Bacterial aerobic degradation of benzene, toluene, ethylbenzene and xylene

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study

Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.

Synchronous removal of gaseous toluene and benzene and degradation process shifts in microbial fuel cell-biotrickling filter system

Illustrating the biodegradation processes of multi-component volatile organic compounds (VOCs) will expedite the implication of biotechnology in purifying industrial exhaust. Here, performance shifts of microbial fuel cell and biotrickling filter combined system (MFC-BTF) are investigated for removing single and dual components of toluene and benzene. Synchronous removal of toluene (95 %) and benzene (97 %) are achieved by MFC-BTF accompanied with the output current of 0.41 mA. Elevated content of extracellular polymeric substance facilitates the mass transfer of benzene with the presence of toluene. Strains of Bacteroidota, Proteobacteria and Chloroflexi contribute to the removal of dual components VOCs. Empty bed reaction time and the VOCs concentration are the important factors influencing their dissolution in the system. The biodegradation of toluene and benzene proceeds with 2-hydroxymuconic semialdehyde and o-hydroxybenzoic acid as the main intermediates. These results provide a comprehensive understanding of multi-component VOCs removal by MFC-BTF and guide the system design, optimization, and scale-up.

Soil processes modify the composition of volatile organic compounds (VOCs) from CO2- and CH4-dominated geogenic and landfill gases: A comprehensive study

Degradation mechanisms affecting non-methane volatile organic compounds (VOCs) during gas uprising from different hypogenic sources to the surface were investigated through extensive sampling surveys in areas encompassing a high enthalpy hydrothermal system associated with active volcanism, a CH4-rich sedimentary basin and a municipal waste landfill. For a comprehensive framework, published data from medium-to-high enthalpy hydrothermal systems were also included. The investigated systems were characterised by peculiar VOC suites that reflected the conditions of the genetic environments in which temperature, contents of organic matter, and gas fugacity had a major role. Differences in VOC patterns between source (gas vents and landfill gas) and soil gases indicated VOC transformations in soil. Processes acting in soil preferentially degraded high-molecular weight alkanes with respect to the low-molecular weight ones. Alkenes and cyclics roughly behaved like alkanes. Thiophenes were degraded to a larger extent with respect to alkylated benzenes, which were more reactive than benzene. Furan appeared less degraded than its alkylated homologues. Dimethylsulfoxide was generally favoured with respect to dimethylsulfide. Limonene and camphene were relatively unstable under aerobic conditions, while α-pinene was recalcitrant. O-bearing organic compounds (i.e., aldehydes, esters, ketones, alcohols, organic acids and phenol) acted as intermediate products of the ongoing VOC degradations in soil. No evidence for the degradation of halogenated compounds and benzothiazole was observed. This study pointed out how soil degradation processes reduce hypogenic VOC emissions and the important role played by physicochemical and biological parameters on the effective VOC attenuation capacity of the soil.

2-Furoic acid associated with the infection of nematodes by Dactylellina haptotyla and its biocontrol potential on plant root-knot nematodes

Dactylellina haptotyla is a typical nematode-trapping fungus that has garnered the attention of many scholars for its highly effective lethal potential for nematodes. Secondary metabolites play an important role in D. haptotyla-nematode interactions, but which metabolites perform which function remains unclear. We report the metabolic functions based on high-quality, chromosome-level genome assembly of wild D. haptotyla YMF1.03409. The results indicate that a large variety of secondary metabolites and their biosynthetic genes were significantly upregulated during the nematode-trapping stage. In parallel, we identified that 2-furoic acid was specifically produced during nematode trapping by D. haptotyla YMF1.03409 and isolated it from fermentation production. 2-Furoic acid demonstrated strong nematicidal activity with an LD50 value of 55.05 µg/mL against Meloidogyne incognita at 48 h. Furthermore, the pot experiment showed that the number of galls of tomato root was significantly reduced in the experimental group treated with 2-furoic acid. The considerable increase in the 2-furoic acid content during the infection process and its virulent nematicidal activity revealed an essential synergistic effect during the process of nematode-trapping fungal infection. IMPORTANCE Dactylellina haptotyla have significant application potential in nematode biocontrol. In this study, we determined the chromosome-level genome sequence of D. haptotyla YMF1.03409 by long-read sequencing technology. Comparative genomic analysis identified a series of pathogenesis-related genes and revealed significant gene family contraction events during the evolution of D. haptotyla YMF1.03409. Combining transcriptomic and metabolomic data as well as in vitro activity test results, a compound with important application potential in nematode biocontrol, 2-furoic acid, was identified. Our result expanded the genetic resource of D. haptotyla and identified a previously unreported nematicidal small molecule, which provides new options for the development of plant biocontrol agents.

Metagenomic analysis reveals specific BTEX degrading microorganisms of a bacterial consortium

Petroleum hydrocarbon contamination is of environmental and public health concerns due to its toxic components. Bioremediation utilizes microbial organisms to metabolism and remove these contaminants. The aim of this study was to enrich a microbial community and examine its potential to degrade petroleum hydrocarbon. Through successive enrichment, we obtained a bacterial consortium using crude oil as sole carbon source. The 16 S rRNA gene analysis illustrated the structural characteristics of this community. Metagenomic analysis revealed the specific microbial organisms involved in the degradation of cyclohexane and all the six BTEX components, with a demonstration of the versatile metabolic pathways involved in these reactions. Results showed that our consortium contained the full range of CDSs that could potentially degrade cyclohexane, benzene, toluene, and (o-, m-, p-) xylene completely. Interestingly, a single taxon that possessed all the genes involved in either the activation or the central intermediates degrading pathway was not detected, except for the Novosphingobium which contained all the genes involved in the upper degradation pathway of benzene, indicating the synergistic interactions between different bacterial genera during the hydrocarbon degradation.

