Biomass carbon measurements and substrate utilization patterns of microbial populations from soils amended with cadmium, copper, or zinc

The microbial mechanisms by which long-term heavy metal contamination affects soil organic carbon levels

Globally, reducing carbon emissions and mitigating soil heavy metal pollution pose pressing challenges. We evaluated the effects of lead (Pb) and cadmium (Cd) contamination in the field over 20 years. The five treatment groups featured Pb concentrations of 40 and 250 mg/kg, Cd concentrations of 10 and 60 mg/kg, and a combination of Pb and Cd (60 and 20 mg/kg, respectively); we also included a pollution-free control group. After 20 years, soil pH decreased notably in all treatments, particularly by 1.02 in Cd10-treated soil. In addition to the increase of SOC in Cd10 and unchanged in Pb40 treatment, the SOC was reduced by 9.62%-12.98% under the other treatments. The α diversities of bacteria and fungi were significantly changed by Cd10 pollution (both p < 0.05) and the microbial community structure changed significantly. However, there were no significant changes in bacterial and fungal communities under other treatments. Cd10 pollution reduced the numbers of Ascomycota and Basidiomycota fungi, and enhanced SOC accumulation. Compared to the control, long-term heavy Cd, Pb, and Pb-Cd composite pollution caused SOC loss by increasing Basidiomycota which promoting carbon degradation, and decreasing Proteobacteria which promoting carbon fixation via the Krebs cycle. Our findings demonstrate that heavy metal pollution mediates Carbon-cycling microorganisms and genes, impacting SOC storage.

Uptake of potentially toxic elements and polycyclic aromatic hydrocarbons from the hydromorphic soil and their cellular effects on the Phragmites australis

The current study provides an information on the combined effect of pollution with potentially toxic elements (PTEs) and polycyclic aromatic hydrocarbons (PAHs) in hydromorphic soils on the accumulation, growth, functional and morphological-anatomical changes of macrophyte plant, i.e., Phragmites australis Cav., as well as information about their bioindication status on the example of small rivers of the Azov basin. The territory of the lower reaches of the Kagalnik River is one of the small rivers of the Eastern Azov region was examined with different levels of PTEs contamination in soils, where the excess of the lithosphere clarkes and maximum permissible concentrations (MPC) for Mn, Cr, Zn, Pb, Cu, and Cd were found. The features of the 16 priority PAHs quantitative and qualitative composition in hydromorphic soils and P. australis were revealed. The influence of soil pollution on accumulation in P. australis, as well as changes in the morphological parameters were shown. It has been observed that morphometric changes in P. australis at sites experiencing the сontamination and salinity are reflected with the changes in the ultrastructure of plastids, mitochondria, and EPR elements of plant cells. PTEs accumulated in inactive organs and damaged cell structures. At the same time, PAHs penetrated through the biomembranes and violated their integrity, increased permeability, resulted cell disorganization, meristem, and conductive tissues of roots. The nature and extent of the structural alterations found are dependent on the type and extent of pollution in the examined regions and can be utilized as bioindicators for evaluating the degree of soil phytotoxicity characterized by the accumulation of PTE and PAHs.

Effects of Amendments and Indigenous Microorganisms on the Growth and Cd and Pb Uptake of Coriander (Coriandrum sativum L.) in Heavy Metal-Contaminated Soils

Heavy metal (HM) contamination of soils is a worldwide problem with adverse consequences to the environment and human health. For the safe production of vegetables in contaminated soil, efficient soil amendments need to be applied such as nano-hydroxyapatite (n-HAP) and poly γ-glutamic acid (γ-PGA), which can mitigate heavy metal uptake and enhance crop yield. However, the combined effects of soil amendments and indigenous microorganisms (IMOs) on HMs immobilisation and accumulation by crops have received little attention. We established a pot experiment to investigate the effects of IMOs combined with n-HAP and γ-PGA on coriander (Coriandrum sativum L.) growth and its Cd and Pb uptake in two acidic soils contaminated with HMs. The study demonstrated that applying n-HAP, with and without IMOs, significantly increased shoot dry biomass and reduced plant Cd and Pb uptake and diethylenetriaminepentaacetic acid (DTPA) extractable Cd and Pb concentrations in most cases. However, γ-PGA, with and without IMOs, only reduced soil DTPA-extractable Pb concentrations in slightly contaminated soil with 0.29 mg/kg Cd and 50.9 mg/kg Pb. Regardless of amendments, IMOs independently increased shoot dry biomass and soil DTPA-extractable Cd concentrations in moderately contaminated soil with 1.08 mg/kg Cd and 100.0 mg/kg Pb. A synergistic effect was observed with a combined IMOs and n-HAP treatment, where DTPA-extractable Cd and Pb concentrations decreased in slightly contaminated soil compared with the independent IMOs and n-HAP treatments. The combined treatment of γ-PGA and IMOs substantially increased shoot dry biomass in moderately contaminated soil. These results indicate that solo n-HAP enhanced plant growth and soil Cd and Pb immobilisation, and mitigated Cd and Pb accumulation in shoots. However, the combination of n-HAP and IMOs was optimal for stabilising and reducing HMs' uptake and promoting plant growth in contaminated soil, suggesting its potential for safe crop production.

Opportunities regarding the use of technologies of energy recovery from sewage sludge

Abstract

Based on the global need to efficiently eliminate highly produced amounts of sewage sludge, alternative technologies are required to be practically developed. Reduction of sewage sludge waste quantities with energy recovery is the most important and modern practice, with least possible impact on the environment. Appropriate technologies for treating and disposal sewage sludge are currently considered: incineration, gasification and pyrolysis. The main products generated during the pyrolysis process are bio-gas, bio-oil and bio-residue, providing sustainable fuels/ biofuels and adsorbents. Compared to other disposal methods of sewage sludge, pyrolysis has advantages in terms of the environment: waste in small quantities, low emissions, low level of heavy metals. From a technological point of view, pyrolysis is the most efficient in relation to its final products, pyrolysis oil, pyrolysis gas and solid residue that can be transformed into CO2 adsorbent with the help of chemical and thermal activation processes. The incineration process of sewage sludge has a number of disadvantages both environmentally and technologically: organic pollutants, heavy metals, toxic pollutants and ash resulting from combustion that needs a disposal process. A comparison of different types of sewage sludge elimination for the energy recovery is described in the present paper.

