Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

Abstract

The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60–70%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50–70% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11–46%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4–9.0%), Pusillimonas (0.7–2.3%), and Bradyrhizobium (0.8–1.8%) did possess genes involved in aliphatic or aromatic compound degradation.

Crude oil induces plant growth and antioxidant production in Leersia hexandra Sw. A hydrophytic grass that rhizodegrades oil in Tabasco, Mexico.

“…Lh also has a rhizosphere colonized by hydrocarbonoclastic bacteria and fungi (González-Moscoso et al 2019). The adaptation of these microorganisms to the presence of crude oil suggests the presence of genes related to hydrocarbon degradation similar to those found in the bacteria Pusillimonas, Dietzia, Bradyrhizobium, Azospirillum, and Azotobacter (Arias-Trinidad et al 2017; Wang et al 2021). When associated with the roots of Lh, these bacteria stimulate the removal of TPH from the soil (Orocio-Carrillo et al 2019).…”

Biotreatment of oily sludge by a bacterial consortium: Effect of bioprocess conditions on biodegradation efficiency and bacterial community structure

“…compared to other AK6 members, this assumption might appear contradictory to the general belief assigning most abundant community members as the most influential in pollutant degradation process. However, this does not have to be always the case and some studies reported a crucial role of the so-called “rare biosphere” or “conditionally rare taxa” in pollutants biodegradation ( Wang et al, 2017 , 2021 ; Xu et al, 2018 ; Pascoal et al, 2020 ).…”

Comparative evaluation of bacterial and fungal removal of indoor and industrial polluted air using suspended and packed bed bioreactors.

“…Hydrogenophaga, Hyphomicrobium and Dokdonella have been linked before to the treatment of alkanes and also of complex hydrocarbons (Pascual et al, 2020;Rojas-Gätjens et al, 2020). Moreover, it has been recently discovered that members of the family Phyllobacteriaceae have the necessary genes for the metabolism of complex alkanes (Wang et al, 2021).…”