Environmental biotechnology offers several promising techniques for the rehabilitation of polluted environments. The modern industrialized world presents novel challenges to the environmental sciences, requiring a constant development and deepening of knowledge to enable the characterization of novel pollutants and a better understanding of the bioremediation strategies as well as their limiting factors. The success of bioremediation depends heavily on the survival and activities of indigenous microbial communities and their interaction with introduced microorganisms. The majority of natural microbiomes remain uncultivated; therefore, further investigations focusing on their intrinsic functions in ecosystems are needed. In this review, we aimed to provide (a) a comprehensive overview of the presence of viable but nonculturable bacteria and yet-to-becultivated cells in nature and their diverse awakening strategies in response to, among other factors, signalling extracellular metabolites (autoinducers, resuscitation promoting factors, and siderophores); (b) an outline of the trends in isolating unculturable bacteria; and (c) the potential applications of these hidden players in rehabilitation processes. Keywords Uncultured bacteria Á Viable but nonculturable bacteria Á Bacterial resuscitation Á Environmental application of VBNC bacteria Á Exploitation of microbial metabolic potential

Rhodococcus erythropolis PR4 is able to degrade diesel oil, normal-, iso-and cycloparaffins and aromatic compounds. The complete DNA content of the strain was previously sequenced and numerous oxygenase genes were identified. In order to identify the key elements participating in biodegradation of various hydrocarbons, we performed a comparative whole transcriptome analysis of cells grown on hexadecane, diesel oil and acetate. The transcriptomic data for the most prominent genes were validated by RT-qPCR. The expression of two genes coding for alkane-1-monooxygenase enzymes was highly upregulated in the presence of hydrocarbon substrates. The transcription of eight phylogenetically diverse cytochrome P450 (cyp) genes was upregulated in the presence of diesel oil. The transcript levels of various oxygenase genes were determined in cells grown in an artificial mixture, containing hexadecane, cycloparaffin and aromatic compounds and six cyp genes were induced by this hydrocarbon mixture. Five of them were not upregulated by linear and branched hydrocarbons. The expression of fatty acid synthase I genes was downregulated by hydrocarbon substrates, indicating the utilization of external alkanes for fatty acid synthesis. Moreover, the transcription of genes involved in siderophore synthesis, iron transport and exopolysaccharide biosynthesis was also upregulated, indicating their important role in hydrocarbon metabolism. Based on the results, complex metabolic response profiles were established for cells grown on various hydrocarbons. Our results represent a functional annotation of a rhodococcal genome, provide deeper insight into molecular events in diesel/hydrocarbon utilization and suggest novel target genes for environmental monitoring projects.

The alkane (pristane) degradation capacity o f Rhodococcus erythropolis PR4 (NBRC 100887), isolated from marine environment, was previously observed. In this study, the ability of this strain for biodegradation of various animal fats, such as pig lards and poultry fats as well as butter, margarine and sunflower cooking oil was studied. Bioconversion of fats and oil was determined as methyl-ester (FAME) derivatives by GC-MS. R. erythropolis PR4 strain could utilize all substrates tested but the bioconversion rate and efficacies varied. The optimum pH for decomposition of pig lard and poultry fat was 8.5, respectively. Addition of carbonate to the media dramatically improved the efficiency o f the process via stabilization of pH o f the fermentation. Biotransformation of poultry fat was complete in four days and around 80% conversion was reached in the case of pig lard in media containing carbonate. The extracellular lipase activity of the R. erythropolis PR4 strain was also demonstrated by various techniques. The results suggest the R. erythropolis PR4 strain studied is a promising candidate in bioremediation/bioconversion of fatcontaining wastes within a relatively short time.