Oil degrading microbiome
Oil contamination in soils causes significant environmental impacts and risks to human health. However, there is still lack of efficient bioremediation approaches to remove the contaminants. Here, culture-independent and culture-dependent methods were used to examine the prokaryotic and the eukaryotic microbiome of different heavily contaminated soils in Kazakhstan. Bacteria and fungi were enriched and isolated from four soils contaminated with crude oil or hydrocarbons. Model hydrocarbons of crude oil such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkanes pristane and heptamethylnonane, the biaromatic compound biphenyl and the condensed aromatic substance anthracene were used as substrates for the enrichment and the isolation experiments. Furthermore, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and phenol and crude oil itself as enrichment substrates. The enrichment process was accompanied by culture-independent tests. At the end, the 110 isolated and taxonomically determined bacterial, yeast and filamentous fungal strains were compared with the results of the Illumina sequencing of the last enrichment cultures.  The majority of these 110 strains from 45 different genera belong to well-described hydrocarbon degraders like Bacilli and Rhodococci as well as to Achromobacter, Gordonia, Pseudomonas, Stenotrophomonas, Aspergillus, Exophiala, Fusarium, Meyerozyma, Penicillium and Trichoderma species. The most abundant species was the ascomycetal yeast Meyerozyma guilliermondii followed by strains of the bacterial genus Peribacillus. Furthermore, we combined the microbiome insights on the enrichment procedures and the isolation of bacteria, yeasts and filamentous fungi with the in-fact degradation potential of the isolated species based on substrate consumption and metabolite formation. In addition to the well-described hydrocarbon degraders, the utilization spectrum of less-studied strains of the genera Leifsonia, Neorhizobium, Purpureocillium, Rhodotorula and Sarocladium could be broadened, so that in the end a complex overview of the degradation of crude oil components emerged.