Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil

In situ remediation of oil-contaminated soils by ozonation: Experimental study and numerical modeling

The goal of the present work is to quantify the performance of ozonation as a method for the in situ remediation of soils polluted at varying degree with different types of hydrocarbons, and assess its applicability, in terms of remediation efficiency, cost factors, and environmental impacts. Ozonation tests are conducted on dry soil beds, for three specific cases: sandy soil contaminated with low, moderate and high concentration of a non-aqueous phase liquid (NAPL) consisting of equal concentrations of n-decane, n-dodecane, and n-hexadecane; sandy soil polluted with diesel fuel; oil-drilling cuttings (ODC). The transient changes of the concentration of the total organic carbon (TOC), total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAHs), and soluble chemical oxygen demand (SCOD) in soil and carbon dioxide (CO2), carbon monoxide (CO), volatile organic compounds (VOCs), and ozone (O3) in exhaust gases are recorded. A numerical model is suggested where the ozone is adsorbed on solid grains, reacts with adsorbed organic species, and desorbed CO2, CO along with unconsumed O3 are released. The model is used to estimate the ozonation kinetic parameters, upscale the process, and estimate the cost and gas emissions per 1 tn of treated soil. Experiments reveal that after 4h of treatment, the TOC decreases profoundly only for the low NAPL concentration (76.4%), the highest and fastest TPH removal efficiency occurs for the moderate NAPL concentration (∼88%), and diesel fuel (87%), while the TPH removal efficiency becomes high enough for oil-drilling cuttings (80%) after 8h of treatment. In all cases, mainly CO2 is detected in exhaust gases, its cumulative mass is fully consistent with the TOC losses, while the O3 consumption is enhanced for heavily polluted soils. The concentration of PAHs is reduced profoundly for both the diesel fuel and ODC. The lowest energy consumption per unit mass of degraded TPH or TOC occurs for the heavily polluted soils. The cost of soil treatment increases with the initial TPH concentration and pollutant complexity increasing.

Degradation and mechanism of PAHs by Fe-based activated persulfate: Effect of temperature and noble metal

The accumulation of contaminants like PAHs in soil due to industrialization, urbanization, and intensified agriculture poses environmental challenges, owing to their persistence, hydrophobic nature, and toxicity. Thus, the degradation of PAHs has attracted worldwide attention in soil remediation. This study explored the effect of noble metal and temperature on the degradation of various polycyclic aromatic hydrocarbons (PAHs) in soil, as well as the types of reactive radicals generated and mechanism. The Fe-Pd/AC and Fe-Pt/AC activated persulfate exhibited high removal efficiency of 19 kinds of PAHs, about 79.95 % and 83.36 %, respectively. Fe-Pt/AC-activated persulfate exhibits superior degradation efficiency than that on Fe-Pd/AC-activated persulfate, due to the higher specific surface area and dispersity of Pt particles, thereby resulting in increased reactive radicals (·OH, SO4-· and ·OOH). Additionally, thermal activation enhances the degradation of PAHs, with initial efficiencies of 64.20 % and 55.49 % on Fe-Pd/AC- and Fe-Pt/AC-activated persulfate systems respectively, increasing to 76.05 % and 73.14 % with elevated temperatures from 21.5 to 50 °C. Metal and thermal activation facilitate S2O82- activation, generating reactive radicals, crucial for the degradation of PAHs via ring opening and oxygen hydrogenation reactions, yielding low-ring oxygen-containing derivatives such as organic acids, keto compounds, ethers, and esters. Furthermore, understanding the impact of parameters such as activation temperature and the types of noble metals on the degradation of PAHs within the activated persulfate system provides a theoretical foundation for the remediation of PAH-contaminated soil.

Effect of site-specific conditions and operating parameters on the removal efficiency of petroleum-originating pollutants by using ozonation

Soil contamination is a worldwide problem, mainly caused by a wide range of organic compounds: e.g., alkanes, aromatics, and polynuclear aromatics. Using ozone to help remediate contaminated soils is gaining interest due to its capability in oxidizing recalcitrant contaminants in short application time., although studies using ozonation for soil remediation are so far limited to the laboratory scale. This review attempts to summarize and discuss the state of the art in the treatment of soils contaminated with recalcitrant organic contaminants by using ozone, emphasizing the influence of operating conditions, such as the content and age of soil organic matter, grain size, moisture content, pH, and ozone dose. Special attention is given to the combination of ozonation and biodegradation. The main advantages in using ozonation as a remediation technique are its high oxidation potential applicable to a wide range of organic pollutants and its oxygen release after chemical decomposition that allow aerobic biodegradation. The review results show that ozonated soils can be reused after ozonation treatment, therefore ozonation can be considered an excellent remediation technique, even if combined with biodegradation, allowing removal percentages of 90% and more.

