Journal of Agronomy and Field Innovations

Background: Organic farming practices in the long run help preserve the health of soils by using fewer synthetic products and improving biological processes. Microbial communities in soils are essential for the proper working of an ecosystem because they facilitate nutrient cycling, carbon storage, and plant growth. Functional metagenomics allows researchers to describe the functional characteristics of microbes without the need to grow them.
Objective: The current research used shotgun sequencing in order to investigate the functional gene characteristics of microorganisms in soils of long-term organic farming practices (more than 15 years of organic farming) and conventional farming practices, concentrating on such features as nutrient cycling, carbon storage, and stress response.
Methods: Samples of soil from (0-15 cm in depth) were obtained from the long-term experimental field on organic and conventional systems of farming. The shotgun metagenomics has been carried out with the use of Illumina NovaSeq sequencing and HUMAnN3 and KEGG databases in order to quantify the activities of functional genes. Statistics were performed with the use of ANOVA, PCA, and PERMANOVA (P < 0.05).
Results: Organic farming land was found to have higher levels of nitrogen fixation (nifH 2.3 times greater), nitrification (amoA 1.8 times greater), and carbon degradation genes compared to conventional farming land. The pathways that support carbon sequestration processes are better equipped with enzymes. Furthermore, microbial functional diversity is higher in soils with organic farming practices (1.6-fold). The COG categories related to carbohydrate and energy metabolism are enriched in the functional metagenomics data.
Conclusion: Organic farming enables the building of the functional capacity of soil microbial systems achieved through improved nutrient cycling and carbon sequestration.