The effect of long-term mercury pollution on the soil microbial community

Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities

Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.

Soil core microbiota drive community resistance to mercury stress and maintain functional stability

Soil microbial communities have resistance to environmental stresses and thus can maintain ecosystem functions such as decomposition, nutrient provisioning, and plant pathogen control. However, predominant factors driving community resistance of soil microbiome to heavy metal pollution stresses and ecosystem functional stability are still unclear, limiting our ability to forecast how soil pollution might affect ecosystem sustainability. Here, we conducted microcosm experiments to estimate the importance of soil microbiome in predicting community resistance to heavy metal mercury (Hg) stress in paired paddy and upland fields. We found that community resistance of soil microbiome was strongly correlated with ecosystem functional stability, so were the individual groups of organisms such as bacteria, saprotrophic fungi, and phototrophic protists. The core phylotypes within soil microbiome had a major contribution to community resistance, which was essential for the maintenance of functional stability. Co-occurrence network further confirmed that community resistances of main ecological clusters were positively correlated with ecosystem functional stability. Together, our results provide new insights into the link between community resistance and functional stability, and highlight the importance of core microbiota in driving community resistance to environmental stresses and maintain functional stability.

Unboxing the black box-one step forward to understand the soil microbiome: A systematic review

Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.

Ecological risk assessment of heavy metals in the sediments and their impacts on bacterial community structure: A case study of Bamen Bay in China

Heavy metal pollution associated with human activity is of big concern in tropical bays. Microorganisms may be highly sensitive to heavy metals. Nonetheless, little is known about effects of heavy metals on microbial structure in tropical bay sediments. In this study, 16S rRNA gene sequencing and potential ecological risk index analysis were used to analyze the relationships between nine metals (arsenic, lead, cadmium, cobalt, chromium, copper, zinc, manganese, and nickel) and bacterial communities in the sediments of Bamen Bay, China. Our results showed that Bamen Bay was under a considerable ecological risk and cadmium had the highest monomial potential ecological risk. In addition, individual metal contamination correlated with bacterial community composition but not with bacterial α-diversity. Arsenic was the metal influencing bacterial community structure the most. Our findings provide a novel insight into the monitoring and remediation of heavy metal pollution in tropical bays.

Demystifying mercury geochemistry in contaminated soil-groundwater systems with complementary mercury stable isotope, concentration, and speciation analyses

Interpretation of mercury (Hg) geochemistry in environmental systems remains a challenge. This is largely associated with the inability to identify specific Hg transformation processes and species using established analytical methods in Hg geochemistry (total Hg and Hg speciation). In this study, we demonstrate the improved Hg geochemical interpretation, particularly related to process tracing, that can be achieved when Hg stable isotope analyses are complemented by a suite of more established methods and applied to both solid- (soil) and liquid-phases (groundwater) across two Hg2+-chloride (HgCl2) contaminated sites with distinct geological and physicochemical properties. This novel approach allowed us to identify processes such as Hg2+ (i.e., HgCl2) sorption to the solid-phase, Hg2+ speciation changes associated with changes in groundwater level and redox conditions (particularly in the upper aquifer and capillary fringe), Hg2+ reduction to Hg0, and dark abiotic redox equilibration between Hg0 and Hg(II). Hg stable isotope analyses play a critical role in our ability to distinguish, or trace, these in situ processes. While we caution against the non-critical use of Hg isotope data for source tracing in environmental systems, due to potentially variable source signatures and overprinting by transformation processes, our study demonstrates the benefits of combining multiple analytical approaches, including Hg isotope ratios as a process tracer, to obtain an improved picture of the enigmatic geochemical behavior and fate of Hg at contaminated legacy sites.

The Effect of Heavy Metals on Microbial Communities in Industrial Soil in the Area of Piekary Śląskie and Bukowno (Poland)

The aim of this study was to determine the activity and structure of microbial communities in soils contaminated with heavy metals (HMs). To achieve this goal, soil samples were taken from two contaminated sites (i.e., Piekary Śląskie and Bukowno) in Poland. A wide range of methods were applied, including: total and metal-tolerant culturable bacteria enumeration; microbial community structure analysis using the phospholipid fatty acid method (PLFA); denaturing gradient gel electrophoresis (PCR-DGGE); and metabolic activity using BIOLOG and EcoPlateTM. Our studies showed that HMs negatively affected microbial community structure and activity in polluted soils. Apart from the contamination with HMs, other soil parameters like soil pH and water also impacted microbial community structure and growth. Metal-tolerant bacterial strains were isolated, identified and tested for presence of genes encoding HM tolerance using the polymerase chain reaction (PCR) methodology. Contamination with HMs in the tested areas was found to lead to development of metallotolerant bacteria with multiple tolerances toward Zn, Ni, Cd and Cu. Different genes (e.g., czcA, cadA and nccA) encoding HM efflux pumps were detected within isolated bacteria. Culturable bacteria isolated belonged to Proteobacteria, Actinobacteria and Bacteroidetes genera. Among non-culturable bacteria in soil samples, a significant fraction of the total bacteria and phyla, such as Gemmatimonadetes and Acidobacteria, were found to be present in all studied soils. In addition, bacteria of the Chloroflexi genus was present in soil samples from Piekary Śląskie, while bacteria of the Firmicutes genus were found in soil samples from Bukowno.

