Comparison of Biostimulation versus Bioaugmentation with Bacterial Strain PM1 for Treatment of Groundwater Contaminated with Methyl Tertiary Butyl Ether (MTBE)

Field Test of In Situ Groundwater Treatment Applying Oxygen Diffusion and Bioaugmentation Methods in an Area with Sustained Total Petroleum Hydrocarbon (TPH) Contaminant Flow

Contamination of groundwater by petroleum hydrocarbons is a widespread environmental problem in many regions. Contamination of unsaturated and saturated zones could also pose a significant risk to human health. The main purpose of the study was to assess the efficiency of biodegradation of total petroleum hydrocarbon (TPH) in situ, in an area with loam and sandy loam soils, and to identify features and characteristics related to groundwater treatment in an area with a persistent flow of pollutants. We used methods of biostimulation (oxygen as stimulatory supplement) and bioaugmentation to improve water quality. Oxygen was added to the groundwater by diffusion through silicone tubing. The efficiency of groundwater treatment was determined by detailed monitoring. Implementation of the applied measure resulted in an average reduction in TPH concentration of 73.1% compared with the initial average concentration (4.33 mg/L), and in the local area, TPH content was reduced by 95.5%. The authors hope that this paper will contribute to a better understanding of the topic of groundwater treatment by in situ biodegradation of TPH. Further studies on this topic are particularly needed to provide more data and details on the efficiency of groundwater treatment under adverse geological conditions.

The Fate of MTBE and BTEX in Constructed Wetlands

Hydrocarbon contamination of water resources is a global issue. These compounds are generated and discharged into the environment in industrial areas from chemical and petrochemical plants, oil refineries, power plants, and so forth. Fuel hydrocarbons, namely, BTEX (benzene, toluene, ethylbenzene, and xylenes) and MTBE (methyl tert-butyl ether), are commonly found in groundwater, posing environmental and health risks to humans and ecosystems. Nature-based technologies represent an alternative solution, providing high efficiency, an environmentally friendly character, simple operation, and cost efficiency, which are characteristics particularly desired by the international petroleum industry. This article discusses the use of the green technology of constructed wetlands to remediate water polluted with hydrocarbons. Although the number of related international experiences and studies is limited, the article presents the latest developments of wetland technology for the removal of MTBE and benzene-BTEX. The discussion includes the overall efficiency of the different wetland types that have been tested and used, the main transformation and removal processes that regulate the fate of BTEX and MTBE in constructed wetlands, and the potential for future investigations.

Use of omic tools to assess methyl tert-butyl ether (MTBE) degradation in groundwater

This study employed innovative technologies to evaluate multiple lines of evidence for natural attenuation (NA) of methyl tertiary-butyl ether (MTBE) in groundwater at the 22 Area of Marine Corps Base (MCB) Camp Pendleton after decommissioning of a biobarrier system. For comparison, data from the 13 Area Gas Station where active treatment of MTBE is occurring was used to evaluate the effectiveness of omic techniques in assessing biodegradation. Overall, the 22 Area Gas Station appeared to be anoxic. MTBE was detected in large portion of the plume. In comparison, concentrations of MTBE at the 13 Area Gas Station were much higher (42,000 μg/L to 2800 μg/L); however, none of the oxygenates were detected. Metagenomic analysis of the indigenous groundwater microbial community revealed the presence of bacterial strains known to aerobically and anaerobically degrade MTBE at both sites. While proteomic analysis at the 22 Area Gas Station showed the presence of proteins of MTBE degrading microorganisms, the MTBE degradative proteins were only found at the 13 Area Gas Station. Taken together, these results provide evidence for previous NA of MTBE in the groundwater at 22 Area Gas Station and demonstrate the effectiveness of innovative-omic technologies to assist monitored NA assessments.

