Mid-project Progress Report

Microbes can directly and indirectly interfere with the Striga life-cycle, either by deterring the parasite or by triggering processes that impair infection of the host roots (Masteling et al., 2019). Direct modes of action include i) pathogenicity towards Striga, ii) antagonism via secondary metabolites or volatile organic compounds, and iii) interference with host-Striga signalling. Indirect modes of action by which microbes could suppress Striga include a) enhancement of nutrient (P, N) acquisition by the host, b) induced systemic resistance (ISR), and c) alteration of root exudation or root architecture (Masteling et al., 2019). To date, most studies on microbe-mediated suppression of Striga and other root parasitic weeds have focused on the activities of single microbial species, mostly fungi and bacteria. In the PROMISE project, the ultimate goal is to design synthetic microbial communities (SynComs) or identify microbial metabolites that consistently suppress Striga infections or trigger suicidal germination of the Striga seed bank. The design of SynComs should involve microbes with complementary modes of action that act together or synergistically, and preferably at different stages of the parasite’s life cycle. This reinforces the need to understand the taxonomic and functional diversity of the sorghum root microbiome and the dynamic changes in the microbiome during plant and parasite development as well as their interaction. Moreover, a microbiome-mediated strategy for Striga control should take into account how each microbial member of the consortium behaves across different soil conditions, how their activities are influenced by the genotypic diversity of the host and parasite as well as by other commonly used agricultural practices used to control Striga (e.g. crop rotation, trap/catch crop).

Figure 1: picture of a sorghum field site in Ethiopia sampled in the PROMISE project to map the Striga seedbank and to characterize the soil and sorghum root microbiome (picture courtesy: Dr. Taye Tessema, EIAR).

In the past 2-3 years of the PROMISE project, we have developed a highly sensitive molecular detection method that allows accurate quantification of Striga seeds in field soils. This technique is now applied in the project to i) quantitatively map the geographic distribution of the Striga seedbank in soils from Ethiopia and other sub-Saharan countries, ii) assess the relation between Striga seedbank and incidence in sorghum fields across different agro-ecologies in Ethiopia, and iii) investigate the impact of existing and new (microbiome-based) approaches that target the Striga seedbank. To identify Striga-antagonistic microbes or microbial metabolites, we developed an automated computer vision tool for image analysis and high-through-put bioassays. To isolate potential members of a microbial SynCom, we determined the core and accessory root microbiome of sorghum. Defining the core microbiome allows us to target microorganisms and traits that are consistently associated with roots of different sorghum genotypes growing in soils from different agroecological zones. To identify specific microbial genera that interfere with the Striga life-cycle we are screening a well-characterized and sequenced bacterial culture collection representing multiple phyla, genera and species. We also established and characterized a large fungal isolate collection (approximately 4,000 isolates) from Ethiopian field soils, sorghum roots and Striga seeds. Several of these significantly interfere with Striga seed germination. Similarly, we established a large collection of P-solubilizing bacteria which are being tested for their abilities to affect the strigolactone-based signalling between host and parasite.

In the context of host-parasite signalling, we identified new putative mechanisms by which the root microbiome can exert a suppressive effect on Striga root infection by manipulation of the host (sorghum) physiology, host-Striga signalling and root cellular traits. These mechanisms are being further explored in the coming year. In this context, we also initiated collaborations with two other projects funded by the Bill & Melinda Gates Foundation, i.e. N2-Africa and ENSA. Together with team members of N2-Africa, experiments on Striga seed bank detection in selected Kenyan soils were initiated. For ENSA, experiments were conducted to evaluate the impact of specific plant genes on root microbiome assembly and Striga infection.

Masteling, R., Lombard, L., De Boer, W., Raaijmakers, J. M., & Dini-Andreote, F. (2019). Harnessing the microbiome to control plant parasitic weeds. Current Opinion in Microbiology, 49(June), 26-33. https://doi.org/10.1016/j.mib.2019.09.006