Periodic Reporting for period 1 - MICROBIS (Metabolites Inducers of Cross-tolerance to Biotic Stress)
Reporting period: 2021-09-15 to 2023-09-14
The exponential increase in world population constitutes a global challenge to ensure food security. Paradoxically, crop quality and productivity are increasingly threatened by more frequent stress factors due to climate change and conversion of suboptimal soils into croplands. Compared to abiotic stressors, pathogens have wider impact on crop yield as they limit plant growth, interfere with post-harvest processes, and affect livestock and human health. Pathogens are responsible of 15% of global crop losses and compromise the equivalent of food for 600 million people. Therefore, deciphering features involved in plant defence is fundamental to complete our understanding about immunity and design biotechnological strategies to prepare plants for adverse environments.
There have been important limitations that precluded our capacity to elucidate mechanisms underlying immunity. First, plant immune responses have been mostly characterised upon pathogen infection in isolation, but not in combination with abiotic stressors as often occurs in nature. Second, immune responses rely on interconnections among multiple biological components and not on individual players, as traditionally addressed. Third, defence strategies characterised in model species might differ in species of agronomical interest due to interspecific barriers. To circumvent such limitations, I investigated plant immunity using sequential designs for abiotic-biotic stressors and systemic analysis in Arabidopsis and crop species.
Previous studies envisaged that metabolome reconfigurations during transient environmental changes tend to be persistent overtime. Thus, I hypothesised whether metabolite changes configured during abiotic stress conditions could act as signatures to retain “stress memory”. The overarching goal of MICROBIS was the identification of metabolic changes in Arabidopsis after exposure to abiotic stressors that enhance resilience against pathogens and set the path for translation into plants of agronomic interest. I addressed four objectives:
1. To characterise Arabidopsis immune responses under sequential stress periods reproducing natural conditions.
2. To recapitulate metabolome rewiring upon sequential stress and isolate candidate features for cross-tolerance.
3. To ascertain the biological relevance of candidate metabolites for cross-tolerance in planta.
4. To initially translate cross-tolerance mechanisms into species of agronomical interest.
The outcome of MICROBIS will contribute to design strategies that efficiently reinforce immunity against frequent pathogens in plants of agronomical interest.
There have been important limitations that precluded our capacity to elucidate mechanisms underlying immunity. First, plant immune responses have been mostly characterised upon pathogen infection in isolation, but not in combination with abiotic stressors as often occurs in nature. Second, immune responses rely on interconnections among multiple biological components and not on individual players, as traditionally addressed. Third, defence strategies characterised in model species might differ in species of agronomical interest due to interspecific barriers. To circumvent such limitations, I investigated plant immunity using sequential designs for abiotic-biotic stressors and systemic analysis in Arabidopsis and crop species.
Previous studies envisaged that metabolome reconfigurations during transient environmental changes tend to be persistent overtime. Thus, I hypothesised whether metabolite changes configured during abiotic stress conditions could act as signatures to retain “stress memory”. The overarching goal of MICROBIS was the identification of metabolic changes in Arabidopsis after exposure to abiotic stressors that enhance resilience against pathogens and set the path for translation into plants of agronomic interest. I addressed four objectives:
1. To characterise Arabidopsis immune responses under sequential stress periods reproducing natural conditions.
2. To recapitulate metabolome rewiring upon sequential stress and isolate candidate features for cross-tolerance.
3. To ascertain the biological relevance of candidate metabolites for cross-tolerance in planta.
4. To initially translate cross-tolerance mechanisms into species of agronomical interest.
The outcome of MICROBIS will contribute to design strategies that efficiently reinforce immunity against frequent pathogens in plants of agronomical interest.
I successfully set up a platform to systematically cultivate Arabidopsis under standard conditions and apply several abiotic stress treatments (temperature, light and water availability) in moderate doses before pathogen challenge. Overall, plants recovered from abiotic stressors displayed enhanced susceptibility against the bacterium Pseudomonas syringae but tolerance against the fungus Botrytis cinerea.
Next, metabolome profiles of Arabidopsis plants were monitored on daily basis to comprehensively cover temporal reconfigurations of metabolites during stress treatments. All treatments led to specific metabolome reconfigurations that persisted when plants returned to standard conditions. Therefore, my analysis supported the irreversibility of metabolome changes as a general trend in abiotic stress responses.
Metabolome datasets were used to elaborate networks to capture a more systemic interpretation of molecular changes during abiotic stress treatments. Network analysis revealed similar reconfigurations among treatments, although the central features operating in response to each stressor was minimally overlapping. Then, I propose a central metabolic response to environmental changes in Arabidopsis, though it should be orchestrated via different components.
To validate my analysis, I extracted the most relevant compounds that could modulate Arabidopsis immune responses based on commonly altered metabolic pathways among abiotic stress treatments and central features in networks. Mutant lines targeting intermediates in selected metabolic pathways were evaluated for immune responses against four different pathogens. More than half of the lines displayed enhanced susceptibility to at least two pathogens, supporting that the identified metabolites indeed sustain defence after environmental changes.
