Tracking beneficial Streptomyces strains in plant shoot, roots and rhizosphere soils

Author: Lovepreet singh Lovepreet Singh

Lovepreet Singh, Lovepreet singh, 2019 Tracking beneficial Streptomyces strains in plant shoot, roots and rhizosphere soils, Flinders University, College of Medicine and Public Health

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Bacteria are ubiquitous in the environment. Among these bacteria, Streptomyces which are an important genus of Actinobacteria can be found in the soil and produce a number of bioactive secondary metabolites. Streptomyces can also be found in plants as endophytes to promote the plant growth and to suppress plant pathogens. Endophytic population also assist in the plant growth by alleviating biotic stresses (disease control) and abiotic stresses such as drought. These endophytes can promote plant growth and yield, suppress pathogens, may help to remove contaminants, solubilize phosphate, or contribute in nutrient acquisition in plants. These treatments were conducted on plants using whole live cells of Streptomyces. Wheat and chickpea plants grown under application of Streptomyces were selected to monitor the presence of bacterial strain. To monitor the presence of these endophytes some techniques needed to be developed. There are many different methods to isolate and characterise bacterial strains, but it is difficult to track a specific strain that was added to a plant. These pitfalls can be avoided by using whole genome next generation sequencing and target conserved genes with high single nucleotide polymorphism. Primer designing on the highly polymorphic region could be helpful to identify and track specific Streptomyces strain in plant and soil samples. To ensure the primer specificity, optimization of strain specific primers was first performed by using in silico bioinformatic tools. Conventional PCR was used to confirm the specificity of designed primers for selected strains versus other closely related Streptomyces strains. Then selected Streptomyces strains were detected and quantified in plant shoots and roots and soil samples using quantitative PCR. Streptomyces strains in different plant and soil samples were detected in seeds and plants roots. The final DNA concentration of specific strains was calculated using a standard curve obtained following serial dilution of the DNA of pure cultures. The presence and quantification of Streptomyces strains will be helpful to optimize the concentration of inoculant.

Keywords: strain tracking, streptomyces, actinomycetes, strain typing, antiSMASH, Geneious, chickpea, wheat, qPCR,PCR.

Subject: Biotechnology thesis

Thesis type: Masters
Completed: 2019
School: College of Medicine and Public Health
Supervisor: Dr. Ricardo Pinto Araujo