A systematic review on mitigation of common indoor air pollutants using plant-based methods: a phytoremediation approach

Environmental pollution, especially indoor air pollution, has become a global issue and affects nearly all domains of life. Being both natural and anthropogenic substances, indoor air pollutants lead to the deterioration of the ecosystem and have a negative impact on human health. Cost-effective plant-based approaches can help to improve indoor air quality (IAQ), regulate temperature, and protect humans from potential health risks. Thus, in this review, we have highlighted the common indoor air pollutants and their mitigation through plant-based approaches. Potted plants, green walls, and their combination with bio-filtration are such emerging approaches that can efficiently purify the indoor air. Moreover, we have discussed the pathways or mechanisms of phytoremediation, which involve the aerial parts of the plants (phyllosphere), growth media, and roots along with their associated microorganisms (rhizosphere). In conclusion, plants and their associated microbial communities can be key solutions for reducing indoor air pollution. However, there is a dire need to explore advanced omics technologies to get in-depth knowledge of the molecular mechanisms associated with plant-based reduction of indoor air pollutants.

Removal of Benzene and Toluene from Synthetic Wastewater by Adsorption onto Magnetic Zeolitic Imidazole Framework Nanocomposites

Considering the risk associated with exposure to benzene and toluene in water resources, researchers have been motivated to conduct studies to remove them from aqueous solutions. Thus, by performing the present study, the potential of Fe₃O₄/zeolite imidazolate framework nanoparticles (Fe₃O₄@ZIF-8) was evaluated for the adsorption of benzene and toluene. Accordingly, the solution pH, Fe₃O₄@ZIF-8 dosage, mixing time, concentration of benzene and toluene, and temperature, were the parameters considered for conducting the batch experiments, for which their effect on adsorption efficiency was evaluated. Our conducted experiments introduced the neutral pH as the best pH range to obtain the maximum removal. Fitting the adsorption data into the various models revealed the aptness of the Langmuir isotherm equation in describing experimental information and highest adsorption capacity; for benzene it was 129.4, 134.2, 137.3, and 148.2 mg g^-1, but for toluene it was 118.4, 125.2, 129.6, and 133.1 mg g^-1, for temperature 20, 30, 40, and 50 °C, respectively. Using obtained optimal conditions, the adsorption efficiencies of benzene and toluene were obtained to be 98.4% and 93.1%, respectively. Kinetic studies showed acceptable coefficients for PSO kinetics and confirmed its suitability. Also, the recyclability results showed that for six consecutive periods of the adsorption-desorption process, the percentage of removal decreased by only 6% for benzene and toluene. Moreover, calculating thermodynamic parameter changes for benzene and toluene removal confirmed the favorability and spontaneity of the studied process and its endothermic nature. Considering the above findings, Fe₃O₄@ZIF-8 was found to be an operative adsorbent for removing pollutants.

Cupriavidus metallidurans CH34 Possesses Aromatic Catabolic Versatility and Degrades Benzene in the Presence of Mercury and Cadmium

Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this study were to analyze the aromatic catabolic potential of C. metallidurans CH34 and to determine the functionality of the predicted benzene catabolic pathway and the influence of cadmium and mercury on benzene degradation. Three chromosome-encoded bacterial multicomponent monooxygenases (BMMs) are involved in benzene catabolic pathways. Growth assessment, intermediates identification, and gene expression analysis indicate the functionality of the benzene catabolic pathway. Strain CH34 degraded benzene via phenol and 2-hydroxymuconic semialdehyde. Transcriptional analyses revealed a transition from the expression of catechol 2,3-dioxygenase (tomB) in the early exponential phase to catechol 1,2-dioxygenase (catA1 and catA2) in the late exponential phase. The minimum inhibitory concentration to Hg (II) and Cd (II) was significantly lower in the presence of benzene, demonstrating the effect of co-contamination on bacterial growth. Notably, this study showed that C. metallidurans CH34 degraded benzene in the presence of Hg (II) or Cd (II).

Toluene Bioremediation by Using Geotextile-Layered Permeable Reactive Barriers (PRBs)

Sources of contamination in a subsurface environment are petrol, diesel fuel, gasoline at oil refineries, underground storage tanks, transmission pipelines, and different industries. The permeable reactive barrier (PRB) is a promising technology to remediate groundwater in-situ. In this study, synthetic groundwater samples containing toluene are treated in three reactor columns by biological processes. PRB-1 consisted of sand and gravel as reactor media, microbial inoculum (bioaugmentation—BA), and nutrients (biostimulation—BS); PRB-2 consisted of sand and gravel as reactor media, microbial inoculum, nutrients, and 12 layers of nonwoven geotextile fabrics; and PRB-3 consisted of only sand and gravel as reactor media (natural attenuation—NA). This study was conducted to assess the impact of geotextile fabric filter, bioaugmentation, and biostimulation on toluene degradation efficiency. After 167 days of treatment, toluene biodegradation efficiencies varied between 88.2% and 93.8% for PRB 1, between 98.0% and 99.3% for PRB 2, and between 14.2% and 68.6% for PRB 3. The effluent toluene concentrations for PRB-2 were less than the guideline value (0.7 mg/L) of the World Health Organization. Reaction rate data were fitted with a first-order kinetic reaction rate model. This study showed that the toluene removal efficiency in the geotextile layered PRB combined with BA and BS process was significantly higher compared to the other processes tested. This lab-scale study introduced a new PRB configuration suitable for the remediation of sites contaminated with toluene.

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers

A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.

