Bioremediation of PAHs and VOCs: Advances in clay mineral–microbial interaction

Bioremediation is an effective strategy for cleaning up organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Advanced bioremediation implies that biotic agents are more efficient in degrading the contaminants completely. Bioremediation by microbial degradation is often employed and to make this process efficient, natural and cost-effective materials can serve as supportive matrices. Clay/modified clay minerals are effective adsorbents of PAHs/VOCs, and readily available substrate and habitat for microorganisms in the natural soil and sediment. However, the mechanism underpinning clay-mediated biodegradation of organic compounds is often unclear, and this requires critical investigation. This review describes the role of clay/modified clay minerals in hydrocarbon bioremediation through interaction with microbial agents in specific scenarios. The vision is on a faster, more efficient and cost-effective bioremediation technique using clay-based products. This review also proposes future research directions in the field of clay modulated microbial degradation of hydrocarbons.     

Bioremediation approaches for organic pollutants: A critical perspective

Due to human activities to a greater extent and natural processes to some extent, a large number of organic chemical substances such as petroleum hydrocarbons, halogenated and nitroaromatic compounds, phthalate esters, solvents and pesticides pollute the soil and aquatic environments. Remediation of these polluted sites following the conventional engineering approaches based on physicochemical methods is both technically and economically challenging. Bioremediation that involves the capabilities of microorganisms in the removal of pollutants is the most promising, relatively efficient and cost-effective technology. However, the current bioremediation approaches suffer from a number of limitations which include the poor capabilities of microbial communities in the field, lesser bioavailability of contaminants on spatial and temporal scales, and absence of bench-mark values for efficacy testing of bioremediation for their widespread application in the field. The restoration of all natural functions of some polluted soils remains impractical and, hence, the application of the principle of function-directed remediation may be sufficient to minimize the risks of persistence and spreading of pollutants. This review selectively examines and provides a critical view on the knowledge gaps and limitations in field application strategies, approaches such as composting, electrobioremediation and microbe-assisted phytoremediation, and the use of probes and assays for monitoring and testing the efficacy of bioremediation of polluted sites.     

Bioremediation approaches for organic pollutants: a critical perspective

Due to human activities to a greater extent and natural processes to some extent, a large number of organic chemical substances such as petroleum hydrocarbons, halogenated and nitroaromatic compounds, phthalate esters, solvents and pesticides pollute the soil and aquatic environments. Remediation of these polluted sites following the conventional engineering approaches based on physicochemical methods is both technically and economically challenging. Bioremediation that involves the capabilities of microorganisms in the removal of pollutants is the most promising, relatively efficient and cost-effective technology. However, the current bioremediation approaches suffer from a number of limitations which include the poor capabilities of microbial communities in the field, lesser bioavailability of contaminants on spatial and temporal scales, and absence of bench-mark values for efficacy testing of bioremediation for their widespread application in the field. The restoration of all natural functions of some polluted soils remains impractical and, hence, the application of the principle of function-directed remediation may be sufficient to minimize the risks of persistence and spreading of pollutants. This review selectively examines and provides a critical view on the knowledge gaps and limitations in field application strategies, approaches such as composting, electrobioremediation and microbe-assisted phytoremediation, and the use of probes and assays for monitoring and testing the efficacy of bioremediation of polluted sites.     

Effect of heavy metals and PAH on soil assessed via dehydrogenase assay

Dehydrogenase enzyme activity (DHA) assay method using resazurin was accommodated for measuring of toxicity of compound contaminants on uncharacterized microbial communities present in any given soil. The method was used to compare the toxic effect of heavy metal and polycyclic aromatic hydrocarbon (PAH) contaminant mixture (Cr, Pb, Cu, Cd, Pyrene) on four typical Estonian soils covering a range of compositions. The method proved to be useable on all soils; the sensitivity of soil microbiology to toxic effect of contaminants was found to have a negative correlation with Ca and organic matter (OM) content and a positive correlation with amorphous phase content of soils.     

New advances in plant growth-promoting rhizobacteria for bioremediation

Plant growth-promoting rhizobacteria (PGPR) are bacteria capable of promoting plant growth by colonizing the plant root. For a long period PGPR were mainly used for assisting plants to uptake nutrients from the environment or preventing plant diseases. Phytoremediation is a new and promising approach to remove contaminants in the environment. But using plants alone for remediation confronts many limitations. Recently, the application of PGPR has been extended to remediate contaminated soils in association with plants. Of all the present contaminants, the profound impacts of organic and heavy metal pollutants have attracted world wide attention. Here we review the progress of PGPR for remediation of soils contaminated with these two sources.     

