Use of Endophytic Microorganisms in Crop Adaptations to Increased Salinity and Resistance to Pests and Diseases

Abstract

Understanding endophytic microorganisms associated with soda lakes shrubs and building a holistic Kenyan soda lake living library of microorganisms while exploring their potential applications in various industries is crucial in the current climate crisis. Lake Magadi and Lake Bogoria are saline alkaline endorheic lakes, in semi-arid regions with erratic rainfall. Vascular shrubs growing along the shores of these lakes must develop adaptive mechanisms to cope with high alkalinity, salinity and erratic environmental conditions. Previous studies on soda lake microorganisms have focused on isolations from water, soil and sediments, leaving behind the plant associated niche. Plant associated microorganisms from harsh environments have previously been shown to harbor diverse metabolic and genetic profiles that play an important role in plant growth, health and survival under stressful conditions. The aim of this study was to collect shrubs growing along the shores of Lake Bogoria and Lake Magadi, and isolate associated bacteria and fungi. The resultant isolates were identified using molecular techniques and consensus sequences aligned with highly homologous sequences in NCBI database. The isolates were screened for production of exo-enzymes, salinity tolerance and inhibition of bean root rot pathogen, Fusarium solani. The ability of the isolates to endophytically colonize bean and tomato seedlings was also evaluated. The effects of endophytic colonization on salinity stress, Fusarium solani and Tetranycus urticae were assessed in green house experiments. Endophytic bacteria were affiliated to three different phyla, Firmicutes, Proteobacteria and Actinobacteria while fungal endophytes were affiliated to two phyla, Basidiomycetes and Ascomycetes. A larger number of bacterial isolates were more salt tolerant while only few fungal isolates indicated growth at 1M NaCl concentration. All tested fungal and bacterial isolates irrespective of the concentration or the method used, endophytically colonized tomato and bean seedlings respectively.. Two bacterial isolates; Bacillus megaterium and Enterobacter hormaechei subsp. Xiangfangensis showed more than 50% bean root rot pathogen, Fusarium solani mycelial inhibition in dual culture assays, completely inhibited germination of the spores in co-culture assays and resulted in its biocontrol in planta. All the four select fungal endophytes significantly enhanced the germination of tomato seeds by 23% under salinity stress. Endophytic colonization of tomato seedlings significantly decreased the quantity of hydrogen peroxide and enhanced total chlorophyll produced under salinity stress compared to non-inoculated seedlings. Exposure of tomato seedlings colonized with fungal endophytesdid not affect the number of eggs laid or the mortality of spider mites. The study gives a first insight into the bacterial and fungal endophytes associated with saline alkaline adapted shrubs. The isolates also provide the potential use of soda lakes derived microorganisms in the agricultural production, an application that has not been widely explored in Kenya.