Phylogenetic affiliation of endophytic actinobacteria associated with red gum tree grown in salinity area and their plant growth promoting properties and suppression of phytopathogens, and genome data mining of selected strains

Eucalyptus is an economic plant of Thailand that can tolerate salt and drought stress. This work aims to report on the study of biodiversity among endophytic actinobacteria isolated from <i>Eucalyptus camaldulensis</i> grown in saline soil, as well as their properties for promoting plant growth and inhibiting fungal pathogens <i>in vitro</i>. Root, twig, and leaf samples of five plants, <i>E. camaldulensis</i> grown in Kalasin Province, Thailand, were collected. The soil samples of each plant were collected, and soil salinity was evaluated by the electrical conductivity of a saturated soil extract (ECe). It was found that the ECe of the soil was between 4.5 and 12 dS/m, and the pH of the soil ranged between 3.9 and 5.2. Based on their morphology and 16S rRNA gene sequences, the majority of the isolates (552, 96.7%) were identified as the genus <i>Streptomyces</i>. The remaining isolates (19, 3.3%), which included ten genera: <i>Cellulosimicrobium</i> (3), <i>Kocuria</i> (3), <i>Brevibacterium</i> (2), <i>Micrococcus</i> (2), <i>Microbacterium</i> (2), <i>Peterkaempfera</i> (2), <i>Tsukamurella</i> (2), <i>Brachybacterium</i> (1), <i>Curtobacterium</i> (1), and <i>Gordonia</i> (1). Two hundred and seventy-three isolates were tested for antifungal activity against two eucalyptus pathogens, <i>Pseudoplagiostroma eucalypti</i> LS6 and <i>Cladosporium</i> sp. LB1. Most isolates showed antifungal activity against <i>P. eucalypti</i> LS6. The plant growth-promoting (PGP) study of 154 selected strains showed that 154 (100%), 18 (11.7%), 14 (9.1%), and 7 (4.5%) isolates could produce indole-3-acetic acid (IAA), 1-aminocyclopropane (ACC) deaminase, solubilize phosphate, and fix nitrogen <i>in vitro</i>, respectively. Identification of non-actinobacteria isolates based on 16S rRNA gene sequence analysis indicated that 10 genera were obtained: <i>Aureimonas, Bacillus, Chryseobacterium, Deinococcus, Massilia, Methylobacterium, Pseudomonas, Serratia, Staphylococcus</i>, and <i>Stenotrophomonas</i>. One selected <i>Streptomyces</i> strain, EWL5.1, was selected for a seed germination test in salinity stress and PGP <i>in planta</i>. The result indicated that this strain could support the seedling length vigor index (SLVI) of eucalyptus seedlings in salinity conditions and significantly increase the fresh weight of eucalyptus seedlings <i>in planta</i>. Four representative <i>Streptomyces</i> strains and one strain of <i>Micrococcus</i> were sequenced for their genomes. The result indicated that these four <i>Streptomyces</i> strains comprise various biosynthesis gene clusters (BGCs) of antibiotic production. Genome data mining also reveals that all strains contain genes encoding PGP properties. These potential strains can be applied to be used as PGPB to support eucalyptus growth in the future.