Metagenomic Insights into Soil Microbial Communities

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Genetics & Plant Breeding

Metagenomic Insights into Soil Microbial Communities and Functional Dynamics in Natural Farming Systems Across Agro-ecological Zones of India

Name of the PI

Dr. D. Shivani, Assistant Professor (Genetics and Plant Breeding), School of Agriculture, Kaveri University, Gowraram (V), Wargal (M), Siddipet – 502279

Abstract

Natural farming systems, with minimal chemical inputs, are gaining importance for enhancing soil health and sustainability. This study uses high-throughput metagenomic sequencing to characterize soil microbial diversity, functional genes, and metabolic pathways in natural farming systems across India’s agro-ecological zones. Comparative analyses with conventional farming will reveal shifts in community composition and functions linked to nutrient cycling, plant growth promotion, and stress tolerance. Findings will identify region-specific microbial signatures and functional traits, providing insights to optimize natural farming practices for productivity and resilience.

Objectives

  1. To characterize and compare soil microbial community structure and diversity in natural and conventional farms across various agroecological zones using metagenomic sequencing.
  2. To identify functionally relevant microbial genes (e.g., nitrogen fixation, phosphorus solubilization, plant growth promoting, disease suppression) enriched in natural farming systems.
    1. To assess the influence of traditional natural farming bio-inputs (Jeevamrit, Beejamrit, Panchagavya) on microbial community dynamics and functional gene profiles.

Technical Details (Brief)

This 2-year project will investigate the taxonomic and functional dynamics of soil microbial communities in natural farming versus conventional farming systems across multiple agro-ecological zones of India. Representative sites will be selected to capture variations in climate, soil type, and cropping patterns.

Sampling Strategy: Soil samples will be collected from rhizosphere and bulk soil under both farming systems, with triplicate sampling to ensure statistical robustness. Sites practicing natural farming will be further categorized based on the use of bio-inputs such as Jeevamrit, Beejamrit, and Panchagavya.

Metagenomic Analysis: High-quality soil DNA will be extracted and subjected to whole metagenome shotgun sequencing (Illumina platform). Bioinformatics pipelines (e.g., MG-RAST, MetaPhlAn, KEGG, eggNOG) will be used for taxonomic profiling (bacteria, archaea, fungi, viruses) and functional annotation. Special focus will be on genes related to nutrient cycling (nitrogen fixation, phosphorus solubilization), plant growth promotion, and disease suppression. 

Data Integration & Analysis: Microbial diversity indices, functional gene abundances, and metabolic pathway profiles will be compared across systems, zones, and bio-input treatments. Environmental metadata (soil pH, organic carbon, nutrient content) will be integrated to identify key drivers of microbial structure and function.

Project Duration

2 years (2026–2027)

Expected Impact

  • Comprehensive metagenomic profiles revealing differences in soil microbial community structure and diversity between natural and conventional farming systems across diverse agroecological zones.
  • Identification of key functional microbial genes involved in nutrient cycling, disease suppression, and plant growth promotion that are enriched in natural farming soils.
  • Detailed characterization of microbial communities and functional gene profiles present in traditional natural farming bio-inputs (Jeevamrit, Beejamrit, Panchagavya) and their influence on soil microbial dynamics.
  • Integrated understanding of how traditional bio-inputs contribute to enhancing beneficial soil microbial functions in natural farming systems.
  • Scientific evidence supporting the use of microbial indicators and bio-inputs for improving soil health and sustainability in natural farming practices.

Collaborating Partners

  1. Krishi Vignan Kedra, Longding, Arunachal Pradesh – 792131
  2. ICAR-Central Potato Research Institute, Regional Station, Muthorai, Ooty, Tamil Nadu, India, 643004

Funding Agency

Competitive Research Grant (CRG),National Mission on Natural Farming

Budget Summary

43,20,000

Kaveri University was established as per the Telangana Private Universities (Establishment & Regulation) Act, 2018 under section 3.

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