Mycoremediation effect of Trichoderma harzianum strain T22 combined with ozonation in diesel-contaminated sand

This study aimed to determine the ability of the fungus Trichoderma harzianum strain T22 (Th-T22) to utilize diesel fuel as a carbon source. The potential use of Th-T22 for diesel bioremediation in an artificial soil was tested by inoculating a diesel-sand mixture with a fungal mycelial suspension of Th-T22. Given the ability of ozone to degrade compounds with low biochemical reactivity, the effect of a pre- and post-ozonation was also evaluated. The survival, growth and sporulation of Th-T22 throughout the bioremediation trial were monitored in all the treatments. In the post-ozonation treatments, the biodegradation percentages of diesel removal were 70.16% and 88.35% in Th-T22-inoculated sand treated or untreated with the antibacterial streptomycin, respectively. The results showed that ozonation alone caused good removal efficiencies (41.9%) but it was much more effective if combined with Th-T22 in a post-ozonation regime, whereas pre-ozonation negatively affected the subsequent biodegradation, likely due to its disinfectant and oxidizing effect on Th-T22. The results obtained demonstrated the significant mycoremediation ability of Th-T22 in diesel-contaminated sand and its possible use as a bioremediation agent for diesel spills in polluted sites.

Joint response of chemistry and functional microbial community to oxygenation of the reductive confined aquifer

Oxygen can enter into reductive aquifer through natural and artificial processes. However, the joint response of groundwater chemistry and functional microbial communities to oxygenation is not well understood due to the gap between taxonomic and functional microbial composition. Here, two wells named CZK15 and CZK22 at the second confined aquifer in Central China were in situ aerated, and the chemical parameters of groundwater and microbial communities in bio-trapping sand sediment were analysed during aeration. The microbial metabolic functions related to C, N, S, Fe transformation were predicted by Functional Annotation of Prokaryotic Taxa (FAPROTAX) approach and some key functional genes, such as phe, nah, narG, and soxB were verified by the real-time quantitative Polymerase Chain Reaction (qPCR) method. The biomass was promoted, microbial diversity fluctuated, and microbial composition changed remarkably with aeration mainly constrained by reduction-oxidation (redox) variation and SO₄^2- concentration. Among functional microbes, aerobic chemoheterotrophs including aromatic compound degraders (also especially for relative abundance of phe and some nah gene) and methylotrophs are dramatically enriched interpreting dissolved oxygen (DO) consumption and total organic carbon (TOC) decomposing in sediment. Whilst fermenters and methanogen expectedly decreased during aeration. Denitrifying microbes and narG gene relative abundance increased corresponding to the NO₃^- increase after aeration, while microbes for N₂ fixation, ammonification, and nitrification decreased relating to the source of NH₄⁺. The sulfide oxidation causing increased SO₄^2- was reflected by the blooming of sulfur-oxidizing microbes and soxB gene. Some sulfate reducers persisted in sediment after aeration due to sufficient SO₄^2- as substrate. Fe(II) was mainly chemically oxidized as iron-oxidizing microbes were of low abundance and tended to decrease with aeration. The iron-reducing bacteria Geobacteraceae increased with aeration corresponding to the increased Fe(III) oxides formation. The findings of this study could have important implications in understanding the biogeochemical behaviours with cyclic redox conditions.

Rapid degradation of long-chain crude oil in soil by indigenous bacteria using fermented food waste supernatant