Article Highlights

Comparing the effect of Cu-based fungicides and pure Cu salts on microbial biomass, microbial community structure and bacterial community tolerance to Cu

The effect of Cu on three different microbial endpoints was studied using different Cu sources, in order to check the usefulness of pure Cu salts to estimate the toxicity of commercial Cu fungicides on soil microbes. Cu additions caused similar dose-response curves of substrate induced respiration (SIR) decreases regardless of Cu source, i.e. the use of pure Cu salts to estimate the effect of Cu fungicides on microbial biomass using SIR may be useful. Phospholipid fatty acid (PLFA) analysis showed that the Cu source was more important for the microbial community structure than Cu concentration. Thus, the use of Cu salts to infer the effects of Cu fungicides on microbial community structure using PLFA analysis is not recommended, since effects of Cu concentration will be confounded with Cu source. Analyzing pollution induced community tolerance (PICT) to Cu showed that the use of pure Cu salts may overestimate Cu effects if Cu salt additions modified the soil pH. The highest doses of Cu salts increased bacterial community tolerance to Cu between 300 and 600 times, while commercial Cu fungicide increases were between 20 and 160 times. Therefore, the use of pure Cu salts to estimate the Cu fungicides effects on soil microbes is not recommended for PLFAs analyses, not suitable for PICT at high Cu concentrations, while useful for SIR.

Microbial Features Indicating the Recovery of Soil Ecosystem Strongly Affected by Mining and Ore Processing

Tailings-derived soils formed from waste materials produced during mineral processing often exhibit extremes of pH, low content of organic matter and limited nutrient availability. The success of site revitalization depends mostly on the ability to maintain natural soil functions. We analyzed technogenic sediments from four selected localities in Slovakia defined as environmental burdens: Slovinky (SLS, SLD), Markušovce (MAS, MAD), Lintich (LIS, LID), Horná Ves (HVS, HVD) in the presented research. None of these sites has long been used for its original purpose. In all localities, the concentrations of several risk elements (As, Ba, Cd, Co, Cr, Cu, Ni, Pb, Zn) still significantly exceed the statutory limit values. Besides the content of risk elements, the amounts of organic carbon, total nitrogen, pH value and moisture level in technogenic substrates were determined. We evaluated selected microbiological parameters, including microbial biomass carbon (MBC), microbial respiration and cellulolytic activity to determine how soil organisms tolerate long-term pollution. In general, the values of microbiological parameters were not as low as one would expect. The results confirmed a negative correlation between MBC content and concentrations of several toxic metals (Co, Cr, Cu, Ni, Zn). The values of assessed microbial indicators were in several cases comparable to those in natural soils. We noticed the lowest metabolic quotient values (qCO₂) in the heavily polluted locality HVS. The microbial quotient (qMic) was low in every locality except HVS, where the substrate availability index (SAI) was highest. The soil microbial community properties have shown that, despite adverse conditions, these emerging soils allow the growth and development of microorganisms to such an extent that they can adequately use available (although limited) nutrients. The data obtained suggest that these severely impacted soil ecosystems can restore their original environmental functions in time.

Competitive redox reaction of Au-NCs/MnO2 nanocomposite: Toward colorimetric and fluorometric detection of acid phosphatase as an indicator of soil cadmium contamination

In this study, by rational regulating the competitive redox reaction of Au-NCs/MnO₂ nanocomposite between the dye indigo carmine (IC) and the enzymatic product L-ascorbic acid (AA), we have established a colorimetric and fluorometric double-channel responsive assay for acid phosphatase (ACP), which could serve as an indicator of soil cadmium (Cd) contamination. Initially, the gold nanoclusters (Au-NCs) were added to the suspension of MnO₂ nanosheets to form Au-NCs/MnO₂ nanocomposite with enhanced oxidative degradation ability. When IC was subsequently added, the blue color of IC faded due to oxidative degradation, and the mixture showed the yellow color of Au-NCs/MnO₂ nanocomposite. Meanwhile, based on the inner filter effect (IFE), the fluorescence of Au-NCs was suppressed by MnO₂ nanosheets during this process. However, with the presence of AA, hydrolyzed from L-ascorbic-2-phosphate (AAP) by ACP, the MnO₂ nanosheets in Au-NCs/MnO₂ nanocomposite were reduced to Mn²⁺ immediately. As a consequence, IC remained its blue color, in the meantime, the fluorescence of Au-NCs recovered, which essentially constituted a new mechanism for ACP detection with colorimetric and fluorometric double-channel response. With the method we developed, soil ACP activity can either be directly visualized by bare eyes or detected reliably through double channels. Furthermore, the dynamic changes of ACP activity during soil Cd contamination could also be monitored; the sharp increase of ACP activity at an appropriate time point could serve as a unique alarm for cadmium (Cd) contamination in soil, which is of great importance for soil quality evaluation and ecological risk assessment.

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.

Soil pH effects on the toxicity of zinc oxide nanoparticles to soil microbial community

We conducted an experiment with two agricultural soils with acidic and alkaline pH levels to assess the effects of zinc oxide nanoparticles (nZnO) on the bacterial community. The effect of the nZnO concentrations (0, 0.1, 1, 10, 100, 1000 mg Zn/kg soil) and contact time between nanoparticles and soil (180 days) was considered. We measured the microbial respiration rate, nitrogen transformation, enzymatic activities (dehydrogenase (DH), acidic phosphatase (ACP), and alkaline phosphatase (ALP)), and the community-level physiological profile (CLPP) soil parameters. Respiration potential and nitrogen transformation were negatively affected only at the highest nZnO concentration. The changes in enzymatic activities were very variable with time and between both soils. A stimulating effect of the nanoparticles on microbial activity was clearly shown at 30 days after the nZnO application in both soils, except for the 1000 mg/kg in calcareous soil, after which time in the latter, the functional richness of the bacterial community was reduced to virtually zero. However, values of the enzymatic activities demonstrated that there was self-adaptation of microbial communities over the study period (180 days). The nZnO 1000 mg/kg dose produced an increase in bacterial growth in the acidic soil, without apparent changes in their metabolic profiles over time. A good correlation was found between microbial respiration rates (calcareous and acidic soils) and microbial metabolic activity (acidic soil) based on extracted Zn concentrations. Our findings suggest the necessity of additional studies to examine the effects of nZnO in natural microorganism populations in soil with different pH levels for extended periods of time.

