Soil bacterial diversity under conservation agriculture-based cereal systems in Indo-Gangetic Plains
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.
KeywordsAcidobacteria 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.
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.
- Blake GR, Hartge KH (1986) Bulk density. In: Methods of soil analysis. Klute A (ed). ASA and SSSA, Madison, Wisconsin, USA, 363–375Google Scholar
- Boch J, Bonas U (2010) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phyto pathol 48:419–436. https://doi.org/10.1146/annurev-phyto-080508-081936 CrossRefGoogle Scholar
- Ceja-Navarro JA, Rivera-Orduna FN, Patino-Zúniga L, Vila-Sanjurjo A, Crossa J, Govaerts B, Dendooven L (2010) Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl Environ Microbiol 76:3685–3691. https://doi.org/10.1128/AEM.02726-09 CrossRefPubMedPubMedCentralGoogle Scholar
- Constancias F, Prévost-Bouré NC, Terrat S, Aussems S, Nowak V, Guillemin JP, Bonnotte A, Biju-Duval L, Navel A, Martins JM, Maron PA (2014) Microscale evidence for a high decrease of soil bacterial density and diversity by cropping. Agron Sustain Dev 34:831–840. https://doi.org/10.1007/s13593-013-0204-3 CrossRefGoogle Scholar
- Degrune F, Theodorakopoulos N, Dufrêne M, Colinet G, Bodson B, Hiel MP, Taminiau B, Nezer C, Daube G, Vandenbol M (2016) No favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium). Agric Ecosyst Environ 224:12–21. https://doi.org/10.1016/j.agee.2016.03.017 CrossRefGoogle Scholar
- FAO Conservation Agriculture Program (2014) CA adoption worldwide. http://www.fao.org/ag/ca/6c.html. Downloaded 26
- Gathala M, Kumar V, Sharma PC, Saharawat Y, Jat HS, Singh M, Kumar A, Jat ML, Humphreys E, Sharma DK, Sharma S, Ladha JK (2013) Optimizing intensive cereal-based cropping systems addressing current and future drivers of agricultural change in the northwestern Indo-Gangetic Plains of India. Agric Ecosyst Environ 177:85–97. https://doi.org/10.1016/j.agee.2013.06.002 CrossRefGoogle Scholar
- Gupta RS (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367–402. https://doi.org/10.1111/j.1574-6976.2000.tb00547.x CrossRefPubMedGoogle Scholar
- Indoria AK, Rao CS, Sharma KL, Reddy KS (2017) Conservation agriculture—a panacea to improve soil physical health. Curr Sci 112(1):52Google Scholar
- Jackson ML (1973) Soil chemical analysis. Prentice Hall of India Pvt. Ltd., New DelhiGoogle Scholar
- Jat RK, Sapkota TB, Singh RG, Jat ML, Kumar M, Gupta RK (2014) Seven years of conservation agriculture in a rice–wheat rotation of eastern gangetic plains of South Asia: yield trends and economic profitability. Field Crops Res 164:199–210. https://doi.org/10.1016/j.fcr.2014.04.015 CrossRefGoogle Scholar
- Jat HS, Datta A, Sharma PC, Kumar V, Yadav AK, Choudhary M, Choudhary V, Gathala MK, Sharma DK, Jat ML, Yaduvanshi NPS (2017) Assessing soil properties and nutrient availability under conservation agriculture practices in a reclaimed sodic soil in cereal-based systems of North-West India. Arch Agron Soil Sci 1–15Google Scholar
- Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. In: The significance and regulation of soil biodiversity. Springer Netherlands, 75–86Google Scholar
- Lienhard P, Terrat S, Prévost-Bouré NC, Nowak V, Régnier T, Sayphoummie S, Panyasiri K, Tivet F, Mathieu O, Levêque J, Maron PA (2014) Pyrosequencing evidences the impact of cropping on soil bacterial and fungal diversity in Laos tropical grassland. Agron Sustain Dev 34:525 –525 33. https://doi.org/10.1007/s13593-013-0162-9 CrossRefGoogle Scholar
- Meisinger DB, Zimmermann J, Ludwig W, Schleifer KH, Wanner G, Schmid M, Bennett PC, Engel AS, Lee NM (2007) In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA). Environ Microbiol 9(6):1523–1534CrossRefPubMedGoogle Scholar
- Navarro-Noya YE, Gómez-Acata S, Montoya-Ciriaco N, Rojas-Valdez A, Suárez-Arriaga MC, Valenzuela-Encinas C, Jiménez-Bueno N, Verhulst N, Govaerts B, Dendooven L (2013) Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem. Soil Biol Biochem 65:86–95CrossRefGoogle Scholar
- Smit E, Leeflang P, Gommans S, Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291. https://doi.org/10.1128/aem.67.5.2284-2291.2001 CrossRefPubMedPubMedCentralGoogle Scholar
- Subbiah BV, Asija GL (1956) A rapid procedure 744 for the determination of available nitrogen in soils. Curr Sci 25:259–260Google Scholar