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

Microbial functional diversity and carbon use feedback in soils as affected by heavy metals

Soil microorganisms are an important indicator of soil fertility and health. However, our state of knowledge about soil microbial activities, community compositions and carbon use patterns under metal contaminations is still poor. This study aimed to evaluate the influences of heavy metals (Cd and Pb) on soil microorganisms by investigating the microbial community composition and carbon use preferences. Metal pollution was approached both singly and jointly with low (25 and 2500 mg kg^-1) and high (50 and 5000 mg kg^-1) concentrations of Cd and Pb, respectively, in an artificially contaminated soil. In a laboratory incubation experiment, bio-available and potentially bio-available metal concentrations, selected soil properties (pH, electrical conductivity, total organic carbon and total nitrogen), and microbial parameters (microbial activity as basal respiration, microbial biomass carbon (MBC) and microbial functional groups) were determined at two sampling occasions (7 and 49 days). Metal contamination had no effect on the selected soil properties, while it significantly inhibited both microbial activity and MBC formation. Contaminated soils had higher microbial quotient (qCO₂), suggesting there was higher energy demand with less microbially immobilized carbon as MBC. Notably, the efficiency of microbial carbon use was repressed as the metal concentration increased, yet no difference was observed between metal types (p > 0.05). Based on the microbial phospholipid fatty acids (PLFA) analysis, total PLFAs decreased significantly under metal stress at the end of incubation. Heavy metals had a greater negative influence on the fungal population than bacteria with respective 5-35 and 8-32% fall in abundances. The contaminant-driven (metal concentrations and types) variation of soil PLFA biomarkers demonstrated that the heavy metals led to the alteration of soil microbial community compositions and their activities, which consequently had an adverse impact on soil microbial carbon immobilization.

Are Fungal Endophytes Merely Mycorrhizal Copycats? The Role of Fungal Endophytes in the Adaptation of Plants to Metal Toxicity

The contamination of soil with toxic metals is a worldwide problem, resulting in the disruption of plant vegetation and subsequent crop production. Thus, remediation techniques for contaminated soil and water remain a constant interest of researchers. Phytoremediation, which utilizes plants to remove or stabilize contaminants, is perceived to be a promising strategy. However, phytoremediation's use to date is limited because of constraints associated with such factors as slow plant growth rates or metal toxicity. Microbial-assisted phytoremediation serves as an alternative solution, since the impact of the microbial symbionts on plant growth and stress tolerance has frequently been described. Endophytic fungi occur in almost every plant in the natural environment and contribute to plant growth and tolerance to environmental stress conditions. Although this group of symbiotic fungi was found to form association with a wide range of hosts, including the non-mycorrhizal Brassicaceae metallophytes, their role in the response of plants to metal toxicity has not been thoroughly elucidated to date. This review summarizes the current knowledge regarding the role of endophytic fungi in the tolerance of plants to toxic metals and highlights the similarities and differences between this group of symbiotic fungi and mycorrhizal associations in terms of the survival of the plant during heavy metal stress.

Establishing a quick screening method by using a microfluidic chip to evaluate cytotoxicity of metal contaminants

Due to rapid industrialization and urbanization, the environment is exposed to many chemicals from natural or anthropogenic sources. The contaminants impact eco-system and human health via food chain. Animals, including humans, are likely to accumulate contaminants in their bodies from direct exposure or feeding behavior, resulting in toxicity. Therefore, evaluation of the toxicity of contaminants is an important issue. Metals are highly toxic but the toxicity depends on many factors, including the valance and the complex form of metals, the organic matter level in the environment, the reducing/oxidizing condition of the environment, and etc. Since the level of metal amount does not directly correlate to bioavailability, cell culture is usually used for toxicity evaluation. In this study, a microfluidic chip was developed to evaluate the cell toxicity from exposure to metals, copper and thallium. Compared to traditional cytotoxicity assay using static state culture with tetrazolium reagent, this microfluidic chip can generate various shear stresses by changing geometry of culture areas or flow rate. Enhancement of shear stresses could increase cell sensitivity toward metal exposure. Therefore, this platform provides a more sensitive platform for quantitative analysis of cell toxicity and could be applied to evaluate toxicity from environmental samples.