Environmental Concentrations of Copper, Alone or in Mixture With Arsenic, Can Impact River Sediment Microbial Community Structure and Functions

In many aquatic ecosystems, sediments are an essential compartment, which supports high levels of specific and functional biodiversity thus contributing to ecological functioning. Sediments are exposed to inputs from ground or surface waters and from surrounding watershed that can lead to the accumulation of toxic and persistent contaminants potentially harmful for benthic sediment-living communities, including microbial assemblages. As benthic microbial communities play crucial roles in ecological processes such as organic matter recycling and biomass production, we performed a 21-day laboratory channel experiment to assess the structural and functional impact of metals on natural microbial communities chronically exposed to sediments spiked with copper (Cu) and/or arsenic (As) alone or mixed at environmentally relevant concentrations (40 mg kg-1 for each metal). Heterotrophic microbial community responses to metals were evaluated both in terms of genetic structure (using ARISA analysis) and functional potential (using exoenzymatic, metabolic and functional genes analyses). Exposure to Cu had rapid marked effects on the structure and most of the functions of the exposed communities. Exposure to As had almost undetectable effects, possibly due to both lack of As bioavailability or toxicity toward the exposed communities. However, when the two metals were combined, certain functional responses suggested a possible interaction between Cu and As toxicity on heterotrophic communities. We also observed temporal dynamics in the functional response of sediment communities to chronic Cu exposure, alone or in mixture, with some functions being resilient and others being impacted throughout the experiment or only after several weeks of exposure. Taken together, these findings reveal that metal contamination of sediment could impact both the genetic structure and the functional potential of chronically exposed microbial communities. Given their functional role in aquatic ecosystems, it poses an ecological risk as it may impact ecosystem functioning.

Individual and combined effects of cadmium and polycyclic aromatic hydrocarbons on the phytoremediation potential of Xanthium sibiricum in co-contaminated soil

Soil contamination with heavy metals and organic pollutants continues to cause major ecological damage and human health problems. Phytoremediation offers a highly promising technology for the recovery of sites contaminated with mixed pollutants. In this study, we performed a greenhouse experiment to investigate the individual and combined effects of cadmium (Cd) and polycyclic aromatic hydrocarbon (PAH) contamination on the growth of Xanthium sibiricum, and also the ability of this species to accumulate and remove Cd and to reduce PAHs over a period of 75 days. Our results demonstrated that individual or combined contamination by Cd and PAHs showed no significant differences to the control treatment except in the high Cd treatment. The reduction of PAH concentration in the soil with the passage of time was similar in the presence or absence of plants. At higher levels of Cd, the removal of pyrene decreased in both planted and non-planted soils; however, this effect might be due to the higher Cd content. Soil dehydrogenase and polyphenol oxidase activities showed that soil contamination did not have a significant effect on the removal of PAHs. Overall, our results suggest that X. sibiricum might be a suitable species for use in the phytoremediation of contaminated soils.

Poly-γ-glutamic acid, a bio-chelator, alleviates the toxicity of Cd and Pb in the soil and promotes the establishment of healthy Cucumis sativus L. seedling

Poly-γ-glutamic acid (γ-PGA) can be used as a chemical stabilizer to chelate heavy metals in polluted soils. We investigated the effects of γ-PGA on cucumber seedlings under Cd and Pb stresses. γ-PGA effectively reduced the growth inhibitory effects of Cd and Pb on cucumber seedlings. Cd and Pb absorption in cucumber seedlings was also decreased. Further, γ-PGA decreased the malondialdehyde content, and increased the proline content and the total antioxidant capacity of cucumber seedlings in a dose-dependent manner. Infrared spectral characterization of γ-PGA-Cd and γ-PGA-Pb showed that Cd²⁺ and Pb²⁺ bind to free carboxyl groups on γ-PGA. Furthermore, γ-PGA-Cd and γ-PGA-Pb were degraded by 22.02 and 24.68%, respectively, within 28 weeks. The chelating rate of γ-PGA-Pb and γ-PGA-Cd reached 27.26 and 14.28%, respectively. Further, γ-PGA alleviated the negative effects of Cd and Pb on soil microorganisms. Thus, γ-PGA can effectively reduce the accumulation of heavy metals in crops caused by heavy metal pollution of farmland, and has significant application value.

Responses of riverbed sediment bacteria to heavy metals: Integrated evaluation based on bacterial density, activity and community structure under well-controlled sequencing batch incubation conditions

Better understanding the responses of riverbed sediment bacteria to heavy metals is a key for considering using riverbed sediment bacterial community as an indicator of river water contamination by heavy metals. For this, integrated evaluation based on bacterial density, activity and community structure through incubation experiments under well-controlled conditions is necessary to obtain more closely relevant findings that are difficult to achieve through field studies. The findings may also include those that can serve as new evidence to clarify contrary findings reported in previous studies. In this study, sequencing batch incubation experiments were performed using sediment suspensions from three rivers with catchment of different land covers and uses. The effects of four metals (Pb, Cr, Cd and Cu) were investigated by spiking them separately under three different concentration levels. Glucose was added once every day as the carbon source throughout the whole incubation lasted for 30 days. The changing trends of the density of general and heterotrophic bacteria showed clearly that the responses of sediment bacteria to Cu were obviously stronger, followed by that to Cd; whereas, the responses to Pb and Cr were not apparent. For incubation with Cu, a short-term inhibition effect appeared in the initial 3 days and was then followed by a long-term promotion effect reflected by obvious increases of bacterial density against control. In regard of bacterial activity evaluated based on the first-order consumption rate for glucose, a trend of decreases was revealed. The results of PCR-DGGE and sequence analysis of extracted 16S rDNA further suggested there were bacterial species that had strong tolerance against the metal and could grow readily to become new dominating ones. The existence of such bacterial species was inferred as the reason leading to the observed increases of bacterial density during incubation with the metal.