Application of magnesium peroxide (MgO2) nanoparticles for toluene remediation from groundwater: batch and column studies

In the present study, magnesium peroxide (MgO₂) nanoparticles were synthesized by electro-deposition process and characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FESEM). The batch experiments were conducted to evaluate the MgO₂ half-life (600 mg/L) in groundwater under various temperatures (4, 15, and 30 °C) and initial pH (3, 7, and 12). The effect of Fe²⁺ ions (enhanced oxidation) on the toluene remediation by MgO₂ was also investigated. Nanoparticles were injected to sand-packed continuous-flow columns, and toluene removal (50 ppm) was studied within 50 days at 15 °C. The results indicated that the half-life of MgO₂ at pH 3 and 12 were 5 and 15 days, respectively, in comparison to 10 days at the initial pH 7 and 15 °C. The nanoparticles showed 20 and 7.5 days half-life at 4 and 30 °C temperatures, respectively. Injection of Fe²⁺ ions indicated an impressive effect on toluene removal by MgO₂, and the contaminant was completely removed after 5 and 10 days, in the batch and column experiments, respectively. Confocal laser scanning microscope (CLSM) analysis indicated that the attached biofilm had a significant role in the decontamination of groundwater. Comparison of bioremediation and enhanced oxidation resulted in a considerable insight into the application of magnesium peroxide in groundwater remediation. Graphical abstract ᅟ.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1

Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay

Metagenomes derived from environmental microbiota encode a vast diversity of protein homologs. How this diversity impacts protein function can be explored through selection assays aimed to optimize function. While artificially generated gene sequence pools are typically used in selection assays, their usage may be limited because of technical or ethical reasons. Here, we investigate an alternative strategy, the use of soil microbial DNA as a starting point. We demonstrate this approach by optimizing the function of a widely occurring soil bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase. We identified a specific ACC deaminase domain region (ACCD-DR) that, when PCR amplified from the soil, produced a variant pool that we could swap into functional plasmids carrying ACC deaminase-encoding genes. Functional clones of ACC deaminase were selected for in a competition assay based on their capacity to provide nitrogen to Escherichia coli in vitro. The most successful ACCD-DR variants were identified after multiple rounds of selection by sequence analysis. We observed that previously identified essential active-site residues were fixed in the original unselected library and that additional residues went to fixation after selection. We identified a divergent essential residue whose presence hints at the possible use of alternative substrates and a cluster of neutral residues that did not influence ACCD performance. Using an artificial ACCD-DR variant library generated by DNA oligomer synthesis, we validated the same fixation patterns. Our study demonstrates that soil metagenomes are useful starting pools of protein-coding-gene diversity that can be utilized for protein optimization and functional characterization when synthetic libraries are not appropriate.

Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary

Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and proved to have excellent capabilities in degrading some common fuel oxygenates like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along with other organic compounds. Here, we report the draft genome sequence of M. sp. strain T29 together with the description of the genome properties and its annotation. The draft genome consists of 608 contigs with a total size of 4,449,424 bp and an average coverage of 150×. The genome exhibits an average G + C content of 68.7 %, and contains 4754 protein coding and 52 RNA genes, including 48 tRNA genes. 71 % of the protein coding genes could be assigned to COG (Clusters of Orthologous Groups) categories. A formerly unknown circular plasmid designated as pT29A was isolated and sequenced separately and found to be 86,856 bp long.

Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.

Gene mdpC plays a regulatory role in the methyl-tert-butyl ether degradation pathway of Methylibium petroleiphilum strain PM1

Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.

Numerical modeling analysis of VOC removal processes in different aerobic vertical flow systems for groundwater remediation

Vertical flow systems filled with porous medium have been shown to efficiently remove volatile organic contaminants (VOCs) from contaminated groundwater. To apply this semi-natural remediation strategy it is however necessary to distinguish between removal due to biodegradation and due to volatile losses to the atmosphere. Especially for (potentially) toxic VOCs, the latter needs to be minimized to limit atmospheric emissions. In this study, numerical simulation was used to investigate quantitatively the removal of volatile organic compounds in two pilot-scale water treatment systems: an unplanted vertical flow filter and a planted one, which could also be called a vertical flow constructed wetland, both used for the treatment of contaminated groundwater. These systems were intermittently loaded with contaminated water containing benzene and MTBE as main VOCs. The highly dynamic but permanently unsaturated conditions in the porous medium facilitated aerobic biodegradation but could lead to volatile emissions of the contaminants. Experimental data from porous material analyses, flow rate measurements, solute tracer and gas tracer test, as well as contaminant concentration measurements at the boundaries of the systems were used to constrain a numerical reactive transport modeling approach. Numerical simulations considered unsaturated water flow, transport of species in the aqueous and the gas phase as well as aerobic degradation processes, which made it possible to quantify the rates of biodegradation and volatile emissions and calculating their contribution to total contaminant removal. A range of degradation rates was determined using experimental results of both systems under two operation modes and validated by field data obtained at different operation modes applied to the filters. For both filters, simulations and experimental data point to high biodegradation rates, if the flow filters have had time to build up their removal capacity. For this case volatile emissions are negligible and total removal can be attributed to biodegradation, only. The simulation study thus supports the use of both of these vertical flow systems for the treatment of groundwater contaminated with VOCs and the use of reactive transport modeling for the assessment of VOCs removal and operation modes in these high performance treatment systems.