The objective of this study is to explore how to stimulate soil indigenous bacteria for the degradation of long-chain crude oil by adding fermented food waste supernatant (FS). Four concentrations of FS (0 mL, 0.1 mL, 1 mL, and 3 mL) were added to two oil-contaminated soils S1 and S2 for 30 days of bioremediation experiments. The results showed that the biodegradation of long-chain alkanes (C₂₉ - C₂₄) could reach up to 1756 mg/kg (49.3%, S1) and 3937 mg/kg (43.9%, S2), which were 3.1 and 3.2 times that of the non-nutrient system. In addition, the logarithmic growth rate of the indigenous hydrocarbon degraders (IHD) reached 41.5%. The long-chain crude oil can be rapidly degraded by indigenous bacteria with FS added in a short time. The glucose and acetic acid accelerated the consumption of ammonia nitrogen (NH₄⁺-N) in the prophase of bioremediation and the molar ratio of consumed carbon (contained in glucose and acetic acid) to consumed NH₄⁺-N (C/N) was high by adding FS. Thus, the IHD can multiply rapidly. The analysis of microbial diversity revealed that the IHD (genera Acinetobacter and Aquabacterium) became the dominant bacteria. Long-chain alkanes became the main carbon sources for IHD after 14 days in soil S1 and 16 days in soil S2. Thus, the rapid biodegradation of long-chain crude oil was achieved. The genus Aquabacterium which was uncultivable on crude oil medium became the dominant bacteria. This study provides an environment-friendly and sustainable remediation technology for bioremediation of oil-contaminated soils.

Enhanced degradation of polycyclic aromatic hydrocarbons by indigenous microbes combined with chemical oxidation

In this study, the removal efficiency PAHs by chemical oxidation combined with microbe remediation was evaluated in two contaminated soils. The number of indigenous soil microbes decreased after the addition of chemical oxidants and then increased by nutrients addition. The total removal efficiencies of PAHs by chemical oxidation and nutrient addition followed the order: activated persulfate > potassium permanganate > modified Fenton reagent > Fenton reagent. There are 24.29-27.97%, 22.00-23.67%, 10.24-13.74% and 1.9-2.5% contributions separately due to nutrient treatment in Fenton, modified Fenton, activated persulfate and potassium permanganate treatment, which show significantly difference. The different chemical oxidants exhibited 78-90% removal efficiency for 5-6 rings PAHs, while 52-85% removal efficiency for 2-4 rings PAHs. With the addition of nutrients, the growth of indigenous microbes was enhanced significantly, and the contents of 2-4 rings PAHs in the soil were further decreased. Furthermore, the removal efficiencies of NAP and ANY were increased by more than 45%, while the removal efficiencies of ANE, FLE and PHE were about 30% at Fenton system. There was a complementary enhancing effect of microbial remediation for PAHs degradation after chemical oxidation.

Impacts of moisture content during ozonation of soils containing residual petroleum

We tested the effect of soil moisture content on the efficiency of gas-phase ozonation for two types of soils containing residual petroleum. For the first soil (BM2), having a total petroleum hydrocarbons (TPH) concentration of 18,000mg/kg soil, a moisture content of 5% benefited oxidation, giving the highest efficiency of ozonation for TPH removal and for producing soluble and biodegradable products. In contrast, higher moisture content hindered O₃ from oxidizing reactive materials in the second soil (BM3), which had a higher TPH concentration, 33,000mg/kg soil. This trend was documented by less TPH removal, less generation of soluble and biodegradable organic products, and a carbon balance that showed retarded carbon oxidation. An unexpected phenomenon was smoldering during ozonation of air-dried (<1% moisture) BM3, which did not occur with the same moisture conditions for BM2. BM3 smoldered was due to its higher TPH content, low heat buffering, and more release of volatiles with low self-ignition points. Smoldering did not occur for ≥ 5% water content, as it suppressed the temperature increase needed to volatilize the organics that initiated smoldering. The findings underscore the importance of controlling water content during ozonation to optimize the effectiveness of ozonation and prevent smoldering.

Biological and analytical techniques used for detection of polyaromatic hydrocarbons

Polycyclic aromatic hydrocarbons contain two or more fused benzene rings that are considered as cosmo-pollutants ubiquitously found in the environment. The identification and monitoring of polycyclic aromatic hydrocarbons (PAHs) are of great interests for rapid and on-site detection. Therefore, many analytical and biological techniques have been proposed for the qualitative and quantitative assessments of PAHs. Non-biological analytical techniques such as infrared, Raman, and fluorescence spectroscopies are commonly exploited as non-destructive techniques while gas chromatography (GC) and high-performance liquid chromatography (HPLC) with multiple detectors are extensively employed for the separation and detection of an analyte. Even though spectroscopy and chromatography are more accurate, convenient, and feasible techniques, often, these methods are expensive and sophisticated which require high maintenance cost. On the other hand, biological approaches, i.e., immunoassay, PCR, and microarray, offer comprehensive high-throughput specificity and sensitivity for a similar analyte. Biosensor- and immunoassay-mediated detections of PAHs have opened up new avenues in terms of low cost, rapid determination, and higher sensitivity. In this review, we have discussed the strengths and limitations of biological and analytical techniques that were explored for precise evaluation and were trusted at both the legislation and research levels.

