Metatranscriptomics of microbial biofilm succession on HDPE foil: uncovering plastic-degrading potential in soil communities

Abstract

Background Microbial communities in soil are a complex and sensitive system which secures soil health, nutrient cycling and the degradation of natural and xenobiotic substances. Even though plastic pollution is increasing worldwide, very little is known about microbial processes that take place once plastic debris gets incorporated into the soil matrix. In this study, we conducted the first metatranscriptome analysis of polyethylene (PE)-associated biofilm communities in a highly polluted landfill soil and compared their gene expressions to those of a forest soil community within a 53-day period.Results Our findings indicate that the microbial population present in soil contaminated with plastic debris carries a predisposition to both inhabit and degrade plastic surfaces. Surprisingly, the microbial community from an undisturbed forest soil contained a diverse array of plastic-associated genes (PETase, alkB etc.), indicating the presence of an enzymatic machinery capable of plastic degradation. Plastic-degrading taxa were upregulated in the early stages of biofilm and the PE-degrading enzymes alkB1/alkM and transporters such as FadL, livG, livF, livH and livM and fatty acid β-oxidation pathway were active during the maturation of the biofilm. We also found an increase in nitrogen fixation genes in the plastic soil community (but not in forest soil), indicating an essential metabolic adaptation of biofilm communities in the plastisphere.Conclusion With this study, we address the underlying patterns of gene expression during biofilm development of a PE-associated plastisphere in soil and address the pressing question whether or not natural microbial communities carry the potential to biodegrade petrochemical-based plastic in the (soil) environment.

Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach

“…In addition to metagenomics, metatranscriptomics would be a useful method, as it indicates the expression of enzymatic machinery capable of plastic degradation. By applying metatranscriptomics to PE films, McLean et al [11] found a variety of plastic-associated genes (e.g. PETase), indicating the presence of potential enzymes for plastic degradation.…”

“…There are many ways to find microbial enzymes that are potentially active in plastic degradation [8][9][10]. The most recently applied and innovative way to find an enzymatic machinery capable of plastic degradation is through metagenomics or metatranscriptomics [11]. While shotgun metagenomics extracts DNA from all cells in a community and then cuts it into tiny fragments that are sequenced independently [12], metatranscriptomics provides information about genes expressed by the community as a whole [13].…”