Biomimetic Nanopillar Silicon Surfaces Rupture Fungal Spores.

The mechano-bactericidal action of nanostructured surfaces is well-documented; however, synthetic nanostructured surfaces have not yet been explored for their antifungal properties toward filamentous fungal species. In this study, we developed a biomimetic nanostructured surface inspired by dragonfly wings. A high-aspect-ratio nanopillar topography was created on silicon (nano-Si) surfaces using inductively coupled plasma reactive ion etching (ICP RIE). To mimic the superhydrophobic nature of insect wings, the nano-Si was further functionalised with trichloro(1H,1H,2H,2H-perfluorooctyl)silane (PFTS). The viability of Aspergillus brasiliensis spores, in contact with either hydrophobic or hydrophilic nano-Si surfaces, was determined using a combination of standard microbiological assays, confocal laser scanning microscopy (CLSM), and focused ion beam scanning electron microscopy (FIB-SEM). Results indicated the breakdown of the fungal spore membrane upon contact with the hydrophilic nano-Si surfaces. By contrast, hydrophobised nano-Si surfaces prevented the initial attachment of the fungal conidia. Hydrophilic nano-Si surfaces exhibited both antifungal and fungicidal properties toward attached A. brasisiensis spores via a 4-fold reduction of attached spores and approximately 9-fold reduction of viable conidia from initial solution after 24 h compared to their planar Si counterparts. Thus, we reveal, for the first time, the physical rupturing of attaching fungal spores by biomimetic hydrophilic nanostructured surfaces.

Silicon-Doped Graphene Oxide Quantum Dots as Efficient Nanoconjugates for Multifunctional Nanocomposites.

Graphene oxide quantum dots (GOQDs) hold great promise as a new class of high-performance carbonaceous nanomaterials due to their numerous functional properties, such as tunable photoluminescence (PL), excellent thermal and chemical stability, and superior biocompatibility. In this study, we developed a facile, one-pot, and effective strategy to engineer the interface of GOQDs through covalent doping with silicon. The successful covalent attachment of the silane dopant with pendant vinyl groups to the edges of the GOQDs was confirmed by an in-depth investigation of the structural and morphological characteristics. The Si-GOQD nanoconjugates had an average dimension of ∼8 nm, with a graphite-structured core and amorphous carbon on their shell. We further used the infrared nanoimaging based on scattering-type scanning near-field optical microscopy to unveil the spectral near-field response of GOQD samples and to measure the nanoscale IR response of its network; we then demonstrated their distinct domains with strongly enhanced near fields. The doping of Si atoms into the sp2-hybridized graphitic framework of GOQDs also led to tailored PL emissions. We then sought to explore the potential applications of Si-GOQDs on the surface of plastic films where poly(dimethylsiloxane) (PDMS) served as a bridge to tightly anchor the Si-GOQDs to the surface. The bi-layered coated films which were built with co-assembly of Si-GOQDs and PDMS contributed to suppressing the transmission of water molecules due to the generation of compact and less accessible passing sites, achieving a nearly twofold reduction in water permeability compared to the single-layered coated films. The nanoindentation and PeakForce quantitative nanomechanical mapping showed that Si-GOQD-coated substrates were softer and more deformable than those coated only with PDMS. The co-assembly of PDMS and Si-GOQDs yielded films that were less stiff than those made from PDMS alone. Our findings provided conceptual insights into the importance of nanoscale surface engineering of GOQDs in conferring excellent dispersibility and enhancing the performance of nanocomposite films.

Rational design of potent ultrashort antimicrobial peptides with programmable assembly into nanostructured hydrogels.

