Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Converting conventional farming to organic system to improve ecosystem health is a trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was therefore conducted to investigate the effects of agricultural managements, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using shotgun metagenome sequencing. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the major keystone (hub) species, and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp., Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, that might suggest their essential roles in transformation of conventional farming to organic system. Moreover, conventional farming diminished the abundance of cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to a lower microbial diversity in this habitat. Altogether, our results demonstrate the response of sugarcane-associated phyllosphere microbiota to the shift of agricultural managements to a more sustainable sugarcane production.