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.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
Alegbeleye OO, Sant'Ana AS (2020) Manure-borne pathogens as an important source of water contamination: an update on the dynamics of pathogen survival/transport as well as practical risk mitigation strategies. Int J Hyg Environ Health 227:113524. https://doi.org/10.1016/j.ijheh.2020.113524
Arcand MM, Levy-Booth DJ, Helgason BL (2017) Resource legacies of organic and conventional management differentiate soil microbial carbon use. Front Microbiol 8:2293. https://doi.org/10.3389/fmicb.2017.02293
Balazs HE, Schmid CAO, Podar D, Hufnagel G, Radl V, Schroder P (2020) Development of microbial communities in organochlorine pesticide contaminated soil: a post-reclamation perspective. Appl Soil Ecol 150:103467. https://doi.org/10.1016/j.apsoil.2019.103467
Cesarano G, De Filippis F, La Storia A, Scala F, Bonanomi G (2017) Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition. Appl Soil Ecol 120:254–264. https://doi.org/10.1016/j.apsoil.2017.08.017
Constancias F, Terrat S, Saby NPA, Horrigue W, Villerd J et al (2015) Mapping and determinism of soil microbial community distribution across an agricultural landscape. MicrobiologyOpen 4:505–517. https://doi.org/10.1002/mbo3.255
De Corato U (2020a) Disease-suppressive compost enhances natural soil suppressiveness against soil-borne plant pathogens: a critical review. Rhizosphere 13:100192. https://doi.org/10.1016/j.rhisph.2020.100192
De Corato U (2020b) Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies. Chem Biol Technol Agric 7(17):1–26. https://doi.org/10.1186/s40538-020-00183-7
Eremeev V, Talgre L, Kuht J, Mäeorg E, Esmaeilzadeh-Salestani K et al (2020) The soil microbial hydrolytic activity, content of nitrogen and organic carbon were enhanced by organic farming management using cover crops and composts in potato cultivation. Acta Agric Scand Sect B Soil Plant Sci 70:87–94. https://doi.org/10.1080/09064710.2019.1673475
Gaiser T, Stahr K (2013) Soil organic carbon, soil formation and soil fertility. In: Lal R, Lorenz K, Huttl R, Schneider B, J vB (eds) ecosystem services and carbon sequestration in the biosphere. Springer, pp 407-418. https://doi.org/10.1007/978-94-007-6455-2_17
Godde CM, Thorburn PJ, Biggs JS, Meier EA (2016) Understanding the impacts of soil, climate, and farming practices on soil organic carbon sequestration: a simulation study in Australia. Front Plant Sci 7:661. https://doi.org/10.3389/fpls.2016.00661
Jackson ML (1973) Soil chemical analysis. Prentice Hall of India Pvt. Ltd., New Delhi
Joshi D, Chandra R, Suyal DC, Kumar S (2019) Impacts of bioinoculants Pseudomonas jesenii MP1 and Rhodococcus qingshengii S10107 on chickpea (Cicer arietinum L.) yield and soil nitrogen status. Pedosphere 29:388–399. https://doi.org/10.1016/S1002-0160(19)60807-6
Kumar S, Suyal DC, Yadav A, Shouche Y, Goel R (2019) Microbial diversity and soil physiochemical characteristic of higher altitude. PLoS One 14:e0213844. https://doi.org/10.1371/journal.pone.0213844
Lazarovits G, Tenuta M, Conn K (2001) Organic amendments as a disease control strategy for soilborne diseases of high-value agricultural crops. Australas Plant Pathol 30:111–117. https://doi.org/10.1071/AP01009
Lernoud J, Willer H (2019) Current statistics on organic agriculture worldwide: area, operators, and market. https://ciaorganico.net/documypublic/486_2020-organic-world-2019.pdf
Liao J, Xu Q, Xu H, Huang D (2019) Natural farming improves soil quality and alters microbial diversity in a cabbage field in Japan. Sustainability 11:3131. https://doi.org/10.3390/su11113131
Mader P, Fliessbach A, Dubois D, Gunst L, Fried P, Niggli U (2002) Soil fertility and biodiversity in organic farming. Science 296:1694–1697. https://doi.org/10.1126/science.1071148
Mandavgane SA, Kulkarni BD (2020) Valorization of cow urine and dung: a model biorefinery. Waste Biomass Valor 11:1–14. https://doi.org/10.1007/s12649-018-0406-7
Meghvansi MK, Varma A (2015) Organic amendments and soil Suppressiveness in plant disease management. Springer, Switzerland. https://doi.org/10.1007/978-3-319-23075-7
Melo J, Carvalho L, Correia P, de Souza SB, Dias T et al (2018) Conventional farming disrupts cooperation among phosphate solubilising bacteria isolated from Carica papaya's rhizosphere. Appl Soil Ecol 124:284–288. https://doi.org/10.1016/j.apsoil.2017.11.015