Microbial resistance to common antibiotics is threatening to cause the next pandemic crisis. In this context, antimicrobial peptides (AMPs) are receiving increased attention as an alternative approach to the traditional small molecule antibiotics. Here, we report the bi-functional rational design of Fmoc-peptides as both antimicrobial and hydrogelator substances. The tetrapeptide Fmoc-WWRR-NH2-termed Priscilicidin-was rationally designed for antimicrobial activity and molecular self-assembly into nanostructured hydrogels. Molecular dynamics simulations predicted Priscilicidin to assemble in water into small oligomers and nanofibrils, through a balance of aromatic stacking, amphiphilicity and electrostatic repulsion. Antimicrobial activity prediction databases supported a strong antimicrobial motif via sequence analogy. Experimentally, this ultrashort sequence showed a remarkable hydrogel forming capacity, combined to a potent antibacterial and antifungal activity, including against multidrug resistant strains. Using a set of biophysical and microbiology techniques, the peptide was shown to self-assemble into viscoelastic hydrogels, as a result of assembly into nanostructured hexagonal mesophases. To further test the molecular design approach, the Priscilicidin sequence was modified to include a proline turn-Fmoc-WPWRR-NH2, termed P-Priscilicidin-expected to disrupt the supramolecular assembly into nanofibrils, while predicted to retain antimicrobial activity. Experiments showed P-Priscilicidin self-assembly to be effectively hindered by the presence of a proline turn, resulting in liquid samples of low viscosity. However, assembly into small oligomers and nanofibril precursors were evidenced. Our results augur well for fast, adaptable, and cost-efficient antimicrobial peptide design with programmable physicochemical properties.

The Impacts of Different Biological Treatments on the Transformation of Explosives Waste Contaminated Sludge.

The dinitrotoluene isomers 2,4 and 2,6-dinitrotoluene (DNT) represent highly toxic, mutagenic, and carcinogenic compounds used in explosive manufacturing and in commercial production of polyurethane foam. Bioremediation, the use of microbes to degrade residual DNT in industry wastewaters, represents a promising, low cost and environmentally friendly alternative technology to landfilling. In the present study, the effect of different bioremediation strategies on the degradation of DNT in a microcosm-based study was evaluated. Biostimulation of the indigenous microbial community with sulphur phosphate (2.3 g/kg sludge) enhanced DNT transformation (82% transformation, from 300 g/L at Day 0 to 55 g/L in week 6) compared to natural attenuation over the same period at 25 °C. The indigenous microbial activity was found to be capable of transforming the contaminant, with around 70% transformation of DNT occurring over the microcosm study. 16S rDNA sequence analysis revealed that while the original bacterial community was dominated by Gammaproteobacteria (30%), the addition of sulphur phosphate significantly increased the abundance of Betaproteobacteria by the end of the biostimulation treatment, with the bacterial community dominated by Burkholderia (46%) followed by Rhodanobacter, Acidovorax and Pseudomonas. In summary, the results suggest biostimulation as a treatment choice for the remediation of dinitrotoluenes and explosives waste.

Antifungal versus antibacterial defence of insect wings.

HYPOTHESIS: The ability exhibited by insect wings to resist microbial infestation is a unique feature developed over 400 million years of evolution in response to lifestyle and environmental pressures. The self-cleaning and antimicrobial properties of insect wings may be attributed to the unique combination of nanoscale structures found on the wing surface. EXPERIMENTS: In this study, we characterised the wetting characteristics of superhydrophobic damselfly Calopteryx haemorrhoidalis wings. We revealed the details of air entrapment at the micro- and nano scales on damselfly wing surfaces using a combination of spectroscopic and electron microscopic techniques. Cryo-focused-ion-beam scanning electron microscopy was used to directly observe fungal spores and conidia that were unable to cross the air-liquid interface. By contrast, bacterial cells were able to cross the air-water interface to be ruptured upon attachment to the nanopillar surface. The robustness of the air entrapment, and thus the wing antifungal behaviour, was demonstrated after 1-week of water immersion. A newly developed wetting model confirmed the strict Cassie-Baxter wetting regime when damselfly wings are immersed in water. FINDINGS: We provide evidence that the surface nanopillar topography serves to resist both fungal and bacterial attachment via a dual action: repulsion of fungal conidia while simultaneously killing bacterial cells upon direct contact. These findings will play an important role in guiding the fabrication of biomimetic, anti-fouling surfaces that exhibit both bactericidal and anti-fungal properties.

