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

Onuma Kaewkla^1,2*Kawintip Kiakhunthod^1,2Sumalee Chukhampang¹Butsayarat Klinjanthasorn^1,2Piriya Klankaew³Winya Dungkaew²

• ¹Department of Biology, Faculty of Science, Mahasarakham University, Mahasarakham province, Thailand
• ²The Northeastern Soil Salinity Research Unit, Faculty of Science, Mahasarakham University, Maha Sarakham Province, 44150, Thailand, Mahasarakham Province, Thailand
• ³Faculty of Science, Omics Science and Bioinformatics Center, Chulalongkorn University, Pathumwan, 10330, Bangkok, Thailand, Bangkok, Thailand

This work was the first report of studying the biodiversity of endophytic actinobacteria isolated from Eucalyptus camaldulensis grown on saline soil and their properties as plant growth-promoting and inhibiting fungal pathogens in vitro. Root, twig, and leaf samples of five plants, E. camaldulensis 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 pH of 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 Streptomyces. The remaining isolates (19, 3.3%), which included ten genera: Cellulosimicrobium (3), Kocuria (3), Brevibacterium (2), Micrococcus (2), Microbacterium (2), Peterkaempfera (2), Tsukamurella (2), Brachybacterium (1), Curtobacterium (1), and Gordonia (1). Two hundred and seventy-three isolates were tested for antifungal activity against two eucalyptus pathogens, Pseudoplagiostroma eucalypti LS6 and Cladosporium sp. LB1. Most isolates showed antifungal activity against P. eucalypti 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 in vitro, respectively. Identification of non-actinobacteria isolates based on 16S rRNA gene sequence analysis showed that 10 genera were obtained: Aureimonas, Bacillus, Chryseobacterium, Deinococcus, Massilia, Methylobacterium, Pseudomonas, Serratia, Staphylococcus, and Stenotrophomonas. One selected Streptomyces strain, EWL5.1, was selected for a seed germination test in salinity stress and PGP in planta. The result showed 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 in planta. Four representative Streptomyces strains and one strain of Micrococcus were sequenced for their genomes. The result showed that these four Streptomyces strains comprise various biosynthesis gene clusters (BGCs) of antibiotic production. Genome data mining also reveals that all strains contain genes encoding PGP properties.