Seasonal trends of mercury bioaccumulation and assessment of toxic effects in Asian clams and microbial community from field study of estuarine sediment

This study investigated seasonal trends in bioaccumulation potential and toxic effects of mercury (Hg) in Asian clams (Corbicula fluminea) and microbial community. For this, a clam-exposure experiment was performed during summer, fall, and winter seasons in four different sites (HS1: control/clean site; HS2, HS3, and HS4: contaminated sites) of Hyeongsan River estuary, South Korea. Total mercury (THg) and methylmercury (MeHg) in whole sediments were highest at HS4 site during fall, sustained similar levels during winter, but decreased during summer. Unlike whole sediment, pore water reported higher levels in summer, and gradually declined during fall and winter. Asian clams from HS4 site collected during summer presented highest bioaccumulations of THg (521.52 μg/kg, dry weight) and MeHg (161.04 μg/kg, dry weight), which also correlated with the higher levels of Hg present in pore water in the same season. Moreover, biota-sediment-pore water accumulation factor (BSpAF) were comparatively greater in clams collected from HS2∼HS4 compared to HS1 sites, suggesting that porewater was a better indicator of accumulation of Hg. Upregulation of biomarker genes responsible for detoxifying process (gsts1), scavenging oxidative stress (cat), and protein reparation (hsp70 and hsp90) were observed in clams collected from HS2∼HS4. The overexpression of these biomarkers implied that Asian clams can be considered as promising warning tools for Hg-contamination. Both bacterial and metabolic diversities were negatively affected by higher levels of THg and MeHg. Phylum Proteobacteria was enriched in HS2∼HS4 compared to HS1. In contrast, phylum Bacteroidetes showed a reverse trend. The metabolic profile was highest in HS1 and lowest in HS4, revealing higher stress of Hg in HS4 site. Overall, the outcomes of this field study broaden the information on seasonal trends of bioaccumulation of Hg and its toxic effects. These findings may be helpful in Hg monitoring and management programs in other river systems.

Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems

Soil pollution is an important stressor affecting biodiversity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.

The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia

The contamination with organic and inorganic pollutants changes significantly soil microbial community structure. These shifts indicate anthropogenic pressure and help to discover new possibilities for soil remediation. In this study, the microbial community structure of Spolic Technosols formed at the territory of a former industrial sludge reservoir near the Kamensk-Shakhtinsky (Southern Russia) was studied using a metagenomics approach. The studied soils contain high concentrations of heavy metals (HM) (up to 72,900 mg kg^-1) and 16 priority polycyclic aromatic hydrocarbons (PAHs) (up to 6670 mg kg^-1). Its microbial communities demonstrate an excellent adaptability level reflected in their complexity and diversity. As shown by the high values of alpha diversity indices (Shannon values up to 10.1, Chao1 values from 1430 to 4273), instead of decreasing quantitatively and qualitatively on the systemic level, microbial communities tend to undergo complex redistribution. Regardless of contamination level, the share of Actinobacteria and Proteobacteria was consistently high and varied from 20 to 50%. Following the results of the Mann-Whitney U test, there were significant changes of less abundant phyla. The abundance of oligotrophic bacteria from Gemmatimonadetes and Verrucomicrobia phyla and autotrophic bacteria (e.g., Nitrospira) decreased due to the high PAH's level. And abundance of Firmicutes and amoebae-associated bacteria such as TM6 and soil Chlamydia increased in highly contaminated plots. In the Spolic Technosols studied, the influence of factors on the microbial community composition decreased from PAHs concentration to soil characteristics (organic carbon content) and phylum-phylum interactions. The high concentrations of HMs influenced weakly on the microbial community composition.

Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants

Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.

Responses of bacterial taxonomic attributes to mercury species in rhizosphere paddy soil under natural sulphur-rich biochar amendment

Biochar and sulphur (S) are important factors regulating the level, speciation and transformation of mercury (Hg), leading to alterations in the assemblage of the soil microbial community. However, variations in the taxonomic attributes of the rhizosphere soil bacterial community arising from the Hg speciation in paddy soil, amended with natural S-rich biochar (NSBC) derived from the pyrolysis of S-rich oilseed rape straw, remain unclear. Herein, a rice pot experiment was conducted. Hg-polluted paddy soils were amended with NSBC and low-S biochar (LSBC) to evaluate the role of Hg chemical form affected by NSBC in regulating the taxonomic attributes of rhizosphere soil, including microbial abundance, composition, and ecological clusters within the co-occurrence network of microbial communities. Results showed that microbial abundance was higher in soils with lower Hg levels, and mean increases of 149 observed operational taxonomic units (OTUs) and 238 predicted OTUs (Chao 1) were observed, with a 1 mg kg^-1 decrease in the total Hg (T-Hg) content. Among the 13 predictor variables, the T-Hg content was the strongest and most consistent predictor of the bacterial taxonomic attributes. This finding may be attributed to the fact that the drastic reduction in T-Hg and Hg bioavailability induced by NSBC results in the decrease of Hg stress on the soil microbiome. Moreover, NSBC amendment shifted the ecological clusters toward the amelioration of Hg pollution.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

