Unraveling Complexity of Rhizosphere Microbiome Affecting on Quality of Crocus sativus

Abstract Saffron (dried stigmas of Crocus sativus) is an aromatic crop belonging to Iridaceae family. The microorganisms in soil are main factors affecting the production and quality of Crocus sativus. We have studied the microbial relationships between Saffron rhizosphere and quality indices of Crocus sativus (crocin, picrocrocin, and safranal) using a Metagenomic approach. It was found that despite the similar climatic conditions, the quality of Saffron in a region is higher than other regions. This can be related to different microbes in root zone or rhizosphere layer. The purpose was to investigate and compare soil microbiome rhizosphere compared to other regions, as a result, to identify the microbiome affecting the quality of Saffron. In this research, rhizosphere soil of different regions in Ghayen(Iran), the center of high quality Saffron, was firstly sampled during harvesting time. In the next step, soil DNA was extracted, and the 16srRNA gene sequence of each sample was identified based on the RNA-Seq method; finally, the microbiome of the samples was analyzed. The results indicated that beneficial bacteria such as Kosakonia, Enterobacter, Salmonella, Plesiomonas, Pasteurella, Lactococcus, and Mitsuaria have a significant impact on increasing Saffron quality. Such bacteria, which affect the quality of Crocus sativus, increase carbon source, nitrogen fixation, auxin synthesis, dissolved phosphate production, γ-Aminobutyric acid (GABA) production, increase the activity of antioxidant enzymes and increase plant growth stimulants; and can improve the quality of Saffron.