Background: Arbuscular mycorrhizal fungí (AMF), especially Glomus intraradices (Rhizophagus irregularis), are a key component of sustainable agriculture because they enhance phosphorus uptake and improve soil structure as well as increase plant tolerance to biotic and abiotic stress. Nonetheless, limitations of traditional culture-dependent approaches have left the full metabolic and ecological potential of amf largely uncharacterized.
Methods: This research combines two metagenomic sequencing techniques—shotgun and amplicon-based—using Illumina, PacBio, and Oxford Nanopore sequencing technologies. Quality control pipelines were utilized to process the raw sequencing data and assemble the data together into a whole using metaSPAdes. Each metagenome was assessed in terms of its taxonomic classification with Kraken2, and in terms of its functional annotation using KEGG, Pfam, and CAZy databases. Multi-omics integration included the assessment of metagenomics, metatranscriptomics, and metabolomics, allowing for a more complete understanding of how the metagenome interacts with the environment and within an ecosystem.
Results: The study found 3 new gene variants of the phosphate transporter (GiPT1–3), 2 uncharacterized nitrogen assimilation pathways and 5 plant growth promoting genes not present in the reference genomes. The study also observed enhanced nutrient pools in plants (up to 47%) through the use of G. intraradices, Bacillus subtilis and Pseudomonas fluorescens together versus un-inoculated controls.
Conclusion: A thorough understanding of the functional capacity of G. intraradices-based biofertilizers is given by multi-omic integration. Results also indicated a decrease of approximately 25-40% in chemical phosphate fertiliser utilised and increased yield of wheat, maize, and legumes as well. This substantiates the potential to create next generation bio-fertilisers using precision agriculture principles and meeting the goal of global sustainbility.