Phenanthrene degradation in soil by ozonation: Effect of morphological and physicochemical properties

The aim of this study was to characterize the ozone reaction with phenanthrene adsorbed in two types of soils (sand and agricultural). The effect of soil physicochemical properties (texture, bulk density, particle density, porosity, elemental composition, permeability, surface area and pore volume) on the phenanthrene decomposition was evaluated. Commercial sand has a uniform morphology (spherical) with a particle size range between 0.178 and 0.150 mm in diameter, regular elemental composition SiO₂, specific density of 1701.38 kg/m³, a true density of 2492.50 kg/m³, with an effective porosity of 31%. On the other hand, the agricultural soil had heterogeneous morphology, particle size between 0.1779 and 0.05 mm in diameter, elemental composition was montmorrillonite silicon oxide, apparent density of 999.52 kg/m³, a true density of 2673.55 kg/m³, surface area of 34.92 m²/g and porosity of 57%. The percentage of phenanthrene decomposition in the sand was 79% after 2 h of treatment. On the other hand, the phenanthrene degradation in the agricultural soil was 95% during the same reaction time. The pore volume of soil limited the crystal size of phenanthrene and increased the contact surface with ozone confirming the direct impact of physicochemical properties of soils on the decomposition kinetics of phenanthrene. In the case of agricultural soil, the effect of organic matter on phenanthrene decomposition efficiency was also investigated. A faster decomposition of initial contaminant and byproducts formed in ozonation was obtained in natural agricultural soil compared to the sand. The partial identification of intermediates and final accumulated products produced by phenanthrene decomposition in ozonation was developed. Among others, phenanthroquinone, hydroquinone, phenanthrol, catechol as well as phthalic, diphenic, maleic and oxalic acids were identified.

Interpreting Interactions between Ozone and Residual Petroleum Hydrocarbons in Soil

We evaluated how gas-phase O₃ interacts with residual petroleum hydrocarbons in soil. Total petroleum hydrocarbons (TPH) were 18 ± 0.6 g/kg soil, and TPH carbon constituted ∼40% of the dichloromethane-extractable carbon (DeOC) in the soil. At the benchmark dose of 3.4 kg O₃/kg initial TPH, TPH carbon was reduced by nearly 6 gC/kg soil (40%), which was accompanied by an increase of about 4 gC/kg soil in dissolved organic carbon (DOC) and a 4-fold increase in 5-day biochemical oxygen demand (BOD₅). Disrupting gas channeling in the soil improved mass transport of O₃ to TPH bound to soil and increased TPH removal. Ozonation resulted in two measurable alterations of the composition of the organic carbon. First, part of DeOC was converted to DOC (∼4.1 gC/kg soil), 75% of which was not extractable by dichloromethane. Second, the DeOC containing saturates, aromatics, resins, and asphaltenes (SARA), was partially oxidized, resulting in a decline in saturates and aromatics, but increases in resins and asphaltenes. Ozone attack on resins, asphaltenes, and soil organic matter led to the production of NO₃^-, SO₄^2-, and PO₄^3-. The results illuminate the mechanisms by which ozone gas interacted with the weathered petroleum residuals in soil to generate soluble and biodegradable products.

Insights into the fluoride-resistant regulation mechanism of Acidithiobacillus ferrooxidans ATCC 23270 based on whole genome microarrays

Acidophilic microorganisms involved in uranium bioleaching are usually suppressed by dissolved fluoride ions, eventually leading to reduced leaching efficiency. However, little is known about the regulation mechanisms of microbial resistance to fluoride. In this study, the resistance of Acidithiobacillus ferrooxidans ATCC 23270 to fluoride was investigated by detecting bacterial growth fluctuations and ferrous or sulfur oxidation. To explore the regulation mechanism, a whole genome microarray was used to profile the genome-wide expression. The fluoride tolerance of A. ferrooxidans cultured in the presence of FeSO4 was better than that cultured with the S(0) substrate. The differentially expressed gene categories closely related to fluoride tolerance included those involved in energy metabolism, cellular processes, protein synthesis, transport, the cell envelope, and binding proteins. This study highlights that the cellular ferrous oxidation ability was enhanced at the lower fluoride concentrations. An overview of the cellular regulation mechanisms of extremophiles to fluoride resistance is discussed.