Anaerobic methyl tert-butyl ether-degrading microorganisms identified in wastewater treatment plant samples by stable isotope probing

Anaerobic methyl tert-butyl ether (MTBE) degradation potential was investigated in samples from a range of sources. From these 22 experimental variations, only one source (from wastewater treatment plant samples) exhibited MTBE degradation. These microcosms were methanogenic and were subjected to DNA-based stable isotope probing (SIP) targeted to both bacteria and archaea to identify the putative MTBE degraders. For this purpose, DNA was extracted at two time points, subjected to ultracentrifugation, fractioning, and terminal restriction fragment length polymorphism (TRFLP). In addition, bacterial and archaeal 16S rRNA gene clone libraries were constructed. The SIP experiments indicated bacteria in the phyla Firmicutes (family Ruminococcaceae) and Alphaproteobacteria (genus Sphingopyxis) were the dominant MTBE degraders. Previous studies have suggested a role for Firmicutes in anaerobic MTBE degradation; however, the putative MTBE-degrading microorganism in the current study is a novel MTBE-degrading phylotype within this phylum. Two archaeal phylotypes (genera Methanosarcina and Methanocorpusculum) were also enriched in the heavy fractions, and these organisms may be responsible for minor amounts of MTBE degradation or for the uptake of metabolites released from the primary MTBE degraders. Currently, limited information exists on the microorganisms able to degrade MTBE under anaerobic conditions. This work represents the first application of DNA-based SIP to identify anaerobic MTBE-degrading microorganisms in laboratory microcosms and therefore provides a valuable set of data to definitively link identity with anaerobic MTBE degradation.

Study of an aquifer contaminated by ethyl tert-butyl ether (ETBE): site characterization and on-site bioremediation

Ethyl tert-butyl ether (ETBE) was detected at high concentration (300mgL(-1)) in the groundwater below a gas-station. No significant carbon neither hydrogen isotopic fractionation of ETBE was detected along the plume. ETBE and BTEX biodegradation capacities of the indigenous microflora Pz1-ETBE and of a culture (MC-IFP) composed of Rhodococcus wratislaviensis IFP 2016, Rhodococcus aetherivorans IFP 2017 and Aquincola tertiaricarbonis IFP 2003 showed that ETBE and BTEX degradation rates were in the same range (ETBE: 0.91 and 0.83 mg L(-1)h(-1) and BTEX: 0.64 and 0.82 mg L(-1)h(-1), respectively) but tert-butanol (TBA) accumulated transiently at a high level using Pz1-ETBE (74 mg L(-1)). An on-site pilot plant (2m(3)) filled with polluted groundwater and inoculated by MC-IFP, successfully degraded four successive additions of ETBE and gasoline. However, an insignificant ETBE isotopic fractionation was also accompanying this decrease which suggested the involvement of low fractionating-strains using EthB enzymes, but required of additional proofs. The ethB gene encoding a cytochrome P450 involved in ETBE biodegradation (present in R. aetherivorans IFP 2017) was monitored by quantitative real-time polymerase chain reaction (q-PCR) on DNA extracted from water sampled in the pilot plant which yield up to 5×10(6) copies of ethB gene per L(-1).

Linking low-level stable isotope fractionation to expression of the cytochrome P450 monooxygenase-encoding ethB gene for elucidation of methyl tert-butyl ether biodegradation in aerated treatment pond systems

