Unraveling whole genome sequence of pesticide degrading and eggplant growth promoting endophytic strain Klebsiella sp. HSTU-Sny5

Abstract

The study is aimed to characterize a pesticide degrading robust endophytic strain on eggplant growth promotion and to revealing their mechanism through genome wide investigation. To this end, ten different endophytic bacteria were isolated from tomato plant root by screening on the chlorpyrifos pesticide containing agar media.The strain was able to degrade the pesticide in liquid culture that is confirmed by FTIR analysis. The isolate was named as Klebsiella sp. HSTU-Sny5. The HSTU-Sny5 showed MR positive, VP negative, catalase positive, oxidase negative, TSI, CIU, sucrose, dextrose,MIU test, lactose, Urease and maltose positivein test. Indole-3 acetic acid (IAA), ACC deaminase activity, nitrogen fixing and phosphate solubilizing test were observed in positive. Further confirmation of growth promotion activity, these isolates was applied on eggplant.The eggplant germination, root length and shoot length was significantlyenhanced by after treatment of the HSTU-Sny5 strain, as consequence, theVigor Indexobtained508.30±8.20 for the untreatedand 734.40±15.11 for the HSTU-Sny5treated egg plants.The whole genome shot gun sequence of the strain showed one single 5,432,112bp chromosome, with an average 57.8% GC content and 5,231 predicted protein coding DNA sequences (CDS). Plant growth promoting such as phosphate metabolism genes (pstC, pstA, phoU, phoR (sphS), phoB (sphR), pstB, pstS), IAA production gene (Tryptophan synthase beta (trpB), Tryptophan synthase alpha (trpA), Anthranilate synthase, aminase component, Indole3-glycerol phosphate synthase) and nitrogen fixation genes (nifE,nifH, nifA, nifB, nifM, nifZ,nifS, nifU, nifN, nifT) were found in the CDS of genome. Also siderophore production genes(fhuB, tonB, fepG, fepB, fhuD, fhuC, fhuA, fntS etc.), chitinase, H2S production and sulfur assimilation, heat shock proteins, cold shock proteins, superoxide dismutase, and heavy metal (Arsenic resistance, Cadmium, Zinc, Cobalt). Pesticides degrading genes especially organophosphorus gene (opdE), and total 27 esterase proteins were found. The analysis of the HSTU-Sny5 genome revealed a large number of genes involved in uptake and exchange of nutrients, chemotaxis, mobilization, plant colonization, stress tolerance, growth promotion, and pesticide metabolism, which suggested the strains capabilityof providing probiotic roles in nature.