Diversity of experimental designs for the fabrication of antifungal surfaces for the built environment.

The fungal infestation in construction industries is a major problem with a very high removal cost that needs to be controlled not only to prevent the fouling of surfaces but also to prevent allergic reactions or respiratory problems especially in immunocompromised individuals. To combat fungal invasion, several experimental approaches to produce antifungal surfaces have been developed. Here, we reviewed the current strategies in designing antifungal surfaces and classified those approaches into two major categories: the chemical and/or physical modification of the actual material surface and nanoparticle-based coating formulations created using the functionalised nanoparticles. KEY POINTS: • Antifungal effect of micro- and nano-structured superhydrophobic surfaces. • Long-term antifungal effect conferred through biocides. • Advanced coatings based on functionalised silica, TiO2 and ZnO nanoparticles.

Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities.

The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.

Real-time detection and identification of nematode eggs genus and species through optical imaging.

Nematode eggs are pervasive pathogens that infect billions of people and livestock every year. Adult parasitic nematode worms can be distinguished based on their size and morphology. However, their eggs, particularly their species Ascaris lumbricoides and Ascaris suum cannot be identified from each other. Identifying eggs of helminths from wastewater and sludge is important from a public health perspective to minimize the spread of Ascaris infections. Numerous methods exist for nematode identification, from a morphological-based approach to high throughput sequencing technology. However, these techniques are not consistent and often laborious and time-consuming. In this study, we demonstrate that non-invasive real-time identification of eggs is possible based on their intrinsic fluorescence. Using confocal microscopy, we investigate the autofluorescence properties of five species of nematode eggs and observe clear differences between genus and for the first time their species in sludge samples. This non-invasive imaging technique could lead to better understanding of these species and may assist in early control of diseases.

Nanoscale Surface Roughness Influences Candida albicans Biofilm Formation.

The microbial contamination of surfaces presents a significant challenge due to the adverse effects associated with biofilm formation, particularly on implantable devices. Here, the attachment and biofilm formation of the opportunistic human pathogen, Candida albicans ATCC 10231, were studied on surfaces with decreasing magnitudes of nanoscale roughness. The nanoscale surface roughness of nonpolished titanium, polished titanium, and glass was characterized according to average surface roughness, skewness, and kurtosis. Nonpolished titanium, polished titanium, and glass possessed average surface roughness (Sa) values of 350, 20, and 2.5 nm; skewness (Sskw) values of 1.0, 4.0, and 1.0; and (Skur) values of 3.5, 16, and 4, respectively. These unique characteristics of the surface nanoarchitecture were found to play a key role in limiting C. albicans attachment and modulating the functional phenotypic changes associated with biofilm formation. Our results suggest that surfaces with a specific combination of surface topographical parameters could prevent the attachment and biofilm formation of C. albicans. After 7 days, the density of attached C. albicans cells was recorded to be 230, 70, and 220 cells mm-2 on nonpolished titanium, polished titanium, and glass surfaces, respectively. Despite achieving a very low attachment density, C. albicanscells were only observed to produce hyphae associated with biofilm formation on nonpolished titanium surfaces, possessing the highest degree of surface roughness (Sa = 350 nm). This study provides a more comprehensive picture of the impact of surface architectures on C. albicans attachment, which is beneficial for the design of antifungal surfaces.

Challenges and Current Status of the Biological Treatment of PFAS-Contaminated Soils.

Per- and polyfluoroalkyl substances (PFAS) are Synthetic Organic Compounds (SOCs) which are of current concern as they are linked to a myriad of adverse health effects in mammals. They can be found in drinking water, rivers, groundwater, wastewater, household dust, and soils. In this review, the current challenge and status of bioremediation of PFAs in soils was examined. While several technologies to remove PFAS from soil have been developed, including adsorption, filtration, thermal treatment, chemical oxidation/reduction and soil washing, these methods are expensive, impractical for in situ treatment, use high pressures and temperatures, with most resulting in toxic waste. Biodegradation has the potential to form the basis of a cost-effective, large scale in situ remediation strategy for PFAS removal from soils. Both fungal and bacterial strains have been isolated that are capable of degrading PFAS; however, to date, information regarding the mechanisms of degradation of PFAS is limited. Through the application of new technologies in microbial ecology, such as stable isotope probing, metagenomics, transcriptomics, and metabolomics there is the potential to examine and identify the biodegradation of PFAS, a process which will underpin the development of any robust PFAS bioremediation technology.

Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems-Fate and Microbial Responses.

Petroleum hydrocarbons represent the most frequent environmental contaminant. The introduction of petroleum hydrocarbons into a pristine environment immediately changes the nature of that environment, resulting in reduced ecosystem functionality. Natural attenuation represents the single, most important biological process which removes petroleum hydrocarbons from the environment. It is a process where microorganisms present at the site degrade the organic contaminants without the input of external bioremediation enhancers (i.e., electron donors, electron acceptors, other microorganisms or nutrients). So successful is this natural attenuation process that in environmental biotechnology, bioremediation has developed steadily over the past 50 years based on this natural biodegradation process. Bioremediation is recognized as the most environmentally friendly remediation approach for the removal of petroleum hydrocarbons from an environment as it does not require intensive chemical, mechanical, and costly interventions. However, it is under-utilized as a commercial remediation strategy due to incomplete hydrocarbon catabolism and lengthy remediation times when compared with rival technologies. This review aims to describe the fate of petroleum hydrocarbons in the environment and discuss their interactions with abiotic and biotic components of the environment under both aerobic and anaerobic conditions. Furthermore, the mechanisms for dealing with petroleum hydrocarbon contamination in the environment will be examined. When petroleum hydrocarbons contaminate land, they start to interact with its surrounding, including physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) interactions. As microorganism (including bacteria and fungi) play an important role in the degradation of petroleum hydrocarbons, investigations into the microbial communities within contaminated soils is essential for any bioremediation project. This review highlights the fate of petroleum hydrocarbons in tertial environments, as well as the contributions of different microbial consortia for optimum petroleum hydrocarbon bioremediation potential. The impact of high-throughput metagenomic sequencing in determining the underlying degradation mechanisms is also discussed. This knowledge will aid the development of more efficient, cost-effective commercial bioremediation technologies.

Elucidation of the microbial diversity in rivers in south-west Victoria, Australia impacted by rural agricultural contamination (dairy farming).

We assessed the water quality of south-west Victorian rivers impacted by the dairy industry using traditional water quality assessment together with culture-dependent (colilert/enterolert) and also culture-independent (next generation sequencing) microbial methods. The aim of the study was to identify relationships/associations between dairy farming intensity and water contamination. Water samples with high total and faecal coliforms (>1000 MPN cfu/100 ml), and with high nitrogen levels (TN) were observed in zones with a high proportion of dairy farming. Members of the genus Nitrospira, Rhodobacter and Rhodoplanes were predominant in such high cattle density zones. Samples from sites in zones with lower dairy farming activities registered faecal coliform numbers within the permissible limits (<1000 MPN cfu/100 ml) and showed the presence of a wide variety of microorganisms. However, no bacterial pathogens were found in the river waters regardless of the proportion of cattle. The data suggests that using the spatially weighted proportion of land used for dairy farming is a useful way to target at-risk sub-catchments across south west Victoria; further work is required to confirm that this approach is applicable in other regions.

Effects of Dietary Fibre from the Traditional Indonesian Food, Green Cincau (Premna oblongifolia Merr.) on Preneoplastic Lesions and Short Chain Fatty Acid Production in an Azoxymethane Rat Model of Colon Cancer.