Multidimensional compound-specific stable isotope analysis (CSIA) was applied in combination with RNA-based molecular tools to characterize methyl tertiary (tert-) butyl ether (MTBE) degradation mechanisms occurring in biofilms in an aerated treatment pond used for remediation of MTBE-contaminated groundwater. The main pathway for MTBE oxidation was elucidated by linking the low-level stable isotope fractionation (mean carbon isotopic enrichment factor [ε(C)] of -0.37‰ ± 0.05‰ and no significant hydrogen isotopic enrichment factor [ε(H)]) observed in microcosm experiments to expression of the ethB gene encoding a cytochrome P450 monooxygenase able to catalyze the oxidation of MTBE in biofilm samples both from the microcosms and directly from the ponds. 16S rRNA-specific primers revealed the presence of a sequence 100% identical to that of Methylibium petroleiphilum PM1, a well-characterized MTBE degrader. However, neither expression of the mdpA genes encoding the alkane hydroxylase-like enzyme responsible for MTBE oxidation in this strain nor the related MTBE isotope fractionation pattern produced by PM1 could be detected, suggesting that this enzyme was not active in this system. Additionally, observed low inverse fractionation of carbon (ε(C) of +0.11‰ ± 0.03‰) and low fractionation of hydrogen (ε(H) of -5‰ ± 1‰) in laboratory experiments simulating MTBE stripping from an open surface water body suggest that the application of CSIA in field investigations to detect biodegradation may lead to false-negative results when volatilization effects coincide with the activity of low-fractionating enzymes. As shown in this study, complementary examination of expression of specific catabolic genes can be used as additional direct evidence for microbial degradation activity and may overcome this problem.

Size Does Matter: Application-driven Approaches for Soil Metagenomics

Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a high-throughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.

Monitoring bioaugmenation with single-well push-pull tests in sediment systems contaminated with trichloroethene

Bioaugmentation to enhance the rate and extent of reductive dechlorination of chlorinated ethenes was investigated in intermediate ( approximately 1 m) scale physical aquifer models (PAMs) designed to simulate the groundwater flow field near an injection well. Push-pull tests were used to quantify the reductive dechlorination of injected trichloroethene (TCE) and trichlorofluoroethene (TCFE) in prepared sediment packs with and without an added dechlorinating culture containing Dehalococcoides spp. Distribution of the added culture throughout the sediment pack was confirmed by microscopic observation. Repeated additions of TCE (100-350 microM) were completely transformed to ethene in 14 days and a subsequent TCFE addition (114 microM) was completely transformed to fluoroethene (FE) in 24 days. Similar transformation rates, product distributions, and time courses for TCE and TCFE transformation were observed when these compounds were added together at similar initial concentrations. In the control PAM (nonbioaugmented), TCE and TCFE were transformed to only cis-DCE and cis-DCFE, respectively, and transformation rates were 6-12 times slower than those in the bioaugmented PAM. The use of TCFE for push-pull tests is shown to be an effective tool for detecting and quantifying the effects of bioaugmentation on TCE transformation.

Evaluation of the effects of low oxygen concentration on stable isotope fractionation during aerobic MTBE biodegradation

Laboratory experiments were performed with two aerobic MTBE degrading strains ( Methylibium sp. PM1 and Aquincola tertiaricarbonaris L108) in order to determine whether conditions of low oxygen availability, typically found in fuel-contaminated aquifers, can influence stable isotope fractionation of MTBE. Although single carbon and hydrogen enrichment factors of the two strains were not significantly or were only slightly (L108) affected by low oxygen concentrations (fully oxic incubation with initial 21% O2 in the headspace tested versus hypoxic conditions always <2% O2), the experiments showed indirect effects caused by competition interactions in mixed cultures. In a mixed culture of PM1 and L108 under oxic and even more so under hypoxic conditions, the total observed carbon isotope enrichment factor was significantly reduced, while hydrogen fractionation was not detectable. This indicates that the low fractionating model strain L108 is more competitive in degrading MTBE compared to strain PM1. Consistently, higher oxygen affinities during MTBE degradation were observed for strain L108. These first studies, conducted with resting cells, may explain the low isotope fractionation observed in some field studies that are not necessarily related to a lack of biodegradation.

Involvement of a novel enzyme, MdpA, in methyl tert-butyl ether degradation in Methylibium petroleiphilum PM1

Methylibium petroleiphilum PM1 is a well-characterized environmental strain capable of complete metabolism of the fuel oxygenate methyl tert-butyl ether (MTBE). Using a molecular genetic system which we established to study MTBE metabolism by PM1, we demonstrated that the enzyme MdpA is involved in MTBE removal, based on insertional inactivation and complementation studies. MdpA is constitutively expressed at low levels but is strongly induced by MTBE. MdpA is also involved in the regulation of tert-butyl alcohol (TBA) removal under certain conditions but is not directly responsible for TBA degradation. Phylogenetic comparison of MdpA to related enzymes indicates close homology to the short-chain hydrolyzing alkane hydroxylases (AH1), a group that appears to be a distinct subfamily of the AHs. The unique, substrate-size-determining residue Thr(59) distinguishes MdpA from the AH1 subfamily as well as from AlkB enzymes linked to MTBE degradation in Mycobacterium austroafricanum.

