The present paper has examined the degrading ability of phenol-oxidizing bacterium, Ralstonia eutropha, for biological removal of methylene blue (MB) from aqueous solutions under aerobic conditions. Results show that MB has been extensively eliminated as a co-metabolism in the presence of supplementary carbon (glucose) and nitrogen (yeast extract and peptone) sources and the experimental observations indicate that MB is initially adsorbed on the cell’s surface, in accordance to Langmuir Theory, then to be degraded by the cell. The type of nitrogen source, initial pH, aeration rate, and the presence of CaCl2 are all influential factors in the process of MB removal. The biodegradation kinetics modeling has determined that while playing an uncompetitive role, MB inhibits its biodegradation at high concentrations. According to the best fit Han-Levenspiel Model, the maximum MB specific biodegradation rate (rmax), half-saturation concentration of MB (KS), maximum allowable MB concentration (Sm), and the shape factors (n and m) have been 7.37 mg gcell-1 h-1, 32.13 mg/L, 158.8 mg/L, 0.27, and 0.76, respectively.

Petroleum refining industries produce large amounts of toxic effluents, causing environmental pollution. Iran is an oil-rich country that encounters oil pollution in its soil and water. Bioremediation of these pollutants is an appropriate solution to tackle them, compared to physical and chemical remediation methods. There are some factors that increase the rate of biodegradation; therefore, this study aims to determine the rate of gasoil bioremediation by two indigenous bacterial isolates (from oil-contaminated soils of an oil refinery south of Tehran) in two different media, namely soil and soil-sawdust mixture. The two superior indigenous bacteria has been isolated through three steps with results indicating that in an optimal environmental condition (temperature= 27±2 °C, humidity of 60%, water holding capacity, and daily manual aeration), bacterial isolates are able to degrade about 78.87% and 93.53% of gasoil during 45 days in soil and soil-sawdust mixture media, respectively. These results imply the role of sawdust in improving aeration, water holding capacity, and-consequently- increasing bioavailability of gasoil to bacteria.

Petroleum-polluted soil samples from Ahvaz oilfield were enriched, using three methods to detect microorganisms with different dibenzothiophene degradation capabilities. Strain NISOC-03, a nitrate-reducing, oxidase negative, catalase, citrate, and urease positive, gram negative rod, showed interesting dibenzothiophene desulfurization behavior, designated as Entreobacter sp. strain NISOC-03 based on phenotype and genotype analyses. Gas chromatography, biomass measurement, and Gibb’s assay showed that in the presence of benzoate as the carbon source, strain NISOC-03 utilized 64% of 0.8 mM dibenzothiophene, producing 0.27 mM phenyl phenol during the exponential growth phase, though the produced phenyl phenol was degraded in the stationary growth phase. In the presence of glucose as the carbon source, however, strain NISOC-03 metabolized only 19.6% of 0.8 mM dibenzothiophene. Furthermore, replacing glucose with ethanol or glycerol led to the same reduction of the dibenzothiophene utilization. It is thus concluded that the chemistry of the potential carbon source(s) in the culture medium has a significant influence on the quality and the rate of dibenzothiophene metablization, and the enrichment designation has a very vital effect on the biodegradation efficiency of the isolated microorganisms.

2,4,6-Tribromophenol (TBP), an intermediate of brominated flame retardants, can easily release to environment and recalcitrant to degradation. Previously, Bacillus sp. GZT, a pure aerobic strain capable of simultaneously debrominating and mineralizing TBP, was successfully isolated by us. To further obtain a practical application and dig up its TBP degradation mechanism, a total of 46.7-fold purification of a novel dehalogenase with a final specific activity of 18.9 U mg−1 and a molecular mass of 63.4 kDa was achieved. Under optimal conditions (35 °C and 200 rpm), up to 80% degradation efficiencies were achieved within 120 min. Adding H2O2, NADPH, Mn2+ and Mg2+ promoted enzyme reaction effectively; while EDTA, methyl viologen, Ni2+, Cu2+, Ca2+ and Fe2+ strongly inhibited reaction activities. The debromination of TBP was catalyzed by the enzyme at a Km of 78 μM and a Vmax of 0.65 min−1 mg protein−1, which indicated that this dehalogenase could specifically eliminate TBP with a high efficiency and stability. Based on MALDI-TOF/TOF analysis, the dehalogenase shared 98% identity with peptide ABC transporter substrate-binding protein. One open reading frame (ORF) encoding this peptide was found in Strain GZT genome, subjected to clone and expressed in Escherichia coli (E. coli) to characterize the encoding gene. Result showed that this recombinant strain could also remove as similar amount of TBP as Bacillus sp. GZT under the identical condition. Based on these results, we suggest that this newly-isolated TBP dehalogenase highlights a new approach for remediating TBP pollution.

The plant waste-products, wheat straw, corn-cobs and sugarcane bagasse took up respectively, 190, 110 and 250% of their own weights crude oil. The same materials harbored respectively, 3.6 × 105, 8.5 × 103 and 2.3 × 106 g−1 cells of hydrocarbonoclastic microorganisms, as determined by a culture-dependent method. The molecular, culture-independent analysis revealed that the three materials were associated with microbial communities comprising genera known for their hydrocarbonoclastic activity. In bench-scale experiments, inoculating oily media with samples of the individual waste products led to the biodegradation of 34.0–44.9% of the available oil after 8 months. Also plant-product samples, which had been used as oil sorbents lost 24.3–47.7% of their oil via their associated microorganisms, when kept moist for 8 months. In this way, it is easy to see that those waste products are capable of remediating spilled oil physically, and that their associated microbial communities can degrade it biologically.

