Microbial Bioremediation of Petroleum Hydrocarbon– Contaminated Marine Environments

Petroleum pollution has become a serious environmental problem, which can cause harmful damage to the environment and human health. This pollutant is introduced into the environment from both natural and anthropogenic sources. Various physicochemical and biological treatments were developed for the cleanup of contaminated environments. However, bioremediation is based on the metabolic capabilities of microorganisms, and it is considered as the most basic and reliable way to eliminate contaminants, particularly petroleum and its recalcitrant compounds. It is more effective alternative comparing to classical remediation techniques. A high diversity of potential hydrocarbon degrader’s microorganisms was reported, and bacteria constitute the most abundant group, which has been well studied for hydrocarbon degradation. Several bioremediation approaches through bioaugmentation or/and biostimulation have been successfully applied. The interest on the optimizing of different parameters to achieve successful bioremediation technologies has been increased. In this chapter, we summarize the diversity and the hydrocarbon degradation potential of microorganism involved in the remediation of contaminated environments. We also present an overview of the efficient bioremediation strategies used for the decontamination of polluted marine environments

Anti-Microbial Peptides: The Importance of Structure-Function Analysis in the Design of New AMPs

In recent years the rapid emergence of drug resistant microorganisms has become a major health problem worldwide. The number of multidrug resistant (MDR) bacteria is in a rapid increase. Therefore, there is an urgent need to develop new antimicrobial agent that is active against MDR. Among the possible candidates, antimicrobial peptides (AMPs) represent a promising alternative. Many AMPs candidates were in clinical development and the Nisin was approved in many food products. Exact mechanism of AMPs action has not been fully elucidated. More comprehensive of the mechanism of action provide a path towards overcoming the toxicity limitation. This chapter is a review that provides an overview of bacterial AMPs named bacteriocin, focusing on their diverse mechanism of action. We develop here the structure–function relationship of many AMPs. A good understanding of AMPS structure–function relationship can helps the scientific in the conception of new active AMPs by the evaluation of the role of each residue and the determination of the essential amino acids for activity. This feature helps the development of the second-generation AMPs with high potential antimicrobial activity and more

Microbial symbionts : a resource for the management of insect-related problems

Microorganisms establish with their animal hosts close interactions. They are involved in many aspects of the host life, physiology and evolution, including nutrition, reproduction, immune homeostasis, defence and speciation. Thus, the manipulation and the exploitation the microbiota could result in important practical applications for the development of strategies for the management of insect-related problems. This approach, defined as Microbial Resource Management (MRM), has been applied successfully in various environments and ecosystems, as wastewater treatments, prebiotics in humans, anaerobic digestion and so on. MRM foresees the proper management of the microbial resource present in a given ecosystem in order to solve practical problems through the use of microorganisms. In this review we present an interesting field for application for MRM concept, i.e. the microbial communities associated with arthropods and nematodes. Several examples related to this field of applications are presented. Insect microbiota can be manipulated: (i) to control insect pests for agriculture; (ii) to control pathogens transmitted by insects to humans, animals and plants; (iii) to protect beneficial insects from diseases and stresses. Besides, we prospect further studies aimed to verify, improve and apply MRM by using the insectsymbiont ecosystem as a model

Ethylene Response Factor Sl-ERF.B.3 Is Responsive to Abiotic Stresses and Mediates Salt and Cold Stress Response Regulation in Tomato

Sl-ERF.B.3 (Solanum lycopersicum ethylene response factor B.3) gene encodes for a tomato transcription factor of the ERF (ethylene responsive factor) family. Our results of real-time RT-PCR showed that Sl-ERF.B.3 is an abiotic stress responsive gene, which is induced by cold, heat, and flooding, but downregulated by salinity and drought. To get more insight into the role of Sl-ERF.B.3 in plant response to separate salinity and cold, a comparative study between wild type and two Sl-ERF.B.3 antisense transgenic tomato lines was achieved. Compared with wild type, Sl-ERF.B.3 antisense transgenic plants exhibited a salt stress dependent growth inhibition. This inhibition was significantly enhanced in shoots but reduced in roots, leading to an increased root to shoot ratio. Furthermore, the cold stress essay clearly revealed that introducing antisense Sl-ERF.B.3 in transgenic tomato plants reduces their cell injury and enhances their tolerance against 14 d of cold stress. All these results suggest that Sl-ERF.B.3 gene is involved in plant response to abiotic stresses and may play a role in the layout of stress symptoms under cold stress and in growth regulation under salinity