Assessing benzene and toluene adsorption with peat depth: Implications on their fate and transport

After a hydrocarbon spill in a peatland, dissolution of water-soluble compounds including benzene and toluene introduces a dissolved-phase plume to the peatland groundwater system, while the adsorption of these solutes onto the peat matrix restrains their distribution velocity. The adsorption of benzene and toluene and its dependency on peat depth, thus degree of decomposition, are investigated. The batch adsorption experiments revealed that benzene and toluene adsorption isotherms in peat are linear, with adsorption coefficients ranging from 16.2 to 48.7 L/kg and 31.6-48.7 L/kg, respectively. In a vertical peat profile benzene adsorption decreased with depth, while toluene adsorption increased. Considering toluene adsorption onto cellulose is significantly less than toluene adsorption onto humic substance, the increase in toluene adsorption was attributed to decreasing cellulose and increasing humic substances with depth. Negligible competition for adsorption was observed between benzene and toluene at the measured concentrations. The retardation factors of benzene and toluene ranged respectively from 3.5 to 10.7 and from 5.4 to 17.7, both increasing with depth. Higher retardation in deeper peat coupled with lower hydraulic conductivity will lead to a weaker solute velocity in deeper peat, thus preferential migration of these dissolved-phase contaminants in shallow layers. The results can help predict the behavior of dissolved hydrocarbons in peatlands after a hydrocarbon spill.

Cometabolic removal of organic micropollutants by enriched nitrite-dependent anaerobic methane oxidizing cultures

The innovative and recently discovered n-damo process, based on anaerobic methane oxidation with nitrite, was developed in a membrane-based bioreactor and evaluated in terms of organic micropollutants (OMPs) removal. The main singularity of this study consisted in the evaluation of organic micropollutants (OMPs) removal in the biological reactor. A strategy consisting on progressively increasing the nitrogen loading rate in order to increase the specific denitrification activity was followed to check if the selected OMPs were co-metabolically biotransformed. Significant nitrite removal rate (24.1 mg N L^-1 d^-1) was achieved after only 30 days of operation. A maximum specific removal of 186.3 mg N gVSS^-1 d^-1 was obtained at the end of the operation, which is one of the highest previously reported. A successfully n-damo bacteria enrichment was achieved, being Candidatus Methylomirabilis the predominant bacteria during the whole operation attaining a maximum relative abundance of about 40 %. The natural hormones (E1 and E2) were completely removed in the bioreactor. The specific removal rates of erythromycin (ERY), fluoxetine (FLX), roxithromycin (ROX) and sulfamethoxazole (SMX) were successfully correlated with the specific nitrite removal rates, suggesting a co-metabolic biotransformation.

The Effect of an Adsorbent Matrix on Recovery of Microorganisms from Hydrocarbon-Contaminated Groundwater

The microbial degradation of recalcitrant hydrocarbons is an important process that can contribute to the remediation of oil and gas-contaminated environments. Due to the complex structure of subsurface terrestrial environments, it is important to identify the microbial communities that may be contributing to biodegradation processes, along with their abilities to metabolize different hydrocarbons in situ. In this study, a variety of adsorbent materials were assessed for their ability to trap both hydrocarbons and microorganisms in contaminated groundwater. Of the materials tested, a porous polymer resin (Tenax-TA) recovered the highest diversity of microbial taxa in preliminary experiments and was selected for additional (microcosm-based) testing. Oxic and anoxic experiments were prepared with groundwater collected from a contaminated aquifer to assess the ability of Tenax-TA to adsorb two environmental hydrocarbon contaminants of interest (toluene and benzene) while simultaneously providing a surface for microbial growth and hydrocarbon biodegradation. Microorganisms in oxic microcosms completely degraded both targets within 14 days of incubation, while anoxically-incubated microorganisms metabolized toluene but not benzene in less than 80 days. Community analysis of Tenax-TA-associated microorganisms revealed taxa highly enriched in sessile hydrocarbon-degrading treatments, including Saprospiraceae, Azoarcus, and Desulfoprunum, which may facilitate hydrocarbon degradation. This study showed that Tenax-TA can be used as a matrix to effectively trap both microorganisms and hydrocarbons in contaminated environmental systems for assessing and studying hydrocarbon-degrading microorganisms of interest.

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods

Water and soil contamination by industrial wastes is a global concern. Biological treatment of industrial wastewater using bioreactors allows the removal of organic matter and nutrients and enables either reuse or safe discharge. Wastewater bioremediation depends in part on the microbial communities present in the bioreactor. To ascertain which communities may play a role in the remediation process, the present study investigates the microbial community structure and diversity of microorganisms found in a full-scale membrane bioreactor (MBR) for industrial wastewater treatment. The study was carried out using high-throughput data observations following a failure (crash) of the MBR and during the extended recovery of the process. Results revealed a positive correlation between the MBR's ability to remove organic matter and its microbial community richness. The significant changes in relative microbial abundance between crash and recovery periods of the MBR revealed the important role of specific bacterial genera in wastewater treatment processes. A whole-genome metagenomics based comparison showed a clear difference in microbial makeup between two functional periods of MBR activity. The crash period was characterized by abundance in bacteria belonging to Achromobacter, Acinetobacter, Halomonas, Pseudomonas and an uncultured MBAE14. The recovery period on the other hand was characterized by Aquamicrobium and by Wenzhouxiangella marina. Our study also revealed some interesting functional pathways characterizing the microbial communities from the two periods of bioreactor function, such as Nitrate and Sulfate reduction pathways. These differences indicate the connection between the bacterial diversity of the MBR and its efficiency to remove TOC.

Degradation of BTEX mixture by a new Pseudomonas putida strain: role of the quorum sensing in the modulation of the upper BTEX oxidative pathway

A new Pseudomonas putida strain (AQ8) was isolated from a decommissioned oil refinery's soil in Italy and characterized for its ability to degrade BTEX. The draft genome of the new strain was sequenced and annotated for genes that encode enzymes putatively involved in BTEX degradation and quorum sensing. The strain was transformed with a plasmid expressing lactonase, which cleaves the autoinducer quorum sensing signal molecule, the acyl-homoserine lactone, to obtain a quorum sensing minus strain. P. putida AQ8 depleted the 40% on average of all the components of the initial BTEX concentration in 36 h. The quorum sensing minus strain, in the same time interval, depleted only the 10% of the initial BTEX concentration. The role of quorum sensing in regulating the expression of the annotated benzene/toluene dioxygenase gene (benzA) and biphenyl/toluene/benzene dioxygenase (bphA) genes, which are involved in BTEX degradation, was studied by quantitative RT-real-time quantitative (q)PCR analysis. The qPCR data showed decreased levels of expression of the benzA and bphA genes in the quorum sensing minus strain. Our results showed, for the first time, quorum sensing modulation of the level of transcription of dioxygenase genes in the upper BTEX oxidation pathway.

