems (Pinus massoniana inoculated with and without ectomycorrhizal fungi) were designed, and each system contained rhizosphere and non-rhizosphere, while bulk soil was sampled as control. The results showed that treatment of ectomycorrhizal fungi inoculation could obviously improved the absorption of soil moisture, total carbon/total nitrogen and nutrients, while reduced the bulk density and heavy metals of soil when compared with control (p＜0.05). The heavy metals accumulating in plants' roots with ectomycorrhizal fungi were greater than that without ectomycorrhizal fungi. Conversely, they were lower in shoots with ectomycorrhizal fungi. The bacterial community were affiliated with 23 bacterial phyla, 70 classes, 115 orders, 201 families, and 363 genera. Constrained Principal Coordinate Analysis and redundancy analysis demonstrated that bacterial communities structure in the soil inoculated with or without ectomycorrhizal fungi and bulk soil were distinguishable, but no difference between rhizosphere and non-rhizosphere. The LEfSe analysis showed Acidobacteria, Actinobacteria, and Proteobacteria were the dominant phyla that contributed to the difference among treatments.

Diversity and phylogenetic composition of bacterial communities and their association with anthropogenic pollutants in sewage sludge

Despite wastewater treatment, sewage sludge is often contaminated with multiple pollutants. Their impact on the phylogenetic composition and diversity of prokaryotic communities in sludge samples remains largely unknown. In this study, we analyzed the phylogenetic structure of bacterial communities and diversity in sludge from six waste water treatment plants (WWTPs) and linked this information with the pollutants identified in these samples: eight potentially toxic metals (PTMs) and four groups of organic pollutants [polychlorinated biphenyls (PCBs), polyromantic hydrocarbons (PAHs), brominated flame retardants (BFRs) and organochlorine pesticides (OCPs)]. Alpha diversity measures and the distribution of dominant phyla varied among the samples, with the community from the thermophilic anaerobic digestion (TAD)-stabilized sample from Prague being the least rich and the least diverse and containing on average 36% of 16S rRNA gene sequence reads of the thermotolerant genus Coprothermobacter of the class Clostridia (phylum Firmicutes). Using weighted UniFrac distance-based redundancy analysis (dbRDA), we found that a collection of 5 PTMs: Cr, Cu, Ni, Pb, Zn, and a pair of BFRs: hexabromocyclododecane (HBCD) and tribromodiphenyl ethers (triBDEs) were significantly associated with the bacterial community structure in mesophilic anaerobic digestion (MAD)-stabilized samples, whereas PCBs were observed to be marginally significant. Altogether, 85% of the variance in bacterial community structure could be ascribed to these pollutants. The data presented here contribute to a greater understanding of the ecological effects of combined pollution on the composition and diversity of bacterial communities, hence have the potential to aid in predicting ecosystem functions and/or disruptions associated with pollution.

Advances in characterizing microbial community change and resistance upon exposure to lead contamination: Implications for ecological risk assessment

Recent advancement in molecular techniques has spurred waves of studies on responses of microorganisms to lead contamination exposure, leveraging detailed phylogenetic analyses and functional gene identification to discern the effects of lead toxicity on microbial communities. This work provides a comprehensive review of recent research on (1) microbial community changes in contaminated aquatic sediments and terrestrial soils; (2) lead resistance mechanisms; and (3) using lead resistance genes for lead biosensor development. Sufficient evidence in the literature, including both in vitro and in situ studies, indicates that exposure to lead contamination inhibits microbial activity resulting in reduced respiration, suppressed metabolism, and reduced biomass as well as altered microbial community structure. Even at sites where microbial communities do not vary compositionally with contamination levels due to extremely long periods of exposure, functional differences between microbial communities are evident, indicating that some microorganisms are susceptible to lead toxicity as others develop resistance mechanisms to survive in lead contaminated environments. The main mechanisms of lead resistance involve extracellular and intracellular biosorption, precipitation, complexation, and/or efflux pumps. These lead resistance mechanisms are associated with suites of genes responsible for specific lead resistance mechanisms and may serving as indicators of lead contamination in association with dominance of certain phyla. This allows for development of several lead biosensors in environmental biotechnology. To promote applications of these advanced understandings, molecular techniques, and lead biosensor technology, perspectives of future work on using microbial indicators for site ecological assessment is presented.

