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Plant-Microbe-Interaction in the nitrification process


Supervisor: Wolfram Weckwerth

PhD student: Arindam Ghatak

Group: Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology






Plant-Microbe-Interaction in the nitrification process – root exudate characterization

The rhizosphere is the narrow zone of soil specifically influenced by the "hidden" part of the plant, the root system. It is a complex, dynamic and highly interactive microenvironment where a number of arthropods, protists, fungi but also microbes like bacteria and archaea fluctuate from thousands to millions in number. Accordingly, the interactions between roots and soil microbes are highly specialized and based on co-evolutionary strength. In the rhizosphere, plant-microbe interactions play important roles in vital ecosystem processes, such as carbon sequestration and nutrient cycling. Biological processes of plant root exudates within the rhizosphere plays an important part in plant development. Recent research suggests that plant root exudates can inhibit nitrification in the soil. Regulation of the nitrification is an important strategy to improve nitrogen (N) recovery and N-use efficiency in agriculture system where the loss of N following nitrification is significant. Root exudates are an important source of nutrients for microorganisms in the rhizosphere. A number of cereals and legumes were tested for BNI activity in their root exudates. Among the tested cereal and legume crops, sorghum [Sorghum bicolor (L.)], pearl millet [Pennisetum glaucum (L.)] and groundnut [Arachis hypogaea (L.)] have shown detectable BNI activity in root exudates. We have characterized the root exudates collected from pearl millet under drought stress condition. In this study, we identified compounds from the tolerant (cv. ICTP8203) and sensitive (cv. 843-22B) cultivars using HPLC/UV. The harvested roots were cleaned in order to remove soil particles and incubated in distilled water for 2 days in 4 °C in airtight glass bottles to limit O2 levels. The aqueous solution was concentrated to near dryness and dissolved in methanol, water and HCl mixture for the HPLC measurement. The chromatograms showed significant peaks of polyphenols, flavonoids and lignans which were abundant in the root exudates. With the same extracts and based on HPLC/UV identifications, further primary metabolites (GC-MS) and secondary metabolites with LC-MS was performed. In total, we have identified ~80 primary metabolites in all the control and stress samples. Moreover, the samples were also measured for the analysis of secondary metabolites in both positive and negative mode in the LC system, which gave us some very interesting candidates for further validation. We have also provided the same extracts for the BNI measurement in JIRCAS Japan, our collaborator who will be looking at the biological nitrification process in pearl millet root exudates. This analysis will give us a complete characterization of the pearl millet root exudates under normal and stress condition and also provide a significant result on how good the pearl millet root exudates can help in the biological nitrification process. Further, we will also look into the NUE (nitrogen use efficiency) of pearl millet under drought stress. This collaborative research aims to demonstrate significant and substantial genotypic variability in BNI capacity of pearl millet. It will also determine whether environmental constraints such as heat and drought influence the occurrence of BNI - and thus its potential use for agriculture in different pedoclimatic conditions. 


Co-Supervision: Silvia Bulgheresi, Gerhard Herndl

International collaborator: Subbarao, JIRCAS, Japan International Research Center for Agricultural Sciences

Please find a list of publications here.

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