Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plan
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ORIGINAL PAPER
Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant Ayomide Emmanuel Fadiji . Ayansina Segun Ayangbenro . Olubukola Oluranti Babalola
Received: 1 June 2020 / Accepted: 11 July 2020 Ó Springer Nature Switzerland AG 2020
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
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10482-020-01463-w) contains supplementary material, which is available to authorized users. A. E. Fadiji A. S. Ayangbenro O. O. Babalola (&) Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa e-mail: [email protected]
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. Keywords Endophytic microbes Fertilizer application Plant associated microbes Shotgun metagenomics Zea mays
Introduction The diversity of microorganisms is still yet to be fully understood, even though about 1.5 million species of bacteria and fungi have been estimated to perform important roles on earth such as symbionts, decomposers and ecosystem pathogens (Akinsanya et al. 2015). Many microbial communities reside in plant tissues and these microbes, especially bacteria, perform important functions in plant health and growth,
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