Identification of metabolomics panels for potential lung cancer screening by analysis of exhaled breath condensate

Exhaled breath condensate (EBC) is one of the less employed biofluids when searching for clinical markers, despite its non-invasive sampling and the potential relationship between its composition and respiratory disease phenotypes such as lung cancer. The advanced stage at which lung cancer is usually detected is the main reason for the high mortality rate of this carcinogenic disease. In this preliminary research, EBC was used as clinical sample to develop a screening tool for lung cancer discrimination from two control groups (with and without risk factor). Three panels of metabolites were configured using the PanelomiX tool to minimize false negatives (specificity) and false positives (sensitivity). The combination of five metabolites led to three panels providing a sensitivity above 77.9%, specificity above 67.5% and the area under the curve (AUC) above 77.5% for the three panels. An additional study was developed as a first approach to study the statistical significance of metabolites at different stages of lung cancer.

Effects of the joint exposure of decabromodiphenyl ether and tetrabromobisphenol A on soil bacterial community structure

Decabromodiphenyl ether (BDE209) and tetrabromobisphenol A (TBBPA) are the main contaminants at electronic waste (e-waste) recycling sites (EWRSs), and their potential toxicological effects have received extensive attention. However, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. Therefore, indoor incubation tests were performed on control and contaminated soil samples to determine the response of soil bacterial community structure in the joint presence of BDE209 and TBBPA for the first time. The results have demonstrated that the soil bacterial diversity generally declined with increasing BDE209 and TBBPA concentrations and moderate and high doses of both chemicals can cause inhibitory effects. PCR-DGGE analysis indicated that the correlations between Shannon-Weaver index and contaminant concentrations could be well represented by a second-order polynomial model. The combined toxicity of the two chemicals was antagonistic during the first 14 days and then synergistic. Pectobacterium carotovorum, Sinorhizobium fredii HH103, and Stenotrophomonas maltophilia were highly tolerant to joint exposure during the entire incubation period. Moreover, some Staphylococcus strains were enriched after 90 days exposed to TBBPA or low concentrations of BDE209, indicating that they might degrade the two chemicals effectively. The results of these observations have provided some basic understanding of potential ecological effects of joint exposure to BDE209 and TBBPA on soil microorganism at EWRSs.

Identification of persulfate oxidation products of polycyclic aromatic hydrocarbon during remediation of contaminated soil

The extent of PAH transformation, the formation and transformation of reaction byproducts during persulfate oxidation of polycyclic aromatic hydrocarbons (PAHs) in coking plant soil was investigated. Pre-oxidation analyses indicated that oxygen-containing PAHs (oxy-PAHs) existed in the soil. Oxy-PAHs including 1H-phenalen-1-one, 9H-fluoren-9-one, and 1,8-naphthalic anhydride were also produced during persulfate oxidation of PAHs. Concentration of 1,8-naphthalic anhydride at 4h in thermally activated (50°C) persulfate oxidation (TAPO) treatment increased 12.7 times relative to the oxidant-free control. Additionally, the oxy-PAHs originally present and those generated during oxidation can be oxidized by unactivated or thermally activated persulfate oxidation. For example, 9H-fluoren-9-one concentration decreased 99% at 4h in TAPO treatment relative to the control. Thermally activated persulfate resulted in greater oxy-PAHs removal than unactivated persulfate. Overall, both unactivated and thermally activated persulfate oxidation of PAH-contaminated soil reduced PAH mass, and oxidized most of the reaction byproducts. Consequently, this treatment process could limit environmental risk related to the parent compound and associated reaction byproducts.