Pollution characteristics of aromatic hydrocarbons in the groundwater of China

Much of the world's groundwater supply has been contaminated by aromatic hydrocarbons originating from anthropogenic sources. To study the occurrence and distribution characteristics of aromatic hydrocarbons in groundwater, 24 aromatic hydrocarbon compounds were selected: Five BTEX compounds (benzene, toluene, ethylbenzene, o-xylene, m-xylene, and p-xylene), 10 alkyl-substituted benzene, and 9 halogenated aromatics. These aromatic hydrocarbons were then analyzed from 355 samples collected from across China. Results indicated that aromatic hydrocarbons were detected in 59 out of 355 samples. Of the selected aromatic hydrocarbons, BTEX compounds were detected with high frequency and at low concentrations; comparatively, halogenated aromatics were detected with low frequency and at high concentrations. The aromatic hydrocarbon characteristics found in both karst and pore groundwater samples were then determined using their respective hydrogeological conditions and corresponding human activities. In karst groundwater, BTEX compounds were the most frequently detected aromatic hydrocarbon. The high detection frequencies of aromatic hydrocarbons were caused by their rapid migration, owing to the developed conduit system in the sampled karst area. The low concentrations of aromatic hydrocarbons in karst groundwater samples were caused by low-intensity human activity along with special hydrogeological conditions with higher redox potential and the unique compositions of aromatic hydrocarbons. Alkyl-substituted aromatics and halogenated aromatics were detected at higher concentrations in pore groundwater, owing to high-intensity human activity. Aromatic hydrocarbon pollution was gradually decreased along piedmont-alluvial plain-coast line, owing to a decrease in aquifer vulnerability. These were positively correlated with the size of the aquifer's particles. Samples with a high accumulative concentration of these aromatic hydrocarbons tended to occur in pore groundwater with a high concentration of either SO₄^2- or Cl^-.

Volatile organic compounds (VOCs) in solid waste landfill cover soil: Chemical and isotopic composition vs. degradation processes

Landfills for solid waste disposal release to the atmosphere a large variety of volatile organic compounds (VOCs). Bacterial activity in landfill cover soils can play an important role in mitigating VOC emission. In order to evaluate the effects of degradation processes and characterize VOCs composition in landfill cover soil, gases from 60 sites and along 7 vertical profiles within the cover soil were collected for chemical and isotopic analysis at two undifferentiated urban solid waste disposal sites in Spain: (i) Pinto (Madrid) and (ii) Zurita (Fuerteventura, Canary Islands). The CO₂/CH₄ ratios and δ¹³C-CO₂ and δ¹³C-CH₄ values were controlled by either oxidation or reduction processes of landfill gas (LFG). VOCs were dominated by aromatics, alkanes and O-substituted compounds, with minor cyclics, terpenes, halogenated and S-substituted compounds. Degradation processes, depending on both (i) waste age and (ii) velocity of the uprising biogas through the soil cover, caused (i) an increase of degradation products (e.g., CO₂, O-substituted compounds) and (ii) a decrease of degradable components (e.g., CH₄, alkanes, alkylated aromatics, cyclic and S-substituted compounds). Terpenes, halogenated compounds, phenol and furans were unaffected by degradation processes and only depended on waste composition. These results highlight the fundamental role played by microbial activity in mitigating atmospheric emissions of VOCs from landfills. Nevertheless, the recalcitrant behaviour shown by compounds hazardous for health and environment remarks the importance of a correct landfill management that has to be carried out for years after the waste disposal activity is completed, since LFG emissions can persist for long time.

Isolation and characterization of 2-butoxyethanol degrading bacterial strains

A total of 11 bacterial strains capable of completely degrading 2-butoxyethanol (2-BE) were isolated from forest soil, a biotrickling filter, a bioscrubber, and activated sludge, and identified by 16S rRNA gene sequence analysis. Eight of these strains belong to the genus Pseudomonas; the remaining three strains are Hydrogenophaga pseudoflava BOE3, Gordonia terrae BOE5, and Cupriavidus oxalaticus BOE300. In addition to 2-BE, all isolated strains were able to grow on 2-ethoxyethanol and 2-propoxyethanol, ethanol, n-hexanol, ethyl acetate, 2-butoxyacetic acid (2-BAA), glyoxylic acid, and n-butanol. Apart from the only gram-positive strain isolated, BOE5, none of the strains were able to grow on the nonpolar ethers diethyl ether, di-n-butyl ether, n-butyl vinyl ether, and dibenzyl ether, as well as on 1-butoxy-2-propanol. Strains H. pseudoflava BOE3 and two of the isolated pseudomonads, Pseudomonas putida BOE100 and P. vancouverensis BOE200, were studied in more detail. The maximum growth rates of strains BOE3, BOE100, and BOE200 at 30 °C were 0.204 h-1 at 4 mM, 0.645 h-1 at 5 mM, and 0.395 h-1 at 6 mM 2-BE, respectively. 2-BAA, n-butanol, and butanoic acid were detected as potential metabolites during the degradation of 2-BE. These findings indicate that the degradation of 2-BE by the isolated gram-negative strains proceeds via oxidation to 2-BAA with subsequent cleavage of the ether bond yielding glyoxylate and n-butanol. Since Gordonia terrae BOE5 was the only strain able to degrade nonpolar ethers like diethyl ether, the degradation pathway of 2-BE may be different for this strain.

Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria

As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.

The versatility of Pseudomonas putida in the rhizosphere environment

This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.

