Actinobacteria in extreme environments: diversity and plant growth promotion for mitigation of abiotic stresses in tomato

Abstract

Extreme environments contain unfavorable conditions for survival of most microorganisms such as high salinity and drought. These environments are attractive for searching beneficial microorganisms including actinobacteria with adaptive mechanisms and ability to produce metabolites or enzyme that can work in extreme environments and can be applied in biotechnology and agriculture. Therefore, our research focused on actinobacteria from limestone habitats (karst, cave, and limestone quarry) and deep-sea sediments as representatives of terrestrial and marine extreme habitats, respectively. Diversity of actinobacteria was investigated in six limestone habitats in northern Thailand. Soil, dripping water and cotton swab samples were collected to isolate actinobacteria. Samples were pretreated with microwave irradiation prior to isolation on five selective media (humic acid vitamin agar, raffinose-histidine agar, R2A agar, starch casein agar, and water proline agar). A total of 133 actinobacteria were isolated from five limestone habitats with the highest number of actinobacteria was obtained from karst landscape (Forest industry organization, Lampang province). The dominant actinobacteria from all habitats were members of rare actinobacteria. For identification at genus level, Chiang Dao cave showed the highest number of actinobacterial genera (8 genera) followed by Muang-on cave (6 genera), Forest industry organization (4 genera), Thampla cave (2 genera) and quarry area of The Siam cement public company limited (2 genera). This is the first report on isolation of the following genera Epidermidibacterium and Promicromonospora (Chiang Dao cave), Mycolicibacterium and Sinomonas (Muang-on cave), Rugosimonospora (Forest industry organization), and Mycolicibacterium (limestone quarry). Phylogenetic analysis of 16S rRNA gene sequence data revealed that 24.1% of actinobacteria may represent novel species. All actinobacteria were evaluated for three plant growth promoting properties (total indole and siderophore production and phosphate solubilization), and drought tolerance ability. One- hundred and six isolates (79.7%) showed at least one plant growth promoting ability. Among 133 isolates, 80 isolates (60.1%) produced total indole in a range of 0.09- 146.94 µg mL-1. For siderophore production, 72 isolates (54.1%) produced 3.82-1014.17 µmol L-1 of hydroxamate siderophore and 66 isolates (49.6%) produced catecholate siderophore between 1.40-274.33 µmol L-1. Fifteen isolates of actinobacteria could solubilize phosphate and released phosphorus in culture broth in a range of 73.78-104.38 µg mL-1. Two drought- tolerant, ACC deaminase producing actinobacteria, Streptomyces sp. isolate MC1-2 and Tsukamurella sp. isolate MC5-5 were selected to investigate their potential for tomato growth promotion under normal and drought conditions in greenhouse condition. At the end of experiment, Streptomyces sp. MC1-2 showed the best performance as it increased the yield of tomato fruits two folds higher than non-inoculated tomatoes, increased shoot length, dry weight, root dry weight, total chlorophyll, and carotenoids and decreased hydrogen peroxide content of tomato leaves under drought. In addition, the inoculation of actinobacteria did not affect vitamin C content and total antioxidants of tomato fruits grown under normal condition. Deep-sea actinobacteria, namely D. abyssi MT1.1T, D. barathri MT2.1T, and D. profundi MT2.2T were evaluated for their plant growth promoting traits and potential to promote the growth of tomato seedlings under 150 mM NaCl. All deep-sea Dermacoccus species exhibited in vitro production of indole-3-acetic acid (IAA), siderophores and phosphate solubilization. The inoculation D. abyssi MT1.1T or D. barathri MT2.1T improved dry weight and chlorophyll content along with a decreased in hydrogen peroxide content of tomato under salt stress. Notably, D. abyssi MT1.1T had ability to colonize tomato roots. Whole genome analysis revealed protein coding sequences involved in plant growth promoting traits and genes related to salt stress mitigation mechanisms. In addition, biosafety of deep-sea Dermacoccusstrains on the representative organisms in environments were evaluated. Different biosafety level of each deep-sea strain was observed. However, D. abyssi MT1.1T and D. barathri MT2.1T would be safe for use in environments. In conclusion, limestone habitats are a rich source of diverse actinobacteria with plant growth promoting abilities. Plant beneficial strains of actinobacteria from both terrestrial (limestone habitats), and marine (deep-sea sediments) extreme environments are able to mitigate drought or salinity stress in tomato which is an environmental friendly approach for sustainable agriculture.