Bacterial structure and dynamics in mango (Mangifera indica) orchards after long term organic and conventional treatments under subtropical ecosystem

Abstract This study explores the comparative effect of conventional and organic treatments on the rhizosphere microbiome of Mangifera indica cv. Dashehari. The long-term exposures (about 20 years) were monitored under a subtropical ecosystem. Based on plant growth properties and acetylene reduction assay, 12 bacterial isolates (7 from G1-organic and 5 from G2-conventional systems) were identified as Pseudomonas and Bacillus spp. In the conventional system, dehydrogenase activity significantly decreased (0.053 µg TPF formed g−1 of soil h−1) and adversely affected the bacterial diversity composition. In comparison, organic treatments had a good impact on dehydrogenase activity (0.784 µg TPF formed g−1 of soil h−1), alkaline phosphatase (139.25 µg PNP g−1 soil h−1), and bacterial community composition. The Metagenomics approach targeted the V3 and V4 regions to see the impact in the phylum, order, family, genus, and species for both the treatments. Results showed that phylum Acidobacteria (13.6%), Firmicutes (4.84%), and Chloroflexi (2.56%) were dominating in the G2 system whereas phylum Bacteroides (14.55%), Actinobacteria (7.45%), and Proteobacteria (10.82%) were abundantly dominated in the G1 system. Metagenome sequences are at the NCBI-GenBank sequence read archive with SRX8289747 (G1) and SRX8289748 (G2) in the study PRJNA631113. Results indicated that conventional and organic conditions affect rhizosphere microbiome and their environment.