Glyphosate-microbial interactions: metagenomic insights and future directions

Glyphosate [N-(phosphonomethyl) glycine] is the most widely used systematic non-selective herbicide worldwide. However, there is increasing concern about its potential impacts on soil microbial communities, which play crucial roles in maintaining soil functions, plant health, and crop productivity. While glyphosate can be inactivated in soil through strong sorption, desorption remains a significant challenge as glyphosate residues and metabolites can exert toxicity effects on agroecosystems, particularly by altering microbial diversity and functionality. This review synthesizes current knowledge on glyphosate's behavior in soils and advancements in metagenomics approaches (including their limitations) to better understand the complex interactions between glyphosate and microbial communities in genetically modified (GM) cropping systems. Glyphosate has demonstrated antimicrobial properties, inhibiting the growth of various bacteria and fungi. Conversely, other studies suggest that glyphosate may enhance microbial richness, promoting the proliferation of potential glyphosate degraders (e.g., Bacillus, Stenetrophomonas, Pseudomonas, Sphingomonas, and Phenylobacterium) and N₂ fixing bacteria (e.g., Bradyrhizobium, Rhizobium, and Devosia) in the bulk soil and rhizosphere of GM crops. These contrasting findings are influenced by factors such as soil types, glyphosate rates, and crop varieties. Moreover, the review highlights that methodological discrepancies, including variations in next-generation sequencing (NGS) platforms and reference databases, contribute significantly to inconsistencies in the literature. These differences stem from varying levels of accuracy or annotation standards in the databases and NGS technologies used. To address these challenges, this study underscores the need for standardized molecular and bioinformatics approaches. Integrating advanced long-read sequencing technologies, such as Oxford Nanopore and PacBio, with compatible reference databases could provide more accurate and consistent analyses of microbial community composition at finer taxonomic levels. Such advancements could improve our understanding of how glyphosate influences the balance between pathogenic microorganisms and plant-growth-promoting microbes in GM cropping systems, ultimately informing sustainable agricultural practices.