Crude oil-derived hydrocarbons constitute the largest group of environmental pollutants worldwide. The number of reports concerning their toxicity and emphasizing the ultimate need to remove them from marine and soil environments confirms the unceasing interest of scientists in this field. Among the various techniques used for clean-up actions, bioremediation seems to be the most acceptable and economically justified. Analysis of recent reports regarding unsuccessful bioremediation attempts indicates that there is a need to highlight the fundamental aspects of hydrocarbon microbiology in a clear and concise manner. Therefore, in this review, we would like to elucidate some crucial, but often overlooked, factors. First, the formation of crude oil and abundance of naturally occurring hydrocarbons is presented and compared with bacterial ability to not only survive but also to utilize such compounds as an attractive energy source. Then, the significance of nutrient limitation on biomass growth is underlined on the example of a specially designed experiment and discussed in context of bioremediation efficiency. Next, the formation of aerobic and anaerobic conditions, as well as the role of surfactants for maintaining appropriate C:N:P ratio during initial stages of biodegradation is explained. Finally, a summary of recent scientific reports focused on the removal of hydrocarbon contaminants using bioaugmentation, biostimulation and introduction of surfactants, as well as biosurfactants, is presented. This review was designed to be a comprehensive source of knowledge regarding the unique aspects of hydrocarbon microbiology that may be useful for planning future biodegradation experiments. In addition, it is a starting point for wider debate regarding the limitations and possible improvements of currently employed bioremediation strategies.

Surfactants not only are widely used in biotechnological processes but also constitute significant contaminants of the modern world. Among many reports, there is a shortage of works which summarize the issue of surfactant sorption to biomass in a way that would elucidate the biological factors for analysts and analytical factors for microbiologists. The main factor, which is not as obvious as one would expect, is associated with the susceptibility of analytical approaches to errors resulting from incorrect handling of biomass. In case of several publications reviewed in the framework of this study, it was not possible to establish whether the decrease of the analytical signal observed by the authors actually resulted from biodegradation of the surfactant. This review emphasizes the necessity to consider the possibility of surfactant sorption to microbial cells, which may result in significant detection errors as well as conceptual inconsistency. In addition, a reference study regarding representative surfactants (cationic, anionic and non-ionic) as well as yeast, Gram-negative, Gram-positive bacteria, and activated sludge was provided to highlight the possible errors which may arise from disregarding sorption processes when determining degradation of surfactants. This particularly applies to systems which include ionic surfactants and activated sludge as sorption may account for 90% of the observed depletion of the surfactant. Therefore, a systematic approach was proposed in order to improve the credibility of the obtained results. Finally, the need to employ additional procedures was highlighted which may be required in order to verify that the decrease of surfactant concentration results from biodegradation processes.

Little is known about the effect of ionic liquids (ILs) on the structure of soil microbial communities and resulting biodiversity. Therefore, we studied the influence of six trihexyl(tetradecyl)phosphonium ILs (with either bromide or various organic anions) at sublethal concentrations on the structure of microbial community present in an urban park soil in 100-day microcosm experiments. The biodiversity decreased in all samples (Shannon's index decreased from 1.75 down to 0.74 and OTU's number decreased from 1399 down to 965) with the largest decrease observed in the microcosms spiked with ILs where biodegradation extent was higher than 80%. (i.e. [P66614][Br] and [P66614][2,4,4]). Despite this general decrease in biodiversity, which can be explained by ecotoxic effect of the ILs, the microbial community in the microcosms was enriched with Gram-negative hydrocarbon-degrading genera e.g. Sphingomonas. It is hypothesized that, in addition to toxicity, the observed decrease in biodiversity and change in the microbial community structure may be explained by the primary biodegradation of the ILs or their metabolites by the mentioned genera, which outcompeted other microorganisms unable to degrade ILs or their metabolites. Thus, the introduction of phosphonium-based ILs into soils at sub-lethal concentrations may result not only in a decrease in biodiversity due to toxic effects, but also in enrichment with ILs-degrading bacteria.

Herbicidal ionic liquids (HILs) constitute a new concept in crop protection products. Their main advantage is the potential to combine the efficiency of traditional herbicides with low vapour pressure and adjustable water solubility which leads to improved environmental safety in the agricultural sector. Among many strategies to obtain new HILs, esterquats seem to be well suited for modification since both the cation and anion may be constituents of herbicides. In the framework of this study 16 new esterquat HILs were synthetized based on standard herbicides: 2,4-D, MCPA, MCPP, 4-CPA, Clopyralid and Dicamba. Germination tests performed on agricultural soil using cornflower indicated the best two HILs. Furthermore, analysis of the toxicological effects of HILs on wheat plants revealed an additional advantage of the two selected HILs. The glutathione (GSH) content and glutathione S-transferase (GST) activity showed a lower oxidative stress level in wheat plants treated with examined HILs, respectively, in comparison to a mixture of reference compounds. Finally the Ames test was applied in order to analyse the mutagenic activity of the two selected HILs.