Loss characteristics of Cd in soil aggregates under simulated rainfall conditions

Soil particles exert a significant influence on the migration of heavy metals in soil and water environments. In this study, a simulated rainfall experiment was conducted to investigate the loss characteristics of cadmium (Cd) from a red soil surface. Two rainfall intensities (50 and 100 mm h^-1) were considered and the distribution of Cd in different fractions (>1, 1-0.25, 0.25-0.05 and <0.05 mm) of aggregates lost from the soil was examined. The result showed that in the artificially polluted soil, the Cd content in different aggregates decreased with particle size, with the lowest Cd content in the <0.05 mm fraction aggregates. In the rainfall experiment, the runoff rate generally increased with the rainfall duration, while the sediment yield rate first increased and then remained stable. The loss rates of various fractions of aggregates in the sediment generally followed the order of (<0.05) mm > 1-0.25 mm > 0.25-0.05 mm > (>1) mm. The proportions of the <0.05 mm-fraction aggregates were the highest in the loss sediment throughout the entire rainfall process. The lost Cd was transported mainly in the sediment-bound form, while only a very small portion of Cd was lost in the water phase of runoff. High rainfall intensity led to greater Cd loss in runoff. In the lost sediment, the concentration of Cd was higher in the macroaggregates. The phenomenon of Cd enrichment in the fine particles was not observed. Although the concentration of Cd in the <0.05 mm fraction was the lowest, the contribution of this fraction to the total Cd content in the sediments was the highest.

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient

Several strains of archaea have the ability to methylate or resist mercury (Hg), and the paddy field is regarded to be conducive to Hg methylation. However, our knowledge of Hg-methylating or Hg-resistant archaea in paddy soils is very limited so far. Therefore, the distribution of archaea and bacteria in the rhizosphere (RS) and bulk soil (BS) of the rice growing in Xiushan Hg-mining area of southwest China was investigated. Bacterial and archaeal 16S rRNA gene amplicon sequencing of the rice rhizosphere along the Hg gradient was conducted. THg concentrations in RS were significantly higher than that in BS at site S1 and S2, while MeHg concentrations in RS was always higher than that in BS, except S6. Bacterial species richness estimates were much higher than that in archaea. The bacterial α-diversity in high-Hg sites was significant higher than that in low-Hg sites based on ACE and Shannon indices. At the genus level, Thiobacillus, Xanthomonas, Defluviicoccus and Candidatus Nitrosoarchaeum were significantly more abundant in the rhizosphere of high-Hg sites, which meant that strains in these genera might play important roles in response to Hg stress. Hg-methylating archaea in the paddy field could potentially be affiliated to strains in Methanosarcina, but further evidence need to be found. The results provide reference to understand archaeal rhizosphere community along an Hg gradient paddy soils.

How autochthonous microorganisms influence physiological status of Zea mays L. cultivated on heavy metal contaminated soils?

The aim of this study was to investigate the effect of autochthonous microorganisms present in soil collected from heavy metal (HM) uncontaminated (Pb ≈ 59 mg kg^-1, Cd ≈ 0.4 mg kg^-1, Zn ≈ 191 mg kg^-1), moderately (Pb ≈ 343 mg kg^-1, Cd ≈ 12 mg kg^-1, Zn ≈ 1876 mg kg^-1), and highly (Pb ≈ 1586 mg kg^-1, Cd ≈ 57 mg kg^-1, Zn ≈ 3280 mg kg^-1) contaminated sites on Zea mays elemental composition, physiological status, and growth parameters. For this purpose, half of the collected soil was sterilized and soil characterization was performed. After 45 days of cultivation, the presence of HM in the soil negatively affected photosynthesis and transpiration rates, relative chlorophyll content, anthocyanins index, chlorophyll fluorescence parameters, and content of oxidative stress products (H₂O₂ and Malondialdehyde) of Zea mays, while soil sterilization had a positive effect on those parameters. Average percentage of colonization of root segments by arbuscular mycorrhiza fungi decreased with an increase of HM contamination in the soil. The increase in shoot concentration of HMs, particularly Cd and Zn, was a result of contaminated soils sterilization. Aboveground biomass of maize cultivated on sterilized soil was 3-fold, 1.5-fold, and 1.5-fold higher for uncontaminated, moderately contaminated and highly contaminated soils respectively when compared to nonsterilized soils. Contrary to our expectation, autochthonous microflora did not improve plant growth and photosynthetic performance; in fact, they had a negative effect on those processes although they did reduce concentration of HMs in the shoots grown on contaminated soils.

