Microbiome change of agricultural soil under organic farming practices

Abstract

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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References

  1. 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

    CAS  Article  PubMed  Google Scholar 

  2. 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

    Article  PubMed  PubMed Central  Google Scholar 

  3. 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

    Article  Google Scholar 

  4. 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

    Article  Google Scholar 

  5. 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

    Article  PubMed  PubMed Central  Google Scholar 

  6. 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

    Article  Google Scholar 

  7. 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

    Article  Google Scholar 

  8. 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

    CAS  Article  Google Scholar 

  9. 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

  10. 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

    Article  PubMed  PubMed Central  Google Scholar 

  11. Jackson ML (1973) Soil chemical analysis. Prentice Hall of India Pvt. Ltd., New Delhi

    Google Scholar 

  12. 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

    Article  Google Scholar 

  13. 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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. 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

    Article  Google Scholar 

  15. 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

  16. 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

    CAS  Article  Google Scholar 

  17. 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

    CAS  Article  PubMed  Google Scholar 

  18. 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

    CAS  Article  Google Scholar 

  19. 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

    Google Scholar 

  20. 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

    Article  Google Scholar 

  21. 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

    Article  PubMed  Google Scholar 

  22. 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

  23. 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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 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

    CAS  Article  Google Scholar 

  25. 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

    CAS  Article  Google Scholar 

  26. 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

    CAS  Article  Google Scholar 

  27. 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

    Article  PubMed  Google Scholar 

  28. 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

  29. Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423

    Article  Google Scholar 

  30. 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

  31. Subbiah B, Asija GL (1956) Alkaline permanganate method of available nitrogen determination. Curr Sci 25:259

  32. 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

    CAS  Article  Google Scholar 

  33. 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

    Google Scholar 

  34. 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

    Article  Google Scholar 

  35. 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

    Article  Google Scholar 

  36. 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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. 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

    CAS  Article  Google Scholar 

  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

    CAS  Article  Google Scholar 

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Acknowledgments

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

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Contributions

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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Keywords

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