The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the “Farmer-2” rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the “Candidatus” category were found to be robustly enriched the rhizosphere of “Moitree”. Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of “Moitree” had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. “Moitree” with a profuse root system exhibited better N fixation and translocation ability due to a good “foraging strategy” for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, “Farmer-2” revealed a better “mining strategy” for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar–microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.

Onion is one of the most widely cultivated high-value vegetables on the globe. The study of variability and genetic divergence in this crop will facilitate judicious parent selection for future breeding. The present study incorporated 20 onion genotypes to determine the genetic variability and diversity through morpho-physiological and molecular markers. The genotypes were tested for two consecutive years to determine the effects on yield-attributing and bulb-quality traits. Diversity at a molecular level with 31 simple sequence repeat (SSR) markers was determined. Adequate genetic variability existed among the genotypes, with a predominance of additive gene action regarding the inheritance of most of the characteristics. Principal component (PC) analysis detected seven PCs contributing to more than 87% of the genetic diversity in the genotypes. Total yield (kg/plot), Grade ‘C’ bulb (equatorial diameter of the bulb between 3.5 and 4.5 cm), individual bulb weight (g) and phenol content were detected as characteristics positively associated with the first two PCs. A total of 16 primers were amplified, and they produced 32 alleles in the genotypes. Genetic diversity at the morphological and molecular levels indicated moderate diversity among the tested genotypes, with the dissolution of the genotypes into six and three clusters, respectively. The present study on onion facilitates the selection of diverse parents that can generate desirable segregants in future breeding programmes.