Investigation on microbial community in remediation of lead-contaminated soil by Trifolium repensL

Trifolium repensL. is a plant with strong adaptability and large biomass, which possess great potential for phytoremediation. However, little is known concerning its remediation effects and changes in rhizosphere microbial activity and community structure under heavy metal pressure. The aims of this study were to evaluate lead accumulation of Trifolium repensL., study microbial lead resistance, metabolism and community structure characteristics in rhizosphere soils. The accumulated Pb concentration of Trifolium repensL. was observed in 100 and 500 mg/kg Pb contained soil at 55.81 and 90.3 mg/kg, respectively, which cause the decrease of acid-soluble fractions in rhizosphere soil. In the progress of lead-contaminated soil phytoremediation by Trifolium repensL., Pb resistance and metabolic activities of microorganisms have been prompted gradually. In addition, the microbial community composition and abundance were investigated using Illumina sequencing and quantitative PCR. The result showed that after phytoremediation, beneficial microorganisms, such as Flavisolibacter, Kaistobacter, and Pseudomonas, increased, becoming the dominant genera. This study has provided insight into the distribution and activity of the microbial community.

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.

Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.

Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals.

Toxic responses of microorganisms to nickel exposure in farmland soil in the presence of earthworm (Eisenia fetida)

Nickel (Ni)-contamination impairs soil ecosystem, threatening human health. A laboratory simulation of Ni-polluted farmland soil study, in the presence or absence of earthworm, was carried out to investigate the toxic responses of soil microorganisms, including microbial biomass C (MBC), soil basal respiration (SBR), metabolic quotient (qCO₂), urease (UA) and dehydrogenase activities (DHA). Additionally, the variations of Ni bioavailability were also explored. Results manifested that MBC and SBR were stimulated at 50 and 100 mg·kg^-1 of Ni but inhibited by further increasing Ni level, showing a Hormesis effect. Earthworm input delayed the occurrence of a maximum SBR inhibition rate under the combined double-factors of time and dose. No specific effect of Ni concentration on the qCO₂ was observed. UA was significantly suppressed at 800 mg·kg^-1 Ni (P < 0.05 or 0.01), whereas DHA was more sensitive and significantly inhibited throughout all the treatments (P < 0.01), indicating a pronounced dose-response relationship. The addition of earthworm facilitated all the biomarkers above. The time-dependent of dose-effect relationship (TDR) on MBC and SBR inhibition rates suggested that the peak responsiveness of microorganisms to Ni stress were approximate on the 21st day. The bioavailable form of per unit Ni concentration declined with time expanded and concentration increased, and the changeable process of the relative amount of bioavailability was mainly controlled by a physicochemical reactions.

Response of bacterial communities to Pb smelter pollution in contrasting soils

Anthropogenic inputs of trace elements (TE) into soils constitute a major public and environmental health problem. Bioavailability of TE is strongly related to the soil physicochemical parameters and thus to the ecosystem type. In order to test whether soil parameters influence the response of the bacterial community to TE pollution, we collected soil samples across contrasting ecosystems (hardwood, coniferous and hydromorphic soils), which have been contaminated in TE and especially lead (Pb) over several decades due to nearby industrial smelting activities. Bacterial community composition was analysed using high throughput amplicon sequencing and compared to the soil physicochemical parameters. Multivariate analyses of the pedological and biological data revealed that the bacterial community composition was affected by ecosystem type in the first place. An influence of the contamination level was also evidenced within each ecosystem. Despite the important variability in bacterial community structure, we found that specific bacterial groups such as γ-Proteobacteria, Verrucomicrobia and Chlamydiae showed a consistent response to Pb content across contrasting ecosystems. Verrucomicrobia were less abundant at high contamination level whereas Chlamydiae and γ-Proteobacteria were more abundant. We conclude that such groups and ratio's thereof can be considered as relevant bioindicators of Pb contamination.

The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China

Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions.

