Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments.

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.

Ecotoxicity Assessment of Graphene Oxides Using Test Organisms from Three Hierarchical Trophic Levels to Evaluate Their Potential Environmental Risk.

After more than a decade of studying the ecotoxicity of graphene oxide nanomaterials (nGOs), it has been concluded that there is limited information available regarding the environmental risk of graphene-based materials. Since existing ecotoxicological studies of nanomaterials have produced contradictory results, it is recommended that case-by-case studies should be conducted to evaluate their effects. This can be carried out by employing several methods, testing species from different trophic levels, and conducting community studies. Our goal was to evaluate the toxicity effects of two GOs (AF 96/97 and PM 995) derived from different graphite precursors on various test organisms from diverse trophic levels (bacteria, protozoa, a freshwater microbial community, plants, and invertebrate animals) in aquatic environments. We compared the effects of both nGO types and estimated the predicted no-effect environmental concentration (PNEC) values to determine their potential environmental risk. Our findings demonstrated the need for a complex ecotoxicity toolkit since the ecotoxicity results varied based on the test organism, the selected endpoints, and the test method used. Additionally, we found that toxicity effects were dependent on the concentration and characteristics of the specific nGO type used, as well as the exposure time. We estimated the PNEC values for GO AF 96/97 and GO PM 995 in the aquatic compartment to be 8 ng/L and 4 ng/L, respectively. Even after applying the worst-case scenario approach, the tested nGOs pose no environmental risk.

The Biolog EcoPlate™ Technique for Assessing the Effect of Metal Oxide Nanoparticles on Freshwater Microbial Communities.

The application of Biolog EcoPlate™ for community-level physiological profiling of soils is well documented; however, the functional diversity of aquatic bacterial communities has been hardly studied. The objective of this study was to investigate the applicability of the Biolog EcoPlate™ technique and evaluate comparatively the applied endpoints, for the characterisation of the effects of metal oxide nanoparticles (MONPs) on freshwater microbial communities. Microcosm experiments were run to assess the effect of nano ZnO and nano TiO2 in freshwater at 0.8-100 mg/L concentration range. The average well colour development, substrate average well colour development, substrate richness, Shannon index and evenness, Simpson index, McIntosh index and Gini coefficient were determined to quantify the metabolic capabilities and functional diversity. Comprehensive analysis of the experimental data demonstrated that short-term exposure to TiO2 and ZnO NPs affected the metabolic activity at different extent and through different mechanisms of action. TiO2 NPs displayed lower impact on the metabolic profile showing up to 30% inhibition. However, the inhibitory effect of ZnO NPs reached 99% with clearly concentration-dependent responses. This study demonstrated that the McIntosh and Gini coefficients were well applicable and sensitive diversity indices. The parallel use of general metabolic capabilities and functional diversity indices may improve the output information of the ecological studies on microbial communities.

Cyclodextrin-mediated quorum quenching in the Aliivibrio fischeri bioluminescence model system - Modulation of bacterial communication.

Bacterial Quorum Sensing is a cell-to-cell communication process, in which, bacteria, performing cooperative behaviour, produce and detect extracellular signalling chemicals, to monitor cell population density. Numerous bacterial processes including bioluminescence, virulence factor production, biofilm formation etc. are known to be influenced by this bacterial communication network. Interest in QS systems has emerged in response to the fact that these processes have significant impact on the environment, human health as well as agriculture. Cyclodextrins-mediated quorum quenching is an innovative approach and the available information about their effects is very scarce. We selected Aliivibrio fischeri, a bacterium, producing light, based on Quorum Sensing, to be the first to investigate the cyclodextrins' effect on this bioluminescence. A systematic study was performed with twelve different cyclodextrin compounds in order to determine their concentration- and time-dependent bioluminescence inhibitory effect in the A. fischeri model system. Especially high quorum quenching effect was found for α-cyclodextrin: 10 mM α-cyclodextrin at 120 min contact time which caused ~64% inhibition of bioluminescence. Experiments with the co-administration of α-cyclodextrin and N-(3-oxohexanoyl)-L-homoserine lactone, the signalling molecule of A. fischeri clearly showed, that the stimulating effect of this signal was diminished by α-cyclodextrin, suggesting, that complexation was responsible for the observed Quorum Sensing suppression. Although ß-cyclodextrin and its hydroxypropyl derivative significantly inhibited bioluminescence at as low as 0.156 mM concentration, their efficiency did not reach the level of α-cyclodextrin. According to our results, the autoinducer-dependent quorum sensing mechanism in Aliivibrio fischeri was markedly inhibited, the quorum quenching effect of cyclodextrins was clearly demonstrated. The efficiency was influenced by several parameters; the size of the interior cavity, the structure and the concentration of the cyclodextrins, as well as the contact time with the cells. The application of a cyclodextrin-trap for complexation of signal molecules may be a novel, promising method for influencing QS interfering strategies, for example, to enhance the efficiency of various biotechnologies, as well as to find alternative approaches against bacterial proliferation and infections. Furthermore, our results could also serve as a basis for further research with bacterial or plant model systems, in which the same chemical signals may induce physiological responses.