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Abstract
Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources. Bacterial isolates belonging to Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps. were isolated for their capacity to utilise diesel oil, bitumen, pyrene, anthracene, dibenzothiphene, and their mixture as sole carbon sources. Pseudomonas, Arthrobacter, Achromobacter and Microbacterium sps. showed plant growth promoting activity, producing indole-3-acetic acid and expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. In parallel to the culturomic approach, in the microbial community of interest, bacterial community metabarcoding and predictive functional metagenomic analysis were adopted to confirm the potentiality of the isolates in terms of their functional representativeness. The combination of isolation and molecular approaches for the characterisation of a TPH contaminated soil microbial community is proposed as an instrument for the construction of an artificial hydrocarbonoclastic microbiota for environmental restoration.
Highlights
In the last century, the development of chemical and petrochemical industries resulted in the production of a variety of xenobiotics, such as solvents, fuels, plastics, and other organic pollutants, which were recalcitrant to biodegradation and persistent in the environment
The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources
After screening of the different morphotypes by amplified ribosomal DNA restriction analysis (ARDRA) analysis, 3 out of the 18 operational taxonomic units (OTUs) were capable of utilising each carbon source and their mixture as sole carbon sources, and the corresponding 16S rDNAs were sequenced for taxonomic identification (Table 2)
Summary
The development of chemical and petrochemical industries resulted in the production of a variety of xenobiotics, such as solvents, fuels, plastics, and other organic pollutants, which were recalcitrant to biodegradation and persistent in the environment. This persistence leads to the natural selection of microorganisms able to transform TPH. These microorganisms might be considered as “extremophiles”, adapted to live in extreme environments, characterised by high toxicity to most living organisms. The biodegradation of contamination should achieve its transformation and eventual mineralisation [3], and the “re-shaping” of the soil as a matrix, offering ecosystem services [4,5]
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