Tailings microbial community profile and prediction of its functionality in basins of tungsten mine

In a circular economy concept, where more than 300 million tons of mining and quarrying wastes are produced annually, those are valuable resources, supplying metals that are extracted today by other processes, if innovative methods and processes for efficient extraction of these elements are applied. This work aims to assess microbiological and chemical spatial distribution within two tailing basins from a tungsten mine, using a MiSeq approach targeting the 16S rRNA gene, to relate microbial composition and function with chemical variability, thus, providing information to enhance the efficiency of the exploitation of these secondary sources. The tailings sediments core microbiome comprised members of family Anaerolineacea and genera Acinetobacter, Bacillus, Cellulomonas, Pseudomonas, Streptococcus and Rothia, despite marked differences in tailings physicochemical properties. The higher contents of Al and K shaped the community of Basin 1, while As-S-Fe contents were correlated with the microbiome composition of Basin 2. The predicted metabolic functions of the microbiome were rich in genes related to metabolism pathways and environmental information processing pathways. An in-depth understanding of the tailings microbiome and its metabolic capabilities can provide a direction for the management of tailings disposal sites and maximize their potential as secondary resources.

Remediation effectiveness of vermicompost for a potentially toxic metal-contaminated tropical acidic soil in China

Potentially toxic metal (PTM) contamination coupled with soil acidification has posed a severe threat to agricultural sustainability of tropical region in the world. In this study, a vermicopomst (VC) produced from vermicomposting cattle manure under tropical environment was applied to remediating a tropical acidic soil in Hainan, China. The effectiveness of VC in reducing available PTMs in soils was evaluated by incubation experiments with a Cd, Cr or Ni spiked soil and a Cd contaminated field soil. The dynamic changes of soil physical, chemical and biological properties after VC amendment were determined to understand the mechanisms of PTM immobilization. The results showed that VC amendment significantly reduced 0.01M CaCl₂ extractable amounts of Cd, Ni and Cr in the spiked soils, and CaCl₂ extractable Cd was reduced by 49.3% when VC was amended to the Cd contaminated field soil. Thermodynamic studies showed that VC had a high adsorption capacity for Cd, Ni and Cr, with the maximum adsorption (obtained from the Langmuir model) of 33.45, 26.17, and 20.88 mg/g, respectively. The reduction in CaCl₂ extractable metals after VC amendment was consistent with the order of maximum adsorption of VC for Cd, Ni, and Cr. Vermicompost amendment increased soil pH by 0.7 to 1.5 units, which is positively related with VC rate, but negatively with the decrease in extractable metals. These results indicates that adsorption of metals onto VC and an increase in soil pH after VC amendment are likely responsible for the decreased availability of Cd, Ni, and Cr in the contaminated soil. In addition, the addition of stable organic substances and subsequent formation of water-stable aggregates may be also beneficial for immobilizing PTMs and improving tropical soil quality.

Characterization of Microbial Communities, Identification of Cr(VI) Reducing Bacteria in Constructed Wetland and Cr(VI) Removal Ability of Bacillus cereus

In this study, the contribution of substrates microorganisms in three different constructed wetlands (CWs) to Cr(VI) purification was discussed. In addition, the microbial communities in the substrate of different CWs were characterized, and rhizosphere Cr(VI) reducing bacteria was also identified. The results showed that microorganisms could improved Cr(VI) removal to 76.5%, and result in that more Cr(VI) was reduced to Cr(III). The dominant strains in the substrates of different CWs were Sphingomonas sp., Cystobacter sp., Acidobacteria bacterium, Sporotrichum and Pellicularia species. The Cr(VI) reducing bacteria from Leersia hexandra Swartz rhizosphere was identified as Bacillus cereus. Furthermore, under suitable conditions, the removal rate of Cr(VI) by Bacillus cereus was close to 100%.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.