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.

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.

The extensive use of engineered nanomaterials, such as graphene oxide (GO), is stimulating research about its potential environmental impacts on the aquatic ecosystem. This study is aimed to comprehensively assess the acute toxicity of a well-characterized GO suspension to Daphnia magna. Conventional ecotoxicological endpoints (lethality, immobilization) and more sensitive, sublethal endpoints (heartbeat rate, feeding activity, and reactive oxygen species (ROS)) production were used. The possible normalization of the heartbeat rate and feeding activity in clean test medium was also investigated. The fate, time-dependent, and concentration-dependent aggregation behaviour of GO was followed by dynamic light scattering, UV-Vis spectroscopy, and zeta potential measurement methods. The EC₂₀ value for immobilization was 50 mg/L, while, for physiological and behavioural endpoints, it ranged from 8.1 mg/L (feeding activity) to 14.8 mg/L (immobilization). The most sensitive endpoint was the ROS production with EC₂₀ = 4.78 mg/L. 24-h recovery experiments revealed that feeding activity was restored only up to a certain level at higher concentrations, indicating that the potential environmental health effects of GO cannot be neglected. Alterations of normal physiology (heart rate) and feeding activity may be associated with increased risk of predation and reproductive decline, highlighting that GO may have impacts on population and food web dynamics in aquatic ecosystems.

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 β-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.