Stronger impacts of long-term relative to short-term exposure to carbon nanomaterials on soil bacterial communities

Environmental impacts of carbon nanomaterials (CNMs) have been attracting increasing concerns in recent years. Knowledge on how short-term exposure to CNMs influences soil microbial communities is available. However, little is known about the possible difference in effects of long-term versus short-term exposure of CNMs on soil microbial communities. In this study, we systematically compared effects of fullerene (C₆₀), single-walled carbon nanotubes (SW), and graphene (GR) on soil bacterial communities over short (30 d) and long (360 d) term exposure durations. Our findings revealed that short-term exposure to all CNMs significantly increased the alpha diversity of soil bacterial communities. SW and GR exposure for 360 d relative to that for 30 d more significantly decreased their alpha diversity. Compared to short-term exposure, a long term exposure to CNMs more strongly altered the beta diversity of soil bacterial communities. LEfSe analysis showed that, GR relative to C₆₀ and SW exposure more strongly altered soil bacterial community composition especially for long-term duration at various taxonomic levels; more taxa were also identified by LEfSe analysis as biomarkers upon long-term GR exposure. More OTUs were affected by long-term GR exposure. These differences resulted from both distinct physicochemical properties of various CNMs and their exposure durations.

Effects of Land Use and Pollution Loadings on Ecotoxicological Assays and Bacterial Taxonomical Diversity in Constructed Wetlands

Freshwater ecosystems are affected by anthropogenic alterations. Different studies have extensively studied the concentrations of metals, nutrients, and water quality as measurements of pollution in freshwater ecosystems. However, few studies have been able to link these pollutants to bioindicators as a risk assessment tool. This study aimed to examine the potential of two bioindicators, plant ecotoxicological assays and sediment bacterial taxonomic diversity, in ecological risk assessment for six freshwater constructed wetlands in a rapidly urbanizing watershed with diverse land uses. Sediment samples were collected summer, 2015 and 2017, and late summer and early fall in 2016 to conduct plant ecotoxicological assays based on plant (Lepidium, Sinapis and Sorghum) growth inhibition and identify bacterial taxonomical diversity by the 16S rRNA gene sequences. Concentrations of metals such as lead (Pb) and mercury (Hg) (using XRF), and nutrients such as nitrate and phosphate (using HACH DR 2800TM spectrophotometer) were measured in sediment and water samples respectively. Analyses of response patterns revealed that plant and bacterial bioindicators were highly responsive to variation in the concentrations of these pollutants. Hence, this opens up the scope of using these bioindicators for ecological risk assessment in constructed freshwater wetland ecosystems within urbanizing watersheds.

Thallium shifts the bacterial and fungal community structures in thallium mine waste rocks

Thallium (Tl) is a highly toxic metalloid and is considered a priority pollutant by the US Environmental Protection Agency (EPA). Currently, few studies have investigated the distribution patterns of bacterial and fungal microbiomes in Tl-impacted environments. In this study, we used high-throughput sequencing to assess the bacterial and fungal profiles along a gradient of Tl contents in Tl mine waste rocks in southwestern China. Our results showed that Tl had an important, but different influence on the bacterial and fungal diversity indices. Using linear regression analysis, we furtherly divided the dominant bacterial and fungal groups into three distinct microbial sub-communities thriving at high, moderate, and low levels of Tl. Furthermore, our results also showed that Tl is also an important environmental variable that regulates the distribution patterns of ecological clusters and indicator genera. Interestingly, the microbial groups enriched in the samples with high Tl levels were mainly involved in metal and nutrient cycling. Taken together, our results have provided useful information about the responses of bacterial and fungal groups to Tl contamination.

Recent advances in exploring the heavy metal(loid) resistant microbiome

Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.

Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution

Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.

Gut microbiota health closely associates with PCB153-derived risk of host diseases

Although the production and use of PCB153 have been banned globally, PCB153 pollution remains because of its persistence and long half-life in the environment. There is ongoing evidence that exposure to PCB153 may influence gut microbiota health and increase the risk of host health. It is needed to illuminate whether there are associations between gut microbiota dysregulation and PCB153-induced host diseases. Importantly, it is urgently needed to find specific strains as biomarkers to monitor PCB153 pollution and associated disorders. The work aims to investigate the change of gut microbiota composition, structure and diversity and various host physiological indexes, to ravel the chain causality of PCB153, gut microbiota health and host health, and to find potential gut microbiota markers for PCB153 pollution. Here, adult female mice were administrated with PCB153. Obtained results indicated that PCB153 led to gut microbiota health deterioration. PCB153 exposure also induced obesity, hepatic lipid accumulation, abdominal adipose tissue depots and dyslipidemia in mice. Furthermore, specific gut microbiota significantly correlated with the host health indexes. This work provides support for the relationship between gut microbiota aberrance derived from PCB153 and risk of host health, and offers some indications of possible indicative functions of gut microbiota on PCB153 pollution.