Microbial activities in soil cultivated with corn and amended with sewage sludge

Background

One of the main concerns related to the increasing use of sewage sludge in the soil is the possible presence of excess nutrients, which could cause environmental problems and detrimental effects on the soil microorganisms, considered essential to soil nutrient cycling. Thus, the objective of this work was to evaluate the microbial biomass and activity and some chemical characteristics of one specific tropical soil, classified as Dark Red Distroferric Latosol, of a loamy/clayey texture, in a long-term field experiment using anaerobically digested household sludge amendment. The sludge doses applied were the recommended dose and 2, 4 and 8 times the recommended dose. The authors hypothesized that the frequent application of this compound to the soil, even when using the recommended dose, could affect the available phosphorus (P_av) and heavy metal contents of the soil, resulting in concentrations above the needs of the culture as well as negatively affecting the activity of the soil microorganisms.

Results

The results demonstrated that successive applications of sludge, calculated considering the recommended dose of N for corn, did not increase the soil P_av contents in relation to the treatment in which the fertilizer was applied considering the nutrient needs of the culture, contrary to what happened with the highest sludge doses. The Cr, Ni and Cu contents increased with increase in sludge dose, but did not surpass the limits considered inadequate. There were no accentuated differences between the treatments with respect to microbial biomass C. Basal respiration and the FDA hydrolysis were considered to be the parameters that most differentiated the effect of increasing sludge doses on the microbial activity.

Conclusion

The application of a sludge dose to a tropical soil, based on the recommended dose, did not affect the P_av or heavy metal contents of the soil even after years of application. Since there were no differences between the treatments with respect to the C_mic values, to the contrary of what happened with the other microbiological parameters evaluated, the possibility of changes in the composition of the microbial community with the higher sludge doses was considered.

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation

Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices.

An integrated insight into the response of sedimentary microbial communities to heavy metal contamination

Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.

Identification of cadmium-resistant fungi related to Cd transportation in bermudagrass [Cynodon dactylon (L.) Pers]

Phytoremediation utilizing plants and microbes has been increasingly adopted as a green technology for cleaning up heavy metal polluted soils. Cd polluted soil and native bermudagrass from Liuyang and Zhuzhou in Hunan province of China were collected to investigate microbial diversity and isolate Cd resistant fungi, and then to determine the effect of Cd resistant fungi on Cd tolerance and transportation of bermudagrass. The functional diversity of microorganisms was evaluated using the BIOLOG Eco method. Cd-resistant fungi strain was isolated and identified as Aspergillus aculeatus based on the ribosomal internal transcribed spacer region sequence analysis. Bermudagrass was exposed to control, Cd only, and Cd plus A. aculeatus (Cd + A. aculeatus) with growth matrix (sawdust/sand = 3/1 in volume). Results indicated that Cd + A. aculeatus treated bermudagrass exhibited a higher photosynthetic activity compared to Cd only treated plants. Inoculation of A. aculeatus resulted in a decrease in stem and leaf Cd concentrations, to a greater extent for Cd-sensitive than for Cd-tolerant genotype. However, inoculation of A. aculeatus increased root Cd concentration under Cd stress conditions, significantly elevated soil pH, and decreased soil water-soluble Cd concentration. These results suggested that A. aculeatus might be potentially applied to improve Cd tolerance and to reduce Cd transportation to shoot of bermudagrass.

Phytoremediation for co-contaminated soils of chromium and benzo[a]pyrene using Zea mays L

A greenhouse experiment was carried out to investigate the single effect of benzo[a]pyrene (B[a]P) or chromium (Cr) and the joint effect of Cr-B[a]P on the growth of Zea mays, its uptake and accumulation of Cr, and the dissipation of B[a]P over 60 days. Results showed that single or joint contamination of Cr and B[a]P did not affect the plant growth relative to control treatments. However, the occurrence of B[a]P had an enhancing effect on the accumulation and translocation of Cr. The accumulation of Cr in shoot of plant significantly increased by ≥ 79 % in 50 mg kg(-1) Cr-B[a]P (1, 5, and 10 mg kg(-1)) treatments and by ≥ 86 % in 100 mg kg(-1) Cr-B[a]P (1, 5, and 10 mg kg(-1)) treatments relative to control treatments. The presence of plants did not enhance the dissipation of B[a]P in lower (1and 5 mg kg(-1)) B[a]P contaminated soils; however, over 60 days of planting Z. mays seemed to enhance the dissipation of B[a]P by over 60 % in 10 mg kg(-1) single contaminated soil and by 28 to 41 % in 10 mg kg(-1)B[a]P co-contaminated soil. This suggests that Z. mays might be a useful plant for the remediation of Cr-B[a]P co-contaminated soil.

Microbial community structure and functioning along metal pollution gradients

Toxic effects of heavy metals on soil microorganisms have been confirmed in a number of laboratory studies. However, most real-field studies do not allow for strong general conclusions due to a range of problems, such as pseudoreplication and confounding factors, which are almost impossible to control for with the most commonly used polluted versus unpolluted or random sampling designs. Effects of metal contamination on soil microbial community traits were measured along 2 pollution gradients in southern Poland. Employing an experimental regression design, using 2 separate gradients, the authors aimed to control for effects of soil properties and beta-diversity of microbial communities. General microbial activity was measured as soil basal respiration rate and substrate-induced respiration, while microbial functional and structural diversity were analyzed with community-level physiological profiles and phospholipid fatty acid patterns, respectively. Metal concentrations were normalized to their toxicity and integrated in a toxicity index (TI). Microbial activity (basal and substrate-induced respiration) decreased in both gradients with increasing TI. Community-level physiological profiles for fungi correlated positively with TI, but no impact of TI on the community-level physiological profiles of bacteria was observed. The phospholipid fatty acids a:15 and i:17 were positively correlated with TI, whereas 16:1ω9 and 18:2ω9 were negatively correlated with TI. The use of 2 gradients (Olkusz and Miasteczko Śląskie) allowed the authors to reveal a clear effect of pollution on general microbial structure and activities, even though they were not able to control completely for all confounding factors. Soil pH, organic matter content, and nutrient level appeared to be at least as important as TI in determining microbial community structure and activities.

