Shotgun metagenomics reveals the functional diversity of root-associated endophytic microbiomes in maize plant

Abstract

In this study, we used shotgun metagenomics to analyze the whole DNA from maize root planted with different fertilization and without fertilization in a bid to profile the impact of fertilizer applications on the functional diversity of endophytic microbiomes. Complete DNA extraction from roots of maize plant grown on different farming sites such as organic (FK), inorganic (NK) and no fertilizer (CK) sites was carried out, and sequenced using a shotgun metagenomic approach. The raw sequenced data obtained were analyzed using an online database called MG-RAST. Through MG-RAST analysis, endophytic microbiome sequences were identified while sequences of maize origin were discarded. The prediction of the functions of the endophytic microbiomes was done using the SEED subsystem. Our results revealed that no significant difference (P > 0.05) exist in the relative abundance of the 28 functional groups identified within the endophytic microbiomes across the sites. Also, some functional groups and metabolic pathways associated with plant growth promotion such as carbohydrate, secondary metabolism, nitrogen metabolism, iron acquisition and metabolism alongside phosphorus metabolism were observed in the endophytes across the sites. Alpha diversity study revealed no significant difference exist among the functional groups of the endophytes across the sites, while beta diversity study indicated that there was a significant difference (P = 0.01) among the functional groups of the endophytes across the fertilizer sites. Going by the high abundance of functional groups observed in this study, especially in FK samples, it is evident that different farming practices influenced the functions of endophytic microbiomes. We recommend that further studies should explore the functional genes in endophytic microbiomes with the aim of assessing their usefulness in promoting sustainable agriculture.