Striga hermonthica, commonly known as witchweed, infests major cereal crops in Sub-Saharan Africa causing severe yield losses and threatening the livelihood of millions of resource poor farmers.... Show moreStriga hermonthica, commonly known as witchweed, infests major cereal crops in Sub-Saharan Africa causing severe yield losses and threatening the livelihood of millions of resource poor farmers. Despite the use of herbicides, Striga-resistant crop varieties and agronomic practices to mitigate the impact of Striga, these are not effective on their own and require high monetary investments by smallholder farmers. My PhD research focuses on the potential of soil microbes to disrupt the early stages of the parasite’s life cycle through the production of volatile organic compounds. More specifically, we developed a computer vision tool that enabled the large-scale screening of a large bacterial collection for its functional potential to suppress Striga seed germination by naturally produced volatile compounds. This was complemented with the identification of several Striga-suppressive volatile compounds and studies into their genomic regulation. We developed a new approach of ‘precursor-directed activation’ of Striga-suppressive soil microbes by amending field soils with amino acid precursors to suppressive volatile compounds. This strategy will enable better deployment of volatile-mediated Striga suppression under field settings, by steering its production in situ and by aiding in the development of future control methods with higher efficacies and lower application costs Show less
The soil-dwelling, filamentous bacteria of the genus Streptomyces are renowned for their production of useful secondary metabolites including antibiotics. The work described in this thesis provides... Show moreThe soil-dwelling, filamentous bacteria of the genus Streptomyces are renowned for their production of useful secondary metabolites including antibiotics. The work described in this thesis provides new insights on the role and regulation of antibiotic production and resistance in these bacteria. It shows that antibiotic resistance is already beneficial at sub-inhibitory antibiotic concentrations. Resistance can even readily evolve at such low concentrations, thereby possibly explaining the level of resistance seen in pristine environments. Antibiotic producers can benefit from spatial structure, as present in the soil, through the preferential allocation of resources and this enables invasion from low frequencies. Streptomyces do not produce all antibiotics continuously, but antibiotic production is instead tightly regulated in response to environmental cues, including those produced by competitors. Streptomyces are most likely to induce antibiotic production in response to a competitor that shares similar secondary metabolite clusters, indicating a possible role for shared signalling. Besides changes in antibiotic production, other responses to competition are revealed on a transcriptomic level, including an increased expression of developmental genes, suggesting earlier sporulation. Show less
Vinasse is a major by-product generated by the sugarcane biofuel industry. It is a source of microbes, nutrients and organic matter and often it is recycled as fertilizer. The research... Show moreVinasse is a major by-product generated by the sugarcane biofuel industry. It is a source of microbes, nutrients and organic matter and often it is recycled as fertilizer. The research described in this thesis addressed how vinasse and sugarcane straw added together with N fertilizer affect the soil microbial community structure and function and N2O emission. The application of vinasse, N fertilizer and combined application of vinasse plus N fertilizer changed in the soil microbial community. However, these changes were restricted to a short period. Vinasse and straw induced changes in the soil microbial community composition and potential functions, but straw additions triggered the stronger changes. The invasive bacteria present in the vinasse were unable to survive in the soil, except of members of the Lactobacillaceae family. Treatments with vinasse and N fertilizer applications increased N2O emissions and the microbial processes involved in N2O production were nitrification by ammonia-oxidizing bacteria (AOB) and archaea and denitrification by bacteria and fungi. However, amoA-AOB (Nitrosospira sp) and fungal nirK were the most important genes related to N2O emissions. These results highlight the importance of vinasse management and can be used as a reference to develop good management practices. Show less
