Sorghum

Introduction

Sorghum (Sorghum bicolor) is a major food security cereal crop that millions of subsistence farmers in the Sub-Saharan Africa (SSA) rely on. It possesses key agronomic traits that made it a referred crop for cultivation in the respective region, and among these, its adaptation to drought prone arid and semi-arid growing conditions, and substantial grain harvest with minimal investment on agricultural inputs (chemical fertilizers, pesticides, herbicides, etc.). However, the scourging impact of Striga (Striga hermonthica, a.k.a. “Witch-weed”) has long remained a major agricultural constraint hampering the productivity of sorghum in SSA. In worst case scenario, yield losses attributable to Striga infestation could mount to 100%, often forcing farmers to totally abandon their fields. Several control and integrated Striga management systems were developed and implemented over the past half a century. The approaches encompass resistance breeding, herbicides (chemical and biological) application, traditional and improved farm management practices, etc. These efforts, to some extent, managed to limit the Striga devastation and improved sorghum production. 

Nonetheless, despite decades of relentless efforts in research and development (R&D), a ‘silver-bullet’ solution to Striga infestation is yet to be realized. As such, multitude of factors are accounted for the persistence of the Striga problem to date, including, (i) the sustainability, accessibility, and affordability of the Striga control technologies; (ii) resistance breakdown of improved sorghum lines; (iii) poor seed production and dissemination systems; (iv) the incredible environmental adaptation potential of the parasite; and (v) the dynamically evolving new races and/or virulence mechanisms of the parasite, etc. 

With recent advances in ‘omics’ technologies, our understanding of physical, physiological, biochemical, and genetic basis of host-parasite interaction is getting comprehensive. Therefore, scientific efforts towards the development of sustainable, accessible, and affordable alternative biological Striga control solutions tools are promising and technically feasible. Plant microbes are evolutionarily coined to their respective hosts, hence, are often regarded as the ‘extended phenotypes’. Practically demonstrated and molecularly supported experimental reports revealed the plant growth promoting (PGP) beneficial roles of microbes, including defence against pathogens like Striga. Hence, integration of microbes into the ongoing and future R&D programmes for Striga eradication, will be instrumental towards the ultimate success. 

Congruent to the above narrations and suggested perspectives, this thesis was designed with the aims of determining: (i) the physicochemical and microbiome community of native soils in which sorghum was believed to be originated and domesticated; (ii) the sorghum root microbiome community (diversity, composition, and function) in the native soils, and factors dictating the community assembly and functional role; (iii) the core, commonly shared, microbial genera and functional attributes transcending the recruitment pressure exerted by the underlying factors related to soil type, sorghum genotype and phenotype differences; (iv) the effectiveness the core microbial taxa members affecting Striga seed germination and the microbial-based volatile organic compounds (VOCs) significantly correlated thereof, and (v) the impact of Striga infestation on the sorghum plant biomass, root metabolome and rhizosphere microbiome community diversity, composition, functional attributes and biosynthetic gene cluster (BGC) profile, by an integrated ‘omics’ approach in distinct sorghum varieties with genotypic and phenotype differences, particularly in Striga resistance trait. 

Results

In this thesis, we selected three physicochemically distinct soils from 48 sorghum field sites and grew 12 genetically diverse sorghum genotypes with varying phenotypic traits (domestication history, Striga resistance, drought tolerance). Amplicon analysis was conducted and a pre-set criteria was used to define the core: i.e., detected in at least 50% of the replicates at a relative abundance threshold of at least 0.01 (1%). Accordingly, 267 amplicon sequence variants (ASVs) belonging to Rubrobacteria, Pseudomonas, and Beijerinckiaceae were identified to dominate the core rhizosphere microbiome irrespective of soil type and sorghum genotype. 

Selective isolation of the core Pseudomonas taxa was made from the respective rhizosphere soils and the identity of the isolates was confirmed using sequence similarity in the 16S rRNA and shotgun metagenome data. In an approach first in its kind in sorghum research, a temporally and spatially synchronized greenhouse experiment was executed to generate metagenomics and untargeted metabolomics data of roots of three sorghum varieties differing in resistance to Striga. The results revealed significant negative effect of Striga on sorghum biomass in a genotype-dependent manner. The pairwise comparison of control and Striga-infested groups revealed fine-tuned changes in the metabolome, microbiome, functional and BGC profiles that are significantly associated with Striga-infestation in sorghum. The research results generated, and supplementary information provided, could serve as a basis for future efforts focused on microbiome based Striga control strategies.

Striga infestation significantly affected shoot biomass of the susceptible sorghum genotypes, Teshale and Shanqui Red. In these genotypes, the Striga attachment count was also higher compared to the resistant genotype SRN39. However, despite the underlying phenotypic and genotypic differences of the three sorghum genotypes, the root dry weight (RDW) remained unaffected following Striga infestation. In overall, apart from the significant effect on the microbiome in the resistant genotype, Striga infestation did not affect the metabolome, functional and BGC profile of sorghum. Rather, it resulted in fine-tuned and calibrated changes that possibly contributed to resistance in SRN39 and potentially linked to alleviation of biotic stress in the susceptible genotypes.  

Per the objectives of this thesis, the potential of the core isolates against Striga development was tested in lab-based bioassay. Using a mechanistic experimental setup, the significant effect of the isolates on Striga seed germination suppression and loss of viability was determined. In addition, the identity of microbial volatile organic compounds (VOCs) that significantly and negatively correlated with seed germination and viability of Striga seeds were identified. The respective experiments confirmed the functional plant growth promoting (PGP) role (i.e., defence against Striga attack) of core microbes in the sorghum rhizosphere as a niche. Studies conducted on several plants identified Pseudomonas as a major plant growth promoting rhizobacteria. Considering both PGPR traits renowned for and the significant antagonistic effect on Striga, the core Pseudomonas will potentially be considered for wider field application and integration into the Striga control schemes. This practicality of the conclusion is based on the greater survival advantage the taxa possess due to the minimal effect of soil and genotype variation effect on its proliferation and repulsive reactions from the resident microbiota.