Deciphering the toxic effects of metals in gold mining area: Microbial community tolerance mechanism and change of antibiotic resistance genes

Mine tailing dumps represent significant threats to ecological environments due to the presence of toxic substances. The present work investigated the relationship among microbial activity, the community, antibiotic resistance genes (ARGs) and trace metals in soil surrounding gold mine tailings. Using microbial metabolic activity and high-throughput sequencing analysis, we found the trace metals Cd and Hg could be main factors influencing the microbial community. According to bacterial co-occurrence pattern analysis, the effects of total cadmium and total mercury on bacterial diversity are potentially mediated by influencing bacteria community in the keystone module II. Additionally, most of metal-resistant bacteria belong to Actinobacteria and Proteobacteria, and the metal tolerance suggested to be linked with various functions including replication, recombination and repair, as well as inorganic ion transport and metabolism based on PICRUSt2 analysis. We also found that metals generated by mining activity may trigger the co-selection of antibiotic resistance in the phyla Actinobacteria and Proteobacteria due to co-resistance or cross resistance. Additionally, PLS-PM analysis revealed that metals could indirectly affect ARGs by influencing bacterial diversity in gold mining areas.

Long-lasting effect of mercury contamination on the soil microbiota and its co-selection of antibiotic resistance

Antibiotic resistance genes (ARGs) in the environment are an exposure risk to humans and animals and is emerging as a global public health concern. In this study, mercury (Hg) driven co-selection of ARGs was investigated under controlled conditions in two Australian non-agricultural soils with differing pH. Soils were spiked with increasing concentrations of inorganic Hg and left to age for 5 years. Both soils contained ARGs conferring resistance to tetracycline (tetA, tetB), sulphonamides (sul1), trimethoprim (dfrA1) and the ARG indicator class 1 integron-integrase gene, intI1, as measured by qPCR. The last resort antibiotic vancomycin resistance gene, vanB and quinolone resistance gene, qnrS were not detected. Hg driven co-selection of several ARGs namely intI1, tetA and tetB were observed in the alkaline soil within the tested Hg concentrations. No co-selection of the experimental ARGs was observed in the neutral pH soil. 16S rRNA sequencing revealed proliferation of Proteobacteria and Bacteriodetes in Hg contaminated neutral and alkaline soils respectively. Multivariate analyses revealed a strong effect of Hg, soil pH and organic carbon content on the co-selection of ARGs in the experimental soils. Additionally, although aging caused a significant reduction in Hg content, agriculturally important bacterial phyla such as Nitrospirae did not regrow in the contaminated soils. The results suggest that mercury can drive co-selection of ARGs in contaminated non-agricultural soils over five years of aging which is linked to soil microbiota shift and metal chemistry in the soil.

Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress

An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil

Mercury (Hg) pollution or organic amendments (OA) may individually induce changes in the microbial community of paddy soils. However, little is known regarding the interaction of Hg and OA and the effect of different OA applications on the microbial community assemblage in Hg-polluted paddy soil. A soil incubation experiment was performed by applying three organic amendments (OA), namely a food-waste compost (FC), and its HA and FA, into an Hg-polluted paddy soil to examine the changes in the microbial community and merA/merB gene abundance. The results showed that the OA treatments promoted total (SOC) and dissolved organic carbon (DOC) in soils, which may harbor copiotrophic bacteria. The HA and FA treatments decreased microbial diversity and richness along with an increase of water-soluble Hg (WHg) through the complexation of DOC to Hg, which may be mainly attributed to the enhanced Hg biotoxicity to soil microbiome induced by the increased WHg under these two treatments. Additionally, the WHg enhancement also contributed to the increase of Hg-resistant bacteria and merA/merB gene abundance, and consequently, induced changes in the microbial community. These results indicated the interaction of Hg and different OA induced the variation of WHg fraction in paddy soil, which played a fundamental role in the distinct responses of the microbial community assemblage. Collectively, the application of FA and HA to Hg-polluted soil should be limited considering Hg risk to microbiome, and FC can be an alternative.

Sources, toxicity, and remediation of mercury: an essence review

Mercury (Hg) is a pollutant that poses a global threat, and it was listed as one of the ten leading 'chemicals of concern' by the World Health Organization in 2017. The review aims to summarize the sources of Hg, its combined effects on the ecosystem, and its remediation in the environment. The flow of Hg from coal to fly ash (FA), soil, and plants has become a serious concern. Hg chemically binds to sulphur-containing components in coal during coal formation. Coal combustion in thermal power plants is the major anthropogenic source of Hg in the environment. Hg is taken up by plant roots from contaminated soil and transferred to the stem and aerial parts. Through bioaccumulation in the plant system, Hg moves into the food chain, resulting in potential health and ecological risks. The world average Hg concentrations reported in coal and FA are 0.01-1 and 0.62 mg/kg, respectively. The mass of Hg accumulated globally in the soil is estimated to be 250-1000 Gg. Several techniques have been applied to remove or minimize elevated levels of Hg from FA, soil, and water (soil washing, selective catalytic reduction, wet flue gas desulphurization, stabilization, adsorption, thermal treatment, electro-remediation, and phytoremediation). Adsorbents such as activated carbon and carbon nanotubes have been used for Hg removal. The application of phytoremediation techniques has been proven as a promising approach in the removal of Hg from contaminated soil. Plant species such as Brassica juncea are potential candidates for Hg removal from soil.

