Molecular insights into plant–microbe interactions for sustainable remediation of contaminated environment

[Display omitted] •Plant-microbe interaction studies provides information for rhizosphere engineering.•Metaomics approaches useful in categorizing potential plant–microbe consortia.•Plant-microbes partnerships dealing to tackle organic and inorganic pollutants.•Examples of improved phytoremediation by omics application are discussed.•Improved clean-up of environmental pollution with new biotechnological tools. The widespread distribution of organic and inorganic pollutants in water resources have increased due to rapid industrialization. Rhizospheric zone-associated bacteria along with endophytic bacteria show a significant role in remediation of various pollutants. Metaomics technologies are gaining an advantage over traditional methods because of their capability to obtain detailed information on exclusive microbial communities in rhizosphere of the plant including the unculturable microorganisms. Transcriptomics, proteomics, and metabolomics are functional methodologies that help to reveal the mechanisms of plant–microbe interactions and their synergistic roles in remediation of pollutants. Intensive analysis of metaomics data can be useful to understand the interrelationships of various metabolic activities between plants and microbes. This review comprehensively discusses recent advances in omics applications made hitherto to understand the mechanisms of plant–microbe interactions during phytoremediation. It extends the delivery of the insightful information on plant-microbiomes communications with an emphasis on their genetic, biochemical, physical, metabolic, and environmental interactions.