Microbiome-Based Framework for Achieving Simultaneous Efficient Transformation of Persistent Organic Pollutants and Restored Biogeochemical Cycling

Persistent organic pollutants (POPs), prevalent across diverse environmental matrices, are highly hazardous and recalcitrant compounds that can be transformed into low-toxicity compounds by diverse microorganisms. Many transformation processes of POPs could intricately interface with elemental biogeochemical cycles, which are fundamental drivers of ecosystem function. While microbial pathways of POPs transformation have been extensively studied, their integration into broader element turnover in the environment remains fragmented. Here, we review the relationship between POPs metabolism and biogeochemical cycles, spanning from single-species enzymatic coupling to multispecies syntrophic interactions. We contend that POPs transformation is not an isolated microbial event but is deeply embedded within elemental metabolism through direct mechanisms of electron transfer and cross-feeding, or indirect modulation of quorum sensing and mineral-interface interactions. Across levels from gene expression to community level-energy and material exchange, microorganisms in the environment mediate POPs transformation while maintaining elemental balance through dynamic metabolic regulation. Furthermore, we propose a strategic framework that leverages functional compensation and integrative strategies of native and engineered microbiomes to reinforce POPs degradation and coordinate element cycling. Future research should focus on integrating microbiome-based approaches with omics analyses, systems modeling, and ecological engineering. These efforts facilitate the predictable regulation of pollutant-element interactions, ultimately restoring ecosystem multifunctionality within POPs-contaminated sites.