Effects of chromium(III) on enzyme activities and bacterial communities during swine manure composting

The present study investigated the effects of different concentrations of chromium (i.e., 200 and 700mgkg^-1 Cr corresponding to Cr200 and Cr700, respectively) on the microorganisms in swine manure compost. The results demonstrated that a high concentration of Cr(III) could inhibit the activity of key microbial enzymes (i.e., dehydrogenase, cellulase, and urease) in the early composting stages, with maximal inhibition rates of 54.9%, 32.8%, and 46.7% for cellulase, urease, and dehydrogenase, respectively. Furthermore, the bacterial abundances were determined by quantitative PCR and their compositions were evaluated by denaturing gradient gel electrophoresis. Cr200 and Cr700 had significant inhibitory effects on the abundances of bacteria. The DGGE results showed that Cr200 and Cr700 changed the bacterial community structure and diversity, where Cr(III) might enhance the abundance of pathogenic bacteria (e.g., Saccharomonospora) and decrease the abundances of bacteria that degrade cellulose and lignin (e.g., Paenibacillus) during composting.

Distribution characteristics of heavy metal(loid)s in aggregates of different size fractions along contaminated paddy soil profile

Soil aggregates exert a significant influence on the retention and availability of heavy metal(loid)s in soil. In this study, the concentration distribution and chemical forms of heavy metals (Cu, Zn, Cd, Pb, and Hg) and a metalloid (As) in different aggregate-sized fractions (2-0.25, 0.25-0.05, 0.05-0.002, and < 0.002 mm) along the profile (0-1, 1-5, 5-15, and 15-25 cm) of a contaminated paddy field were investigated. The results showed that the values of pH, free Fe oxides (Fe_d), bulk density, and catalase activity gradually increased, whereas the soil organic matter (SOM), cation exchange capacity (CEC), electrical conductivity (EC), microbial biomass carbon (MBC), and urease activity decreased with depth. Long-term heavy metal pollution might impact the catalase activity but showed no obvious influence on the urease activity. Additionally, there was a notable difference in physicochemical properties among the soil aggregates of various particle sizes. The 2-0.25-mm fraction aggregates contained more organic matter, whereas the highest values of CEC and Fe_d were observed in the < 0.002-mm fraction. The concentrations of all six heavy metals/metalloid decreased with depth. In different layers, Cu and Cd showed the highest concentrations in the 2-0.25 mm-fraction, followed by the < 0.002-mm fraction, whereas the highest concentrations of Zn, Pb, and As appeared in the < 0.002-mm fraction. No obvious distribution regularity was observed for Hg among the aggregates. All of the metal(loid)s had lower activity in the deeper soil layers, except for Hg. Furthermore, Cu and Cd displayed more stable forms in the < 0.002-mm fraction aggregates.

Microbial diversity in solar greenhouse soils in Round-Bohai Bay-Region, China: The influence of cultivation year and environmental condition

Round-Bohai Bay (RBB)-Region is an important crop production area in China, where vegetables are mainly produced in solar greenhouses. However, excessive fertilization and monoculture have caused serious deterioration of soil quality in this region. Soil microbial communities play pivotal roles in many ecosystem processes and are recognized as integrative components of soil quality. Therefore, in this study, we investigated bacterial and fungal diversity in solar greenhouse soils covering a wide range of cultivation year (CY) and sampling site (SS), by using pyrosequencing technology. Surprisingly, CY and SS had little influence on bacterial and fungal relative abundance and diversity. However, environmental factors (EF) and soil available potassium (K) in particular made a significant contribution to the variation of soil bacterial and fungal communities. Specifically, K showed significant (P < 0.05) correlations with dominant bacterial phyla Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes and fungal phyla Ascomycota and Basidiomycota. These results suggested that soil EF appeared more important than CY and SS in shaping the compositions of bacterial and fungal communities. In addition, since fertilizer K has been in the long-term abused in RBB-Region, future vegetable production should pay more attention to K input to reduce the negative effect on soil microbial communities.

Cloning and characterization of iron-superoxide dismutase in Antarctic yeast strain Rhodotorula mucilaginosa AN5

A novel superoxide dismutase gene from Antarctic yeast Rhodotorula mucilaginosa AN5 was cloned, sequenced, and then expressed in Escherichia coli. The R. mucilaginosa AN5 SOD (RmFeSOD) gene was 639 bp open reading frame in length, which encoded a protein of 212 amino acids with a deduced molecular mass of 23.5 kDa and a pI of 7.89. RmFeSOD was identified as iron SOD type with a natural status of homodimer. The recombinant RmFeSOD showed good pH stability in the pH 1.0-9.0 after 1 h incubation. Meanwhile, it was found to behave relatively high thermostability, and maintained more than 80% activity at 50 °C for 1 h. By addition of 1 mM metal ions, the enzyme activity increased by Zn²⁺ , Cu²⁺ , Mn²⁺ , and Fe³⁺ , and inhibited only by Mg²⁺ . RmFeSOD showed relatively low tolerance to some compounds, such as PMSF, SDS, Tween-80, Triton X-100, DMSO, β-ME, and urea. However, DTT showed no inhibition to enzyme activity. Using copper stress experiment, the RmFeSOD recombinant E. coli exhibited better growth than non-recombinant bacteria, which revealed that RmFeSOD might play an important role in the adaptability of heavy metals.

