Metagenomic and Metatranscriptomic Analysis of the Rhizosphere Soils Under Organic and Inorganic Nutrition and Functional Screening of Garden Soil Metagenomic Library

Abstract

Intensification of agriculture has resulted in deterioration of soil health which newlinehas shifted the focus towards the need of managing the soils through organic newlineamendments for sustenance of soil health. The knowledge of microbial community newlinestructure in the soils enriched with organic manures is essential for sustainability of newlineagriculture through organic farming. With this view, the current study describes the newlineeffect of application of the organic and inorganic nutrition on bacterial community newlinestructure enriched in soil rhizosphere at various crop growth stages of different crops. newlineWe utilized PCR-DGGE method targeting variable regions V3 and V5 of 16S rRNA newlinegene for the identification of bacterial community structure associated with the ectorhizosphere newlineof the different crops. The highest Shannon diversity index and range newlineweighted richness was recorded at vegetative stage of all organically managed crops as newlinecompared to inorganic management and no nutrient control. The moving window newlineanalysis indicated that ecto-rhizosphere bacterial community structure reduced over the newlinegrowth stages in organic management whereas under inorganic management, the rate of newlinethe change in the bacterial communities increased with the growth stages. Whole newlinemetagenomic and metatranscriptomic sequencing was also applied to discover the newlinemicrobial structure thriving in the soil rhizosphere of maize. Whole metagenome newlinesequencing of FYM, RDF applied soils and no nutrient control soils at vegetative newlinegrowth indicated that the alpha diversity of the FYM treated soils (478) was highest as newlinecompared to RDF (466) and no nutrient control soils (364). The maximum percentage newlineof rare phyla was found in FYM treated soils (6.03%) as compared to no nutrient newlinecontrol (4.63 %). Proteobacteria dominated the soil rhizosphere followed by the newlineActinobacteria, Acidobacteria, Firmicutes and Bacteriodetes. To uncover functional newlinepotential of soil microbes, garden soil metagenomic library was constructed and newlinescreened, through which four clones positive for phosphate solubilisatio