Green cincau (Premna oblongifolia Merr.) is a traditional food of Indonesia and provides a natural source of dietary fibre and antioxidants. This study evaluated the ability of green cincau, and other dietary fibres with or without the addition of anti-oxidant, epigallocatechin-3-gallate (EGCG), to prevent colorectal cancer in a 12 week azoxymethane (AOM) rat model. While all dietary treatments stimulated short chain fatty acid production (SCFA) in the digesta and faeces, no one treatment was able to significantly protect against aberrant crypt formation (ACF), when compared to the control diet. However, feeding green cincau leaves or extracts did not result in an increase in ACF compared to the control diet. Unexpectedly, when the dietary fibre source was pectin, 0.1% EGCG increased proliferative activity and liver lipid peroxidation when compared to the control diet containing cellulose. Examination of faecal microbial communities identified the presence of short chain acid producing bacteria, but a distinct community profile was not observed from any individual diet group. Overall, this research implies that combining dietary fibre with an antioxidant does not automatically equate to a beneficial response. Further work is required to investigate the health-promoting properties of green cincau.

Large scale treatment of total petroleum-hydrocarbon contaminated groundwater using bioaugmentation.

Bioaugmentation or the addition of microbes to contaminated sites has been widely used to treat contaminated soil or water; however this approach is often limited to laboratory based studies. In the present study, large scale bioaugmentation has been applied to total petroleum hydrocarbons (TPH)-contaminated groundwater at a petroleum facility. Initial TPH concentrations of 1564 mg L-1 in the field were reduced to 89 mg L-1 over 32 days. This reduction was accompanied by improved ecotoxicity, as shown by Brassica rapa germination numbers that increased from 52 at day 0 to 82% by the end of the treatment. Metagenomic analysis indicated that there was a shift in the microbial community when compared to the beginning of the treatment. The microbial community was dominated by Proteobacteria and Bacteroidetes from day 0 to day 32, although differences at the genus level were observed. The predominant genera at the beginning of the treatment (day 0 just after inoculation) were Cloacibacterium, Sediminibacterium and Brevundimonas while at the end of the treatment members of Flavobacterium dominated, reaching almost half the population (41%), followed by Pseudomonas (6%) and Limnobacter (5.8%). To the author's knowledge, this is among the first studies to report the successful large scale biodegradation of TPH-contaminated groundwater (18,000 L per treatment session) at an offshore petrochemical facility.

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils.

Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active 13C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event (14C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.

A modified assay for the enumeration of ascaris eggs in fresh raw sewage.

Soil-transmitted helminths (STHs) pose a significant public health problem, infecting approximately 2 billion people globally. Despite relatively low prevalence in developed countries, the removal of STHs from wastewater remains crucial to allow the safe use of biosolids or recycled water for agriculture. Wastewater helminth egg count data can contribute to an assessment of the need for, or success of, a parasite management program. Although the World Health Organisation (WHO) has recommended a standard method for counting helminth eggs in raw sewage based on the method of Bailenger (Ayres et al., 1996), the method generally results in low percentage egg recoveries. Given the importance of determining the presence of STHs, it is essential to develop novel techniques that optimise the recovery rate of eggs from raw sewage. In the present study: •The method described by Bowman et al. (2003) was optimized for the concentration and enumeration of helminth eggs in raw sewage from municipal sewage treatment plants.•The method is simple and reproducible and recovers a greater percentage of helminth eggs compared to the WHO method.

Degradation mechanisms of DDX induced by the addition of toluene and glycerol as cosubstrates in a zero-valent iron pretreated soil.

Abiotic and biotic processes can be used to remediate DDX (DDT, DDD, DDE, and DDNS) contaminated soils; these processes can be fostered using specific carbon-amendments to stimulate particular soil indigenous microbial communities to improve rates or extent of degradation. In this study, toluene and glycerol were evaluated as cosubstrates under aerobic and anoxic conditions to determine the degradation efficiencies of DDX and to elucidate possible degradation mechanisms. Slurry microcosms experiments were performed during 60 days using pretreated soil with zero-valent iron (ZVI). Toluene addition enhanced the percentage of degradation of DDX. DDNS was the main compound degraded (around 86%) under aerobic conditions, suggesting cometabolic degradation of DDX by toluene-degrading soil bacteria. Glycerol addition under anoxic conditions favored the abiotic degradation of DDX mediated by sulfate-reducing bacteria activity, where DDT was the main compound degraded (around 90%). The 16S rDNA metagenomic analyses revealed Rhodococcus ruber and Desulfosporosinus auripigmenti as the predominant bacterial species after 40 days of treatment with toluene and glycerol additions, respectively. This study provides evidence of biotic and abiotic DDX degradation by the addition of toluene and glycerol as cosubstrates in ZVI pretreated DDX-contaminated soil.

