Diversity and probiotic activities of endophytic bacteria associated with the coastal halophyte Messerschmidia sibirica

There is an increasing interest for exploitation and utilization of endophyte resources. However, little was known about endophytic bacteria (EB) associations with halophytes. It is hypothesized that EB from halophytes have evolved mechanisms that promote plant growth, while improving host-plant resistance to biotic and abiotic stress. The present study is the first to examine culturable EB colonization in Messerschmidia sibirica, a salt-secreting halophyte grown in coastal zone of Shandong peninsula in China. Total 198 EB strains were isolated from 450 samples of healthy M. sibirica leaf, stem, and root tissues. Phylogenetic analysis of 16S rRNA gene identified 40 EB genera, indicating a high degree of diversity. Pseudomonas alcaliphila had the highest colonization frequency in leaves and roots, whereas Bacillus subtilis was highest in stems. Diversity and species richness were greater in leaves and stems than in roots. Notably, cultivation-independent and -dependent analyses identified different bacterial species, especially when abundance is low, indicating the necessity of combining the two methods. Most (92.39%) strains exhibited at least one plant growth promotion trait. Respectively, 68.69%, 75.25%, 47.98%, 21.21%, and 48.48% of strains exhibited 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, IAA secretion, siderophore production, and N-fixation, and P-solubilization. In addition, 13.64% of strains showed antimicrobial activity against one or more plant pathogens, including Phytophthora nicotianae, Alternaria alternata, Ralstonia solanacearum, Acidovorax citrulli, Pseudomonas syringae pv. lachrymans, and Erwinia carotovora subsp. Carotovora. Overall, our results supported the habitat-adapted symbiosis hypothesis, demonstrating that M. sibirica naturally harbors a diverse array of EB with different traits beneficial to the host plant.