Rhizosphere microbiome analysis of healthy and infected cumin (Cuminum cyminum L.) varieties from Gujarat, India

Abstract

Cumin (Cuminum cyminum L.; Jeera) is a popular herbal seed spice used in culinary preparation in India. Gujarat and Rajasthan are the largest producer states of cumin seeds from India, while India is also the largest supplier and exporter of cumin across the globe. However, production of cumin is suffering from loss of crop production due to the plant pathogen infections, especially from Fusarium oxysporium sp. Rhizomicrobiome is the key modulator of plant health, revitalizing nutrients and disease response against plant pathogens. The secretion of different metabolites such as root exudates plays an important role in host plant rhizosphere microbial interactions influencing the plant health, growth and development, nutrient acquisition, and disease resistance. Therefore, in this research study, we have examined the microbial diversity from the healthy and fungal infected rhizosphere samples of the three different Gujarat Cumin (GC-2, GC-3, and GC-4) varieties using 16S ribosomal RNA (rRNA) gene sequencing on Ion Torrent S5 sequencing platform. The findings revealed the major dominant family represented by Bacillaceae, Solibacteraceae, Nostocaceae, Paenibacillaceae, Scytonemataceae, and Halothiobacillaceae, while at genera level of taxonomic abundance were represented by Bacillus, Candidatus Solibacter, Synechococcus, Nostoc, Anabaena, and Oscillatoria. The research findings should enhance our understanding of healthy and infected plant rhizosphere microbiome for better crop productivity, disease resistance and management of the crop varieties against plant pathogens.

Keywords

• Rhizosphere
• Fungal infection
• Host plant pathogen
• Microbiome, Co-occurrence network
• Infection