Patterns and determinants of halophilic Archaea (class Halobacteria) diversity in Tunisian endorheic salt lakes and sebkhet systems

We examined the diversity and community structure of members of the halophilic Archaea (class Halobacteria) in samples from central and southern Tunisian endorheic salt lakes and sebkhet (also known as sebkha) systems using targeted 16S rRNA gene diversity survey and quantitative PCR (qPCR) approaches. Twenty-three different samples from four distinct locations exhibiting a wide range of salinities (2% to 37%) and physical characteristics (water, salt crust, sediment, and biofilm) were examined. A total of 4,759 operational taxonomic units at the 0.03 (species-level) cutoff (OTU0.03s) belonging to 45 currently recognized genera were identified, with 8 to 43 genera (average, 30) identified per sample. In spite of the large number of genera detected per sample, only a limited number (i.e., 2 to 16) usually constituted the majority (>/=80%) of encountered sequences. Halobacteria diversity showed a strong negative correlation to salinity (Pearson correlation coefficient = -0.92), and community structure analysis identified salinity, rather than the location or physical characteristics of the sample, as the most important factor shaping the Halobacteria community structure. The relative abundance of genera capable of biosynthesis of the compatible solute(s) trehalose or 2-sulfotrehalose decreased with increasing salinities (Pearson correlation coefficient = -0.80). Indeed, qPCR analysis demonstrated that the Halobacteria otsB (trehalose-6-phosphatase)/16S rRNA gene ratio decreases with increasing salinities (Pearson correlation coefficient = -0.87). The results highlight patterns and determinants of Halobacteria diversity at a previously unexplored ecosystem and indicate that genera lacking trehalose biosynthetic capabilities are more adapted to growth in and colonization of hypersaline (>25% salt) ecosystems than trehalose producers.Peer reviewedMicrobiology and Molecular Genetic

The RadioP1 – An Integrative Web Resource for Radioresistant Prokaryotes

The extremely radioresistant eubacterium Deinococcus radiodurans and the phenotypically related prokaryotes, whose genomes have been completely sequenced, are presently used as model species in several laboratories to study the lethal effects of DNA-damaging and protein-oxidizing agents, particularly the effects of ionizing radiation (IR). Unfortunately, providing relevant information about radioresistant prokaryotes (RP) in a neatly centralized and organized manner still remains a need. In this study, we designed RadioP1 Web resource (www.radiop.org.tn) to gather information about RP defined by the published literature with specific emphasis on (i) predicted genes that produce and protect against oxidative stress, (ii) predicted proteins involved in DNA repair mechanisms and (iii) potential uses of RP in biotechnology. RadioP1 allows the complete RP proteogenomes to be queried using various patterns in a user-friendly and interactive manner. The output data can be saved in plain text, Excel or HyperText Markup Language (HTML) formats for subsequent analyses. Moreover, RadioP1 provides for users a tool “START ANALYSIS”, including the previously described R-packages “drc” and “lethal”, to generate exponential or sigmoid survival curves with D10 and D50 values. Furthermore, when accessible, links to external databases are provided. Supplementary data will be included in the future when the sequences of other RP genomes will become available

Aqueous extracts from tunisian diplotaxis: phenol content, antioxidant and anti-acetylcholinesterase activities, and impact of exposure to simulated gastrointestinal fluids

