Project topics and materials
Get Complete Project Material File(s) Now! »
Regulation of plant colonization, stress response and biofilm formation in bacteria of the Bacillus subtilis group
“For the effective establishment of PGPR beneficial effects, the ability to colonize plant roots by introduced bacteria is an important trait” (Bouizigarne, 2013). PGPR use flagella to move to the root surface (Nihorimbere et al., 2011). In the soil, PGPR overcome opposition from plants and other soil
microorganisms to successfully colonize plants. The PGPR colonization process involves seed attachment, respond to seed exudates, root surface attachment and root colonization, “it includes the following steps: attraction, recognition, adherence, colonization and growth and other strategies to establish interaction” (Nihorimbere et al., 2011). Successful plant colonization involves several aspects, including but not limited to: mechanisms to withstand environmental stresses, efficient chemotaxis, effective communication within bacteria and between bacteria and plant which is performed by quorum sensing auto inducers (Lengeler et al., 1999) as well as transcriptional adaptation. “To establish sufficient population on the host roots, compatibility with the host root exudates and other compounds released by the rhizosphere microorganisms is crucial” (THCFarmer Community, 2017). To understand the genetic mechanisms underlying interaction between Bacillus PGPR and the host plant is important for their effective use as biofertilizers and biopesticides; however there are only a few gene regulation studies during plant colonization from Bacillus subtilis group (Fan et al., 2012). B. subtilis produces biofilm: an extracellular matrix that holds the cells together in multicellular communities (Beauregard et al., 2013). The biofilm is used to attach on root surface where the bacteria provide the plant with many benefits (Vlamakis et al., 2013). B. subtilis coordinates the expression of matrix genes in response to shifting environmental conditions using a complex regulatory network (Vlamakis et al., 2013).
When bacteria colonize plant roots, they encounter different stress conditions from plants and the environment. Bacteria are able to survive stressful environments by altering their gene expression which is controlled at transcription level (Borukhov and Nudler, 2003). Bacillus subtilis cells’ adaptation to stress and starvation is crucial for survival in nature because these unfavorable conditions are the rule in natural ecosystems (Petershon et al., 2001).
Plant colonization, stress response and biofilm formation in the bacteria are controlled at transcription level. Transcription factors involved in the processes are explained in section 1.2.3. The B. subtilis group has a σ/B-dependent general stress regulon with more than 200 genes which are expressed following bacterial exposure to heat, acid, ethanol, salt stress, entry into stationary phase, or starvation for glucose, oxygen or phosphate (Petershon et al., 2001, Price et al., 2001). The group has other sigma factors which respond to different stress conditions. SigI controls a class of heat shock genes. SigL controls the utilization of arginin, acetoin and fructose, required for cold adaptation. SigM controls adaptation to inhibitors of the peptidoglycan synthesis. SigV controls resistance to lytic enzymes. SigX controls resistance to cationic antimicrobial peptides (Subtiwiki.uni-goettingen.de, 2017).
Chapter 1: LITERATURE REVIEW
1.1 Overview of the application of plant growth promoting bacteria in agriculture
1.1.1 The problem of food security around the world and in developing countries
1.1.2 Plant growth promoting bacteria as biofertilizers and biopesticides
1.2. Bacillus as a paradigm of PGPR
1.2.1 Systematic and phylogeny of the Bacillus subtilis group
1.2.2 Regulation of plant colonization, stress response and biofilm formation in bacteria of the Bacillus subtilis group .
1.2.3 Transcription regulation and important transcription factors in PGPR Bacillus
1.2.4 Application of genomics and transcriptomics approaches to elucidate the mechanisms of positive action of the PGPR Bacillus
1.2.5 Simulation of plant colonization by root exudates
1.3 Problem statement
REFERENCES .
CHAPTER 2: EVALUATING THE PLANT PROMOTION AND PLANT PROTECTION ACTIVITIES OF THE BACILLUS STRAINS
2.1 Introduction
2.2 Materials and methods
2.2.1 Cultivation of the Bacillus
2.2.2 Bacillus growth on root exudates
2.2.3 Re-isolation of Bacillus strains from the wheat roots
2.2.4 Plant growth promotion
2.2.5 Inhibition of phytopathogenic fungi
2.2.6 Inducing drought tolerance in plants by treatments with Bacillus .
2.3 Results and Discussion
2.3.1 Bacillus growth on root exudates .
2.3.2 Re-isolation of Bacillus strains from wheat roots .
2.3.3 Plant growth promotion
2.3.4 Inhibition of phytopathogenic fungi
2.3.5 Induction of drought tolerance in plants by treatments with Bacillu
2.4 Conclusion
REFERENCES
Chapter 3: REGULATION OF GENE EXPRESSION IN BACILLUS ATROPHAEUS UCMB-5137
STIMULATED BY MAIZE ROOT EXUDATES
3.1 Introduction
3.2 Materials and methods .
3.2.1. Root exudates preparation
3.2.2. Bacterial growth conditions and RNA preparation
3.2.3. Total RNA extraction and sequencing
3.2.4. Complete genome sequence of B. atrophaeus UCMB-513
3.2.5. Gene orthology and phylogenetic studies
3.2.6. Gene co-expression analysis
3.2.7. Identification of the differentially expressed non-coding RNA
3.3 Results and Discussion
3.3.1. A complete genome sequence of the strain UCMB-5137 and its phylogeny .
3.3.2. Gene expression profiling .
3.3.3 Superimposition of the gene regulation profile in B. atrophaeus over the regulatory network of B. subtilis
3.3.4. The role of ncRNA in gene regulation under root exudates stimuli
3.3.5. A comparison of the gene expression profiles of the B. atrophaeus UCMB-5137 and the
B. amyloliquefaciens FZB42 stimulated by the root exudates
3.4 Conclusion
GENERAL CONCLUSION AND RECOMMENDATIONS
