Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant

Abstract

This study investigated the diversity, structure and nutrient pathways of the root-associated bacterial endophytes of maize plant cultivated using different fertilizers to verify the claim that inorganic fertilizers have some toxic effects on plant microbiome and not are ecofriendly. Whole DNA was extracted from the roots of maize plants cultivated with organic fertilizer, inorganic fertilizer and maize planted without any fertilizer at different planting sites in an experimental field and sequenced using shotgun metagenomics. Our results using the Subsystem database revealed a total of 28 phyla and different nutrient pathways in all the samples. The major phyla observed were Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, Tenericutes, Planctomycetes, Cyanobacteria, and Chlorobi. Bacteroidetes dominated maize from organic fertilizer sites, Firmicutes dominated the no fertilizers site while Proteobacteria dominated Inorganic fertilizer. The diversity analysis showed that the abundance of endophytic bacteria in all the sites is in the order organic fertilizer (FK) > no fertilizer (CK) > inorganic fertilizer (NK). Furthermore, the major nutrient cycling pathways identified are linked with nitrogen and phosphorus metabolism which were higher in FK samples. Going by the results obtained, this study suggests that organic fertilizer could be a boost to sustainable agricultural practices and should be encouraged. Also, a lot of novel endophytic bacteria groups were identified in maize. Mapping out strategies to isolate and purify this novel endophytic bacteria could help in promoting sustainable agriculture alongside biotechnological applications in future.

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Data accessibility

Sequence data obtained in this work have been deposited in the NCBI Sequence Read Archive under Accession Number PRJNA607664.

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Acknowledgements

AEF appreciates National Research Foundation, South Africa/The World Academy of Science African Renaissance (Ref: UID116107) for the stipend which was of great help in his Ph.D. studies. ASA appreciates North-West University for a postdoctoral fellowship award. OOB appreciates the National Research Foundation, South Africa for the research Grant (UID123634) that supported research in her laboratory.

Funding

The study was funded by the National Research Foundation, South Africa (UID123634).

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AEF handled the literature findings, carried out the planting and laboratory work, performed the all necessary analyses, interpreted the results, and wrote the manuscript. ASA provided technical input and proofread the manuscript. OOB provided academic and technical input intensively critiqued the manuscript, and funded the research. All authors agreed that the manuscript is published.

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Correspondence to Olubukola Oluranti Babalola.

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Fadiji, A.E., Ayangbenro, A.S. & Babalola, O.O. Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant. Antonie van Leeuwenhoek 113, 1559–1571 (2020). https://doi.org/10.1007/s10482-020-01463-w

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Keywords

  • Endophytic microbes
  • Fertilizer application
  • Plant associated microbes
  • Shotgun metagenomics
  • Zea mays