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Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach

  • Microbial Genetics • Original Paper
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Abstract

To ensure food security for the ever-increasing world’s population, it is important to explore other alternatives for enhancing plant productivity. This study is aimed at identifying the putative plant growth–promoting (PGP) and endophytic gene clusters in root-associated endophytic microbes from maize root and to also verify if their abundance is affected by different farming practices. To achieve this, we characterize endophytic microbiome genes involved in PGP and endophytic lifestyle inside maize root using the shotgun metagenomic approach. Our results revealed the presence of genes involved in PGP activities such as nitrogen fixation, HCN biosynthesis, siderophore, 4-hydroxybenzoate, ACC deaminase, phenazine, phosphate solubilization, butanediol, methanol utilization, acetoin, nitrogen metabolism, and IAA biosynthesis. We also identify genes involved in stress resistance such as glutathione, catalase, and peroxidase. Our results further revealed the presence of putative genes involved in endophytic behaviors such as aerotaxis, regulator proteins, motility mechanisms, flagellum biosynthesis, nitrogen regulation, regulation of carbon storage, formation of biofilm, reduction of nitric oxide, regulation of beta-lactamase resistance, type III secretion, type IV conjugal DNA, type I pilus assembly, phosphotransferase system (PTS), and ATP-binding cassette (ABC). Our study suggests a high possibility in the utilization of endophytic microbial community for plant growth promotion, biocontrol activities, and stress mitigation. Further studies in ascertaining this claim through culturing of the beneficial isolates as well as pot and field experiments are necessary.

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Acknowledgments

AEF appreciates NRF/TWAS African Renaissance scholarship (UID116107) which was of great encouragement for his Ph.D. studies. OOB acknowledged the National Research Foundation, South Africa, for the research grant (UID123634) that supported research in her laboratory.

Funding

The funding for this project was provided by the National Research Foundation, South Africa (UID123634).

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Authors and Affiliations

  1. Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa

    Ayomide Emmanuel Fadiji, Ayansina Segun Ayangbenro & Olubukola Oluranti Babalola

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  1. Ayomide Emmanuel Fadiji
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  2. Ayansina Segun Ayangbenro
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  3. Olubukola Oluranti Babalola
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Contributions

AEF handled the literature findings, carried out the planting and laboratory work, performed the analyses, interpreted the results, and wrote the manuscript. ASA provided technical input, result interpretation, and proofread the manuscript. OOB initiated the metagenomic research, provided academic and technical inputs to the co-authors, critiqued and helped shape the research, verified the analytical methods, and secured funding for the research.

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Correspondence to Olubukola Oluranti Babalola.

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Communicated by: Agnieszka Szalewska-Palasz

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Fadiji, A.E., Ayangbenro, A.S. & Babalola, O.O. Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach. J Appl Genetics 62, 339–351 (2021). https://doi.org/10.1007/s13353-021-00611-w

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