Two Decades of Rhizosphere Microbiome Research under Sewage Sludge Amendment: From Petri Dishes to High-Throughput Sequencing (2006–2026)

Recycling organic waste in agriculture is a pivotal process to maintain soil fertility, as it contributes to providing plants with nutrients, improving the physical structure and chemical properties of soils, and enhancing their biological activity, but the impact of these residues varies according to climate, soil type, and waste treatment, especially in light of the increase in environmental pollutants resulting from human activities such as industrial chemicals, pesticides, and sewage waste over the past two decades. In 2006, the original study relied on traditional planting and counting methods to detect six microbial groups in the roots of bean and winter wheat crops, grown in forest soils mixed with biomaterials of different proportions and concentrations. and metagenome, metatranscriptome) along with qPCR technology to measure the density of functional genes. Recent findings confirm the findings of a 2006 study on increasing the abundance and activity of microorganisms, while revealing new dimensions such as the presence of antibiotic resistance genes in sludge-treated soils. The study relied on the analysis of 28 peer-reviewed papers published between 2015 and 2026, according to specific criteria including the use of modern sequencing or qPCR techniques, the presence of control samples, and conducting experiments in realistic agricultural environments. The study aims to provide an objective comparison between traditional and modern methods, and to propose a practical framework that integrates them, in order to contribute to the development of safer and more sustainable sludge management, environmental protection, crop safety, and food security.