Screening method for detection of hydrocarbon-oxidizing bacteria in oil-contaminated water and soil specimens

Costus speciosus (Koen ex. Retz.) Sm.: a suitable plant species for remediation of crude oil and mercury-contaminated soil

The aim of this study was to evaluate the efficiency of Costus speciosus (Koen ex. Retz.) Sm. in the degradation of crude oil and reduction of mercury (Hg) from the contaminated soil in pot experiments in the net house for 180 days. C. speciosus was transplanted in soil containing 19150 mg kg-1 crude oil and 3.2 mg kg-1 Hg. The study includes the evaluation of plant biomass, height, root length, total petroleum hydrocarbon (TPH) degradation, and Hg reduction in soil, TPH, and Hg accumulation in plants grown in fertilized and unfertilized pots, chlorophyll production, and rhizospheric most probable number (MPN) at 60-day interval. The average biomass production and heights of C. speciosus in contaminated treatments were significantly (p < 0.05) lower compared to the unvegetated control. Plants grown in contaminated soil showed relatively reduced root surface area compared to the uncontaminated treatments. TPH degradation in planted fertilized, unplanted, and planted unfertilized pot was 63%, 0.8%, and 38%, respectively. However, compared to unvegetated treatments, TPH degradation was significantly higher (p < 0.05) in vegetated treatments. A comparison of fertilized and unfertilized soils showed that TPH accumulation in plant roots and shoots was relatively higher in fertilized soils. Hg degradation in soil was significantly (p < 0.05) more in planted treatment compared to unplanted treatments. The fertilized soil showed relatively more Hg degradation in soil and its accumulation in roots and shoots of plants in comparison to unfertilized soil. MPN in treatments with plants was significantly greater (p < 0.05) than without plants. The plant's ability to produce biomass, chlorophyll, break down crude oil, reduce Hg levels in soil, and accumulate TPH and Hg in roots and shoots of the plant all point to the possibility of using this plant to remove TPH and Hg from soil.

Solid medium for the direct isolation of bacterial colonies growing with polycyclic aromatic hydrocarbons or 2,4,6-trinitrotoluene (TNT)

Isolation of hydrocarbon-degrading bacteria is a key step for the study of microbiological diversity, metabolic pathways, and bioremediation. However current strategies lack simplicity and versatility. We developed an easy method for the screening and isolation of bacterial colonies capable of degrading hydrocarbons, such as diesel or polycyclic aromatic hydrocarbons (PAHs), as well as the pollutant explosive, 2,4,6-trinitrotoluene (TNT). The method uses a two-layer solid medium, with a layer of M9 medium, and a second layer containing the carbon source deposited through the evaporation of ethanol. Using this medium we grew hydrocarbon-degrading strains, as well as TNT-degrading isolates. We were able to isolate PAHs-degrading bacterial colonies directly from diesel-polluted soils. As a proof of concept, we used this method to isolate a phenanthrene-degrading bacteria, identified as Acinetobacter sp. and determined its ability to biodegrade this hydrocarbon.

Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts

Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.

Toxicity assessment of fresh and weathered petroleum hydrocarbons in contaminated soil- a review

Soil contamination with total petroleum hydrocarbons (TPH) is widespread throughout the globe due to the massive production of TPH anthropogenically and its occurrence in the soil. TPH is toxic to beneficial soil organisms and humans and thus has become a serious concern among the public. Traditionally TPH toxicity in the soil is estimated based on chemical fractions and a range of bioassays including plants, invertebrates and microorganisms. There is a large inconsistency among ecotoxicology data using these assays due to the nature of TPH and their weathering. Therefore, in this article, we critically reviewed the weathered conditions of TPH, the potential fate in soil and the bioindicators for the assessment of the ecotoxicity. Based on the current research and the state-of-the-art problem, we also highlighted key recommendations for future research scope for the real-world solution of the ecotoxicological studies of hydrocarbons.

Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds.