Geochemical and microbiological characteristics during in situ chemical oxidation and in situ bioremediation at a diesel contaminated site

While in situ chemical oxidation with persulfate has seen wide commercial application, investigations into the impacts on groundwater characteristics, microbial communities and soil structure are limited. To better understand the interactions of persulfate with the subsurface and to determine the compatibility with further bioremediation, a pilot scale treatment at a diesel-contaminated location was performed consisting of two persulfate injection events followed by a single nutrient amendment. Groundwater parameters measured throughout the 225 day experiment showed a significant decrease in pH and an increase in dissolved diesel and organic carbon within the treatment area. Molecular analysis of the microbial community size (16S rRNA gene) and alkane degradation capacity (alkB gene) by qPCR indicated a significant, yet temporary impact; while gene copy numbers initially decreased 1-2 orders of magnitude, they returned to baseline levels within 3 months of the first injection for both targets. Analysis of soil samples with sequential extraction showed irreversible oxidation of metal sulfides, thereby changing subsurface mineralogy and potentially mobilizing Fe, Cu, Pb, and Zn. Together, these results give insight into persulfate application in terms of risks and effective coupling with bioremediation.

Effect of elevated CO2, O3, and UV radiation on soils

In this work, we have attempted to review the current knowledge on the impact of elevated CO2, O3, and UV on soils. Elevated CO2 increases labile and stabile soil C pool as well as efficiency of organic pollutants rhizoremediation and phytoextraction of heavy metals. Conversely, both elevated O3 and UV radiation decrease inputs of assimilates to the rhizosphere being accompanied by inhibitory effects on decomposition processes, rhizoremediation, and heavy metals phytoextraction efficiency. Contrary to elevated CO2, O3, or UV-B decreases soil microbial biomass, metabolisable C, and soil N t content leading to higher C/N of soil organic matter. Elevated UV-B radiation shifts soil microbial community and decreases populations of soil meso- and macrofauna via direct effect rather than by induced changes of litter quality and root exudation as in case of elevated CO2 or O3. CO2 enrichment or increased UV-B is hypothesised to stimulate or inhibit both plant and microbial competitiveness for soluble soil N, respectively, whereas O3 favours only microbial competitive efficiency. Understanding the consequences of elevated CO2, O3, and UV radiation for soils, especially those related to fertility, phytotoxins inputs, elements cycling, plant-microbe interactions, and decontamination of polluted sites, presents a knowledge gap for future research.

Impact of organic carbon and nutrients mobilized during chemical oxidation on subsequent bioremediation of a diesel-contaminated soil

Remediation with in situ chemical oxidation (ISCO) impacts soil organic matter (SOM) and the microbial community, with deleterious effects on the latter being a major hurdle to coupling ISCO with in situ bioremediation (ISB). We investigate treatment of a diesel-contaminated soil with Fenton's reagent and modified Fenton's reagent coupled with a subsequent bioremediation phase of 187d, both with and without nutrient amendment. Chemical oxidation mobilized SOM into the liquid phase, producing dissolved organic carbon (DOC) concentrations 8-16 times higher than the untreated field sample. Higher aqueous concentrations of nitrogen and phosphorous species were also observed following oxidation; NH4(+) increased 14-172 times. During the bioremediation phase, dissolved carbon and nutrient species were utilized for microbial growth-yielding DOC concentrations similar to field sample levels within 56d of incubation. In the absence of nutrient amendment, the highest microbial respiration rates were correlated with higher availability of nitrogen and phosphorus species mobilized by oxidation. Significant diesel degradation was only observed following nutrient amendment, implying that nutrients mobilized by chemical oxidation can increase microbial activity but are insufficient for bioremediation. While all bioremediation occurred in the first 28d of incubation in the biotic control microcosm with nutrient amendment, biodegradation continued throughout 187d of incubation following chemical oxidation, suggesting that chemical treatment also affects the desorption of organic contaminants from SOM. Overall, results indicate that biodegradation of DOC, as an alternative substrate to diesel, and biological utilization of mobilized nutrients have implications for the success of coupled ISCO and ISB treatments.

Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis

The functional dynamics of microbial communities are largely responsible for the clean-up of hydrocarbons in the environment. However, knowledge of the distinguishing functional genes, known as the metabolic footprint, present in hydrocarbon-impacted sites is still scarcely understood. Here, we conducted several multivariate analyses to characterise the metabolic footprints present in a variety of hydrocarbon-impacted and non-impacted sediments. Non-metric multi-dimensional scaling (NMDS) and canonical analysis of principal coordinates (CAP) showed a clear distinction between the two groups. A high relative abundance of genes associated with cofactors, virulence, phages and fatty acids were present in the non-impacted sediments, accounting for 45.7 % of the overall dissimilarity. In the hydrocarbon-impacted sites, a high relative abundance of genes associated with iron acquisition and metabolism, dormancy and sporulation, motility, metabolism of aromatic compounds and cell signalling were observed, accounting for 22.3 % of the overall dissimilarity. These results suggest a major shift in functionality has occurred with pathways essential to the degradation of hydrocarbons becoming overrepresented at the expense of other, less essential metabolisms.