Effects of Various Carbon Nanotubes on Soil Bacterial Community Composition and Structure

Carbon nanotubes (CNTs) have huge industrial potential, and their environmental impacts need to be evaluated. Knowledge of CNT impacts on soil microbial communities is still limited. To address this knowledge gap, we systematically examined dynamic effects of one type of single-walled carbon nanotubes (SWs) and three multiwalled carbon nanotubes (MWs) with different outer diameters on the soil bacterial community in an agricultural soil over 56 days. The results showed that SWs differently affected soil bacterial abundance, diversity, and composition as compared to MWs. The differences could have resulted from the materials' distinct physical structure and surface composition, which in turn affected their bioavailability in soil. For certain treatments, soil bacterial diversity and the relative abundance of certain predominant phyla were correlated with their exposure duration. However, many phyla recovered to their initial relative abundance within 56 days, reflecting resilience of the soil bacterial community in response to CNT-induced disturbance. Further analysis at the genus level showed differential tolerance to MWs, as well as size- and dose-dependent tolerance among bacterial genera. Predictive functional profiling showed that while CNTs initially caused fluctuations in microbial community function, community function largely converged across all treatments by the end of the 56 day exposure.

Critical mercury concentration in tropical soils: Impact on plants and soil biological attributes

Mercury is a toxic element that becomes a problem when present at high concentrations in soils. Mercury toxicity in soils varies depending on chemical species, concentration, exposure routes, and organism vulnerability. There is little information regarding the toxicity of Hg in tropical soils, especially for establishing safe levels of this pollutant. The purpose of this study was to investigate Hg concentrations in two tropical soils and their effect on oats and common beans, as well as on soil biological attributes. The experiment was carried out in a greenhouse, following ISO 11.269-2 and OECD-208 guidelines. Oat and common bean were cultivated in a Typic Hapludox (TyHpx) and Rhodic Acrudox (RhAcx) contaminated with HgCl₂ at the following concentrations: 0, 2.5, 5.0, 10.0, 20.0, 40.0, and 80.0 mg of Hg kg^-1 of dry soil. The biological variables analyzed were seedling emergence, vegetative growth, chlorophyll content (SPAD index), gas exchange (photosynthetic rate, internal CO₂ concentration, transpiration rate, and stomatal conductance), and Hg concentration and accumulation in shoot dry matter. Microbial biomass carbon, soil basal respiration, and metabolic quotient (qCO₂) were also analyzed. Due to the sorptive characteristics of TyHpx, it had higher Hg concentrations than RhAcx. Mercury showed toxic effects on both oat and common bean species. However, common bean was affected only at concentrations higher than 20 mg kg^-1. The microbial community showed high sensitivity to soil Hg concentrations, but external factors, such as the plant species cultivated, influenced the sensitivity of the community. The microbiota was most sensitive in pots with common bean, and this effect was more pronounced at low clay and low organic matter contents (TyHpx). In this study, the concentration of 0.36 mg kg^-1 was critical for Hg in these soils, based on its deleterious effects on oat and common bean and on biological soil attributes.

Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

BACKGROUND

The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.

RESULTS

We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).

CONCLUSIONS

Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.

NMR-based metabolic toxicity of low-level Hg exposure to earthworms

Mercury is a globally distributed toxicant to aquatic animals and mammals. However, the potential risks of environmental relevant mercury in terrestrial systems remain largely unclear. The metabolic profiles of the earthworm Eisenia fetida after exposure to soil contaminated with mercury at 0.77 ± 0.09 mg/kg for 2 weeks were investigated using a two-dimensional nuclear magnetic resonance-based (¹H-¹³C NMR) metabolomics approach. The results revealed that traditional endpoints (e.g., mortality and weight loss) did not differ significantly after exposure. Although histological examination showed sub-lethal toxicity in the intestine as a result of soil ingestion, the underlying mechanisms were unclear. Metabolite profiles revealed significant decreases in glutamine and 2-hexyl-5-ethyl-3-furansulfonate in the exposed group and remarkable increases in glycine, alanine, glutamate, scyllo-inositol, t-methylhistidine and myo-inositol. More importantly, metabolic network analysis revealed that low mercury in the soil disrupted osmoregulation, amino acid and energy metabolisms in earthworms. A metabolic net link and schematic diagram of mercury-induced responses were proposed to predict earthworm responses after exposure to mercury at environmental relevant concentrations. These results improved the current understanding of the potential toxicity of low mercury in terrestrial systems.