Finally, a similar methodology is being employed for species of agronomical interest, namely tomato and rice. The same platform was used to test abiotic stress responses and immune phenotypes and generate plant material for metabolome analysis. Remarkably, both tomato and rice immunity against compatible pathogen could be manipulated by previous abiotic stress treatments. System-wide analysis of metabolites is ongoing.
Next, metabolome profiles of Arabidopsis plants were monitored on daily basis to comprehensively cover temporal reconfigurations of metabolites during stress treatments. All treatments led to specific metabolome reconfigurations that persisted when plants returned to standard conditions. Therefore, my analysis supported the irreversibility of metabolome changes as a general trend in abiotic stress responses.
Metabolome datasets were used to elaborate networks to capture a more systemic interpretation of molecular changes during abiotic stress treatments. Network analysis revealed similar reconfigurations among treatments, although the central features operating in response to each stressor was minimally overlapping. Then, I propose a central metabolic response to environmental changes in Arabidopsis, though it should be orchestrated via different components.
To validate my analysis, I extracted the most relevant compounds that could modulate Arabidopsis immune responses based on commonly altered metabolic pathways among abiotic stress treatments and central features in networks. Mutant lines targeting intermediates in selected metabolic pathways were evaluated for immune responses against four different pathogens. More than half of the lines displayed enhanced susceptibility to at least two pathogens, supporting that the identified metabolites indeed sustain defence after environmental changes.
Finally, a similar methodology is being employed for species of agronomical interest, namely tomato and rice. The same platform was used to test abiotic stress responses and immune phenotypes and generate plant material for metabolome analysis. Remarkably, both tomato and rice immunity against compatible pathogen could be manipulated by previous abiotic stress treatments. System-wide analysis of metabolites is ongoing.
The publication of the results with Arabidopsis contributed to move the field forward in several directions. My work extends the concept of “stress memory” to metabolites and posed them as modulators of plant immunity. Due to the usage of wide range of stressors and pathogens with different lifestyles, my results suggest as a new general mechanism during sequential stress in Arabidopsis. I stablished an innovative and original Systems Biology approach to investigate metabolome reconfigurations. Furthermore, the outcome from the part derived from crops could represent a new comparative strategy to investigate conserved stress response mechanisms among evolutionary distant species.
I am currently integrating data from crops for direct comparisons of metabolic responses to abiotic stressors among Arabidopsis, tomato and rice. This approach will unravel tentative compounds conserved in distant plant species to be tested as modulators for immunity. Due to limitations in genetic engineering of tomato and rice I will validate candidate metabolites by ectopic treatment with compounds to evaluate resilience to pathogens. To reinforce the relevance of the results I will investigate the effect of the treatments in other species of agronomic interest, namely aubergine and oilseed rape. Therefore, the outcome of MICROBIS will render treatments that generally or individually will confer cross-tolerance against pathogens.
The outcome of MICROBIS contributes to the Societal Challenge 2 of the Work Programme H2020: Food Security, Sustainable Agriculture and Forestry, Marine, Maritime and Inland Water Research and the Bioeconomy since it addresses key challenges that our planet is facing for the years to come, i.e. ensuring food security while adapting to climate change. Indeed, MICROBIS has set an inventive strategy to elucidate candidates and set biotechnological designs to prepare plants for adverse environments. Since the potential treatments are based in natural compounds and might have relatively low cost of production, it could be envisaged that the biotechnological approaches derived from MICROBIS could be easily implemented while minimising environmental and economic impacts. In consequence, the outcome of this action could be of interest for researcher on the one hand to adopt new perspectives about plant immunity and agronomic companies on the other hand to develop innovative products in the near future.
I am currently integrating data from crops for direct comparisons of metabolic responses to abiotic stressors among Arabidopsis, tomato and rice. This approach will unravel tentative compounds conserved in distant plant species to be tested as modulators for immunity. Due to limitations in genetic engineering of tomato and rice I will validate candidate metabolites by ectopic treatment with compounds to evaluate resilience to pathogens. To reinforce the relevance of the results I will investigate the effect of the treatments in other species of agronomic interest, namely aubergine and oilseed rape. Therefore, the outcome of MICROBIS will render treatments that generally or individually will confer cross-tolerance against pathogens.
The outcome of MICROBIS contributes to the Societal Challenge 2 of the Work Programme H2020: Food Security, Sustainable Agriculture and Forestry, Marine, Maritime and Inland Water Research and the Bioeconomy since it addresses key challenges that our planet is facing for the years to come, i.e. ensuring food security while adapting to climate change. Indeed, MICROBIS has set an inventive strategy to elucidate candidates and set biotechnological designs to prepare plants for adverse environments. Since the potential treatments are based in natural compounds and might have relatively low cost of production, it could be envisaged that the biotechnological approaches derived from MICROBIS could be easily implemented while minimising environmental and economic impacts. In consequence, the outcome of this action could be of interest for researcher on the one hand to adopt new perspectives about plant immunity and agronomic companies on the other hand to develop innovative products in the near future.