Many hypersaline environments are often contaminated with petroleum compounds. Among these, oil and natural gas production sites all over the world and hundreds of kilometers of coastlines in the more arid regions of Gulf countries are of major concern due to the extent and magnitude of contamination. Because conventional microbiological processes do not function well at elevated salinities, bioremediation of hypersaline environments can only be accomplished using high salt-tolerant microorganisms capable of degrading petroleum compounds. In the last two decades, there have been many reports on the biodegradation of hydrocarbons in moderate to high salinity environments. Numerous microorganisms belonging to the domain Bacteria and Archaea have been isolated and their phylogeny and metabolic capacity to degrade a variety of aliphatic and aromatic hydrocarbons in varying salinities have been demonstrated. This article focuses on our growing understanding of bacteria and archaea responsible for the degradation of hydrocarbons under aerobic conditions in moderate to high salinity conditions. Even though organisms belonging to various genera have been shown to degrade hydrocarbons, members of the genera Halomonas Alcanivorax, Marinobacter, Haloferax, Haloarcula, and Halobacterium dominate the published literature. Despite rapid advances in understanding microbial taxa that degrade hydrocarbons under aerobic conditions, not much is known about organisms that carry out similar processes in anaerobic conditions. Also, information on molecular mechanisms and pathways of hydrocarbon degradation in high salinity is scarce and only recently there have been a few reports describing genes, enzymes and breakdown steps for some hydrocarbons. These limited studies have clearly revealed that degradation of oxygenated and non-oxygenated hydrocarbons by halophilic and halotolerant microorganisms occur by pathways similar to those found in non-halophiles.

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Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments

Nanotechnology is currently at the forefront of scientific research and technological developments that have resulted in the manufacture of novel consumer products and numerous industrial applications using engineered nanomaterials (ENMs). With the increasing number of applications and uses of ENMs comes an increasing likelihood of nanoscale materials posing potential risks to the environment and engineered technical systems such as wastewater treatment plants (WWTPs). Recent scientific data suggests that ENMs that are useful in, for example, medical applications due to their novel physicochemical properties, may also cause adverse effects to the bacterial populations used in wastewater treatment systems. In this review, the toxicological effects of titanium nanoparticles (nTiO2), zinc oxide (nZnO), carbon nanotubes (CNTs), fullerenes (C60) and silver nanoparticles (AgNPs) to bacteria were examined. The results suggest that the potential ENMs risks to bacteria are non-uniform (need to be assessed case-by-case), and are dependent on numerous factors (e.g. size, pH, surface area, natural organic matter). Currently available data are therefore insufficient for evaluating the risks that ENMs pose in WWTPs. To fill these knowledge gaps, we recommend scenario specific studies aimed at improving our understanding on: (i) estimated volumes of ENMs in effluents, (ii) the antibacterial sensitivity of cultures within WWTPs towards selected ENMs, and (iii) processes improving the stability of ENMs in solutions. Two factors that merit consideration for elucidating the potential risks systematically are the toxicity mechanisms of ENMs to bacteria, and the influencing factors based on inherent physicochemical properties and environmental factors. Furthermore, the complexity of behaviour and fate of ENMs in real WWTPs requires case studies for assessing the ENMs risks to bacteria in vivo. The current laboratory results derived using simplified exposure media do not reflect actual environmental conditions.

The antibacterial effects of engineered nanomaterials: implications for wastewater treatment plants

© 2013 Pampanin and Sydnes, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Polycyclic Aromatic Hydrocarbons a Constituent of Petroleum: Presence and Influence in the Aquatic Environment

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Polycyclic Aromatic Hydrocarbons a Constituent of Petroleum: Presence and Influence in the Aquatic Environment

Pseudomonas aeruginosa is both a model biofilm-forming organism and an opportunistic pathogen responsible for chronic lung infections in cystic fibrosis (CF) patients and infections in burn patients, among other maladies. Here we describe the development of an efficient high-throughput screen to identify small-molecule modulators of biofilm formation. This screen has been run with 66,095 compounds to identify those that prevent biofilm formation without affecting planktonic bacterial growth. The screen is a luminescence-based attachment assay that has been validated with several strains of P. aeruginosa and compared to a well-established but low-throughput crystal violet staining biofilm assay. P. aeruginosa strain PAO1 was selected for use in the screen both because it forms robust biofilms and because genetic information and tools are available for the organism. The attachment-inhibited mutant, strain PAO1 DeltafliC, was used as a screening-positive control. We have also developed and validated a complementary biofilm detachment assay that can be used as an alternative primary screen or secondary screen for the attachment screening-positive compounds. We have determined the potencies of 61 compounds against biofilm attachment and have identified 30 compounds that fall into different structural classes as biofilm attachment inhibitors with 50% effective concentrations of less than 20 microM. These small-molecule inhibitors could lead to the identification of their relevant biofilm targets or potential therapeutics for P. aeruginosa infections.

High-Throughput Screens for Small-Molecule Inhibitors of Pseudomonas aeruginosa Biofilm Development

Update on the cometabolism of organic pollutants by bacteria.