Impact of copper on the abundance and diversity of sulfate-reducing prokaryotes in two chilean marine sediments

We studied the abundance and diversity of the sulfate-reducing prokaryotes (SRPs) in two 30-cm marine chilean sediment cores, one with a long-term exposure to copper-mining residues, the other being a non-exposed reference sediment. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and showed that SRPs are sensitive to high copper concentrations, as the mean number of SRPs all along the contaminated sediment was two orders of magnitude lower than in the reference sediment. SRP diversity was analyzed by using the dsrB-sequences-based PCR-DGGE method and constructing gene libraries for dsrB-sequences. Surprisingly, the diversity was comparable in both sediments, with dsrB sequences belonging to Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae, SRP families previously described in marine sediments, and to a deep branching dsrAB lineage. The hypothesis of the presence of horizontal transfer of copper resistance genes in the microbial population of the polluted sediment is discussed.

Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure

Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

Links between bacterial communities in marine sediments and trace metal geochemistry as measured by in situ DET/DGT approaches

Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT--diffusive equilibration or diffusive gradients in thin-films) and relate the results with two commonly used microbiological variables (bacterial biomass and bacterial diversity as revealed by DGGE). No previous studies have used such in situ approaches in microbial ecology. For biomass and most of the investigated trace metals (Ag, Cd, Sn, Cr, Ni, Cu, Pb, and Al) no significant correlations were found. The exceptions were Fe, Mn, Co, and As which behave like micronutrients. For bacterial diversity, no relevant relationships were found. We conclude that in situ methods are more adapted tools for microbial ecologists but that ex situ approaches are still necessary.

Analysis of the metabolic utilization of carbon sources and potential functional diversity of the bacterial community in lab-scale horizontal subsurface-flow constructed wetlands

Microorganisms are an integral part of the biogeochemical processes in wetlands. To improve the performance of constructed wetlands, it is very important to know the metabolic properties and functional diversity of the microbial communities. The purpose of this study is to analyze the metabolic properties and functional diversity of the microbial community in a horizontal subsurface-flow constructed wetland (CW) in a laboratory study through the sole-carbon-source utilization profiles using Biolog-ECO microplates. The technique has advantages over traditional cell culture techniques, such as molecular-level techniques-RNA amplification, which are time-consuming, expensive, and only applicable to the small number of species that may be cultured. This CW was designed to treat rural eutrophic water in China, using the plant L. This study showed that the metabolic activities of upper front substrate microorganisms (UF) were greater than those of the lower back substrate microorganisms (LB) in the CW. Integrated areas under average well color development (AWCD) curves of substrate microorganisms in the UF were 131.9, 4.8, and 99.3% higher than in the lower front part (LF), the upper back part (UB), and the LB part of the CW, respectively. Principal components analysis showed significant differences in both community structure and metabolic utilization of carbon sources between substrate microorganisms from different sampling sites. Carbon source utilization of polymers, carbohydrates, carboxylic acids, and amino acids was higher in UF than in LF, but that of amines and phenolic compounds was very similar in UF and LF. The richness, evenness, and diversity of upper substrate microbial communities were significantly higher than those of lower substrate. The LF substrate microbial communities had lower evenness than the other sampling plots, and the lowest richness of substrate microbial community was found in the LB part of the CW.

Biomass estimation across the benthic community in polluted freshwater sediment--a promising endpoint in microcosm studies?

With respect to the ecological relevance of endpoints, biomass as an endpoint might be promising regarding ecotoxicological assessments of benthic communities. In a freshwater microcosm study the effect of two cadmium (Cd) concentrations (50 and 400 mg Cd kg(-1) dw) on biomass and abundance of a benthic community were investigated over a period of seven months. Specifically, the sensitivity of both endpoints in distinguishing differential effects was compared. While bacteria were found to be unaffected by Cd, abundance and biomass of protozoans and metazoans decreased. In a short-term comparison, differences between control and Cd treatments were, overall, more pronounced for flagellate biomass and for metazoan abundance with strong differences between the taxonomic groups; furthermore, over the long-term, the differences among organisms and endpoints changed. Based on toxicant sensitivity, the reasonably low variance of the data and the workload involved, biomass can provide a useful additional endpoint in microcosm studies.

Phytoremediation for co-contaminated soils of benzo[a]pyrene (B[a]P) and heavy metals using ornamental plant Tagetes patula

Pot-culture experiments were conducted to investigate the single effect of benzo[a]pyrene (B[a]P) and the joint effect of metal-B[a]P on the growth of Tagetes patula and its uptake, accumulation and dissipation of heavy metals and B[a]P. Results showed that the low concentration of B[a]P (≤10 mg kg(-1)) could facilitate plant growth and resulted in an increase in biomass at the rate of 10.0-49.7% relative to the control. There were significantly positive correlations between the concentrations of B[a]P accumulated in tissues of the plants and soil B[a]P (P<0.001). However, the occurrence of Cd, Cu and Pb had inhibitive effects on plant growth and B[a]P uptake and accumulation on the whole. T. patula still exhibited a steady feature of Cd-hyperaccumulator under combined contaminated soils. By contrast, the effectiveness of Cu and Pb absorption in the plants was very weak. Plant-promoted biodegradation of B[a]P was the dominant contribution, 79.2-92.4% and 78.2-92.9% of dissipation of B[a]P came from plant-biodegradation under single B[a]P and metal-B[a]P contaminated soils, respectively. Therefore, T. patula might be useful for phytoremediation of B[a]P and B[a]P-Cd contaminated sites.

Temporal bacterial diversity associated with metal-contaminated river sediments

The temporal activity, abundance and diversity of microbial communities were evaluated across a metal-contamination gradient around a Superfund site in Montana. In order to analyze short-term variability, samples were collected from six sites on four occasions over 12 months. Measurements of community activity, diversity and richness, quantified by dehydrogenase activity and through denaturant gradient gel electrophoresis (DGGE), respectively, were higher at contaminated sites adjacent to the smelter, relative to reference sites. 16S rRNA gene copy numbers, measured by quantitative PCR, showed seasonal variability, yet were generally higher within polluted sediments. Jaccard similarity coefficients of DGGE profiles, found sites to cluster based primarily on geographical proximity rather than geochemical similarities. Intra-site clustering of the most polluted sites also suggests a stable metal-tolerant community. Sequences from DGGE-extracted bands were predominantly Beta and Gammaproteobacteria, although the communities at all sites generally maintained a diverse phylogeny changing in composition throughout the sampling period. Spearman's rank correlations analysis found statistically significant relationships between community composition and organic carbon (r-value = 0.786) and metals (r-values As = 0.65; Cu = 0.63; Zn = 0.62). A diverse and abundant community at the most polluted site indicates that historical contamination selects for a metal-resistant microbial community, a finding that must be accounted for when using the microbial community within ecosystem monitoring studies. This study highlights the importance of using multiple time-points to draw conclusions on the affect of metal contamination.

