Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil

Abstract

This study investigated the impacts of crude oil, diesel, and gasoline on the diversity of indigenous microbial communities as well as culturable microorganisms in the studied soil. Oil contamination led to shifts in the diversity of the soil's microbial communities, regardless of the contaminant applied. Unpolluted soils were more diverse and evenly distributed than contaminated samples. The domain Bacteria accounted for 65.15% of the whole microbial community. The bacterial phylum Proteobacteria dominated in all samples, followed by Actinobacteria and Acidobacteria. Pseudomonas with 28.15% of reads dominated in Proteobacteria, while Rhodococcus (3.07%) dominated in Actinobacteria, and Blastocatella (2.53%) dominated in Acidobacteria. The dominant fungal phyla across all samples were Ascomycota dominated by Penicillium (50.48% of sequences), and Zygomycota dominated by Mortierella (16.87%). Sequences similar to the archaeal phyla, Euryarchaeota and Thaumarchaeota, were also detected. The number of culturable microorganisms increased following the contamination and was higher in contaminated samples than in clean samples. Oil contamination also resulted in the enrichment of oil-degrading strains. Two bacteria, Serratia marcescens strain PL and Raoultella ornithinolytica PS, which were isolated from crude oil-contaminated soil, exhibited strong crude oil degradation ability. Strain PL was the most efficient strain and degraded 75.10% of crude oil, while strain PL degraded 65.48%, after 20 days of incubation. However, the mixed culture of the two strains was more effective than single strain and could achieve up to 96.83% of crude oil degradation, with a complete abatement of straight-chain hydrocarbons (from C12 to C25), and more than 91% removal of highly branched hydrocarbons, phytane and pristane, which are known to be more recalcitrant to biodegradation. Strains PS and PL are two newly isolated crude oil degraders that are not among the most prominent crude oil-degrading strains referenced in the literature. Therefore, their high degradation capacity makes them perfect candidates for the bioremediation of petroleum hydrocarbon contaminated environments.

Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons

“…Furthermore, such enrichment of specific ASVs likely corresponds to the original presence of either crude oil or diesel. It was shown that different sources of PHCs varying in their chemical compositions were associated with different microbial communities, including PHC-degrading populations ( 55 – 58 ). It should be noted, though, that the soil texture also varied between the two contaminated soils ( 12 ), which may have contributed to different patterns of microbial succession as well.…”

Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage

“…Overall, microbial methods can be divided into culture-dependent and culture-independent approaches, each method with its own purpose and limitations (Van Hamme et al 2003;Knight et al 2018). As molecular technologies advanced, recent hydrocarbon biodegradation studies have focused on characterizing microbial diversity and potential hydrocarbon degraders through marker-gene sequencing (Bidja Abena et al 2020) and on characterizing high resolution taxonomy and function through determining which genes are present in a community through metagenomics and through determining which genes are expressed in a community through metatranscriptomics (Narasimhan et al 2016;Tremblay et al 2019). These metrics provide insight into biodegradation and bioremediation potential as the sequence data from natural unpolluted environments can be mined for known hydrocarbon biodegradative microorganisms and key hydrocarbon biodegradative genes.…”

Microbial community succession during crude oil-degrading bacterial enrichment cultivation and construction of a degrading consortium

“…Therefore, exploring the community succession of crude oil degrading bacteria enrichment culture and revealing the microbial community structure under enrichment culture will help to provide a reference for the construction of consortium in the selection of strains. With the development of high-throughput sequencing technology, the microbial diversity in crude oil-contaminated soil (Bidja Abena et al, 2020;Wang et al, 2020;Huang et al, 2021), water bodies (Harayama et al, 2004), and sediments (Chen et al, 2017) has been continuously described. However, the changes in the microbial community during the process of enrichment cultivation is poorly understood.…”