PANOMICS at the interface of root–soil microbiome and BNI

Understanding the complex nature of root exudate and soil microbiome interaction at the root–soil interface has greatly intensified recently. Biological nitrification inhibition (BNI) can help to reduce excess nitrogen leaching into the outer soil layers, improving nitrogen use efficiency (NUE) and reducing the negative impact of excess nitrogen fertilization on the environment. Single omics analysis will not help understand complex interactions at the root–soil interface. Instead, a PANOMICS approach can determine the spatiotemporal dynamics of root exudates and microbiome. Root exudates mediate plant–microbe interactions, facilitating nutrient uptake and specifically inhibiting soil nitrification, thereby reducing our dependency on fertilizer. Metabolomics of root exudates is widely studied in different crops and germplasm under diverse environmental conditions; combining this with rhizosphere microbiota metabolomics is an upcoming trend. Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome–root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses. Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome–root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses. efforts taken naturally or artificially to maintain the soil composition, soil fertility, root composition, root exudate compounds, and soil microbes. a natural ability of some plants and few crop species to release inhibitors from their roots that block the nitrification process, thus reducing soil nitrification, nitrous oxide (N2O) emission, and N leaching. the biological process of reduction of nitrate (NO3–) into nitrite (NO2–), followed by the reduction of nitrate into nitrogen (N) gas, which mainly results in the release of nitrogen to the air. panomics data and dynamical systems modeling are integrated for a holistic and causal understanding of the genotype–phenotype relation in an environmental context. nonreactive nitrogen gas is hydrogenated to produce biologically available ammonia (NH3), also known as the artificial nitrogen fixation method. a biological activated (bacteria and archaea) process of oxidation of ammonia (NH3) into nitrite (NO2–), which is then followed by the oxidation of nitrite into nitrate (NO3–). the loss of soluble nitrate (NO3–) from the soil, usually through excess water, below the root zone, from where it enters the deeper layer contaminating the groundwater. integrating single omics platforms (such as genomics, transcriptomics, proteomics, metabolomics, etc.) to understand complex systems. nutrients, exudates, border cells, and mucilage, released by the plant roots, that attract microbes. the area of soil surrounding the root, where the chemical communication between the root exudates and the soil microbes occurs. naturally occurring compounds (primary and secondary metabolites) released from the roots of the plants in the nearby soil (rhizosphere), setting up a communication between plant and soil microbes. a method that is environmentally beneficial for farming and allows the production of crops without damage to natural systems or humans. an interdisciplinary approach that uses the biomathematical models to conceptualize dynamic processes, to predict responses to new conditions, and to understand and optimize the plants’ life cycle.