A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons

Simone Becarelli; Ilaria Chicca; Salvatore La China; Giovanna Siracusa; Alessandra Bardi; Maria Gullo; Giulio Petroni; David Bernard Levin; Simona Di Gregorio

doi:10.3389/fmicb.2021.647373

A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons

Front Microbiol. 2021 Jun 8:12:647373. doi: 10.3389/fmicb.2021.647373. eCollection 2021.

Authors

Simone Becarelli^{1

2}, Ilaria Chicca^{1

3}, Salvatore La China⁴, Giovanna Siracusa¹, Alessandra Bardi⁵, Maria Gullo⁴, Giulio Petroni¹, David Bernard Levin^{2

3}, Simona Di Gregorio¹

Affiliations

¹ Department of Biology, University of Pisa, Pisa, Italy.
² BD Biodigressioni, Pisa, Italy.
³ Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada.
⁴ Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy.
⁵ Department of Civil and Environmental Engineering, University of Florence, Florence, Italy.

Abstract

A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.

Keywords: Ciboria sp.; dye-decolorizing peroxidases DyP; functional metagenomic prediction; generalist bacterial species; mycoremediation; specialist bacterial species; total petroleum hydrocarbons.