Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology.

Krishnendu Pramanik,Joydeep Banerjee,Arpita Das,Rishu Sharma,Shayree Chatterjee,Shiv Kumar,Sanjeev Gupta,Anupam Das

doi:10.3390/ijms21238895

Abstract

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.

Highlights

Plant roots interface diverse groups of microbiotas including bacteria, fungi, algae, viruses, and archaea in soil [1,2], which are considered the host’s second genome [3]
Plant Attributes of the Test Cultivars. Both the lentil cultivars responded in significantly different (p = 0.034) manner under rice-fallow ecology
The varied performance of lentil cultivars under rice-fallow ecology was attributed to their divergent grain nutrient content, shoot–root ratio, and root characteristics

Summary

Introduction

Plant roots interface diverse groups of microbiotas including bacteria, fungi, algae, viruses, and archaea in soil [1,2], which are considered the host’s second genome [3]. Culinaris) is a globally important cool-season food legume which plays a major role in household nutritional security in developing countries. This protein-rich crop is an ideal candidate for rice-fallow areas aimed at its intensification to meet the protein demand of vegetarian society. Soils of rice-fallow areas are different from the soils of other lentil growing areas due to alterations from the anaerobic condition during rice growing season to the aerobic condition which strikingly alters the microbial population dynamics, leading to a reduction in biological nitrogen fixation (BNF) and P availability in the succeeding lentil crop [15,16]

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Results

Discussion

Conclusion