‘OMICS’ Studies on Rhizosphere-Microorganism Interactions in Soils

Soil is an ecosystem in which millions of microorganisms live and interact with plant roots. It has phytoremediation properties, sequestering pollutants such as heavy metals (cadmium, lead, and sulfur, among others), microplastics, and a great diversity of products of anthropogenic origin. Recently, the indiscriminate discharge of pharmaceuticals into public sewage systems has become a major concern, resulting in a public health problem due to the multi-resistance of clinically important bacteria and fungi to these pharmaceuticals. Similarly, the constant use of soil for agriculture, as well as the application of pesticides to combat economically important pests, has damaged both the native soil microbiome and impoverished both the biotic and abiotic properties of the soil. This issue is further exacerbated by the detrimental effects of global climate change. This has led to the search for methods to detoxify soils and reduce the deleterious effects of pollutants. Thus, omics tools, such as metabolomics, metagenomics, proteomics, genomics, and transcriptomics, detect the presence of these pollutants and develop detoxification strategies. For example, in soils exposed to copper (Cu), the earthworm Eisenia fetida induces metabolites such as pyruvic acid. In China, the restoration of black soils is possible due to the metabolomic profiling of 287 detected metabolites, which permitted the identification of specific biomarker metabolites that serve for the restoration of degraded soil. Thus, omics tools have become indispensable for the monitoring, diagnosis, and remediation of soils with a high rate of alteration due to anthropogenic activities.