Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging 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 management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. 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 the 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 potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
Highlights
Over the past decades, conventional farming practice that mainly relies on agrochemical inputs has significantly increased the global per capita agricultural production (Pretty, 2008)
This study revealed that organic farming promoted a higher microbial diversity with a more complex and stable network structure
Transition farming was predominated by numerous toxic compound degraders, which might importantly contribute to the restoration of damaged agroecosystems such as remediation of agrochemical residues
Summary
Conventional farming practice that mainly relies on agrochemical inputs has significantly increased the global per capita agricultural production (Pretty, 2008) This effort raises production costs and causes serious problems to the environment including soil contamination and degradation, emission of fertilizers and pesticides, loss of biodiversity, and several negative impacts on human health (Rivera et al, 2017). Organic farming is much closer to natural ecosystems because it depends less on agrochemicals and increases more on nutrient recycling systems This farming has been shown to be more effective in reducing the negative impacts of agricultural practices on the environment and promoting biodiversity (Bengtsson et al, 2005). Another research showed that organic fertilization improved the abundance of microbial nitrogen (N)-cycle genes, which were associated with N availability in the soil (Morugán-Coronado et al, 2019)
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