Isolation of marine xylene-utilizing bacteria and characterization of Halioxenophilus aromaticivorans gen. nov., sp. nov. and its xylene degradation gene cluster

Seven xylene-utilizing bacterial strains were isolated from seawater collected off the coast of Japan. Analysis of 16S rRNA gene sequences indicated that six isolates were most closely related to the marine bacterial genera Alteromonas, Marinobacter or Aestuariibacter. The sequence of the remaining strain, KU68FT, showed low similarity to the 16S rRNA gene sequences of known bacteria with validly published names, the most similar species being Maricurvus nonylphenolicus strain KU41ET (92.6% identity). On the basis of physiological, chemotaxonomic and phylogenetic data, strain KU68FT is suggested to represent a novel species of a new genus in the family Cellvibrionaceae of the order Cellvibrionales within the Gammaproteobacteria, for which the name Halioxenophilus aromaticivorans gen. nov., sp. nov. is proposed. The type strain of Halioxenophilus aromaticivorans is KU68FT (=JCM 19134T = KCTC 32387T). PCR and sequence analysis revealed that strain KU68FT possesses an entire set of genes encoding the enzymes for the upper xylene methyl-monooxygenase pathway, xylCMABN, resembling the gene set of the terrestrial Pseudomonas putida strain mt-2.

Comprehensive genomic analysis of an indigenous Pseudomonas pseudoalcaligenes degrading phenolic compounds

Environmental contamination with aromatic compounds is a universal challenge. Aromatic-degrading microorganisms isolated from the same or similar polluted environments seem to be more suitable for bioremediation. Moreover, microorganisms adapted to contaminated environments are able to use toxic compounds as the sole sources of carbon and energy. An indigenous strain of Pseudomonas, isolated from the Mahshahr Petrochemical plant in the Khuzestan province, southwest of Iran, was studied genetically. It was characterized as a novel Gram-negative, aerobic, halotolerant, rod-shaped bacterium designated Pseudomonas YKJ, which was resistant to chloramphenicol and ampicillin. Genome of the strain was completely sequenced using Illumina technology to identify its genetic characteristics. MLST analysis revealed that the YKJ strain belongs to the genus Pseudomonas indicating the highest sequence similarity with Pseudomonas pseudoalcaligenes strain CECT 5344 (99% identity). Core- and pan-genome analysis indicated that P. pseudoalcaligenes contains 1,671 core and 3,935 unique genes for coding DNA sequences. The metabolic and degradation pathways for aromatic pollutants were investigated using the NCBI and KEGG databases. Genomic and experimental analyses showed that the YKJ strain is able to degrade certain aromatic compounds including bisphenol A, phenol, benzoate, styrene, xylene, benzene and chlorobenzene. Moreover, antibiotic resistance and chemotaxis properties of the YKJ strain were found to be controlled by two-component regulatory systems.

Novel investigation of the performance of continuous packed bed bioreactor (CPBBR) by isolated Bacillus sp. M4 and proteomic study

The present study reveals the benzene degrading potential of bacterial species isolated from petroleum contaminated soil. Genomic analysis suggests that Bacillus sp. M4 was found to be dominating species. The process parameters were optimized and found to be pH 7.0 ± 0.2, temperature 32 ± 5 °C, immobilization time (20 days) and benzene concentration 400 mg/L. The maximum removal efficiency of benzene was calculated and found to be 93.13% at elimination capacity156 (mg/L/day) and inlet loading rate 192 (mg/L/day) achieved in 54th days of operation. In the study, the residual metabolites were analyzed by GC/MS analysis and identified as benzene-1,2-diol. In order to identify the responsible protein involved in the process of benzene biodegradation The proteomic study was performed and proteins were identified by MALDI-TOF analysis. The molecular docking was confirmed by the benzene biodegradation.

Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7

BACKGROUND

Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organic molecules including aliphatic, aromatic, polycyclic aromatic compounds (PAHs), phenols, and nitriles. In accordance with their immense catabolic diversity, Rhodococcus spp. possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. The present study aimed to identify genes involved in the o-xylene degradation in R. opacus strain R7 through a genome-based approach.

RESULTS

Using genome-based analysis we identified all the sequences in the R7 genome annotated as dioxygenases or monooxygenases/hydroxylases and clustered them into two different trees. The akb, phe and prm sequences were selected as genes encoding respectively for dioxygenases, phenol hydroxylases and monooxygenases and their putative involvement in o-xylene oxidation was evaluated. The involvement of the akb genes in o-xylene oxidation was demonstrated by RT-PCR/qPCR experiments after growth on o-xylene and by the selection of the R7-50 leaky mutant. Although the akb genes are specifically activated for o-xylene degradation, metabolic intermediates of the pathway suggested potential alternative oxidation steps, possibly through monooxygenation. This led us to further investigate the role of the prm and the phe genes. Results showed that these genes were transcribed in a constitutive manner, and that the activity of the Prm monooxygenase was able to transform o-xylene slowly in intermediates as 3,4-dimethylphenol and 2-methylbenzylalcohol. Moreover, the expression level of phe genes, homologous to the phe genes of Rhodococcus spp. 1CP and UPV-1 with a 90% identity, could explain their role in the further oxidation of o-xylene and R7 growth on dimethylphenols.

CONCLUSIONS

These results suggest that R7 strain is able to degrade o-xylene by the Akb dioxygenase system leading to the production of the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for several monooxygenases/phenol hydroxylases, supports the involvement of other oxygenases converging in the o-xylene degradation pathway in R7 strain.

The Degradation of O-ethyltoluene and 1,3,5-Trimethylbenzene in Lake Naivasha Wetland, Kenya

The primary degradation of benzene derivatives in aquatic environments occurs via microbial and chemical processes. This study investigated the kinetic degradation of o-ethyltoluene and 1,3,5-trimethylbenzene in the wetland of Lake Naivasha. Sediment samples were collected from 6:00 AM to 6:00 PM at intervals of 3 h during the dry season of December 2017. The sediment samples were air dried, ground into powder, followed by soxhlet extraction in a binary mixture of methanol and hexane in the ratio of 1:1. The extract was analyzed using gas chromatograph with mass selective detector. Variation in the concentrations of o-ethyltoluene and 1,3,5-trimethylbenzene with time was monitored kinetically. Accordingly, the half-lives for the degradation of o-ethyltoluene and 1,3,5-trimethylbenzene were 4.9 and 5.4 h, respectively, and their corresponding decay rate constants were 3.93 × 10^-5 and 3.56 × 10^-5 S^-1. 1,3,5-Trimethylbenzene was the most persistent contaminants in the wetland.

Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics

Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d^-1, accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (Λ^{H/C nitrate} = 12 ± 3 compared to Λ^{H/C sulfate} = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.

Muconic Acid Production via Alternative Pathways and a Synthetic "Metabolic Funnel"

Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production. A fourth pathway proceeding via p-hydroxybenzoate, protocatechuate, and catechol was accordingly developed, though with muconic acid titers by this route reaching just 819 mg/L, its performance lagged behind that of the established, "3-dehydroshikimiate-derived" route. Finally, these two most promising pathways were coexpressed in parallel to create a synthetic "metabolic funnel" that, by enabling maximal net precursor assimilation and flux while preserving native chorismate biosynthesis, nearly doubled muconic acid production to up to >3.1 g/L at a glucose yield of 158 mg/g while introducing only a single auxotrophy. This generalizable, "funneling" strategy is expected to have broad applications in metabolic engineering for further enhancing production of muconic acid, as well as other important bioproducts of interest.

Metabolic phasing of anoxic-PDBR for high rate treatment of azo dye wastewater

The treatment of azo dye wastewater was studied in a periodic discontinuous batch reactor (PDBR) at high loading condition (1250mg/l) under anoxic microenvironments. PDBR performance was evaluated by varying the time period of aerobic microenvironment during the cycle operation [before multiphasing (BMP; Control), 0.014; after multiphasing (AMP): AMPI, 0.84; AMPII, 0.73; AMPIII, 0.65]. Induction of air in anoxic-PDBR facilitated the simultaneous oxidation and reduction conditions and thus resulted higher dye removal efficiency with AMPIII strategy (65%) followed by AMPII (59.4%) and AMPI (54.4%) than the corresponding control operation (BMP: 49.4%). Relatively higher azo reductase enzyme activity was documented with AMP than corresponding BMP operation correlating well with azo dye decolorization. UV- UV-Significant transformational changes of azo dye peaks (618nm) were documented before and after multiphase operations. Cyclic voltammogram profiles depicted increment in redox catalytic currents during AMPIII operation and also supports the involvement of reducing equivalents towards the dye removal. Derivatives of voltammograms illustrated the involvement of various redox mediators viz., cytochrome-C, quinones, Fumarate/Succinate, Fe(CN)₆^3-/Fe(CN)₆^4-, and flavoproteins. Flexibility in phasing the multiple microenvironments in single bioreactor (PDBR) provides new insights in embodying the required capabilities to treat the recalcitrant azo dye wastewater especially at higher dye load operations.

Assessment of biodegradation potential at a site contaminated by a mixture of BTEX, chlorinated pollutants and pharmaceuticals using passive sampling methods - Case study

The present study describes a pilot remediation test of a co-mingled plume containing BTEX, chlorinated pollutants and pharmaceuticals. Remediation was attempted using a combination of various approaches, including a pump and treat system applying an advanced oxidation process and targeted direct push injections of calcium peroxide. The remediation process was monitored intensively and extensively throughout the pilot test using various conventional and passive sampling methods, including next-generation amplicon sequencing. The results showed that the injection of oxygen-saturated treated water with residual hydrogen peroxide and elevated temperature enhanced the in situ removal of monoaromatics and chlorinated pollutants. In particular, in combination with the injection of calcium peroxide, the conditions facilitated the in situ bacterial biodegradation of the pollutants. The mean groundwater concentration of benzene decreased from 1349μg·L^-1 prior to the test to 3μg·L^-1 within 3months after the calcium peroxide injections; additionally, monochlorobenzene decreased from 1545μg·L^-1 to 36μg·L^-1, and toluene decreased from 143μg·L^-1 to 2μg·L^-1. Furthermore, significant degradation of the contaminants bound to the soil matrix in less permeable zones was observed. Based on a developed 3D model, 90% of toluene and 88% of chlorobenzene bound to the soil were removed during the pilot test, and benzene was removed almost completely. On the other hand, the psychopharmaceuticals were effectively removed by the employed advanced oxidation process only from the treated water, and their concentration in groundwater remained stagnant due to inflow from the surroundings and their absence of in situ degradation. The employment of passive sampling techniques, including passive diffusion bags (PDB) for volatile organic pollutants and their respective transformation products, polar organic compound integrative samplers (POCIS) for the pharmaceuticals and in situ soil microcosms for microbial community analysis, was proven to be suitable for monitoring remediation in saturated zones.

Bacterial Degraders of Coexisting Dichloromethane, Benzene, and Toluene, Identified by Stable-Isotope Probing

Most bioremediation studies on volatile organic compounds (VOCs) have focused on a single contaminant or its derived compounds and degraders have been identified under single contaminant conditions. Bioremediation of multiple contaminants remains a challenging issue. To identify a bacterial consortium that degrades multiple VOCs (dichloromethane (DCM), benzene, and toluene), we applied DNA-stable isotope probing. For individual tests, we combined a ¹³C-labeled VOC with other two unlabeled VOCs, and prepared three unlabeled VOCs as a reference. Over 11 days, DNA was periodically extracted from the consortia, and the bacterial community was evaluated by next-generation sequencing of bacterial 16S rRNA gene amplicons. Density gradient fractions of the DNA extracts were amplified by universal bacterial primers for the 16S rRNA gene sequences, and the amplicons were analyzed by terminal restriction fragment length polymorphism (T-RFLP) using restriction enzymes: HhaI and MspI. The T-RFLP fragments were identified by 16S rRNA gene cloning and sequencing. Under all test conditions, the consortia were dominated by Rhodanobacter, Bradyrhizobium/Afipia, Rhizobium, and Hyphomicrobium. DNA derived from Hyphomicrobium and Propioniferax shifted toward heavier fractions under the condition added with ¹³C-DCM and ¹³C-benzene, respectively, compared with the reference, but no shifts were induced by ¹³C-toluene addition. This implies that Hyphomicrobium and Propioniferax were the main DCM and benzene degraders, respectively, under the coexisting condition. The known benzene degrader Pseudomonas sp. was present but not actively involved in the degradation.