Monitoring microbial biomass and respiration in different soils from the Czech Republic--a summary of results

The microbial biomass (Cbio), respiration (basal respiration (BR) and potential respiration (PR)), and derived indices for 520 independent soil samples of 117 different soils from the Czech Republic were statistically analysed. The broad range of soil samples allowed the stepwise breakdown of the database into six reasonable categories of soil: arable soils, loamy grassland soils, sandy grassland soils with weak organic matter content, sandy grassland soils with moderate organic matter content, forest soils with moderate organic matter content, and forest organic soils with rich organic matter content. Because soil microbiology lacks benchmarking values, the ranges of the microbial characteristics for these categories were stated and are presented here. The separation into soil groups narrowed the ranges enough to be useful for comparative purposes. The groups displayed significant differences in basal microbial parameters. The lowest microbial biomass was found in arable soils and grassland sandy soils with weak organic matter content. The highest microbial biomass was shown by loamy grassland soils and organic forest soils. Respiration displayed similar results to the microbial biomass. The derived indices revealed less significant differences confirming their inner-standard nature. The relationships between the soil contamination and microbial parameters were not explored because of the confounding effect of soil organic matter. However, it was not shown by the category of grassland sandy soils with weak organic matter content suggesting they could be especially suitable for the biomonitoring of harmful effects of chemicals on soil microorganisms.     

Impact of arbuscular mycorrhizal fungi on uranium accumulation by plants

Contamination by uranium (U) occurs principally at U mining and processing sites. Uranium can have tremendous environmental consequences, as it is highly toxic to a broad range of organisms and can be dispersed in both terrestrial and aquatic environments. Remediation strategies of U-contaminated soils have included physical and chemical procedures, which may be beneficial, but are costly and can lead to further environmental damage. Phytoremediation has been proposed as a promising alternative, which relies on the capacity of plants and their associated microorganisms to stabilize or extract contaminants from soils. In this paper, we review the role of a group of plant symbiotic fungi, i.e. arbuscular mycorrhizal fungi, which constitute an essential link between the soil and the roots. These fungi participate in U immobilization in soils and within plant roots and they can reduce root-to-shoot translocation of U. However, there is a need to evaluate these observations in terms of their importance for phytostabilization strategies.     

Naphthalene biodegradation kinetics in an aerobic slurry-phase bioreactor

The research was focused on the slurry-phase biodegradation of naphthalene in soil. Among ex situ techniques, the slurry phase offers the advantage of increased availability of contaminants to bacteria. From naphthalene contaminated soil, a Pseudomonas putida M8 strain capable to degrade naphthalene was selected. Experiments were performed in a stirred and oxygenated reactor. In this study, the influence of air flow rate and agitation rate on volatilisation and biodegradation of naphthalene was investigated. The hydrocarbon disappearance, the carbon dioxide production, and the ratio of total heterotrophic and naphthalene-degrading bacteria was monitored. The results obtained confirm that the selected bioremediation technology is successful in the treatment of contaminated soils.     

Residues and source identification of persistent organic pollutants in farmland soils irrigated by effluents from biological treatment plants

Sewage and industrial effluents from biological treatment plant have been widely used for agricultural irrigation in north part of China. However, effluents after biological treatment still contain heavy metals and persistent organic contaminants. The persistent organic contaminants accumulated in soil may transfer through the food chains and cause adverse health effects on human or biological effects on soil fauna and flora after long-term application. In present study, field surveys were carried out in the farmlands irrigated by effluents from biological treatment plants that receive sewage wastewater and industrial discharges. Residues of polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in the soils irrigated using both ground water and effluents were compared. The origins of PAHs in the soils were discussed. The results showed that wastewater irrigation could cause accumulation of PAHs in soils close to the pollution discharge. Significantly higher concentrations of PAHs were observed in the sampling sites close to the entrance of main channel in contrast to those along branches and the reference sites. There was no significant relationship between the accumulation of persistent organic pollutants and organic matter content in soil (TOC). Soil contamination of these persistent organic pollutants as affected by effluent irrigation was characterized by the dominant accumulation of high-molecular-weight PAHs (HMW-PAHs). In the case study, concentration of benzo[a]pyrane (BaP, 45.6 ng/g), indeno[1,2,3-cd]pyrene (IcP, 86.3 ng/g), benzo[g,h,i]perlene (BgP, 66.9 ng/g) could exceed the limits of the soil quality standard for biodegraded soils. In identification of the sources, the IcP/BgP values of PAHs in soils were more close to that in air particulates from coal/coke source (1.09+/-0.03 ng/g) [Dickhut RM, Canuel EA, Gustafson KE, Liu K, Arzayus KM, Walkers E, et al. Automotive sources of carcinogenic polycyclic aromatic hydrocarbons associated with particulate matter in the chesapeake bay region. Environ Sci Technol 2000;34:4635-40]. Therefore, both of the PAHs residues in effluents and emission from a nearby coal/coke plant were responsible. Also in this case study, low levels of the OCPs were observed and were not of significant concern in this wastewater irrigation area. Among the different OCPs analyzed, DDTs (mean 8.41 ng/g) and HCHs (mean 2.91 ng/g) were the major components. From the ratios of DDT/DDTs and beta-HCH/HCHs, it indicated that OCPs residues should be from historical usage.     