A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of Proteobacteria, mainly the Gammaproteobacteria, was found, and OTUs (operational taxonomic units) affiliated to Pseudomonas responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease of Firmicutes and Bacteroidetes was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced.

The present study aimed to investigate biodegradation mechanisms of black carbon (BC)-bound contaminants in BC-amended sediment when BC was applied to control organic pollution. The single-point Tenax desorption technique was applied to track the species changes of nonylphenol (NP) during biodegradation process in the rice straw carbon (RC)-amended sediment. And the correlation between the biodegradation and desorption of NP was analyzed. Results showed that microorganisms firstly degraded the rapid-desorbing NP (6 h Tenax desorption) in RC-amended sediment. The biodegradation facilitated the desorption of slow-desorbing NP, which was subsequently degraded as well (192 h Tenax desorption). Notably, the final amount of NP degradation was greater than that of NP desorption, indicating that absorbed NP by RC amendment can be degraded by microorganisms. Finally, the residual NP amount in RC-amended sediment was decided by RC content and its physicochemical property. Moreover, the presence of the biofilm was observed by the confocal laser scanning microscope (CLSM) and scanning electron microscope (SEM) so that microorganisms were able to overcome the mass transfer resistance and directly utilized the absorbed NP. Therefore, single-point Tenax desorption alone may not be an adequate basis for the prediction of the bioaccessibility of contaminants to microorganisms or bioremediation potential in BC-amended sediment.

In April of 2010, the Macondo well blowout in the northern Gulf of Mexico resulted in an unprecedented release of oil into the water column at a depth of approximately 1500 m. A time series of surface and subsurface sediment samples were collected to the northwest of the well from 2010 to 2013 for molecular biomarker and bulk carbon isotopic analyses. While no clear trend was observed in subsurface sediments, surface sediments (0–3 cm) showed a clear pattern with total concentrations of n-alkanes, unresolved complex mixture (UCM), and petroleum biomarkers (terpanes, hopanes, steranes) increasing from May to September 2010, peaking in late November 2010, and strongly decreasing in the subsequent years. The peak in hydrocarbon concentrations were corroborated by higher organic carbon contents, more depleted Δ14C values and biomarker ratios similar to those of the initial MC252 crude oil reported in the literature. These results indicate that at least part of oil discharged from the accident sedimented to the seafloor in subsequent months, resulting in an apparent accumulation of hydrocarbons on the seabed by the end of 2010. Sediment resuspension and transport or biodegradation may account for the decrease in sedimented oil quantities in the years following the Macondo well spill.

With the phaseout of perfluorooctane sulfonate (PFOS) production in most countries and its well known recalcitrance, there is a need to quantify the potential release of PFOS from precursors previously or currently being emitted into the environment. Aerobic biodegradation of N-ethyl perfluorooctane sulfonamidoethanol (EtFOSE) was monitored in two soils from Indiana, USA: an acidic forest silt loam (FRST-48, pH = 5.5) and a high pH agricultural loam (PSF-49, pH = 7.8) with similar organic carbon contents (2.4 and 2.6%) for 210 d and 180 d, respectively. At designated times, triplicate samples were sacrificed for which headspace samples were taken followed by three sequential extractions. Extracts were analyzed using HPLC-tandem mass spectrometry. Measured profiles of EtFOSE degradation and generation/degradation of subsequent metabolites were fitted to the Indiana soils data as well as to a previously published data set for a Canadian soil using an R-based model (KinGUII) to explore pathways and estimate half-lives (t1/2) for EtFOSE and metabolites. EtFOSE degradation ranged from a few days to up to a month. PFOS yields ranged form 1.06–5.49 mol% with the alkaline soils being four to five times higher than the acidic soil. In addition, a direct pathway to PFOS had to be invoked to describe the early generation of PFOS in the Canadian soil. Of all metabolites, the sulfonamidoacetic acids were the most persistent (t1/2 ≥ 3 months) in all soils. We hypothesized that while pH-pKa dependent speciation may have impacted rates, differences in microbial communities between the 3 soils arising from varied soil properties including pH, nutrient levels, soil management, and climatic regions are likely the major factors affecting pathways, rates, and PFOS yields.

Bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soils requires a higher microbial viability and an increased PAH bioavailability. The clay/modified clay-modulated bacterial degradation could deliver a more efficient removal of PAHs in soils depending on the bioavailability of the compounds. In this study, we modified clay minerals (smectite and palygorskite) with mild acid (HCl) and alkali (NaOH) treatments (0.5–3 M), which increased the surface area and pore volume of the products, and removed the impurities without collapsing the crystalline structure of clay minerals. In soil incubation studies, supplements with the clay products increased bacterial growth in the order: 0.5 M HCl ≥ unmodified ≥0.5 M NaOH ≥3 M NaOH ≥3 M HCl for smectite, and 0.5 M HCl ≥3 M NaOH ≥0.5 M NaOH ≥3 M HCl ≥ unmodified for palygorskite. A14C-tracing study showed that the mild acid/alkali-treated clay products increased the PAH biodegradation (5–8%) in the order of 0.5 M HCl ≥ unmodified > 3 M NaOH ≥ 0.5 M NaOH for smectite, and 0.5 M HCl > 0.5 M NaOH ≥ unmodified ≥ 3 M NaOH for palygorskite. The biodegradation was correlated (r = 0.81) with the bioavailable fraction of PAHs and microbial growth as affected particularly by the 0.5 M HCl and 0.5 M NaOH-treated clay minerals. These results could be pivotal in developing a clay-modulated bioremediation technology for cleaning up PAH-contaminated soils and sediments in the field.