Organic Farming Enhances the Diversity and Community Structure of Endophytic Archaea and Fungi in Maize Plant: a Shotgun Approach

This study compares, for the first time, the diversity and community structure of the endophytic archaea and fungi inhabiting the roots of maize plant cultivated using two different fertilizer regimes and the control field via shotgun metagenomics. This was used to verify our hypothesis that organic farming positively influences the diversity, beneficial effects, and abundance of plant endophytic communities as compared with conventional farming. Total DNA extraction was carried out using the roots of maize plants cultivated with organic fertilizer (FK), inorganic fertilizer (NK), and without any fertilizer (CK) at different farming sites in an experimental field and sequenced using shotgun metagenomics. In all, 3 archaea phyla, namely, Crenarchaeota, Euryarchaeota, and Thaumarchaeota, and 2 fungi phyla, namely, Ascomycota and Basidiomycota, were identified in the samples with higher abundance in samples from the FK site. Our diversity results revealed that the abundance of endophytic archaea and fungi species across the farming sites are in the order NK < CK < FK. The results indicate that organic farming enhances the abundance of endophytic archaea and fungi which might be a boost to sustainable agricultural practices. Furthermore, some new genera of endophytic archaea and fungi were identified from the maize roots. Future studies into how these novel endophytes can be cultured are important in a bid to explore their functions in sustainable agriculture as well as identify their biotechnological importance.