Novel approach to monitoring of the soil biological quality

In this study, a new approach to interpretation of results of the simple microbial biomass and respiration measurements in the soil microbiology is proposed. The principle is based on eight basal and derived microbial parameters, which are standardized and then plotted into sunray plots. The output is visual presentation of one plot for each soil, which makes possible the relative comparison and evaluation of soils in the monitored set. Problems of soil microbiology, such as the lack of benchmarking and reference values, can be avoided by using the proposed method. We found that eight parameters provide enough information for evaluation of the status of the soil microorganisms and, thus, for evaluation of the soil biological quality. The usage of rare parameters (potential respiration PR, ratio of potential and basal respiration PR/BR, biomass-specific potential respiration PR/C(bio), available organic carbon C(ext), and biomass-specific available organic carbon C(ext)/C(bio)) can be recommended, besides classical and well-known parameters (microbial biomass C(bio), basal respiration BR, metabolic coefficient qCO(2)). The combination of basal parameters and derived coefficients can also extend our knowledge about the condition of the soil microorganisms. In monitoring the case studies presented, we observed that soils evaluated to possess good biological quality displayed generally higher values of organic carbon, total nitrogen, clay, and cation exchange capacity. The soils of good biological quality can display higher levels of contaminants. This is probably related with the higher content of organic carbon and clay in these soils.     

An overview of BORIS: Bioavailability of Radionuclides in Soils

The ability to predict the consequences of an accidental release of radionuclides relies mainly on the level of understanding of the mechanisms involved in radionuclide interactions with different components of agricultural and natural ecosystems and their formalisation into predictive models. Numerous studies and databases on contaminated agricultural and natural areas have been obtained, but their use to enhance our prediction ability has been largely limited by their unresolved variability. Such variability seems to stem from incomplete knowledge about radionuclide interactions with the soil matrix, soil moisture, and biological elements in the soil and additional pollutants, which may be found in such soils. In the 5th European Framework Programme entitled Bioavailability of Radionuclides in Soils (BORIS), we investigated the role of the abiotic (soil components and soil structure) and biological elements (organic compounds, plants, mycorrhiza, and microbes) in radionuclide sorption/desorption in soils and radionuclide uptake/release by plants. Because of the importance of their radioisotopes, the bioavailability of three elements, caesium, strontium, and technetium has been followed. The role of one additional non-radioactive pollutant (copper) has been scrutinised in some cases. Role of microorganisms (e.g., K(d) for caesium and strontium in organic soils is much greater in the presence of microorganisms than in their absence), plant physiology (e.g., changes in plant physiology affect radionuclide uptake by plants), and the presence of mycorrhizal fungi (e.g., interferes with the uptake of radionuclides by plants) have been demonstrated. Knowledge acquired from these experiments has been incorporated into two mechanistic models CHEMFAST and BIORUR, specifically modelling radionuclide sorption/desorption from soil matrices and radionuclide uptake by/release from plants. These mechanistic models have been incorporated into an assessment model to enhance its prediction ability by introducing the concept of bioavailability factor for radionuclides.     