Biodegradation can achieve complete and cost-effective elimination of aromatic pollutants through harnessing diverse microbial metabolic processes. Aromatics biodegradation plays an important role in environmental cleanup and has been extensively studied since the inception of biodegradation. These studies, however, are diverse and scattered; there is an imperative need to consolidate, summarize, and review the current status of aromatics biodegradation. The first part of this review briefly discusses the catabolic mechanisms and describes the current status of aromatics biodegradation. Emphasis is placed on monocyclic, polycyclic, and chlorinated aromatic hydrocarbons because they are the most prevalent aromatic contaminants in the environment. Among monocyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene; phenylacetic acid; and structurally related aromatic compounds are highlighted. In addition, biofilms and their applications in biodegradation of aromatic compounds are briefly discussed. In recent years, various biomolecular approaches have been applied to design and understand microorganisms for enhanced biodegradation. In the second part of this review, biomolecular approaches, their applications in aromatics biodegradation, and associated biosafety issues are discussed. Particular attention is given to the applications of metabolic engineering, protein engineering, and “omics” technologies in aromatics biodegradation.

Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches

BTEX biodegradation by a mixed community of micro-organisms offers a promising approach in terms of cost-effectiveness and elimination of secondary pollution. Two bacterial strains, Pseudomonas putida F1 and Pseudomonas stutzeri OX1 were chosen to formulate synthetic consortia based on their ability to biodegrade the mono-aromatic compounds. Benzene and toluene supported the growth of both the strains; while ethyl benzene and o-xylene were only utilized as growth substrates by P. putida F1 and P. stutzeri OX1, respectively. In a mixed substrate system, P. putida F1 exhibited incomplete removal of o-xylene while P. stutzeri OX1 displayed cometabolic removal of ethyl benzene with dark coloration of the growth medium. The biodegradation potential of the two Pseudomonas species complemented each other and offered opportunities to explore their performance as a co-culture for enhanced BTEX biodegradation. Several microbial formulations were concocted and their BTEX biodegradation characteristics were evaluated. Mixed culture biodegradation ascertained the advantages of the co-culture over the individual Pseudomonas species. This study also emphasized the significance of inoculum density and species proportion while concocting preselected micro-organisms for enhanced BTEX biodegradation.

Formulation of microbial cocktails for BTEX biodegradation

Species-specific enumeration of mixed community is invaluable as it facilitates a better understanding of the significance of the individual strains, their interactions, and the underlying mechanisms of community dynamics. Mixed microbial community has been characterized by microbiological, biochemical, or molecular biology-based methods. While microbiological and biochemical techniques do not provide adequate quantitative information of the members of the consortia and require additional techniques for a more comprehensive analysis, molecular biology-based methods analyze the microbial consortium based on specific DNA sequences and do not require isolation and culturing of bacteria for quantitative analysis. These methods outshine conventional culture-based techniques in terms of better sensitivity, reproducibility, and reliability. Quantitative molecular biology methods have been classified as PCR-based and probe hybridization methods. The PCR-based methods includes quantitative real-time PCR and terminal restriction fragment length polymorphism, while fluorescent in situ hybridization and DNA microarrays fall under probe hybridization methods. The workflow, the quantification methods, and their potential applications are discussed in this review by highlighting their advantages and possible limitations.

Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations

Molecular biological methods for mixed culture analysis outshine conventional culture-based techniques in terms of better sensitivity and reliability. The majority of these methods exploit the 16S rRNA sequences of the community DNA, which often fall short for the analysis of closely related microorganisms. This research details the development and validation of a comprehensive methodology to differentiate and quantitatively characterize two Pseudomonas species in a mixed culture. A bioinformatics tool based on whole-genome polymorphism comparison was used to identify marker sequences to differentiate the two bacteria using quantitative real-time PCR. The quantification of the two species was achieved through a correlation of the genomic DNA versus cell number (genomic DNA purification) and threshold cycle number versus genomic DNA (real-time PCR). Several factors including the limitation of genomic DNA purification, effects of substrate concentrations and growth phase on cellular DNA, and choice of simplex or duplex reaction for real-time PCR were considered and evaluated. The developed method was experimentally validated against synthetically constructed consortia.

Bioinformatics and molecular biology for the quantification of closely related bacteria

The paper explores the effectiveness of hands-on learning (HOL) as a student-centered model to train first year chemical engineering undergraduates. The pedagogical design of the course uses laboratory sessions, lectures, reflection sessions, projects, and assessments to achieve the course learning outcomes. The adopted assessment methodology (100% continuous assessment with no end-of-semester examination) aims at evaluating the quality of learning and mastery of higher order skills by students. The student feedback has been encouraging with many students finding the HOL methodology useful in offering meaningful opportunities to gain knowledge and acquire a breadth of higher-order skills.

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Karthiga Nagarajan

Papers

Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches

Formulation of microbial cocktails for BTEX biodegradation

Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations

Bioinformatics and molecular biology for the quantification of closely related bacteria

Hands-On Learning: An Experiential Approach to Train Chemical Engineering Students.