Microbiome change of agricultural soil under organic farming practices


The agricultural practices are known to affect the soil ecosystem, which ultimately influences the environment and human health. In this perspective, soil nutrient status and microbial diversity of ten year’s long organically managed soil were compared with its conventional counterpart at Pantnagar, India (29.03° N/79.46° E). A combination of farmyard manure and vermicompost was used under an organic farming system along with a mixture of neem oil and cow urine as a biopesticide. Organic amendments have improved carbon, nitrogen, and phosphorus content in the soil. Moreover, the copy numbers of diazotrophs and phosphate solubilizers were also found to increase under the organic system which can be evident from their dominance in the organic soil metagenome. Further, several clinically important bacterial genera viz. Corynebacterium, Mycobacterium, Enterococcus, Staphylococcus, Ruminococcus, Prevotella, Coxiella, Neisseria, Haemophilus, Actinobacillus, Treponema, and Mycoplasma were observed only in conventional soil and were completely absent in organic soil sample. These findings revealed that besides enhancing soil fertility and microbial diversity, organic practices have an impact on the soil-borne pathogens and, in general, on the soil microbiome. It will impart value addition to the organic products and lead us towards healthy agricultural practices and products.

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We are extremely grateful to G.B. Pant University of Agriculture and Technology, Pantnagar (Uttarakhand) for providing financial assistance and space to conduct experiments.

Author information




DCS: Conducted the experiments, data analysis and preparation of first draft of the manuscript.

RS: Data analysis, Editing and review of the manuscript.

DKS: In-charge of experimental fields and has provided the necessary facilities.

RG: Conceptualization of the work, laboratory facilities, finalization of the manuscript.

Corresponding author

Correspondence to Reeta Goel.

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The authors declare that there is no conflict of interest.

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NGS data have been submitted to NCBI Sequence Read Archive (SRA) under the accession number PRJNA607339.

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Suyal, D.C., Soni, R., Singh, D.K. et al. Microbiome change of agricultural soil under organic farming practices. Biologia (2021). https://doi.org/10.2478/s11756-021-00680-6

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  • Organic farming
  • Pathogenic microorganisms
  • Next-generation sequencing
  • Soil fertility