Organic amendments enhance crop yield by improving rhizospheric microbiome diversity

Rhizosphere associated plant microbiome plays an important role in nutrient acquisition, plant growth promotion, and stress tolerance. Abundance and diversity in the rhizospheric microbiome, which is host specific, has been correlated with plant productivity. In addition to host specificity, it is largely affected by use of agro-chemicals during crop cultivation. In this study, the effect of organic biostimulant viz., Soil Rejuvenator HPP-P3 on the rhizospheric bacterial community was analyzed in three crops viz. Cotton, Soybean, Turmeric and Pigeon pea using full length 16S rRNA gene amplicon sequencing. The crops were grown at the same location to avoid environmental factors affecting soil microbiome composition. This comparative metagenomics study revealed that the organic amendment improves crop specific rhizospheric bacterial communities with respect to its composition and abundance of dominant species. Overall, Proteobacteria, Firmicutes, Acidobacteria & Bacteroidetes were found to be the most dominant bacterial phyla collectively constituting more than 85% of total bacterial diversity of every rhizospheric soil. As compared to control plots the rhizospheric microbiome composition varies significantly in treatment plots as indicated by differential taxa abundance at every level of taxonomic hierarchy viz. Phylum, Class, Order, Family, Genus and Species. Interestingly, there is differential abundance of dominating bacterial genera specific to each crop, suggesting selective enrichment of microbes at rhizosphere depending on host plant physiology. Nitrospora, Sphingomoans and Gemmata were the top three genera dominating in cotton rhizosphere as compared to control plot. In case of Pigeon pea Vicinamibacter, Pseudomonas and Peribacillus were selectively enriched bacteria genera as compared to control plot. However, for Turmeric Bacillus, Peribacillus and Ornithibacillus were the top three dominant genera. For Soybean Vicinamibacter, Haliangium and Pseudomonas were dominating genera compared to control plot. The improved rhizospheric microbiome resulted in an increase in crop yield by 15-20 % as compared to control plot. The study reveals the mode of action of organic amendment through effective microbiome modulation at the rhizosphere.