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Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

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Abstract

Main conclusion

This review is an effort to provide in-depth knowledge of microbe’s interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture.

Abstract

Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

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Acknowledgements

The authors extend their appreciation to the Deputyship for Research & Innovation, Ministry of Education and Saudi Arabia for funding this re-search work through the project number (Qu-IF-1-1- 1). The authors also thank to the technical support of Qassim University, Buraydah, Saudi Arabia.

Funding

This research was funded by the Deputyship for Research & Innovation, Ministry of Education Saudi Arabia for funding this research work through the project number (Qu-IF-1-1- 1).

Author information

Authors and Affiliations

  1. Department of Biotechnology, SHEPA, Varanasi, India

    Shalini Rai

  2. Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia

    Ayman F. Omar, Medhat Rehan & Ahmad Al-Turki

  3. Department of Plant Pathology, Plant Pathology and Biotechnology Laboratory and EPCRS Excellence Center, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt

    Ayman F. Omar

  4. Department of Genetics, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt

    Medhat Rehan

  5. Department of Microbiology, MIET, Meerut, India

    Alka Sagar

  6. Department of Botany, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan

    Noshin Ilyas

  7. Asian PGPR Society, Auburn Venture, Auburn, AL, USA

    R. Z. Sayyed

  8. Department of Agronomy, Faculty of Agriculture, Sher-E-Bangla Agricultural University (SAU), Sher-E-Bangla Nagar, Dhaka, 1207, Bangladesh

    Mirza Hasanuzzaman

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Correspondence to Shalini Rai, Ayman F. Omar or R. Z. Sayyed.

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Rai, S., Omar, A.F., Rehan, M. et al. Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture. Planta 257, 27 (2023). https://doi.org/10.1007/s00425-022-04052-5

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