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems

Exoelectrogenic biofilms capable of extracellular electron transfer are important in advanced technologies such as those used in microbial electrochemical remediation systems (MERS) Few bacterial strains have been, nevertheless, obtained from MERS exoelectrogenic biofilms and characterized for bioremediation potential. Here we report the identification of one such bacterial strain, Citrobacter sp. KVM11, a petrophilic, iron reducing bacterial strain isolated from hydrocarbon fed MERS, producing anodic currents in microbial electrochemical systems. Fe(III) reduction of 90.01 ± 0.43% was observed during 5 weeks of incubation with Fe(III) supplemented liquid cultures. Biodegradation screening assays showed that the hydrocarbon degradation had been carried out by metabolically active cells accompanied by growth. The characteristic feature of diazo dye decolorization was used as a simple criterion for evaluating the electrochemical activity in the candidate microbe. The electrochemical activities of the strain KVM11 were characterized in a single chamber fuel cell and three electrode electrochemical cells. The inoculation of strain KVM11 amended with acetate and citrate as the sole carbon and energy sources has resulted in an increase in anodic currents (maximum current density) of 212 ± 3 and 359 ± mA/m2 with respective coulombic efficiencies of 19.5 and 34.9% in a single chamber fuel cells. Cyclic voltammetry studies showed that anaerobically grown cells of strain KVM11 are electrochemically active whereas aerobically grown cells lacked the electrochemical activity. Electrobioremediation potential of the strain KVM11 was investigated in hydrocarbonoclastic and dye detoxification conditions using MERS. About 89.60% of 400 mg l-1 azo dye was removed during the first 24 h of operation and it reached below detection limits by the end of the batch operation (60 h). Current generation and biodegradation capabilities of strain KVM11 were examined using an initial concentration of 800 mg l-1 of diesel range hydrocarbons (C9-C36) in MERS (maximum currentdensity 50.64 ± 7 mA/m2; power density 4.08 ± 2 mW/m2, 1000 ω, hydrocarbon removal 60.14 ± 0.7%). Such observations reveal the potential of electroactive biofilms in the simultaneous remediation of hydrocarbon contaminated environments with generation of energy.

Identification of Electrode Respiring, Hydrocarbonoclastic Bacterial Strain Stenotrophomonas maltophilia MK2 Highlights the Untapped Potential for Environmental Bioremediation

Electrode respiring bacteria (ERB) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (MERS) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. Very few ERB have been isolated from MERS, those exhibited a bioremediation potential toward organic contaminants. Here we report once such bacterial strain, Stenotrophomonas maltophilia MK2, a facultative anaerobic bacterium isolated from a hydrocarbon fed MERS, showed a potent hydrocarbonoclastic behavior under aerobic and anaerobic environments. Distinct properties of the strain MK2 were anaerobic fermentation of the amino acids, electrode respiration, anaerobic nitrate reduction and the ability to metabolize n-alkane components (C8–C36) of petroleum hydrocarbons (PH) including the biomarkers, pristine and phytane. The characteristic of diazoic dye decolorization was used as a criterion for pre-screening the possible electrochemically active microbial candidates. Bioelectricity generation with concomitant dye decolorization in MERS showed that the strain is electrochemically active. In acetate fed microbial fuel cells (MFCs), maximum current density of 273 ± 8 mA/m² (1000 Ω) was produced (power density 113 ± 7 mW/m²) by strain MK2 with a coulombic efficiency of 34.8%. Further, the presence of possible alkane hydroxylase genes (alkB and rubA) in the strain MK2 indicated that the genes involved in hydrocarbon degradation are of diverse origin. Such observations demonstrated the potential of facultative hydrocarbon degradation in contaminated environments. Identification of such a novel petrochemical hydrocarbon degrading ERB is likely to offer a new route to the sustainable bioremedial process of source zone contamination with simultaneous energy generation through MERS.

Enhanced xylose fermentation and hydrolysate inhibitor tolerance of Scheffersomyces shehatae for efficient ethanol production from non-detoxified lignocellulosic hydrolysate

Effective conversion of xylose into ethanol is important for lignocellulosic ethanol production. In the present study, UV-C mutagenesis was used to improve the efficiency of xylose fermentation. The mutated Scheffersomyces shehatae strain TTC79 fermented glucose as efficiently and xylose more efficiently, producing a higher ethanol concentration than the wild-type. A maximum ethanol concentration of 29.04 g/L was produced from 71.31 g/L xylose, which was 58.95 % higher than that of the wild-type. This mutant also displayed significantly improved hydrolysate inhibitors tolerance and increased ethanol production from non-detoxified lignocellulosic hydrolysates. The ethanol yield, productivity and theoretical yield by TTC79 from sugarcane bagasse hydrolysate were 0.46 g/g, 0.20 g/L/h and 90.61 %, respectively, while the corresponding values for the wild-type were 0.20 g/g, 0.04 g/L/h and 39.20 %, respectively. These results demonstrate that S. shehatae TTC79 is a useful non-recombinant strain, combining efficient xylose consumption and high inhibitor tolerance, with potential for application in ethanol production from lignocellulose hydrolysates.

Heavy metal-immobilizing organoclay facilitates polycyclic aromatic hydrocarbon biodegradation in mixed-contaminated soil

Soils contaminated with a mixture of heavy metals and polycyclic aromatic hydrocarbons (PAHs) pose toxic metal stress to native PAH-degrading microorganisms. Adsorbents such as clay and modified clay minerals can bind the metal and reduce its toxicity to microorganisms. However, in a mixed-contaminated soil, an adsorption process more specific to the metals without affecting the bioavailability of PAHs is desired for effective degradation. Furthermore, the adsorbent should enhance the viability of PAH-degrading microorganisms. A metal-immobilizing organoclay (Arquad(®) 2HT-75-bentonite treated with palmitic acid) (MIOC) able to reduce metal (cadmium (Cd)) toxicity and enhance PAH (phenanthrene) biodegradation was developed and characterized in this study. The MIOC differed considerably from the parent clay in terms of its ability to reduce metal toxicity (MIOC>unmodified bentonite>Arquad-bentonite). The MIOC variably increased the microbial count (10-43%) as well as activities (respiration 3-44%; enzymatic activities up to 68%), and simultaneously maintained phenanthrene in bioavailable form in a Cd-phenanthrene mixed-contaminated soil over a 21-day incubation period. This study may lead to a new MIOC-assisted bioremediation technique for PAHs in mixed-contaminated soils.