MALDI-TOF MS for the Identification of Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near Unconventional Natural Gas Extraction Sites

Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.

Electrobioremediation of oil spills

Annually, thousands of oil spills occur across the globe. As a result, petroleum substances and petrochemical compounds are widespread contaminants causing concern due to their toxicity and recalcitrance. Many remediation strategies have been developed using both physicochemical and biological approaches. Biological strategies are most benign, aiming to enhance microbial metabolic activities by supplying limiting inorganic nutrients, electron acceptors or donors, thus stimulating oxidation or reduction of contaminants. A key issue is controlling the supply of electron donors/acceptors. Bioelectrochemical systems (BES) have emerged, in which an electrical current serves as either electron donor or acceptor for oil spill bioremediation. BES are highly controllable and can possibly also serve as biosensors for real time monitoring of the degradation process. Despite being promising, multiple aspects need to be considered to make BES suitable for field applications including system design, electrode materials, operational parameters, mode of action and radius of influence. The microbiological processes, involved in bioelectrochemical contaminant degradation, are currently not fully understood, particularly in relation to electron transfer mechanisms. Especially in sulfate rich environments, the sulfur cycle appears pivotal during hydrocarbon oxidation. This review provides a comprehensive analysis of the research on bioelectrochemical remediation of oil spills and of the key parameters involved in the process.

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

The destruction of benzene by calcium peroxide activated with Fe(II) in water

The ability of Fe(II)-activated calcium peroxide (CaO₂) to remove benzene is examined with a series of batch experiments. The results showed that benzene concentrations were reduced by 20 to 100% within 30 min. The magnitude of removal was dependent on the CaO₂/Fe(II)/Benzene molar ratio, with much greater destruction observed for ratios of 4/4/1 or greater. An empirical equation was developed to quantify the destruction rate dependence on reagent composition. The presence of oxidative hydroxyl radicals (HO^•) and reductive radicals (primarily O₂^•-) was identified by probe compound testing and electron paramagnetic resonance (EPR) tests. The results of the EPR tests indicated that the application of CaO₂/Fe(II) enabled the radical intensity to remain steady for a relatively long time. The effect of initial solution pH was also investigated, and CaO₂/Fe(II) enabled benzene removal over a wide pH range of 3.0~9.0. The results of radical scavenging tests showed that benzene removal occurred primarily by HO^• oxidation in the CaO₂/Fe(II) system, although reductive radicals also contributed. The intermediates in benzene destruction were identified to be phenol and biphenyl. The results indicate that Fe(II)-activated CaO₂ is a feasible approach for treatment of benzene in contaminated groundwater remediation.

Micropollutant degradation via extracted native enzymes from activated sludge

A procedure was developed to assess the biodegradation of micropollutants in cell-free lysates produced from activated sludge of a municipal wastewater treatment plant (WWTP). This proof-of-principle provides the basis for further investigations of micropollutant biodegradation via native enzymes in a solution of reduced complexity, facilitating downstream protein analysis. Differently produced lysates, containing a variety of native enzymes, showed significant enzymatic activities of acid phosphatase, β-galactosidase and β-glucuronidase in conventional colorimetric enzyme assays, whereas heat-deactivated controls did not. To determine the enzymatic activity towards micropollutants, 20 compounds were spiked to the cell-free lysates under aerobic conditions and were monitored via LC-ESI-MS/MS. The micropollutants were selected to span a wide range of different biodegradabilities in conventional activated sludge treatment via distinct primary degradation reactions. Of the 20 spiked micropollutants, 18 could be degraded by intact sludge under assay conditions, while six showed reproducible degradation in the lysates compared to the heat-deactivated negative controls: acetaminophen, N-acetyl-sulfamethoxazole (acetyl-SMX), atenolol, bezafibrate, erythromycin and 10,11-dihydro-10-hydroxycarbamazepine (10-OH-CBZ). The primary biotransformation of the first four compounds can be attributed to amide hydrolysis. However, the observed biotransformations in the lysates were differently influenced by experimental parameters such as sludge pre-treatment and the addition of ammonium sulfate or peptidase inhibitors, suggesting that different hydrolase enzymes were involved in the primary degradation, among them possibly peptidases. Furthermore, the transformation of 10-OH-CBZ to 9-CA-ADIN was caused by a biologically-mediated oxidation, which indicates that in addition to hydrolases further enzyme classes (probably oxidoreductases) are present in the native lysates. Although the full variety of indigenous enzymatic activity of the activated sludge source material could not be restored, experimental modifications, e.g. different lysate filtration, significantly enhanced specific enzyme activities (e.g. >96% removal of the antibiotic erythromycin). Therefore, the approach presented in this study provides the experimental basis for a further elucidation of the enzymatic processes underlying wastewater treatment on the level of native proteins.

Carbon and Hydrogen Stable Isotope Fractionation Associated with the Aerobic and Anaerobic Degradation of Saturated and Alkylated Aromatic Hydrocarbons

Saturated hydrocarbons (alkanes) and alkylated aromatic hydrocarbons are abundant environmental compounds. Hydrocarbons are primarily removed from the environment by biodegradation, a process usually associated with moderate carbon and significant hydrogen isotope fractionation allowing monitoring of biodegradation processes in the environment. Here, we review the carbon and hydrogen stable isotope fractionation associated with the cleavage of C-H bonds at alkyl chains of hydrocarbons. Propane, <i>n</i>-butane and ethylbenzene were used as model components for alkyl moieties of aliphatic and aromatic hydrocarbons with emphasis on the cleavage of the C-H bond without the involvement of molecular oxygen. The carbon and hydrogen isotope fractionation factors were further used to explore the diagnostic potential for characterizing the mode of bond cleavage under oxic and anoxic conditions. &#x039B; factors, calculated to correlate carbon and hydrogen fractionation, allowed to distinguish between aerobic and anaerobic biodegradation processes in the environment.

