A metagenomic approach to predict the role of microbiome in a plant-microbe system for degrading the model azo dye methyl red.

Azo dye contamination poses significant environmental challenges due to its persistence and toxicity. Plant-microbe integrated systems offer a sustainable solution for dye bioremediation, yet the functional roles of microbial communities and their interactions within community and with host plants during bioremediation remain underexplored. This study presents an integrated, multi omics approach to dissect the microbial diversity, functional potential, and plant-microbe interactions within a plant-microbe integrated bioremediation system for model azo dye, methyl red degradation. The microbial diversity of various organisms enriched under different treatment conditions for effective azo dye treatment was explored. A read-based approach using HUMAnN 3 pipeline was adopted to extract metabolic information from the shotgun metagenomic reads. Diversity analysis showed the enrichment of microorganisms capable of growing in the presence of the pollutant methyl red in an oligotrophic condition. The metabolic potential of the enriched organisms in dye removal was studied. Based on the enzymatic abundance, a pathway for the degradation of methyl red is proposed. Endophytic bacteria such as Klebsiella pneumoniae and Klebsiella varicola were responsible for encoding major dye-degrading enzymes in plant-integrated systems. In the plant-microbe integrated system both endophytic and intestinal microorganisms such as Kluyvera intestini and Escherichia coli are among the top 5 contributors of genes encoding downstream aromatic compound degradation enzymes. Notably Enterococcus casseliflavus showed highest enzyme abundance for azobenzene reductase in plant -microbe integrated strategy with 11.5-fold greater abundance than the treatment system containing only microbial inoculum. Metabolomics data from root exudates experiment revealed the role of root exudates in selective recruitment of microbial community. The role of biofilm and quorum sensing pathways in enhancing the bioremediation potential of the microbiome and the potential microbe-microbe and plant-microbe interaction was analysed. Deciphering the metabolic contribution of each microorganism and the microbiome as a whole is crucial to design engineered bioremediation systems. ENVIRONMENTAL IMPLICATIONS: Understanding the potential of microorganisms, their enrichments, and survival will help in designing specific consortia for effective degradation of pollutants. Metagenomic analysis reveal that the functional complementation in the microbiome is responsible for the pollutant degradation and the presence of plants through the root exudates, provide the nutrients lacking in the oligotrophic conditions observed in many waste streams, thereby enriching suitable microorganisms. This metagenomic study along with the metabolomics component, provides the justification for the efficiency of the plant microbe treatment of model dye methyl red and this could be exploited in real time situations.