The hydrocarbon-degrading bacteria and fungi in oil contaminated soils of Kazakhstan: microbiome composition, enrichment, isolation and bioremediation potential

Felix Müller, Haitao Wang, Anne Reinhard, Anel A. Omirbekova, Ramza Zh. Berzhanova, Togzhan D. Mukasheva, Tim Urich, Annett Mikolasch

2026

Full text Open access: Gold Metadata (CSL-JSON)
DOI 10.1186/s40793-026-00866-y
Data confidence 70 medium
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Abstract

BACKGROUND: Oil contamination in soils causes significant environmental impacts and risks to human health. Oil components can be naturally reduced by indigenous microorganisms, that are able to degrade such substrates. We used culture-independent and culture-dependent methods to examine the prokaryotic and the eukaryotic microbiome of different heavily oil contaminated soils in Kazakhstan. Bacteria and fungi were enriched and isolated from four soils contaminated with crude oil or hydrocarbons. Aliphatic, aromatic and condensed aromatic model hydrocarbons of crude oil and crude oil itself were used as substrates for the enrichment and the isolation experiments. The enrichment process was accompanied by culture-independent tests. RESULTS: The results of the Illumina sequencing of the contaminated soils and the enrichment cultures were compared with the results of the culture-dependent isolation and determination of bacterial, yeast and filamentous fungal strains. 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. CONCLUSION: In the end a complex overview of the indigenous microorganisms and their degradation ability of crude oil components emerged and demonstrates the great potential of bioremediation for Kazakhstan soils.