Microbial remediation of recalcitrant pollutants in soil and geo-environmental engineering systems

Polycyclic aromatic hydrocarbons (PAHs), petroleum hydrocarbons, chlorinated compounds, pesticides, pharmaceuticals, per- and polyfluoroalkyl substances and heavy metals are all examples of pollutants that are more difficult to degrade in the environment, are toxic, and persist in the environment for an extended period. Traditional remediation practices are often high-cost, high energy, and can have a negative impact on soil ecosystems. Microbial remediation has proven to be an emerging sustainable and eco-friendly technology using bacteria, fungi, actinomycetes, and microbial consortia to degrade, transform, immobilize, and/or detoxify contaminants through a variety of processes such as biodegradation, biosorption, bioaccumulation, biotransformation, biomineralization, co-metabolism, and biofilm-mediated processes. This review covers the types of pollutants that are recalcitrant, the microbial communities in the soil, and the most significant microbial processes associated with the remediation of recalcitrant pollutants. Additionally, the most important applications of geo-environmental engineering (GE) are critically discussed, including biostimulation, bioaugmentation, rhizoremediation, mycoremediation, microbially induced carbonate precipitation (MICP), and permeable reactive biobarriers. The factors affecting remediation effectiveness, advanced monitoring methods, existing challenges, and emerging innovations such as synthetic biology, engineered microbial consortia, nanobioremediation, and artificial intelligence are also pointed out. Microbial processes combined with geo-environmental engineering can be a promising way to restore the soil sustainably and to protect the environment for the long term.