The prevalence of antimicrobial resistance (AMR) in bacterial pathogens resulting from the intensive usage of antibiotics and antibiotic compounds is acknowledged as a significant global concern that impacts both human and animal health. In this study, we sequenced and analyzed the genomes of two emergent onion-pathogenic species of Burkholderia, B. cenocepacia CCRMBC56 and B. orbicola CCRMBC23, focusing on genes that are potentially associated with their high level of antibiotic and copper resistance. We also identified genes contributing to the copper resistance of B. cenocepacia CCRMBC56 through high-throughput analysis of mutated genes in random transposon mutant populations that were differentially enriched in a copper-containing medium. The results indicated that genes involved in DNA integration, recombination, and cation transport are important for the survival of B. cenocepacia CCRMBC56 in copper-stressed conditions. Furthermore, the fitness effect analysis identified additional genes crucial for copper resistance, which are involved in functions associated with the oxidative stress response, the ABC transporter complex, and the cell outer membrane. In the same analysis, genes related to penicillin binding, the TCA cycle, and FAD binding were found to hinder bacterial adaptation to copper toxicity. This study provides potential targets for reducing the copper resistance of B. cenocepacia and other copper-resistant bacterial pathogens.

One of the challenges in the practical application of plant growth-promoting bacteria (PGPB) is predicting their effectiveness under field conditions. Performance can vary due to environmental factors and the recruitment of genotype-specific microbiota through root exudates. In addition, the viability of PGPB during storage and delivery must be maintained to avoid inconsistent field performance. Lyophilization (freeze-drying) is a promising method for preserving bacterial cells; however, this process subjects bacterial cells to extreme thermal and osmotic stresses that can lead to irreversible cellular damage. In this study, the addition of crude soybean seed extract, with 10% glycine betaine and 5% cellobiose as cryoprotective agents, improved bacterial viability after freeze-drying with high recovery rates of 82–98% after preservation, which is essential to ensure the efficacy of beneficial soil bacteria used as biotic agents. To our knowledge, this is the first study to report optimal preservation conditions for beneficial soil bacteria shown to promote soybean growth, providing a basis for improving soybean yield through microbial applications.