3 Biotech

, 8:304 | Cite as

Soil bacterial diversity under conservation agriculture-based cereal systems in Indo-Gangetic Plains

  • Madhu ChoudharyEmail author
  • Parbodh C. Sharma
  • Hanuman S. Jat
  • Abhinandita Dash
  • Balaji Rajashekar
  • Andrew J. McDonald
  • Mangi L. Jat
Original Article


In Indo-Gangetic plains (IGP) of India, natural resources (soil, water, and environment) are degrading under the conventional–till (CT)-based management practices in rice–wheat cropping system. A long-term field experiment was conducted to understand the soil bacterial diversity and abundance under different sets of management scenarios (Sc). The study comprised of four scenarios, namely, -Sc.I CT-based rice–wheat system (farmers’ practice); Sc.II, partial conservation agriculture (CA) based in which rice is under CT—wheat and mungbean under zero-tillage (ZT); Sc.III, full CA-based in which rice–wheat–mungbean are under ZT and Sc.IV, where maize–wheat–mungbean are under ZT. These scenarios varied in cropping system, tillage, and crop residue management practices. Using Illumina MiSeq sequencing technology, the variable regions V3–V4 of 16S rRNA were sequenced and the obtained reads were analyzed to study the diversity patterns in the scenarios. Results showed the presence of 53 bacterial phyla across scenarios. The predominant phyla in all scenarios were Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes which accounted for more than 70% of the identified phyla. However, the rice-based systems (Sc.I, Sc.II, and Sc.III) were dominated by phylum Proteobacteria; however, maize-based system (Sc.IV) was dominated by Acidobacteria. The class DA052 and Acidobacteriia of Acidobacteria and Bacteroidetes of Bacteroidia were exceptionally higher in Sc.IV. Shannon diversity index was 8.8% higher in Sc.I, 7.5% in Sc.II, and 2.7% in Sc.III compared to Sc.IV. The findings revealed that soil bacterial diversity and abundance are influenced by agricultural management practices as bacterial diversity under full CA-based management systems (Sc.III and Sc.IV) was lower when compared to farmer’s practice (Sc.I) and partial CA (Sc.II) scenarios.


Acidobacteria Bacterial diversity Conservation agriculture Metagenome Proteobacteria 



We acknowledge that this research was undertaken in collaboration with International Maize and Wheat Improvement Centre (CIMMYT) under Cereal Systems Initiative for South Asia (CSISA) project supported by Bill and Melinda Gates Foundation (BMGF), USAID and CGIAR Research Programs on Climate Change, Agriculture and Food Security (CCAFS), and Wheat Agri-food Systems (WHEAT). We also acknowledge the support received from the Director, ICAR-CSSRI, Karnal.

Author contributions

MC, PS, and HS designed the study; AM, ML, and HS gave the idea of study and supported the design; MC conducted the research; AD and BR analyzed the data; MC wrote the manuscript and HS assisted with revising the draft manuscript. All authors have read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest in the publication.

Supplementary material

13205_2018_1317_MOESM1_ESM.docx (18 kb)
Supplementary material 1 (DOCX 17 KB)
13205_2018_1317_MOESM2_ESM.pdf (1.5 mb)
Supplementary material 2 (PDF 1558 KB)
13205_2018_1317_MOESM3_ESM.tif (10.8 mb)
Supplementary material 3 (TIF 11037 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Madhu Choudhary
    • 1
    Email author
  • Parbodh C. Sharma
    • 1
  • Hanuman S. Jat
    • 2
  • Abhinandita Dash
    • 3
  • Balaji Rajashekar
    • 3
  • Andrew J. McDonald
    • 4
  • Mangi L. Jat
    • 2
  1. 1.Division of Soil and Crop ManagementICAR-Central Soil Salinity Research Institute (ICAR-CSSRI)KarnalIndia
  2. 2.International Maize and Wheat Improvement Centre (CIMMYT)New DelhiIndia
  3. 3.Genotypic Technology Pvt. Ltd.BengaluruIndia
  4. 4.International Maize and Wheat Improvement Centre (CIMMYT)KathmanduNepal

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