Objective  Culture methods for and detection of the antibiotic resistance genes (ARGs) in the endophytic bacteria of Azolla were established to monitor and find means to curtail the drug pollution in aquatic environment.

  Method  Three selected media were used to culture the endophytic bacteria in Azolla microphylla for metagenome sequencing and bioinformatical analysis on ARGs.

  Result  A total of 48.66G clean data was obtained to yield 54 180 predicted ORFs. Through the taxonomic information database NR, 1 712 microbial species were annotated belonging to 38 phyla. On species abundance of the bacteria from the 3 cultures, Proteobacteria accounted for more than 99.14% of all at the phyla level, while at genus level, Herbaspirillum approximately 91% and Burkholderia 1.2%. Blasted with the ARDB database, 3 samples were annotated with 10 genes associated with the resistance to bacitracin and chloramphenicol. Compared to CARD, there were 212 antibiotic related genes (AROs) found in the samples. The genes resistant to antibiotics (AR) accounted for more than 88% of total AROs, while those sensitive to antibiotics (AS) approximately 7% and those resistant to target antibiotics (AT) 4-6%.

  Conclusion  The community structure and ARG types of the endophytic bacteria in Azolla cultured in the 3 different media were basically same.