Assessment of the chemical, microbiological and toxicological aspects of post-processing water from underground coal gasification

The purpose of this paper is to provide a comprehensive characterisation (including chemical, microbiological and toxicological parameters) of water after the underground coal gasification (UCG) process. This is the first report in which these parameters were analysed together to assess the environmental risk of the water generated during the simulation of the underground coal gasification (UCG) process performed by the Central Mining Institute (Poland). Chemical analysis of the water indicated many hazardous chemical compounds, including benzene, toluene, ethylbenzene, xylene, phenols and polycyclic aromatic hydrocarbons (PAHs). Additionally, large quantities of inorganic compounds from the coal and ashes produced during the volatilisation process were noted. Due to the presence of refractory and inhibitory compounds in the post-processing water samples, the microbiological and toxicological analyses revealed the high toxicity of the UCG post-processing water. Among the tested microorganisms, mesophilic, thermophilic, psychrophilic, spore-forming, anaerobic and S-oxidizing bacteria were identified. However, the number of detected microorganisms was very low. The psychrophilic bacteria dominated among tested bacteria. There were no fungi or Actinomycetes in any of the water samples. Preliminary study revealed that hydrocarbon-oxidizing bacteria were metabolically active in the water samples. The samples were very toxic to the biotests, with the TU50 reaching 262. None of biotests was the most sensitive to all samples. Cytotoxicity and genotoxicity testing of the water samples in Vicia uncovered strong cytotoxic and clastogenic effects. Furthermore, TUNEL indicated that all of the water samples caused sporadic DNA fragmentation in the nuclei of the roots.

Field note: phytoremediation of petroleum sludge contaminated field using sedge species, Cyperus rotundus (Linn.) and Cyperus brevifolius (Rottb.) Hassk

The aim of this study was to degrade total petroleum hydrocarbon (TPH) in a petroleum sludge contaminated site (initial TPH concentration of 65,000-75,000 mg kg(-1)) with two native sedge species namely Cyperus rotundus (Linn.) and Cyperus brevifolius (Rottb.) Hassk. Fertilized and unfertilized treatments were maintained separately to record the influence of fertilizer in TPH degradation. The average biomass production (twenty plants from each treatment) of C. rotundus was 345.5 g and that of C. brevifolius was 250.6 g in fertilized soil during 360 days. Decrease in soil TPH concentration was higher in fertilized soil (75% for C. rotundus and 64% for C. brevifolius) than in unfertilized soil (36% for C. rotundus and 32% for C. brevifolius). In unvegetated treatments, decrease in soil TPH concentration in fertilized (12%) and unfertilized soil (8%) can be attributed to natural attenuation and microbial degradation. TPH accumulation in roots and shoots was significantly higher in fertilized soil in comparison to unfertilized soils (p < 0.05). Most probable number (MPN) in planted treatments was significantly higher than in unplanted treatments (p < 0.05).

Impact of hydrocarbon type, concentration and weathering on its biodegradability in soil

The objective of this research was to investigate the impact of the hydrocarbon type and concentration, as well as the total effect of the natural weathering process to hydrocarbon biodegradability in sandy soil and the environment. In this experiment, sandy soil was separately contaminated with 0.5%, 1.0%, 2.0% and 3.5% of diesel and crude oils. Oil contaminated soil was taken from the Oil Refinery dumping sites after 9 years of weathering, and its concentration was adjusted to the above-mentioned levels. The biodegradation process was monitored by measuring CO(2), evolution rate, hydrocarbon degradation rate and dehydrogenase activity. The favourable concentration ranges for the soil contaminated with diesel oil were 1.0%, with concentrations at about 2.0% causing slightly adverse effects to CO(2) production which was overcome after 2 weeks, and with 3.5% diesel oil causing significant toxicity. For soil contaminated with crude oil, 2.0% was found to be optimum for effective biodegradation, with 3.5% crude oil also causing adverse effects to CO(2) production, although less so than the same concentration of diesel oil. No adverse effect was obtained for any concentration of the weathered oil, as after the weathering process, the remaining contaminants in the soil were mostly poorly degradable constituents like asphaltenes, resins etc. It has been proposed that such residual material from oil degradation is analogous to, and can even be regarded as, humic material. Due to its inert characteristics, insolubility and similarity to humic materials it is unlikely to be environmentally hazardous.