Luminescent lanthanide nanoparticles as labels in DNA microarrays for quantification of methyl tertiary butyl ether degrading bacteria

We report application of lanthanide nanoparticles for DNA quantification in a microarray platform as a substitute for conventional organic fluorophores. A non-PCR based DNA microarray assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether (MTBE) was demonstrated. Probe DNA was immobilized on a glass surface, hybridized with biotinylated target DNA and subsequently incubated with Neutravidin-biofunctionalized nanoparticles. The fluorescence spot intensities, measured by a commercial laser scanner, show a linear relationship (R2 = 0.98) with bacterial 16S rDNA over a range of target DNA concentrations, while the background fluorescence remained low. In addition, nanoparticles fluorescence shows a stronger intensity than Quasar570 (Cy3). Present sensitivity of the assay is 10 pM of target DNA. The selectivity of the DNA-nanoparticle-probes to discriminate a non-target DNA with two base pairs mismatch in the 16S rDNA gene sequence was shown. The use of Eu:Gd2O3 nanoparticles as biolabels provides a relatively non-toxic, inexpensive, rapid and sensitive alternative to the materials currently used in DNA microarrays.

Method for measuring substrate preferences by individual members of microbial consortia proposed for bioaugmentation

In this study we used the assimilation of isotope labeled CO(2) to measure the substrate preferences by two different bioaugmentation mixtures proposed for bioremediation of diesel oil contamination. All active microorganisms assimilate CO(2) in various carboxylation processes involved in growth. The CO(2) assimilation by the two mixtures was measured upon addition of glucose, diesel oil or specific compounds present in diesel oil (naphthalene, toluene, hexadecane, and octane). It was shown that within short term incubations with diesel oil (<5 h), one bioaugmentation mixture was superior to the other regarding the assimilation of CO(2). This observation was confirmed in a labor-intensive long term microcosm study (60 days). The applied method open various possibilities for fast pre-testing of substrate-preferences by microbial-bioaugmentation mixtures without microcosm experiments, on-site tests, and complicated chemical analysis. This study also demonstrates the possibility to obtain further information on the substrate preferences at a single cell level of phylogenetically defined microbial subgroups in bioaugmentation mixtures, based on combined analyses of microautoradiography and fluorescence in situ hybridization.

A proteomics strategy for the analysis of bacterial biodegradation pathways

Bacterial biodegradation (bioremediation) is the use of microorganisms to break down organic materials into simpler compounds; it plays a pivotal role in the clean-up of hazardous wastes in the environment. Following the completion of genome sequencing in bacteria capable of biodegradation, functional genomic studies have played a major role in obtaining information on bacterial biodegradation pathways. Novel proteomics technologies have recently been developed to make it possible to analyze global protein expression. Proteomics can also provide important information on the life cycle, regulation, and post-translational modification of proteins induced under specific conditions. Proteomics technologies have been applied to the comprehensive study of bacterial biodegradation. In this paper, we introduce the proteomics technologies applicable to bacterial biodegradation studies, review the results of the proteomics analysis of representative biodegrading bacteria, and discuss the potential use of proteomics technologies in future biodegradation studies.

Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol

High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of tert-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in M. petroleiphilum PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.

Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1

Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an approximately 4-Mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (approximately 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

Biodegradability of imidazolium and pyridinium ionic liquids by an activated sludge microbial community