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

Functional gene expression of oil-degrading bacteria resistant to hexadecane toxicity

Contamination with oil poses a threat to the environment and to human health worldwide. Biological methodologies have proved to be economical, versatile and efficient for the remediation of pollutants. In this paper, a highly efficient oil-degrading bacterial strain USTB-2 was isolated from an oil production well of Dagang oil field in Tianjin, China. The 16S rRNA sequence of USTB-2 showed 100% similarity with that of Bacillus subtilis BSn5. Hexadecane is one of the most important components in petroleum. The half inhibitory ratio (IC₅₀) of hexadecane inhibited organisms, determined by microcalorimetry, was lower in USTB-2 than in B. BSn5. The results indicate that the strain USTB-2 degrades hexadecane to make it less toxic compared with the normal strain. RT-PCR was used to evaluate the expression of oil-degrading enzymes, specifically 4-hydroxyphenylacetate 3-monooxygenase genes (HPMO). A sharp increase in the expression of HPMO genes was observed for USTB-2, while the expression of HPMO genes in reference strain B. BSn5 remained relatively stable. These methods can be used to study the metabolic potential of microorganisms for in situ oil decontamination.

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

Spatial variations of hydrocarbon contamination and soil properties in oil exploring fields across China

Successful site remediation is critically based on a comprehensive understanding of distribution of contaminants, soil physico-chemical and microbial properties in oil contaminated sites. One hundred and ten topsoils were sampled from seven typical oil fields in different geoclimate regions across north to south China to investigate the spatial variances of oil contaminations and soil parameters. Oil concentrations and compositions, soil geochemical properties and microbial populations were analyzed and statistic analysis methods were used to analyze the spatial pattern of soil variables. The results indicated that oil contaminations were serious in most oil exploring areas in China, especially with high levels of polycyclic aromatic hydrocarbons (PAHs) from petrogenic origin. Ordination analyses indicated a relatively distinct spatial pattern that all soil samples grouped mainly by geographic locations, instead of distributing along contamination or other geochemical variable gradient. Microbial populations were found to be statistically positively correlated with soil nitrogen, phosphorus and water content, and negatively correlated with salt pH and soluble salts (P<0.05). This study provided insights into the spatial variability of soil variables in hydrocarbon-contaminated fields across large spatial scales, which is important for the environmental protection and further remediation in oil contaminated sites according to local conditions.

Use of functional gene arrays for elucidating in situ biodegradation

Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.

Detailed characterization of polar compounds of residual oil in contaminated soil revealed by Fourier transform ion cyclotron resonance mass spectrometry

Effects of remediation technologies on polar compounds of crude oil in contaminated soils have not been well understood when compared to hydrocarbons. In this study, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize the changes in NSO polar compounds of crude oil and residual oil after long-term natural attenuation, biostimulation and subsequent ozonation following biostimulation of contaminated soils. N1 and O1 species, which were abundant in the crude oil, were selectively biodegraded, and species with higher double bond equivalent values and smaller carbon numbers appeared to be more resistant to microbial alteration. O2-O6 species were enriched by biodegradation and contained a large number of compounds with a high degree of unsaturation. Ozone could react with a variety of polar compounds in residual oil after biodegradation and showed high reactivity with polar species containing aromatic or multi-aliphatic rings, including the residual N1 and O1 species, naphthenic acids and unsaturated O3-O6 compounds. Fatty acids and O3-O8 species dominated by saturated alkyl compounds were resistant to ozonation or the primarily incomplete ozonation products. Principal component analysis of identified peaks in the FT-ICR MS spectra provided a comprehensive overview of the complex samples at the molecular level and the results were consistent with the detailed analysis. Taken together, these results showed the high complexity of polar compounds in residual oils after biodegradation or ozonation in contaminated soil and would contribute to a better understanding of bioremediation and ozonation processes.