Antioxidants have been considered essential for preventing cell damage by scavenging deleterious free radicals. The consumption of antioxidant-rich plants is associated with a reduced risk of some chronic diseases. This study evaluates the antioxidant and acetylcholinesterase inhibition activities of aqueous extracts obtained from different parts of Diplotaxis simplex and Diplotaxis harra from Tunisia. The study also aimed to investigate the action of simulated gastrointestinal juice on antioxidant activities of both extracts. The total phenolic, flavone and flavonol, and flavanone and dihydroflavonol contents were determined by Folin-Ciocalteau, aluminum chloride and 2,4-dinitrophenylhydrazine colorimetric methods, respectively. The metal ion chelating activity, acetylcholinesterase inhibition capacity, and free radical scavenging potential of the extracts towards ABTS (2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid), DPPH (2,2-diphenyl-1-picrylhydrazyl), hydroxyl, superoxide and nitric oxide were also evaluated. The action of simulated gastro-intestinal fluids on the flavone and flavonol content and total antioxidant activity of the flower extracts was surveyed. Extracts from the seeds and flowers of D. simplex and D. harra displayed the highest amounts of phenols (2691.7 and 2694.5 mg Caffeic Acid Equivalent (CAE)/100 mg; 3433.4 and 2647.2 mg CAE/100 mg, respectively) and flavonols/flavones (2144.4 and 2061.1 mg Rutin Equivalent (RE)/100 g; 1922.6 and 1461.1 mg RE/100 g, respectively). The flower and seed extracts exhibited the highest rates of antioxidant and acetylcholinesterase inhibition activities. A decrease in the flavonoid content and antioxidant activity was observed after extract exposure to simulated saliva. Antioxidant and acetylcholinesterase inhibition activities were noted to depend on plant species and plant parts. In vitro gastrointestinal digestion is useful in assessing the bio-accessibility of compounds with biological activities from food. The simulated gastrointestinal fluids influenced the flavonoid concentration and antioxidant activity

Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments

Halocins, Bacteriocin-Like Antimicrobials Produced by the Archaeal Domain: Occurrence and Phylogenetic Diversity in <em>Halobacteriales</em>

Members of extremely halophilic archaea, currently consisting of more than 56 genera and 216 species, are known to produce their specific bacteriocin-like peptides and proteins called halocins, synthesized by the ribosomal pathway. Halocins are diverse in size, consisting of proteins as large as 35 kDa and peptide “microhalocins” as small as 3.6 kDa. Today, about fifteen halocins have been described and only three genes, halC8, halS8 and halH4, coding C8, S8 and H4 halocins respectively have been identified. In this study, a total of 1858 of complete and nearly complete genome sequences of Halobacteria class members were retrieved from the IMG and Genbank databases and then screened for halocin encoding gene content, based on the BLASTP algorithm. A total of 61 amino acid sequences belonging to three halocins classes (C8, HalH4 and S8) were identified within 15 genera with the abundance of C8 class. Phylogenetic analysis based on amino acids sequences showed a clear segregation of the three halocins classes. Halocin S8 was phylogenetically more close to HalH4. No clear segregation on species and genera levels was observed based on halocin C8 analysiscontrary to HalH4 based analysis. Collectively, these results give an overview on halocins diversity within halophilic archaea which can open new research topics that will shed light on halocins as marker for haloarchaeal phylogentic delineation

Efficacy of Natural and Synthetic Biofilm Inhibitors Associated with Antibiotics in Eradicating Biofilms Formed by Multidrug-Resistant Bacteria

Biofilms formed by multidrug resistant (MDR) bacteria like methicillin-resistant Staphylococcus aureus (MRSA) and others are the main causes of infections that represent a serious public health issue. Persistent MDR infections are mostly derived from biofilm formation which in turn leads to resistance to conventional antimicrobial therapy. Inhibition of bacterial surface attachment is the new alternative strategy without affecting the bacterial growth. Thus, the discovery of compounds that interfere with biofilm production, virulence factors release and quorum sensing (QS) detection in pathogens is a promising processus. Among these compounds, natural and synthetic molecules are a compelling alternative to attenuate pathogenicity. The combination of these compounds with antibiotics makes the bacteria more vulnerable to the later, once used alone. This combination can restore antibiotic effectiveness against MDR bacteria. Among these molecules, 3-phenylpropan-1-amine (3-PPA) has been found to inhibit Serratia marcescens biofilm formation, PAβN has been proven to inhibit biofilm prodcution in A. baumannii, while brominated Furanone C-30 has been reported to be a potent inhibitor of the QS system and P. aeruginosa biofilm. Therefore, the combination between biofilm-inhibitors and antibiotics represents a promising strategy to mitigate antibiotic resistance in MDR pathogens, which has become a major threat to public healthcare around the globe