Microbial diversity and function during different bioremediation strategies of diesel-polluted soil

In numerous hydrocarbon-polluted sites, oxygen and pollutant bioavailability constitutes the main limiting factors for biodegradation because of the strong adsorption of hydrocarbons on organic soil particles (clay and peat). Therefore, several strategies such as biostimulation (with air/H2O2 and/or nutrients) or bioaugmentation are used, but often without understanding the endogenous microflora degrading capacity. This lack of differentiation between indigenous and added microorganisms could lead to poor predictability of the biodegradation efficiency. In addition, anaerobic degradation remains less applied in industrial settings for such compounds (especially for saturated hydrocarbons) as this process remains slow.
In this context, the main objective of our study was to understand how the bacterial community evolves, in terms of species and degrading gene diversities, during the application of three different bioremediation strategies in a heavily diesel-polluted clay soil: (i) anaerobic natural attenuation, (ii) bioventing and (iii) bioaugmentation with Rhodococcus erythropolis T902.1. In addition to the supply of new degrading genes, bioaugmentation with this biosurfactant-producing strain should facilitate the bioassimilation of desorbed hydrocarbons by the whole degrading microflora. This hypothesis is strengthened by previous results obtained during several microcosm- and pilot-scale experiments.
Aerobic and anaerobic microcosms were set up with three different soil samples coming from the same polluted site. Initially, their global organic content was identical but their hydrocarbon and peat concentrations were different, which led to differential oxygen consumption. Soils were sampled every 10 days to extract the DNA to measure changes in bacterial populations (with RISA analysis and 16S rRNA gene sequencing) and function (with qPCR and sequencing of degrading genes). Further analyses of the hydrocarbon content by GC-MS and of the genetic diversity by MiSeq metagenomic analysis provided detailed chemical and functional microbial data related to compound degradation and relative gene increases. Initial results showed significant differences in the microbial community structure. Moreover, Rhodococci seem to be maintained in the soil after inoculation.