Chemical composition and Zn bioavailability of the soil solution extracted from Zn amended variable charge soils

A study on variable charge soils (volcanic Italian and podzolic Scottish soils) was performed to investigate the influence of soil properties on the chemical composition of soil solution. Zinc speciation, bioavailability and toxicity in the soil solution were examined. The soils were spiked with increasing amounts of Zn (0, 100, 200, 400 and 1000 mg/kg) and the soil solutions were extracted using rhizon soil moisture samplers. The pH, total organic carbon (TOC), base cations, anions, total Zn and free Zn2+ in soil solution were analysed. A rapid bioassay with the luminescent bacterium Escherichia coli HB101 pUCD607 was performed to assess Zn toxicity. The influence of soil type and Zn treatments on the chemical composition of soil solution and on Zn toxicity was considered and discussed. Different trends of total and free Zn concentrations, base cations desorption and luminescence of E. coli HB101 pUCD607 were observed. The soil solution extracted from the volcanic soils had very low total and free Zn concentrations and showed specific Zn2+/Ca2+ exchange. The soil solution from the podzolic soil had much higher total and free Zn concentrations and showed no evidence of specific Zn2+/Ca2+ exchange. In comparison with the subalkaline volcanic soils, the acidic podzol showed enhanced levels of toxic free Zn2+ and consequently stronger effects on E. coli viability.

Molecular and functional assessment of bacterial community convergence in metal-amended soils

Species diversity and the structure of microbial communities in soils are thought to be a function of the cumulative selective pressures within the local environment. Shifts in microbial community structure, as a result of metal stress, may have lasting negative effects on soil ecosystem dynamics if critical microbial community functions are compromised. Three soils in the vicinity of a copper smelter, previously contaminated with background, low and high levels of aerially deposited metals, were amended with metal-salts to determine the potential for metal contamination to shape the structural and functional diversity of microbial communities in soils. We hypothesized that the microbial communities native to the three soils would initially be unique to each site, but would converge on a microbial community with similar structure and function, as a result of metal stress. Initially, the three different sites supported microbial communities with unique structural and functional diversity, and the nonimpacted site supported inherently higher levels of microbial activity and biomass, relative to the metal-contaminated sites. Amendment of the soils with metal-salts resulted in a decrease in microbial activity and biomass, as well as shifts in microbial community structure and function at each site. Soil microbial communities from each site were also observed to be sensitive to changes in soil pH as a result of metal-salt amendment; however, the magnitude of these pH-associated effects varied between soils. Microbial communities from each site did not converge on a structurally or functionally similar community following metal-salt amendment, indicating that other factors may be equally important in shaping microbial communities in soils. Among these factors, soil physiochemical parameters like organic matter and soil pH, which can both influence the bioavailability and toxicity of metals in soils, may be critical.

Copper dynamics and impact on microbial communities in soils of variable organic status

The effect of soil organic status on copper impact was investigated by means of a microcosm study carried out on a vineyard soil that had been amended with varying types of organic matter during a previous long-term field experiment. Soil microcosms were contaminated at 250 mg Cu kg(-1) and incubated for 35 days. Copper distribution and dynamics were assessed in the solid matrix by a sequential extraction procedure and in the soil solution by measuring total and free exchangeable copper concentrations. Copper bioavailability was also measured with a whole-cell biosensor. Modifications of microbial communities were assessed by means of biomass-C measurements and characterization of genetic structure using ARISA (automated-ribosomal-intergenic-spacer-analysis). The results showed that copper distribution, speciation, and bioavailability are strongly different between organically amended and nonamended soils. Surprisingly, in solution, bioavailable copper correlated with total copper but not with free copper. Similarly the observed differential copper impact on micro-organisms suggested that organic matter controlled copper toxicity. Bacterial-ARISA modifications also correlated with the estimated metal bioavailability and corresponded to the enrichment of the Actinobacteria. Contrarily, biomass-C and fungal-ARISA measurements did not relate trivially to copper speciation and bioavailability, suggesting that the specific composition of the indigenous-soil communities controls its sensitivity to this metal.

Growth response of Zea mays L. in pyrene-copper co-contaminated soil and the fate of pollutants

Phytoremediation, use of plants for remediation, is an emerging technology for treating heavy metals or a final polishing step for the high-level organic contamination, and may be suitable for remediation of heavy metal and organic co-contaminated soil. The aim of this study was to investigate the influence of co-contamination on the growth of Zea mays L. and the fate of both heavy metal and organic pollutants, using Cu and pyrene as the model pollutants. Results showed that shoot and root biomass were affected by the copper-pyrene co-contamination, although maize grown in spiked soils showed no outward signs of phytotoxicity. With the initial concentration of 50,100 and 500 mg/kg, pyrene tended to alleviate the inhibition of Cu to Z. mays L. Pyrene in both planted and non-planted soil was greatly decreased at the end of the 4-week culture, accounting for 16-18% of initial extractable concentrations in non-planted soil and 9-14% in planted soil, which indicated that the dissipation of soil pyrene was enhanced in the presence of vegetation probably due to the biodegradation and association with the soil matrix. With the increment of Cu level, residual pyrene in the planted soil tended to increase. The pyrene residual in the presence of high concentration of Cu was even higher in the planted soil than that in the non-planted soil, which suggested that the change of the microbial composition and microbial activity or the modified root physiology under Cu stress was probably unbeneficial to the dissipation of pyrene. A more thorough understanding of the mechanisms by which metals affect the dissipation of organic pollutants in the rhizosphere could provide a much better framework on which to base manipulation. Unlike pyrene, heavy metal copper cannot be degraded. Decontamination of Cu from contaminated soils in this system required the removal of Cu by plants. It was observed that the ability of Cu phytoextraction would be inhibited under co-contamination of high level of pyrene in highly Cu-polluted soil. In the treatment of 400 mg Cu/kg and 500 mg pyrene/kg, the accumulation of Cu was less than half of that in 400 mg Cu/kg treatment.