Are the existing guideline values adequate to protect soil health from inorganic mercury contamination?

Currently, data that guide safe concentration ranges for inorganic mercury in the soil are lacking and subsequently, threaten soil health. In the present study, a species sensitivity distribution (SSD) approach was applied to estimate critical mercury concentration that has little (HC₅) or no effect (PNEC) on soil biota. Recently published terrestrial toxicity data were incorporated in the approach. Considering total mercury content in soils, the estimated HC₅ was 0.6 mg/kg, and the PNEC was 0.12-0.6 mg/kg. Whereas, when only water-soluble mercury fractions were considered, these values were 0.04 mg/kg and 0.008-0.04 mg/kg, respectively.

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil

In this study, we analysed the impact of heavy metals and plant rhizodeposition on the structure of indigenous microbial communities in rhizosphere and bulk soil that had been exposed to heavy metals for more than 150 years. Samples of the rhizosphere of Silene vulgaris and non-rhizosphere soils 250 and 450 m from the source of emission that had different metal concentrations were collected for analyses. The results showed that soils were collected 250 m from the smelter had a higher number of Cd-resistant CFU compared with the samples that were collected from 450 m, but no significant differences were observed in the number of total and oligotrophic CFU or the equivalent cell numbers between rhizosphere and non-rhizosphere soils that were taken 250 and 450 m from the emitter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of the denaturing gradient gel electrophoresis (DGGE) profiles, as well as a cluster analysis that was generated on the phospholipid fatty acid (PLFA) profiles, showed that the bacterial community structure of rhizosphere soils depended more on the plant than on the distance and metal concentrations. The sequencing of the 16S rDNA fragments that were excised from the DGGE gel revealed representatives of the phyla Bacteroidetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Betaproteobacteria in the analysed soil with a predominance of the first three groups. The obtained results demonstrated that the presence of S. vulgaris did not affect the number of CFUs, except for those of Cd-resistant bacteria. However, the presence of S. vulgaris altered the soil bacterial community structure, regardless of the sampling site, which supported the thesis that plants have a higher impact on soil microbial community than metal contamination.

Application of Denaturing Gradient Gel Electrophoresis to the Analysis of Bacterial Communities Associated With Asymptomatic and Symptomatic Pericoronitis

PURPOSE

Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities associated with asymptomatic and symptomatic pericoronitis. The aim of the study was to compare the fingerprinting patterns of these 2 clinical conditions.

MATERIALS AND METHODS

The microbiota of mandibular third molar pockets associated with asymptomatic or symptomatic pericoronitis cases were collected and profiled by the polymerase chain reaction DGGE method. Banding patterns were compared by cluster analysis techniques.

RESULTS

Thirteen symptomatic pericoronitis and 7 asymptomatic pericoronitis samples were collected. Comparative analysis of the 2 clinical conditions showed bands that were common to the symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique to the clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles was 23.8 ± 4.2 (range, 19 to 34) for samples from symptomatic cases and 24.1 ± 2.4 (range, 21 to 29) for those from asymptomatic cases. Cluster analysis and multidimensional scaling analysis of the DGGE banding pattern showed a distinction in the similarity of banding patterns according to the presence or absence of symptoms.

CONCLUSIONS

These results suggest that the diversity of pericoronal pocket microbiota in asymptomatic pericoronitis cases differs markedly from that of symptomatic cases.

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover

The use of biopurification systems can mitigate the effects of pesticide contamination on farms. The primary aim of this study was to evaluate the effect of pesticide dissipation on microbial communities in a pilot biopurification system. The pesticide dissipation of atrazine, chlorpyrifos and iprodione (35 mg kg^-1 active ingredient [a.i.]) and biological activity were determined for 40 days. The microbial communities (bacteria, actinomycetes and fungi) were analyzed using denaturing gradient gel electrophoresis (DGGE). In general, pesticide dissipation was the highest by day 5 and reached 95%. The pesticides did not affect biological activity during the experiment. The structure of the actinomycete and bacterial communities in the rhizosphere was more stable during the evaluation than that in the communities in the control without pesticides. The rhizosphere fungal communities, detected using DGGE, showed small and transitory shifts with time. To conclude, rhizosphere microbial communities were not affected during pesticide dissipation in a pilot biopurification system.

Response of soil microbial activities and microbial community structure to vanadium stress

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC₅₀) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions.