Bioremediation potential of diesel-contaminated Libyan soil.

Bioremediation is a broadly applied environmentally friendly and economical treatment for the clean-up of sites contaminated by petroleum hydrocarbons. However, the application of this technology to contaminated soil in Libya has not been fully exploited. In this study, the efficacy of different bioremediation processes (necrophytoremediation using pea straw, bioaugmentation and a combination of both treatments) together with natural attenuation were assessed in diesel contaminated Libyan soils. The addition of pea straw was found to be the best bioremediation treatment for cleaning up diesel contaminated Libyan soil after 12 weeks. The greatest TPH degradation, 96.1% (18,239.6mgkg(-1)) and 95% (17,991.14mgkg(-1)) were obtained when the soil was amended with pea straw alone and in combination with a hydrocarbonoclastic consortium respectively. In contrast, natural attenuation resulted in a significantly lower TPH reduction of 76% (14,444.5mgkg(-1)). The presence of pea straw also led to a significant increased recovery of hydrocarbon degraders; 5.7log CFU g(-1) dry soil, compared to 4.4log CFUg(-1) dry soil for the untreated (natural attenuation) soil. DGGE and Illumina 16S metagenomic analyses confirm shifts in bacterial communities compared with original soil after 12 weeks incubation. In addition, metagenomic analysis showed that original soil contained hydrocarbon degraders (e.g. Pseudoxanthomonas spp. and Alcanivorax spp.). However, they require a biostimulant (in this case pea straw) to become active. This study is the first to report successful oil bioremediation with pea straw in Libya. It demonstrates the effectiveness of pea straw in enhancing bioremediation of the diesel-contaminated Libyan soil.

A quantitative PCR approach for quantification of functional genes involved in the degradation of polycyclic aromatic hydrocarbons in contaminated soils.

Polycyclic aromatic hydrocarbons (PAHs) are major pollutants globally and due to their carcinogenic and mutagenic properties their clean-up is paramount. Bioremediation or using PAH degrading microorganisms (mainly bacteria) to degrade the pollutants represents cheap, effective methods. These PAH degraders harbor functional genes which help microorganisms use PAHs as source of food and energy. Most probable number (MPN) and plate counting methods are widely used for counting PAHs degraders; however, as culture based methods only count a small fraction (<1%) of microorganisms capable of carrying out PAH degradation, the use of culture-independent methodologies is desirable.•This protocol presents a robust, rapid and sensitive qPCR method for the quantification of the functional genes involved in the degradation of PAHs in soil samples.•This protocol enables us to screen a vast number of PAH contaminated soil samples in few hours.•This protocol provides valuable information about the natural attenuation potential of contaminated soil and can be used to monitor the bioremediation process.

Commercial feasibility of lignocellulose biodegradation: possibilities and challenges.

The main source of energy supply worldwide is generated from fossil fuels, which undoubtedly are finite and non-environmental friendly resources. Bioethanol generated from edible resources also has economic and environmental concerns. Despite the immense attention to find an alternative (inedible) source of energy in the last two decades, the total commercial production of 1st generation biofuels is limited and equivalent only to approximately 3% of the total road transport fuel consumption. Lignocellulosic waste represents the most abundant biomass on earth and could be a suitable candidate for producing valuable products including biofuels. However, cellulosic bioethanol has not been produced on a large scale due to the technical barriers involved that make the commercial production of cellulosic bioethanol not economically feasible. This review examines some of the current barriers to commercialization of the process.