The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.

Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating pollution. This study aimed to determine individual cultures’ and a strain mixture’s ability to utilize alkanes (single alkanes and crude oil). The proper study of pure cultures is necessary to design synergistically working consortia. The Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13 strains isolated from a wastewater treatment plant of a crude oil refinery can grow in media containing various aromatic and aliphatic hydrocarbons. The genome of the strain ICP1 contains four genes encoding alkane hydroxylases, whose transcription depended on the length of the alkane in the media. We observed that the hydrophobic cells of the strain ICP1 adhered to hydrophobic substrates, and their biofilm formation increased the bioavailability and biodegradation of the hydrocarbons. Although strain ICTN13 also has one alkane hydroxylase-encoding gene, the growth of the strain in a minimal medium containing alkanes was weak. Importantly, the growth of the mixture of strains in the crude oil-containing medium was enhanced compared with that of the single strains, probably due to the specialization in the degradation of different hydrocarbon classes and co-production of biosurfactants.

Background: The utilization of Pseudomonas putida was explored in this study as a promising approach for lignin valorization. To this end, dry hydrolysis lignin was used as a feedstock for the first time. Hydrolysis lignin is a product of the enzymatic hydrolysis and separation of cellulose and hemicellulose from the lignin backbone in diverse lignocellulosic sources. Various fractionation techniques were applied to obtain lignin monomers and multimers in solution for use as a growth medium for P. putida , whose tolerance of inhibitory phenolic compounds distinguishes it from most bacteria. Results: Physiological evaluations revealed that Pseudomonas putida strains KT2440 and PaW85 exhibited broad pH tolerance ranges, with robust growth observed at elevated pH levels. Batch fermentations using hydrolysis lignin (HL) solutions showed complete consumption of sugars within 24 hours, demonstrating the viability of fractionated HL as a substrate for P. putida cultivation. HPLC analysis of HL monomer concentrations during simulated fed-batch fermentation revealed rapid catabolism of catechol and increased CCMA concentration, followed by stabilization, indicating that CCMA is synthesized more quickly than degraded when the initial catechol concentration is high. Filtered alkaline HL fractionations yielded more than twice as much catechol as unfiltered fractionations. Screening of indigenous bacterial strains isolated from various soil and water samples (CELMS Collection, website http://eemb.ut.ee ) identified five new candidate strains for CCMA production, two for PCA production, and three for vanillic acid production. Conclusions: The novel use of fractionated hydrolysis lignin as a growth medium shows potential for lignin valorization and chemical production. Filtered alkaline fractionation yields more catechol and is superior for cis,cis -muconic acid production; however, unfiltered fractionations may be more suitable for other compounds and upscaling. Further investigation of screened strains could reveal more efficient enzymes, which could be optimized and transformed into P. putida in future research.