Effects of cadmium-resistant fungi Aspergillus aculeatus on metabolic profiles of bermudagrass [Cynodondactylon (L.)Pers.] under Cd stress

Plants' tolerance to heavy metal stress may be induced by the exploitation of microbes. The objectives of this study were to investigate the effect of cadmium (Cd)-resistant fungus, Aspergillus aculeatus, on tolerance to Cd and alteration of metabolites in bermudagrass under Cd stress, and identify the predominant metabolites associated with Cd tolerance. Two genotypes of bermudagrass with contrasting Cd tolerance (Cd-sensitive 'WB92' and Cd-tolerant 'WB242') were exposed to 0, 50, 150 and 250 mg kg^-1 Cd for 21 days. Physiological responses of bermudagrass to Cd stress were evaluated based on the relative growth rate (RGR) and normalized relative transpiration rate (NRT). Plants inoculated with A. aculeatus exhibited higher RGR and NRT under Cd stress than those of non-inoculated plants, regardless of genotypes. A total of 32 Cd-responsive metabolites in leaves and 21 in roots were identified in the two genotypes, including organic acids, amino acids, sugars, and fatty acids and others. Interestingly, under Cd stress, the leaves of inoculated 'WB92' accumulated less citric acid, aspartic acid, glutamic acid, sucrose, galactose, but more sorbose and glucose, while inoculated 'WB242' leaves had less citric acid, malic acid, sucrose, sorbose, but more fructose and glucose, compared to non-inoculated plants. In 'WB92' roots, the A. aculeatus reduced mannose content, but increased trehalose and citric acid content, while in 'WB242', it decreased sucrose, but enhanced citric acid content, compared to Cd regime. The results of this study suggest that A. aculeatus may induce accumulation of different metabolites associated with Cd tolerance in bermudagrass.

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation

Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH₄⁺-N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.

Detection of Bacillus and Stenotrophomonas species growing in an organic acid and endocrine-disrupting chemical-rich environment of distillery spent wash and its phytotoxicity

Sugarcane molasses-based distillery spent wash (DSW) is well known for its toxicity and complex mixture of various recalcitrant organic pollutants with acidic pH, but the chemical nature of these pollutants is unknown. This study revealed the presence of toxic organic acids (butanedioic acid bis(TMS)ester; 2-hydroxysocaproic acid; benzenepropanoic acid, α-[(TMS)oxy], TMS ester; vanillylpropionic acid, bis(TMS)), and other recalcitrant organic pollutants (2-furancarboxylic acid, 5-[[(TMS)oxy] methyl], TMS ester; benzoic acid 3-methoxy-4-[(TMS)oxy], TMS ester; and tricarballylic acid 3TMS), which are listed as endocrine-disrupting chemicals. In addition, several major heavy metals were detected, including Fe (163.947), Mn (4.556), Zn (2.487), and Ni (1.175 mg l^-1). Bacterial community analysis by restriction fragment length polymorphism revealed that Bacillus and Stenotrophomonas were dominant autochthonous bacterial communities belonging to the phylum Firmicutes and γ-Proteobacteria, respectively. The presence of Bacillus and Stenotrophomonas species in highly acidic environments indicated its broad range adaptation. These findings indicated that these autochthonous bacterial communities were pioneer taxa for in situ remediation of this hazardous waste during ecological succession. Further, phytotoxicity assay of DSW with Phaseolus mungo L. and Triticum aestivum revealed that T. aestivum was more sensitive than P. mungo L. in the seed germination test. The results of this study may be useful for monitoring and toxicity assessment of sugarcane molasses-based distillery waste at disposal sites.

Soil contamination assessment for Pb, Zn and Cd in a slag disposal area using the integration of geochemical and microbiological data

Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted. Metal availability was evaluated based on the geoaccumulation index (I _geo), ecological risk ([Formula: see text]), Risk Assessment Code (RAC) and experimental data, and different reference values were tested to assist in the interpretation of the indices. The soil pH was slightly acidic to neutral, the Eh values indicated oxidized conditions and the average SOM content varied from 12.10 to 53.60 g kg^-1. The average pseudo-total concentrations of metals were in the order of Zn > Pb > Cd. Pb and Zn were mainly bound to the residual fraction and Fe-Mn oxides, and a significant proportion of Cd was bound to the exchangeable and carbonate fractions. The topsoil (0-20 cm) is highly contaminated (I _geo) with Cd and has a very high potential ecological risk ([Formula: see text]). Higher bacterial diversity was mainly associated with higher metal concentrations. It is concluded that the integration of geochemical and microbiological data can provide an appropriate evaluation of mining waste-contaminated areas.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.

Responses of soil ammonia oxidizers to a short-term severe mercury stress

The responses of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to mercury (Hg) stress were investigated through a short-term incubation experiment. Treated with four different concentrations of Hg (CK, Hg25, Hg50, and Hg100, denoting 0, 25, 50, and 100mgHg/kg dry soil, respectively), samples were harvested after 3, 7, and 28day incubation. Results showed that the soil potential nitrification rate (PNR) was significantly inhibited by Hg stress during the incubation. However, lower abundances of AOA (the highest in CK: 9.20×10(7)copies/g dry soil; the lowest in Hg50: 2.68×10(7)copies/g dry soil) and AOB (the highest in CK: 2.68×10(7)copies/g dry soil; the lowest in Hg50: 7.49×10(6)copies/g dry soil) were observed only at day 28 of incubation (P<0.05). Moreover, only the community structure of soil AOB obviously shifted under Hg stress as seen through DGGE profiles, which revealed that 2-3 distinct AOB bands emerged in the Hg treatments at day 28. In summary, soil PNR might be a very useful parameter to assess acute Hg stress on soil ecosystems, and the community structure of soil AOB might be a realistic biological indicator for the assessment of heavy metal stress on soil ecosystems in the future.

