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Doctoral thesis, 2014

Genome-wide analyses of Bacillus amyloliquefaciens strains provide insights into their beneficial role on plants

Niazi, Adnan


The innate immunity system of plants provides a basal defence barrier to most microorganisms. However, many plant pathogens have evolved to overcome this defence. Certain bacteria in the PGPB (plant growth promoting bacteria) category that improve plant growth have also been found to improve plant defence against insect pests and pathogens. Some bacteria of the genus Bacillus are known to be associated with plant roots, and have potential as possible biocontrol agents and biofertilizers in agriculture. For instance, Bacillus amyloliquefaciens subsp. plantarum strains can support plant growth and protection to stress after developing physical and biochemical contacts with plants. This thesis provides detailed descriptions of the genomic structure of three B. amyloliquefaciens subsp. plantarum strains with ability to promote plant growth and to suppress disease from several pathogens. The Bacillus genomes contain the basic genetic traits required for survival in the rhizosphere and plant growth promotion including chemotaxis and motility, root colonization, and biosynthesis of phytohormones. Besides growth promotion, the genomes have the capability to encode several antibacterial and antifungal compounds that effectively protect plant from pathogenic microorganisms. Several of the predicted traits were confirmed by experimental analysis. Genome-wide comparative analysis of the Bacillus strains indicates that the genomes are very similar although variation has been observed in phenotypes associated with plant growth promotion and disease suppression. A possible explanation could be mutations in one or more putative genes. Genomic comparison with other non-plant associated Bacillus species indicates the genomic polymorphism has a crucial role in loss and gain of function in the two groups of Bacillus species.


Bacillus amyloliquefaciens; Genome sequencing; Plant growth promoting rhizobacteria; PGPR; biocontrol; bacterial genome analysis; comparative genome analysis

Published in

Acta Universitatis Agriculturae Sueciae
2014, number: 2014:66
ISBN: 978-91-576-8080-8, eISBN: 978-91-576-8081-5
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

Authors' information

Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Bioinformatics and Systems Biology
Agricultural Science

URI (permanent link to this page)