Changes in the composition of an acid mine drainage microbial community upon successive transfers in medium containing low-grade copper sulfide

A consortium of microorganisms from acid mine drainage samples was cultured in modified 9 K medium containing low-grade copper sulfide. The culture was maintained for sixty days and then transferred to fresh medium. This process was repeated three more times and a final consortium exhibiting a copper extraction rate of 89.3% was obtained. RFLP and microarrays analysis of 16S rRNA sequences retrieved from the consortia showed that Acidithiobacilluscaldus, Leptospirillumferriphilum, Sulfobacillus sp., Acidiphilium sp., and Sulfolobus spp. were represented in higher numbers in the consortia obtained in the copper-containing medium than in the original consortium. In contrast, a decrease in Acidithiobacillus ferrooxidans, Alicyclobacillus sp., Pseudomonas sp., and Sulfobacillus thermosulfidooxidans was observed. The abundance of genes related to sulfur metabolism from At. caldus and Sulfolobus spp., iron oxidation from Leptospirillum sp. and metal resistance from most of the detected microorganisms increased as the consortium was successively transferred into fresh medium.

The effect of the introduction of exogenous strain Acidithiobacillus thiooxidans A01 on functional gene expression, structure and function of indigenous consortium during pyrite bioleaching

Acidithiobacillus thiooxidans A01 was added to a consortium of bioleaching bacteria including Acidithiobacilluscaldus, Leptospirillumferriphilum, Acidithiobacillus ferrooxidans, Sulfobacillus thermosulfidooxidans, Acidiphilium spp., and Ferroplasma thermophilum cultured in modified 9 K medium containing 0.5% (w/v) pyrite, and 10.7% increase of bioleaching rate was observed. Changes in community structure and gene expression were monitored with real-time PCR and functional gene arrays (FGAs). Real-time PCR showed that addition of At. thiooxidans caused increased numbers of all consortium members except At. caldus, and At. caldus, L. ferriphilum, and F. thermophilum remained dominant in this community. FGAs results showed that after addition of At. thiooxidans, most genes involved in iron, sulfur, carbon, and nitrogen metabolisms, metal resistance, electron transport, and extracellular polymeric substances of L. ferriphilum, F. thermophilum, and Acidiphilium spp., were up-regulated while most of these genes were down-regulated at 70-78 h in At. caldus and up-regulated in At. ferrooxidans, then down-regulated at 82-86 h.

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

Background

Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes.

Results

First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.

Conclusions

We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Stability of the total and functional microbial communities in river sediment mesocosms exposed to anthropogenic disturbances

River systems are exposed to anthropogenic disturbances, including chemical pollution and eutrophication. This may affect the phylogenetic diversity as well as the abundance of various functional groups within sediment-associated microbial communities. To address such potential effects, mesocosms filled with Ebro delta sediment covered with river water were exposed to chlorinated organic compounds or to a high nutrient concentration as used for fertilization. Changes in the abundance of selected functional microbial groups, i.e. total aerobes, nitrate, sulfate and iron reducers, organohalide-respiring microorganisms as well as methanogens, were examined using culture-dependent most probable number and culture-independent PCR methods targeting phylogenetic as well as functional gene markers. It was concluded that the abundance of functional groups was neither affected by pollution with 1,2-dichloroethane and tetrachloroethene nor by elevated nutrient loads, although changes in the bacterial community composition were observed using 16S rRNA gene-targeted fingerprint techniques. This study reinforced the notion that complementary culture-dependent and molecular methods, focusing on different fractions of the microbial community (cultivable, active or total), should be used in combination for a comprehensive description of phylogenetic diversity and functional potential.

Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies

A functional gene array (FGA), GeoChip 2.0, was used to assess the biogeochemical cycling potential of microbial communities associated with healthy and Caribbean yellow band diseased (YBD) Montastraea faveolata. Over 6700 genes were detected, providing evidence that the coral microbiome contains a diverse community of archaea, bacteria and fungi capable of fulfilling numerous functional niches. These included carbon, nitrogen and sulfur cycling, metal homeostasis and resistance, and xenobiotic contaminant degradation. A significant difference in functional structure was found between healthy and YBD M. faveolata colonies and those differences were specific to the physical niche examined. In the surface mucopolysaccharide layer (SML), only two of 31 functional categories investigated, cellulose degradation and nitrification, revealed significant differences, implying a very specific change in microbial functional potential. Coral tissue slurry, on the other hand, revealed significant changes in 10 of the 31 categories, suggesting a more generalized shift in functional potential involving various aspects of nutrient cycling, metal transformations and contaminant degradation. This study is the first broad screening of functional genes in coral-associated microbial communities and provides insights regarding their biogeochemical cycling capacity in healthy and diseased states.