Non-Ferrous Metal Industry Waste Disposal Sites As A Source Of Poly-Extremotolerant Bacteria

Waste disposal sites from non-ferrous metal industry constitute environments very hostile for life due to the presence of very specialized abiotic factors (pH, salt concentration, heavy metals content). In our experiments microflora of two waste disposal sites in Slovakia – brown mud disposal site from aluminium production near Ziar nad Hronom and nickel sludge disposal site near Sered - was analyzed for cultivable bacteria. Isolated bacteria were characterized by a combination of classical microbiological approaches and molecular methods and the most of isolated bacteria shown a poly-extremotolerant phenotype. The most frequently halotolerant (resistant to the high level of salt concentrations) and alkalitolerant (resistant to the high pH level) bacteria belonging to the Actinobacteria class were detected. The most of bacteria shown very high level of heavy metal resistance e.g. more than 500 μg/ml for Zn2+ or Cu2+. Based on our data, waste disposal sites thus on one side represents an important environmental burden but on other side they are a source of new poly-extremotolerant bacterial strains and species possibly used in many biotechnology and bioremediation applications.

Applications of organic and inorganic amendments induce changes in the mobility of mercury and macro- and micronutrients of soils

Both soil organic matter and sulfur (S) can reduce or even suppress mercury (Hg) mobility and bioavailability in soil. A batch incubation experiment was conducted with a Chernozem and a Luvisol artificially contaminated by 440 mg·kg⁻¹ Hg showing wide differences in their physicochemical properties and available nutrients. The individual treatments were (i) digestate from the anaerobic fermentation of biowaste; (ii) fly ash from wood chip combustion; and (iii) ammonium sulfate, and every treatment was added with the same amount of S. The mobile Hg portion in Chernozem was highly reduced by adding digestate, even after 1 day of incubation, compared to control. Meanwhile, the outcome of these treatments was a decrease of mobile Hg forms as a function of incubation time whereas the contents of magnesium (Mg), potassium (K), iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), and phosphorus (P) were stimulated by the addition of digestate in both soils. The available calcium (Ca) contents were not affected by the digestate addition. The experiment proved digestate application as the efficient measure for fast reduction of mobile Hg at extremely contaminated soils. Moreover, the decrease of the mobile mercury portion was followed by improvement of the nutrient status of the soils.

Extraction of the metagenomic DNA and assessment of the bacterial diversity from the petroleum-polluted sites

The assessment of the microbial diversity of the entire community of a given habitat requires the extraction of the total environmental DNA. Metagenomic investigations of a petroleum-polluted habitat have its unique challenges. The specific methods were developed for the extraction of high-quality metagenome in good quantity from the petroleum-polluted saline and non-saline sites in Gujarat (India). The soil samples were washed to remove the toxic, hazardous organic pollutants which might interfere with the recovery of the metagenomic DNA. The metagenomic DNA extraction results were encouraging with the mechanical bead beating, soft lysis, and combination of both. The extracted DNA was assessed for its purity and yield followed by its application in the amplification of the 16S rRNA region. The amplicons were used for judging the molecular diversity by the denaturing gradient gel electrophoresis (DGGE). The microbial diversity was also analyzed statistically by calculating various diversity indices and principal component analysis (PCA). The results on the metagenomic diversity of the bacterial population among the three cohorts based on the culture-independent technique exhibited significant difference among the PAH sites and Okha-Madhi and Porbandar Madhavpur habitats.

Patterns of bacterial diversity along a long-term mercury-contaminated gradient in the paddy soils

Mercury (Hg) pollution is usually regarded as an environmental stress in reducing microbial diversity and altering bacterial community structure. However, these results were based on relatively short-term studies, which might obscure the real response of microbial species to Hg contamination. Here, we analysed the bacterial abundance and community composition in paddy soils that have been potentially contaminated by Hg for more than 600 years. Expectedly, the soil Hg pollution significantly influenced the bacterial community structure. However, the bacterial abundance was significantly correlated with the soil organic matter content rather than the total Hg (THg) concentration. The bacterial alpha diversity increased at relatively low levels of THg and methylmercury (MeHg) and subsequently approached a plateau above 4.86 mg kg(-1) THg or 18.62 ng g(-1) MeHg, respectively. Contrasting with the general prediction of decreasing diversity along Hg stress, our results seem to be consistent with the intermediate disturbance hypotheses with the peak biological diversity under intermediate disturbance or stress. This result was partly supported by the inconsistent response of bacterial species to Hg stress. For instance, the relative abundance of Nitrospirae decreased, while that of Gemmatimonadetes increased significantly along the increasing soil THg and MeHg concentrations. In addition, the content of SO(4)(2-), THg, MeHg and soil depth were the four main factors influencing bacterial community structures based on the canonical correspondence analysis (CCA). Overall, our findings provide novel insight into the distribution patterns of bacterial community along the long-term Hg-contaminated gradient in paddy soils.

Stability of soil microbial structure and activity depends on microbial diversity

Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.