Molecular diversity of 16S rRNA and gyrB genes in copper mines

The molecular diversities of the microbial communities from four sites impacted by acid mine drainage (AMD) at Dexing Copper Mine in Jiangxi province of China were studied using 16S rRNA sequences and gyrB sequences. Of the four sampled sites, each habitat exhibited distinct geochemical characteristics and the sites were linked geographically allowing us to correlate microbial community structure to geochemical characteristics. In the present study, we examined the molecular diversity of 16S rRNA and gyrB genes from water at these sites using a PCR-based cloning approach. We found that the microbial community appears to be composed primarily of Proteobacteria, Acidobacteria, Actinobacteria, Nitrospira, Firmicutes, Chlorella and unknown phylotypes. Of clones affiliated with Nitrospira, Leptospirillum ferrooxidans, Leptospirillum ferriphilum and Leptospirillum group III were all detected. Principal-component analysis (PCA) revealed that the distribution of the microbial communities was influenced greatly by geochemical characteristics. The overall PCA profiles showed that the sites with similar geochemical characteristics had more similar microbial community structures. Moreover, our results also indicated that gyrB sequence analysis may be very useful for differentiating very closely related species in the study of microbial communities.

Effects of 2,4-dichlorophenol, pentachlorophenol and vegetation on microbial characteristics in a heavy metal polluted soil

The aim of this study was to evaluate the soil microbial characteristics in historically heavy-metal polluted soil, which was also affected by organic co-contaminants, 2,4-dichlorophenol or pentachlorophenol, which often occur due to the conventional use of pesticides. It was observed that the normalized microbial biomass (microbial biomass per unit soil organic C) of the contaminated soil was very low, less than 1% in both non-planted and ryegrass planted soil, and showed a decreasing trend with the treatment of organic co-contaminants. The microbial biomass and substrate-induced respiration (SIR) in the ryegrass planted soil were much larger, as compared with the non-planted soil with or without organic pollutants. The different resistant bacterial community and its physiological diversity in the rhizosphere further suggested that the effect of vegetation on microbial activity was not just a general increase in the mass or activity of pre-existing microorganisms, but rather acted selectively on microbial growth so that the relative abundance of different microbial groups in soil was changed. In sum, high concentrations of organic co-contaminants, especially pentachlorophenol (PCP), could strengthen the deterioration of microbial ecology. The adverse effect of heavy metal-organic pollutants on the soil microbial biomass and activity might be the reason for the slow degradation of PCP that has high chlorinated and high toxicity. Vegetation might be the efficient way to assist in improving and restoring the utilization of agricultural ecosystems. The beneficial microbial effect of vegetation could cause the rapid dissipation of 2,4-dichlorophenol (2,4-DCP) that has less chlorinated and less toxicity in the planted soils.

Effect of heavy metals on substrate utilization pattern, biomass, and activity of microbial communities in a reclaimed mining wasteland of red soil area

The microbial biomass, basal respiration, and substrate utilization pattern in a copper mining wasteland of red soil area, southern China, were investigated, and indicated that soil microflora were obviously affected by heavy metals. Microbial biomass and basal respiration were negatively affected by comparatively high heavy metal levels. Two important microbial ecophysiological parameters, namely, the microbial biomass C (C(mic))/microbial biomass N (N(mic)) ratio and the metabolic quotient (qCO(2)) were significantly correlated to heavy metal stress. There was a significant decrease in the C(mic)/N(mic) ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters could have great potential as sensitive, effective, and liable indicators of the stresses or perturbations in soils of mining ecosystems.

Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils

The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using B- and F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.

Influence of lead acetate on soil microbial biomass and community structure in two different soils with the growth of Chinese cabbage (Brassica chinensis)

A greenhouse pot experiment was conducted to evaluate the impact of different concentrations of lead acetate on soil microbial biomass and community structure during growth of Chinese cabbage (Brassica chinensis) in two different soils. The field soils were used for a small pot, short-term 60-day growth chamber study. The soils were amended with different Pb concentrations, ranging from 0 to 900mgkg(-1) soil. The experimental design was a 2 soilx2 vegetation/non-vegetationx6 treatments (Pb)x3 replicate factorial experiment. At 60 days the study was terminated and soils were analyzed for microbial parameters, namely, microbial biomass, basal respiration and PLFAs. The results indicated that the application of Pb at lower concentrations (100 and 300mgkg(-1)) as lead acetate resulted in a slight increase in soil microbial biomass, whereas Pb concentrations >500mgkg(-1) caused an immediate gradual significant decline in biomass. However, the degree of impact on soil microbial biomass and basal respiration by Pb was related to management (plant vegetation) or the contents of clay and organic matter in soils. The profiles of 21 phospholipid fatty acids (PLFAs) were used to assess whether observed changes in functional microbial parameters were accompanied by changes in the composition of the microbial communities after Pb application at 0, 300 and 900mg Pbkg(-1) soil. The results of principal component analyses (PCA) indicated that there were significant increases in fungi biomarkers of 18:3omega6c, 18:1omega9c and a decrease in cy17:0, which is an indicator of gram-negative bacteria for the high levels of Pb treatments In a word, soil microbial biomass and community structure, therefore, may be sensitive indicators reflecting environmental stress in soil-Pb-plant system. However, further studies will be needed to better understand how these changes in microbial community structure might actually impact soil microbial community function.

Adherent bacteria in heavy metal contaminated marine sediments

The eubacterial communities adherent to sediment particles were studied in heavy metal contaminated coastal sediments. Six sampling sites on the Belgian continental plate and presenting various metal loads, granulometries, and organic matter content, were compared. The results indicated that the total microbial biomass (attached + free-living bacteria) was negatively correlated to HCl-extractable metal levels (p<0.05) and that the percentage of cells adherent to sediment particles was close to 100% in every site even in highly contaminated sediments. Consequently, it seems that heavy metal contamination does affect total bacterial biomass in marine sediments but that the ratio between attached and free living microorganisms is not affected. The composition of the eubacterial communities adherent to the fine fraction of the sediments (<150 microm) was determined using fluorescent in situ hybridisation (FISH). The FISH results indicated that the proportion of gamma- and delta-Proteobacteria, and Cytophaga-Flexibacter-Bacteroides (CFB) bacteria, was not related to the HCl extractable metal levels. Most of the 79 complete 16S rRNA sequences obtained from the attached microbial communities were classified in the gamma- and delta-Proteobacteria and in the CFB bacteria. A large proportion of the attached gamma-Proteobacterial sequences found in this study (56%) was included in the uncultivated GMS clades that are indigenous to marine sediments.