Soil organic horizons as a major source for radiocesium biorecycling in forest ecosystems

Here we review some of the main processes and key parameters affecting the mobility of radiocesium in soils of semi-natural areas. We further illustrate them in a collection of soil surface horizons which largely differ in their organic matter contents. In soils, specific retention of radiocesium occurs in a very small number of sorbing sites, which are the frayed edge sites (FES) born out of weathered micaceous minerals. The FES abundance directly governs the mobility of trace Cs in the rhizosphere and thus its transfer from soil to plant. Here, we show that the accumulation of organic matter in topsoils can exert a dilution of FES-bearing minerals in the thick humus of some forest soils. Consequently, such accumulation significantly contributes to increasing 137Cs soil-to-plant transfer. Potassium depletion and extensive exploration of the organic horizons by plant roots can further enhance the contamination hazard. As humus thickness depends on both ecological conditions and forest management. our observations support the following ideas: (1) forest ecosystems can be classified according to their sensitivity to radiocesium bio-recycling, (2) specific forest management could be searched to decrease such bio-recycling.     

Sources and remediation techniques for mercury contaminated soil

Mercury (Hg) in soils has increased by a factor of 3 to 10 in recent times mainly due to combustion of fossil fuels combined with long-range atmospheric transport processes. Other sources as chlor-alkali plants, gold mining and cement production can also be significant, at least locally. This paper summarizes the natural and anthropogenic sources that have contributed to the increase of Hg concentration in soil and reviews major remediation techniques and their applications to control soil Hg contamination. The focus is on soil washing, stabilisation/solidification, thermal treatment and biological techniques; but also the factors that influence Hg mobilisation in soil and therefore are crucial for evaluating and optimizing remediation techniques are discussed. Further research on bioremediation is encouraged and future study should focus on the implementation of different remediation techniques under field conditions.     

Mixotrophic cyanobacteria and microalgae as distinctive biological agents for organic pollutant degradation

Millions of natural and synthetic organic chemical substances are present in both soil and aquatic environments. Toxicity and/or persistence determine the polluting principle of these substances. The biological responses to these pollutants include accumulation and degradation. The responses of environments with organic pollutants are perceptible from the dwindling degradative abilities of microorganisms. Among different biological members, cyanobacteria and microalgae are highly adaptive through many eons, and can grow autotrophically, heterotrophically or mixotrophically. Mixotrophy in cyanobacteria and microalgae can provide many competitive advantages over bacteria and fungi in degrading organic pollutants. Laboratory culturing of strict phototrophic algae has limited the realization of their potential as bioremediation agents. In the natural assemblages, mixotrophic algae can contribute to sequestration of carbon, which is otherwise emitted as carbon dioxide to the atmosphere under heterotrophic conditions by other organisms. Molecular methods and metabolic and genomic information will help not only in identification and selection of mixotrophic species of cyanobacteria and microalgae with capabilities to degrade organic pollutants but also in monitoring the efficiency of remediation efforts under the field conditions. These organisms are relatively easier for genetic engineering with desirable traits. This review presents a new premise from the literature that mixotrophic algae and cyanobacteria are distinctive bioremediation agents with capabilities to sequester carbon in the environment.     

Soil and soil environmental quality monitoring in China: A review

Over the past few decades, numerous concerns have been raised in China over the issue of environmental sustainability. Various soil survey and monitoring programs have been carried out in China to study soil quality, and to provide a scientific basis for environment policy making. This paper provides an overview of past and current soil quality surveys and monitoring activities in China. This paper includes a summary of concerns over background concentrations of elements in soil, and soil environmental standards and guidelines in China. Levels of pollution in urban soil, agricultural soil, and soil in mining and smelting areas were compared using the concentrations and pollution indexes. In addition to soil surveys, soil monitoring is essential to study the data and to examine the effects of contaminants in soils. However, the current soil quality monitoring system was insufficient to accurately determine the soil quality status of soils across China. For accurate soil monitoring in China, it will be necessary to set up routine monitoring systems at various scales (national, provincial, and local scales), taking into consideration monitoring indicators and quality assurance. This is currently an important priority for the environmental protection administration of China.     

Agronomic and remedial benefits and risks of applying biochar to soil: Current knowledge and future research directions

‘Biochar’ represents an emerging technology that is increasingly being recognized for its potential role in carbon sequestration, reducing greenhouse gas emissions, waste management, renewable energy, soil improvement, crop productivity enhancement and environmental remediation. Published reviews have so far focused mainly on the above listed agronomic and environmental benefits of applying biochar, yet paid little or no attention to its harmful effects on the ecological system. This review highlights a balanced overview of the advantages and disadvantages of the pyrolysis process of biochar production, end-product quality and the benefits versus drawbacks of biochar on: (a) soil geochemistry and albedo, (b) microflora and fauna, (c) agrochemicals, (d) greenhouse gas efflux, (e) nutrients, (f) crop yield, and (g) contaminants (organic and inorganic). Future research should focus more on the unintended long-term consequences of biochar on biological organisms and their processes in the soil.     