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.

Changes in the heavy metal distributions in whole soil and aggregates affected by the application of alkaline materials and phytoremediation

The combined effect of alkaline materials and plants on the distribution of copper and cadmium in whole soil and aggregates was explored by a 3 yearin situexperiment.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

Microbial Diversity of Chromium-Contaminated Soils and Characterization of Six Chromium-Removing Bacteria

Three soil samples obtained from different sites adjacent to a chromium slag heap in a steel alloy factory were taken to examine the effect of chromium contamination on soil bacterial diversity as determined by construction of 16S rDNA clone libraries and sequencing of selected clones based on restriction fragment length polymorphism (RFLP) analysis. Results revealed that Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Alphaproteobacteria occurred in all three soil samples, although the three samples differed in their total diversity. Sample 1 had the highest microbial diversity covering 12 different classes, while Sample 3 had the lowest microbial diversity. Strains of six different species were successfully isolated, one of which was identified as Zobellella denitrificans. To our knowledge, this is the first report of a strain belonging to the genus Zobellella able to resist and reduce chromium. Among all isolates studied, Bacillus odysseyi YH2 exhibited the highest Cr(VI)-reducing capability, with a total removal of 23.5 % of an initial Cr(VI) concentration of 350 mg L(-1).

An ecological risk assessment of heavy metal contamination in the surface sediments of Bosten Lake, northwest China

Bosten Lake, a typical rump lake in an oasis in northwest China, was chosen to evaluate the distribution, sources, pollution status, and potential ecological risk of heavy metals. Sediment samples were collected from the lake, and results showed that the values of the eight heavy metals all fell within the Second Soil National Standard, while the average and maximum values of the metals were higher than the background values of the study. Multivariate statistical analysis showed that sediment concentrations of Cd, Pb, Hg, and Zn were mainly influenced by man sources. In comparison, Cu, Ni, Cr, and As were primarily natural in origin. Enrichment factor analysis (EF) and the geo-accumulation index evaluation method (I geo) showed that Cd, Hg, and Pb fell under low and partial serious pollution levels, while Zn, As, Cr, Ni, and Cu mainly were characterized under no pollution and low pollution levels. The potential ecological hazards index (RI) showed that among the eight heavy metals, Pb, Hg, and Cd posed the highest potential ecological risk, with potential ecological hazards indices (RI) of 29.06, 27.71, and 21.54 %, respectively. These findings demonstrated that recent economic development in the area of the basin has led to heavy metal accumulation in the surface sediments of the lake.

Different responses of soil microbial metabolic activity to silver and iron oxide nanoparticles

The knowledge regarding the effects of metal or metal oxide nanoparticles on soil microbial metabolic activity and key ecological functions is limited, relative to the information about their species diversity. For this reason, the responses of soil microbial metabolic activity to silver (AgNPs) and iron oxide (FeONPs) nanoparticles, along concentration gradients of each, were evaluated by microcalorimetry and soil nitrification potential. The changes in abundances of bacteria, eukaryotes and ammonia-oxidizing bacteria were measured by real time quantitative PCR. It was found that AgNP (at 0.1, 1 and 10 mg kg(-1) soil) amendments decreased soil microbial metabolic activity, nitrification potential and the abundances of bacteria and ammonia-oxidizing bacteria; on the contrary, FeONPs had the positive effects on soil microbial metabolic activity (at 1 and 10 mg kg(-1) soil) and soil nitrification potential (at 0.1 and 1 mg kg(-1) soil). Specific microbial metabolic activity and specific nitrification potential further revealed that metal or metal oxide nanoparticles could change the C and N cycles of the agricultural soil through influencing soil microbial metabolism. These findings could deepen the understanding of the influence of NPs on soil microorganisms and their driven soil ecology process.