Ethylbenzene Dehydrogenase and Related Molybdenum Enzymes Involved in Oxygen-Independent Alkyl Chain Hydroxylation

Ethylbenzene dehydrogenase initiates the anaerobic bacterial degradation of ethylbenzene and propylbenzene. Although the enzyme is currently only known from a few closely related denitrifying bacterial strains affiliated to the Rhodocyclaceae, it clearly marks a universally occurring mechanism used for attacking recalcitrant substrates in the absence of oxygen. Ethylbenzene dehydrogenase belongs to subfamily 2 of the DMSO reductase-type molybdenum enzymes together with paralogous enzymes involved in the oxygen-independent hydroxylation of p-cymene, the isoprenoid side chains of sterols and even possibly n-alkanes; the subfamily also extends to dimethylsulfide dehydrogenases, selenite, chlorate and perchlorate reductases and, most significantly, dissimilatory nitrate reductases. The biochemical, spectroscopic and structural properties of the oxygen-independent hydroxylases among these enzymes are summarized and compared. All of them consist of three subunits, contain a molybdenum-bis-molybdopterin guanine dinucleotide cofactor, five Fe-S clusters and a heme b cofactor of unusual ligation, and are localized in the periplasmic space as soluble enzymes. In the case of ethylbenzene dehydrogenase, it has been determined that the heme b cofactor has a rather high redox potential, which may also be inferred for the paralogous hydroxylases. The known structure of ethylbenzene dehydrogenase allowed the calculation of detailed models of the reaction mechanism based on the density function theory as well as QM-MM (quantum mechanics - molecular mechanics) methods, which yield predictions of mechanistic properties such as kinetic isotope effects that appeared consistent with experimental data.

Hydrocarbon degrading microbial communities in bench scale aerobic biobarriers for gasoline contaminated groundwater treatment

BTEX compounds (benzene, toluene, ethylbenzene and xylenes) and methyl tert-butyl ether (MTBE) are some of the main constituents of gasoline and can be accidentally released in the environment. In this work the effect of bioaugmentation on the microbial communities in a bench scale aerobic biobarrier for gasoline contaminated water treatment was studied by 16S rRNA gene sequencing. Catabolic genes (tmoA and xylM) were quantified by qPCR, in order to estimate the biodegradation potential, and the abundance of total bacteria was estimated by the quantification of the number of copies of the 16S rRNA gene. Hydrocarbon concentration was monitored over time and no difference in the removal efficiency for the tested conditions was observed, either with or without the microbial inoculum. In the column without the inoculum the most abundant genera were Acidovorax, Bdellovibrio, Hydrogenophaga, Pseudoxanthomonas and Serpens at the beginning of the column, while at the end of the column Thauera became dominant. In the inoculated test the microbial inoculum, composed by Rhodococcus sp. CE461, Rhodococcus sp. CT451 and Methylibium petroleiphilum LMG 22953, was outcompeted. Quantitative PCR results showed an increasing in xylM copy number, indicating that hydrocarbon degrading bacteria were selected during the treatment, although only a low increase of the total biomass was observed. However, the bioaugmentation did not lead to an increase in the degradative potential of the microbial communities.

Microbial respiration and natural attenuation of benzene contaminated soils investigated by cavity enhanced Raman multi-gas spectroscopy

Soil and groundwater contamination with benzene can cause serious environmental damage. However, many soil microorganisms are capable to adapt and are known to strongly control the fate of organic contamination. Innovative cavity enhanced Raman multi-gas spectroscopy (CERS) was applied to investigate the short-term response of the soil micro-flora to sudden surface contamination with benzene regarding the temporal variations of gas products and their exchange rates with the adjacent atmosphere. (13)C-labeled benzene was spiked on a silty-loamy soil column in order to track and separate the changes in heterotrophic soil respiration - involving (12)CO2 and O2- from the natural attenuation process of benzene degradation to ultimately form (13)CO2. The respiratory quotient (RQ) decreased from a value 0.98 to 0.46 directly after the spiking and increased again within 33 hours to a value of 0.72. This coincided with the maximum (13)CO2 concentration rate (0.63 μmol m(-2) s(-1)), indicating the highest benzene degradation at 33 hours after the spiking event. The diffusion of benzene in the headspace and the biodegradation into (13)CO2 were simultaneously monitored and 12 days after the benzene spiking no measurable degradation was detected anymore. The RQ finally returned to a value of 0.96 demonstrating the reestablished aerobic respiration.

Can ornamental potted plants remove volatile organic compounds from indoor air? A review

Volatile organic compounds (VOCs) are found in indoor air, and many of these can affect human health (e.g. formaldehyde and benzene are carcinogenic). Plants affect the levels of VOCs in indoor environments, thus they represent a potential green solution for improving indoor air quality that at the same time can improve human health. This article reviews scientific studies of plants' ability to remove VOCs from indoor air. The focus of the review is on pathways of VOC removal by the plants and factors affecting the efficiency and rate of VOC removal by plants. Laboratory based studies indicate that plant induced removal of VOCs is a combination of direct (e.g. absorption) and indirect (e.g. biotransformation by microorganisms) mechanisms. They also demonstrate that plants' rate of reducing the level of VOCs is influenced by a number of factors such as plant species, light intensity and VOC concentration. For instance, an increase in light intensity has in some studies been shown to lead to an increase in removal of a pollutant. Studies conducted in real-life settings such as offices and homes are few and show mixed results.

Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs

The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO₂, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.