Ionic liquids (ILs) are novel organic salts that have enormous potential for industrial use as green replacements for harmful volatile organic solvents. Varying the cationic components can alter the chemical and physical properties of ILs, including solubility, to suit a variety of industrial processes. However, to complement designer engineering, it is crucial to proactively characterize the biological impacts of new chemicals, in order to fully define them as environmentally friendly. Before introduction of ILs into the environment, we performed an analysis of the biodegradability of six ILs by activated sludge microorganisms collected from the South Bend, Indiana wastewater treatment plant. We examined biodegradability of 1-butyl, 1-hexyl and 1-octyl derivatives of 3-methyl-imidazolium and 3-methyl-pyridinium bromide compounds using the standard Organisation for Economic Cooperation and Development dissolved organic carbon Die-Away Test, changes in total dissolved nitrogen concentrations, and 1H-nuclear magnetic resonance analysis of initial and final chemical structures. Further, we examined microbial community profiles throughout the incubation period using denaturing gradient gel electrophoresis (DNA-PCR-DGGE). Our results suggest that hexyl and octyl substituted pyridinium-based ILs can be fully mineralized, but that imidazolium-based ILs are only partially mineralized. Butyl substituted ILs with either cation, were not biodegradable. Biodegradation rates also increase with longer alkyl chain length, which may be related to enhanced selection of a microbial community. Finally, DGGE analysis suggests that certain microorganisms are enriched by ILs used as a carbon source. Based on these results, we suggest that further IL design and synthesis include pyridinium cations and longer alkyl substitutions for rapid biodegradability.

Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria

A Gram-negative, rod-shaped, motile, non-pigmented, facultative aerobe that grew optimally at pH 6.5 and 30 degrees C (strain PM1T) was isolated for its ability to completely degrade the gasoline additive methyl tert-butyl ether. Analysis of the 16S rRNA gene sequence indicated that this bacterium was a member of the class Betaproteobacteria in the Sphaerotilus-Leptothrix group. The 16S rRNA gene sequence identity to other genera in this group, Leptothrix, Aquabacterium, Roseateles, Sphaerotilus, Ideonella and Rubrivivax, ranged from 93 to 96 %. The chemotaxonomic data including Q-8 as the major quinone, C16 : 1omega7c and C16 : 0 as the major fatty acids and a DNA G+C content of 69 mol%, support the inclusion of strain PM1T in the class Betaproteobacteria. It differed from other members of the Sphaerotilus-Leptothrix group by being a facultative methylotroph that used methanol as a sole carbon source, and by also being able to grow heterotrophically in defined media containing ethanol, toluene, benzene, ethylbenzene and dihydroxybenzoates as sole carbon sources. On the basis of the morphological, physiological, biochemical and genetic information, a new genus and species, Methylibium petroleiphilum gen. nov., sp. nov., is proposed, with PM1T (=ATCC BAA-1232T=LMG 22953T) as the type strain.

Is bioaugmentation a feasible strategy for pollutant removal and site remediation?

Microorganisms can degrade numerous organic pollutants owing to their metabolic machinery and to their capacity to adapt to inhospitable environments. Thus, microorganisms are major players in site remediation. However, their efficiency depends on many factors, including the chemical nature and the concentration of pollutants, their availability to microorganisms, and the physicochemical characteristics of the environment. The capacity of a microbial population to degrade pollutants within an environmental matrix (e.g. soil, sediment, sludge or wastewater) can be enhanced either by stimulation of the indigenous microorganisms by addition of nutrients or electron acceptors (biostimulation) or by the introduction of specific microorganisms to the local population (bioaugmentation). Although it has been practiced in agriculture and in wastewater treatment for years, bioaugmentation is still experimental. Many factors (e.g. predation, competition or sorption) conspire against it. However, several strategies are currently being explored to make bioaugmentation a successful technology in sites that lack significant populations of biodegrading microorganisms. Under optimal local conditions, the rate of pollutant degradation might increase upon addition of an inoculant to remediate a chemical spill; however, the most successful cases of bioaugmentation occur in confined systems, such as bioreactors in which the conditions can be controlled to favour survival and prolonged activity of the exogenous microbial population.

Natural attenuation and enhanced bioremediation of organic contaminants in groundwater

An area of intense scientific and practical interest is the biogeochemical and microbial processes determining the success of natural attenuation, biostimulation and/or bioaugmentation treatments for organic contaminants in groundwater. Recent studies in this area have focused on the reductive dechlorination of chlorinated solvents, the degradation of the fuel additive methyl tert-butyl ether, and the removal of long-term hydrocarbon contamination. These studies have been facilitated by the use of stable isotope analysis to demonstrate in situ bioremediation and push-pull tests, in which isotopes are injected into aquifers and then quickly retrieved and analyzed, to measure in situ activity. Molecular tools such as quantitative PCR, the detection of mRNA expression, and numerous DNA fingerprinting methods have also proved valuable, being employed to identify and sometimes quantify environmentally important organisms or changes in communities. Methods to track bacteria and tools to characterize bacterial attachment properties have also offered insight into bacterial transport in situ.