A Survey of Soil Enzyme Activities along Major Roads in Beijing: The Implications for Traffic Corridor Green Space Management

Soil quality is critical to the management of urban green space, in particular, along traffic corridors where traffic-related air pollution is significant. Soil quality can be evaluated by soil enzyme activities, which show quick responses to both natural and anthropogenic disturbances. In this study, we investigated three soil enzyme activities (i.e., dehydrogenase, catalase and urease) along the major roads in urban areas of Beijing. Results show the activities of dehydrogenase, catalase and urease in urban samples were 58.8%, 68.2% and 48.5% less than the rural sample, respectively. The content of fluorescent amino acids as indicators of microbial activities was also consistently lower in urban samples than the rural. We observed two times greater exposure of particulate material along the roadsides in urban areas than rural areas. Although traffic air pollutants provide some nutrient sources to stimulate the URE activity, the exposure to traffic-related air pollution leads to the substantial decrease in enzyme activities. There were significant negative correlations for exposure to PM10 with DHA (r = −0.8267, p = 0.0017) and CAT (r = −0.89, p = 0.0002) activities. For the urban soils URE activity increased with the increasing of PM. We conclude that the degraded soil quality can negatively affect the target of developing plants and green spaces along the traffic corridors to mitigate the traffic impact. This study suggests the investigation of integrated strategies to restore the soil quality, reinforce the ecological service functions of green spaces along the traffic corridors and reduce the traffic pollutants.

Development of an NDIR CO₂ sensor-based system for assessing soil toxicity using substrate-induced respiration

The eco-toxicological indicators used to evaluate soil quality complement the physico-chemical criteria employed in contaminated site remediation, but their cost, time, sophisticated analytical methods and in-situ inapplicability pose a major challenge to rapidly detect and map the extent of soil contamination. This paper describes a sensor-based approach for measuring potential (substrate-induced) microbial respiration in diesel-contaminated and non-contaminated soil and hence, indirectly evaluates their microbial activity. A simple CO2 sensing system was developed using an inexpensive non-dispersive infrared (NDIR) CO2 sensor and was successfully deployed to differentiate the control and diesel-contaminated soils in terms of CO2 emission after glucose addition. Also, the sensor system distinguished glucose-induced CO2 emission from sterile and control soil samples (p ≤ 0.0001). Significant effects of diesel contamination (p ≤ 0.0001) and soil type (p ≤ 0.0001) on glucose-induced CO2 emission were also found. The developed sensing system can provide in-situ evaluation of soil microbial activity, an indicator of soil quality. The system can be a promising tool for the initial screening of contaminated environmental sites to create high spatial density maps at a relatively low cost.

Influence of removal of organic matter and iron and manganese oxides on cadmium adsorption by red paddy soil aggregates

Different soil components in various aggregates were selectively removed for evaluating their influence on Cd adsorption.

Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon-contaminated and uncontaminated soils following willow (Salix spp. L.) planting

Phytoremediation is a potentially inexpensive alternative to chemical treatment of hydrocarbon-contaminated soils, but its success depends heavily on identifying factors that govern the success of root-associated microorganisms involved in hydrocarbon degradation and plant growth stimulation. Arbuscular mycorrhizal fungi (AMF) form symbioses with many terrestrial plants, and are known to stimulate plant growth, although both species identity and the environment influence this relationship. Although AMF are suspected to play a role in plant adaptation to hydrocarbon contamination, their distribution in hydrocarbon-contaminated soils is not well known. In this study, we examined how AMF communities were structured within the rhizosphere of 11 introduced willow cultivars as well as unplanted controls across uncontaminated and hydrocarbon-contaminated soils at the site of a former petrochemical plant. We obtained 69 282 AMF-specific 18S rDNA sequences using 454-pyrosequencing, representing 27 OTUs. Contaminant concentration was the major influence on AMF community structure, with different AMF families dominating at each contaminant level. The most abundant operational taxonomic unit in each sample represented a large proportion of the total community, and this proportion was positively associated with increasing contamination, and seemingly, by planting as well. The most contaminated soils were dominated by three phylotypes closely related to Rhizophagus irregularis, while these OTUs represented only a small proportion of sequences in uncontaminated and moderately contaminated soils. These results suggest that in situ inoculation of AMF strains could be an important component of phytoremediation treatments, but that strains should be selected from the narrow group that is both adapted to contaminant toxicity and able to compete with indigenous AMF species.