Soil Microbiome and Nutrient Cycling: Implications for Sustainable Agriculture
Nidhi Kamboj *
Department of Soil Science, CCSHAU, Hisar, India.
Shivam Dinkar
Department of Forestry, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar, Raipur, Chhattisgarh- 492012, India.
Swati Singh
Department of Agronomy, Sardar Vallabhbhai Patel University of Agriculture and Technology, Modipuram, Meerut 250110, India.
Sunil
Department of Biochemistry, CCSHAU, Hisar, India.
Manish Kumar
Department of Agronomy, Rajasthan College of Agriculture, MPUAT, Udaipur 313001 (Rajasthan), India.
Girish K
Department of Microbiology, Government College for Women (Autonomous), Mandya, Mandya University, Karnataka, India.
Suparna Deepak
Department of Biotechnology, Pillai College of Arts, Commerce & Science (Autonomous), Navi Mumbai, India.
Shubhendu Singh
Department of Agronomy, Banaras Hindu University, India.
*Author to whom correspondence should be addressed.
Abstract
Soil microbial communities—including bacteria, archaea, fungi, and viruses—play a pivotal role in mediating critical nutrient cycling processes (carbon, nitrogen, and phosphorus transformations) that underpin agricultural productivity and ecosystem resilience. Recent advancements in high-throughput sequencing, multi-omics (metagenomics, metatranscriptomics, metabolomics), exudate chemistry, isotope-tracing, and synthetic microbiome engineering (SynComs, microbial inoculants) have enabled mechanistic insights into how soil microbiomes regulate nutrient fluxes under diverse agroecosystem contexts. This review synthesizes findings from 2019–2025 regarding: (1) microbial community composition and functional potential; (2) microbial mechanisms underlying N, P, and C cycling; (3) the impact of agricultural practices (fertilizer regimes, tillage, crop rotations, cover cropping, organic amendments) on soil microbiomes and nutrient dynamics; (4) emerging technologies and strategies for microbiome-based nutrient management—including SynCom design, host genotypic selection, and precision agriculture tools; and (5) major challenges such as context dependency, reproducibility, scale-up logistics, and socio-economic barriers. We propose research priorities including trait- and interaction-focused approaches, coordinated multi-site field trials, host-microbiome co-selection, digital decision-support integration, and supportive policy mechanisms to realize robust, field-deployable microbiome-based strategies for sustainable agriculture.
Keywords: Soil microbiome, nutrient cycling, nitrogen fixation, phosphorus solubilization, carbon decomposition, sustainable agriculture