Isolation, characterization and phylogenetic analysis of endophytic bacteria in rice plant cultivated on soil of Phu Yen province, Vietnam

Abstract

Endophytic bacterial diversity in Rice plant cultivated on soil of Phu Yen province, Vietnam was studied. Rice plant samples were taken in eight sites (districts) of Phu Yen provinces of this region. Endophytic bacteria were isolated in three kinds of medium (LGI, NFb, RMR) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 561 isolates were isolated on three media and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 73 isolates having the best characteristics and they were identified as rice endophytes and nifH gene. The sequences from selected endophytic bacteria (73 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). From 73 isolates, 23 isolates belonged to Bacillus (31.54%), 44 isolates were Proteobacteria (60.24%), while 6 isolates were Bacteroides (8.22%). Based on Pi value (nucleotide diversity), Bacteroides group had the highest theta values in comparison of three groups and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Bacteroides group had the highest values in comparison of three group. From these results showed that thirteen strains (Bacillus megaterium TANa5, Bacillus methylotrophicus TAN17, Bacillus megaterium TALa14, Pseudomonas putida TAL1, Bacillus subtilis TAL4, Burkholderia kururiensis TAL22, Azospirillum amazonense SHL70, Bacillus subtilis DXL 136, Burkholderia kururiensis PHL87, Burkholderia vietnamiensis PHL103, Bacillus megaterium PHL105, Bacillus megaterium DHL154 and Bacillus subtilis SHIM60) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor soils and high-yielding rice because they are not only famous strains but also are safety strains for agricultural sustainable.