Effects of lead contamination on soil microbial activity and rice physiological indices in soil-Pb-rice (Oryza sativa L.) system

The effect of lead (Pb) treatment on the soil microbial activities (soil microbial biomass and soil basal respiration) and rice physiological indices were studied by greenhouse pot experiment. Pb was applied as lead acetate at six different levels in two different paddy soils, namely 0 (control), 100, 300, 500, 700, 900 mg kg-1 soil. The results showed that the application of Pb at lower level (<300 mg kg-1) as lead acetate resulted in a slight increase in soil microbial activities compared with the control, and had an inhibitory influence at high concentration (>500 mg Pb kg-1 soil), which might be the critical concentration of Pb causing a significant decline in the soil microbial activities. However, the degree of influence on soil microbial activities by Pb was related to the clay and organic matter contents of the soils. On the other hand, when the level of Pb treatments increased to 500 mg kg-1, there was ecological risk for both soil microbial activities and plants. The results also revealed that there was a consistent trend that the chlorophyll contents increased initially, and then decreased gradually with increase in Pb concentration. Pb was effective in inducing proline accumulation and its toxicity causes oxidative stress in rice plants. In a word, soil microbial activities and rice physiological indices, therefore, may be sensitive indicators reflecting environmental stress in soil-Pb-rice system.

Evaluation of dissipation mechanisms by Lolium perenne L, and Raphanus sativus for pentachlorophenol (PCP) in copper co-contaminated soil

Though phytoremediation is widely studied in remediation of metal contaminated soils or organic contaminated soils, little information is available regarding the effectiveness and processes of phytoremediation of sites co-contaminated with organic and metal pollutants. Sites co-contaminated with organic and metal pollutants are common and considered to be a more complex problem as the two components often cause a synergistic effect on cytotoxicity as measured both by growth inhibition and colony-forming ability. In this paper, the dissipation mechanisms for pentachlorophenol (PCP) in copper co-contaminated soil by Lolium perenne L, and Raphanus sativus was investigated in a greenhouse experiment by monitoring the growth response of plants, evaluating the removal efficiency of extractable PCP, differentiating PCP residuals in strongly and loosely adhering rhizosphere soils, and analyzing the microbial activity in the rhizosphere. In copper co-contaminated soil with the initial PCP concentration of 50 mg/kg, plants grew better with the increment of soil Cu level (0, 150, 300 mg/kg), which implied that combinations of inorganic and organic pollutants sometimes exerted antagonistic effects on plant cytotoxicity. The observed higher PCP dissipation in soil spiked with 50 mg/kg PCP in the presence of Cu and the less difference of PCP residual between strongly and loosely adhering soils further suggests the occurrence of Cu-PCP interaction and the enhanced degradation and mass flow are two possible explanations. In copper co-contaminated soil with the initial PCP concentration of 100 mg/kg, however, both plant growth and microbial activity were inhibited with the increment of soil Cu level. The lowered degrading activity of microorganisms and the reduced mass flow were probably responsible for the significantly lower levels of PCP dissipation in copper co-contaminated soil. These results showed that remediation of sites co-contaminated with organic and metal pollutants is a complex problem and a more thorough understanding of the extent and mechanisms by which metals inhibit organic degradation is needed to develop phytoremediation of co-contaminated sites.

Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure

A greenhouse experiment was performed to analyze a potential effect of genetically modified potatoes expressing antibacterial compounds (attacin/cecropin, T4 lysozyme) and their nearly isogenic, nontransformed parental wild types on rhizosphere bacterial communities. To compare plant transformation-related variations with commonly accepted impacts caused by altered environmental conditions, potatoes were cultivated under different environmental conditions, for example using contrasting soil types. Further, plants were challenged with the blackleg pathogen Erwinia carotovora ssp. atroseptica. Rhizosphere soil samples were obtained at the stem elongation and early flowering stages. The activities of various extracellular rhizosphere enzymes involved in the C-, P- and N-nutrient cycles were determined as the rates of fluorescence of enzymatically hydrolyzed substrates containing the highly fluorescent compounds 4-methylumbelliferone or 7-amino-4-methyl coumarin. The structural diversity of the bacterial communities was assessed by 16S rRNA-based terminal restriction fragment length polymorphism analysis, and 16S rRNA gene clone libraries were established for the flowering conventional and T4 lysozyme-expressing Desirée lines grown on the chernozem soil, each line treated with and without E. carotovora ssp. atroseptica. Both genetic transformation events induced a differentiation in the activity rates and structures of associated bacterial communities. In general, T4 lysozyme had a stronger effect than attacin/cecropin. In comparison with the other factors, the impact of the genetic modification was only transient and minor, or comparable to the dominant variations caused by soil type, plant genotype, vegetation stage and pathogen exposure.

Bioluminescent bacterial biosensors for the assessment of metal toxicity and bioavailability in soils

A major factor governing the toxicity of heavy metals in soils is their bioavailability. Traditionally, sequential extraction procedures using different extractants followed by chemical analysis have been used for determining the biologically available fraction of metals in soils. Yet, the transfer of results obtained on non-biological systems to biological ones is certainly questionable. Therefore, bioluminescence-based bacterial biosensors have been developed using genetically engineered microorganisms, constructed by fusing transcriptionally active components of metal resistance mechanisms to lux genes from naturally bioluminescent bacteria like Vibrio fischeri for the assessment of metal toxicity and bioavailability in polluted soils. As compared to chemical methods, bacterial biosensors present certain advantages, such as selectivity, sensitivity, simplicity, and low cost. Despite certain inherent limitations, bacterial bioluminescent systems have proven their usefulness in soils under laboratory and field conditions. Finally, green fluorescent protein-based bacterial biosensors are also applicable for determining with high sensitivity the bioavailability of heavy metals in soil samples.