Negatu B, Vermeulen R, Mekonnen Y, Kromhout H (2018) Neurobehavioural symptoms and acute pesticide poisoning: a cross-sectional study among male pesticide applicators selected from three commercial farming systems in Ethiopia. Occup Environ Med 75:283–289. https://doi.org/10.1136/oemed-2017-104538
Olsen SR (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. Circular (United States. Department of Agriculture), no. 939. US Department of Agriculture, Washington, D.C
Orr CH, Leifert C, Cummings SP, Cooper JM (2012) Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects. PLoS One 7:e52891. https://doi.org/10.1371/journal.pone.0052891
Rajwar J, Chandra R, Suyal DC, Tomer S, Kumar S, Goel R (2018) Comparative phosphate solubilizing efficiency of psychrotolerant Pseudomonas jesenii MP1 and Acinetobacter sp. ST02 against chickpea for sustainable hill agriculture. Biologia 73:793–802. https://doi.org/10.2478/s11756-018-0089-3
Rawat N, Sharma M, Suyal DC, Singh DK, Joshi D, Singh P, Goel R (2019) Psyhcrotolerant bio-inoculants and their co-inoculation to improve Cicer arietinum growth and soil nutrient status for Sustainable Mountain agriculture. J Soil Sci Plant Nutr 19:639–647. https://doi.org/10.1007/s42729-019-00064-5
Sanderman J, Baldock JA (2010) Accounting for soil carbon sequestration in national inventories: a soil scientist's perspective. Environ Res Lett 5:034003. https://doi.org/10.1088/1748-9326/5/3/034003
Scheuerell SJ, Mahaffee WF (2004) Compost tea as a container medium drench for suppressing seedling damping-off caused by Pythium ultimum. Phytopathology 94:1156–1163. https://doi.org/10.1094/PHYTO.2004.94.11.1156
Schierstaedt J, Grosch R, Schikora A (2019) Agricultural production systems can serve as reservoir for human pathogens. FEMS Microbiol Lett 366:fnaa016. https://doi.org/10.1093/femsle/fnaa016
Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423
Siddiqui Y, Naidu Y, Ali A (2015) Bio-intensive Management of Fungal Diseases of fruits and vegetables utilizing compost and compost teas. In: Meghvansi M, Varma a (eds) organic amendments and soil Suppressiveness in plant disease management. Soil biology, vol 46. Springer, Cham. https://doi.org/10.1007/978-3-319-23075-7_14
Subbiah B, Asija GL (1956) Alkaline permanganate method of available nitrogen determination. Curr Sci 25:259
Suyal DC, Yadav A, Shouche Y, Goel R (2015) Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences. Biologia 70:305–313. https://doi.org/10.1515/biolog-2015-0048
Suyal DC, Joshi D, Debbarma P, Soni R, Das B, Goel R (2019) Soil Metagenomics: Unculturable microbial diversity and its function. In: Varma A, Choudhary DK (eds) Mycorrhizosphere and Pedogenesis. Springer, Singapore, pp 355–362. https://doi.org/10.1007/978-981-13-6480-8_20
Tautges NE, Sullivan TS, Reardon CL, Burke IC (2016) Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system. Appl Soil Ecol 108:258–268. https://doi.org/10.1016/j.apsoil.2016.09.003
Tomer S, Suyal DC, Shukla A, Rajwar J, Yadav A, Shouche Y, Goel R (2017) Isolation and characterization of phosphate solubilizing bacteria from Western Indian Himalayan soils. 3. Biotech 7:1–5. https://doi.org/10.1007/s13205-017-0738-1
van Gils S, Tamburini G, Marini L, Biere A, van Agtmaal M et al (2017) Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer. PLoS One 12:e0179695. https://doi.org/10.1371/journal.pone.0179695
Walkley A, Black IA (1934) An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Sci 37(1):29–38
Ye L, Zhao X, Bao E, Li J, Zou Z, Cao K (2020) Bio-organic fertilizer with reduced rates of chemical fertilization improves soil fertility and enhances tomato yield and quality. Sci Rep 10:1–11. https://doi.org/10.1038/s41598-019-56954-2
We are extremely grateful to G.B. Pant University of Agriculture and Technology, Pantnagar (Uttarakhand) for providing financial assistance and space to conduct experiments.
Conflict of interest
The authors declare that there is no conflict of interest.
Availability of data and material
NGS data have been submitted to NCBI Sequence Read Archive (SRA) under the accession number PRJNA607339.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
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
- Organic farming
- Pathogenic microorganisms
- Next-generation sequencing
- Soil fertility