Soil-plant transfer of plutonium and americium in contaminated regions of Belarus after the Chernobyl catastrophe

Experimental data are presented for the soil to plant transfer of plutonium and americium into the main species of grass vegetation of Belarusian grasslands contaminated as a result of the Chernobyl catastrophe of 1986. The content of radionuclides in pore soil solutions and the total reserve of biologically available forms of plutonium and americium in rooting layers of different soil varieties have been established. The distribution coefficients of (239,240)Pu and 241Am between the solid phase and pore waters of soils have been evaluated. The migration ability and biological availability of radionuclides in soils with different structures of the absorbing complex have been analyzed for various landscape conditions. The dependence of soil to plant transfer of plutonium and americium on the content and composition of organic matter, and other characteristics of the soil complex has been studied. On the basis of these data, predictions of the contamination levels of the main grass species of natural and agricultural ecosystems by 241Am are presented.     

Biogeochemical C and N cycles in urban soils

The percentage of urban population is projected to increase drastically. In 2030, 50.7 to 86.7% of the total population in Africa and Northern America may live in urban areas, respectively. The effects of the attendant increases in urban land uses on biogeochemical C and N cycles are, however, largely unknown. Biogeochemical cycles in urban ecosystems are altered directly and indirectly by human activities. Direct effects include changes in the biological, chemical and physical soil properties and processes in urban soils. Indirect effects of urban environments on biogeochemical cycles may be attributed to the introductions of exotic plant and animal species and atmospheric deposition of pollutants. Urbanization may also affect the regional and global atmospheric climate by the urban heat island and pollution island effect. On the other hand, urban soils have the potential to store large amounts of soil organic carbon (SOC) and, thus, contribute to mitigating increases in atmospheric CO(2) concentrations. However, the amount of SOC stored in urban soils is highly variable in space and time, and depends among others on soil parent material and land use. The SOC pool in 0.3-m depth may range between 16 and 232 Mg ha(-1), and between 15 and 285 Mg ha(-1) in 1-m depth. Thus, depending on the soil replaced or disturbed, urban soils may have higher or lower SOC pools, but very little is known. This review provides an overview of the biogeochemical cycling of C and N in urban soils, with a focus on the effects of urban land use and management on soil organic matter (SOM). In view of the increase in atmospheric CO(2) and reactive N concentrations as a result of urbanization, urban land use planning must also include strategies to sequester C in soil, and also enhance the N sink in urban soils and vegetation. This will strengthen soil ecological functions such as retention of nutrients, hazardous compounds and water, and also improve urban ecosystem services by promoting soil fertility.     

An overview of the effect of organic matter on soil-radiocaesium interaction: implications in root uptake

This paper aims to give an overview of the effect of organic matter on soil-radiocaesium interaction and its implications on soil-to-plant transfer. Studies carried out after the Chernobyl accident have shown that high 137CS soil-to-plant transfer persists in organic soils over years. In most of these soils, the specific sites in clays control radiocaesium adsorption, organic compounds having an indirect effect. Only in organic soils with more than 95% of organic matter content and negligible clay content does adsorption occur mostly on non-specific sites. After a contamination event, two main factors account for the high transfer: the low solid-liquid distribution coefficient, which is due to the low clay content and high NH4+ concentration in the soil solution, and the low K+ availability, which enhances root uptake. The estimation of the reversibly adsorbed fraction, by means of desorption protocols, agrees with the former conclusions, since it cannot be correlated with the organic matter content and shows the lack of specificity of the adsorption in the organic phase. Moreover, the time-dependent pattern of the exchangeable fraction is related to soil-plant transfer dynamics.     

Chemical associations of artificial radionuclides in Cumbrian soils

The distributions of radionuclides in the surface layer of four soils of contrasting types from west Cumbria, UK, have been studied in detail. All the soils contain enhanced levels of artificial radionuclides derived from low-level discharges both to sea and to atmosphere from the British Nuclear Fuels reprocessing plant at Sellafield. The bulk of the activity is held in the top 15 cm of soil profiles, suggesting that radionuclide mobility is limited. Sequential extraction experiments have identified major associations of plutonium with organic matter and of caesium with silicates but there is no preferential association of ruthenium with any single soil component.