Periodic Reporting for period 5 - RESISTANCE (Resistance evolution in response to spatially variable pathogen communities)
Période du rapport: 2022-03-01 au 2022-08-31
RESISTANCE studied the evolution and functionality of disease resistance when accounting for the diversity of pathogens that are attacking the same host. The project focuses on plants, but the mechanisms of diseases and immunity are very similar in other species as well. The aim was to uncover how individuals and populations survive and develop their resistance under continuous attack by multiple pathogens.
The work was carried out on the ribwort plantain across the 4,000 meadows which have been mapped and are annually surveyed in Åland Islands since the 1990s. The intention was to create projections of how the structure of disease communities can influence the growth and reproduction of individuals. At the same time, we gathered information on the factors that underlie the formation of disease communities. We uncovered how resistance functions when the same host is simultaneously or sequentially attacked by multiple different pathogen species, and how resistance evolves under the realistic scenario of pathogen exposure.
The results contribute knowledge that is urgently needed to develop alternative, non-pesticide reliant management strategies in the battle against plant diseases. The current over-reliance on pesticides weighs heavily on our ecosystems and has generated a biased food production situation globally as developing countries lack the funds needed for effective pesticides. Host priming is one alternative method, in which broad spectrum resistance may be triggered by ‘priming' the host’s defences using a biotic (or abiotic) elicitor. Currently more data is needed on how priming functions under natural ecological conditions, and for this purpose results of Objective 3 will be most valuable.
The work was carried out on the ribwort plantain across the 4,000 meadows which have been mapped and are annually surveyed in Åland Islands since the 1990s. The intention was to create projections of how the structure of disease communities can influence the growth and reproduction of individuals. At the same time, we gathered information on the factors that underlie the formation of disease communities. We uncovered how resistance functions when the same host is simultaneously or sequentially attacked by multiple different pathogen species, and how resistance evolves under the realistic scenario of pathogen exposure.
The results contribute knowledge that is urgently needed to develop alternative, non-pesticide reliant management strategies in the battle against plant diseases. The current over-reliance on pesticides weighs heavily on our ecosystems and has generated a biased food production situation globally as developing countries lack the funds needed for effective pesticides. Host priming is one alternative method, in which broad spectrum resistance may be triggered by ‘priming' the host’s defences using a biotic (or abiotic) elicitor. Currently more data is needed on how priming functions under natural ecological conditions, and for this purpose results of Objective 3 will be most valuable.
Objective 1. Towards this end, in 2017 we carried out sampling of natural Plantago lanceolata populations, as well as survey of factors that may play a role in determining these communities. Following RNA extractions, the samples were sent to Switzerland for small RNA sequencing to reveal local virus communities and DNA samples were sent to LGC Genomics GmbH for sequencing of the fungal communities. We analyzed these data using our bioinformatics pipelines and used Joint Species Disribution Models, Markov random fields and conditional random fields to analyse these data. Analysis of the virus communities revealed the importance of both direct and conditional virus-virus interactions for the community assembly. Joint analysis of the virus and fungus communities revealed that early season viruses have a significant impact on colonization of fungi on the same host plant later in the season (Sallinen et al. In prep). We also carried out additional field surveys of fungal infections with controlled inoculations to determine how pathogen diversity shape their dynamics and occurrence patterns. Jointly our results highlight the importance of biotic interactions for pathogen community assembly.
Objective 2. As we had virus primers ready and had identified plant genotypes that differ in their resistance, contrary to the plan, we carried out the field trap plant experiment already in summer 2017 instead of in 2018 as was stated in the original plan. This work was carried out by PhD student Sallinen. The project also hosted MSc students Maarit Numminen and Vanja Milenkovic, who successfully completed their MSc theses. RNA and DNA has been extracted from most samples and those samples have been characterized for viruses using primers. We find host genotype to have a striking impact on within-host pathogen community structure. The common garden experiment of Objective 2 was set up at Lammi Biological Station in summer 2018, and it further confirmed the effect role of host genotype affecting pathogen communities.
Objective 3. Using the temporal samples collected from the field trial in Objective 1, and virus specific primers, we analysed how the arrival sequence of viruses impacts the late season virus community structure. We found that some viruses had both positive and negative impacts on later arriving species, and that the effect is mediated by host plant genotype. The manuscript analysing priority effects mediated by host genotype is being finalized for submission to ISME J. A manuscript demonstrating the importance of induced host immune responses in shaping pathogen communities both under natural epidemics and in a controlled field trials was published in Nature Ecology & Evolution. PhD student Jokinen developed a qPCR protocol to quantify virus titer and the multifactorial greenhouse experiment addressing question 1 was completed in the summer 2022. PhD student Jokinen has funding for her PhD studies to finalize analysis and writing of this study.
Objective 4. The common garden experiment of Objective 2 was set up at Lammi Biological Station in summer 2018, and was monitored and sampled for two years. We discovered that the composition of the pathogen community has a significant effect on the fitness consequences of infection suffered by the host. The manuscript is currently revised for Evolution.
Objective 5. This year we completed the study analysing consequences of past infection for host population ecology and evolution and it has been published in Nature Communications. We demonstrated that the selection intensity which natural pathogen populations impose on their host population depends on the degree of host population isolation and that eco-evolutionary feedback loops shape the outcome of host-pathogen coevolution.
Objective 2. As we had virus primers ready and had identified plant genotypes that differ in their resistance, contrary to the plan, we carried out the field trap plant experiment already in summer 2017 instead of in 2018 as was stated in the original plan. This work was carried out by PhD student Sallinen. The project also hosted MSc students Maarit Numminen and Vanja Milenkovic, who successfully completed their MSc theses. RNA and DNA has been extracted from most samples and those samples have been characterized for viruses using primers. We find host genotype to have a striking impact on within-host pathogen community structure. The common garden experiment of Objective 2 was set up at Lammi Biological Station in summer 2018, and it further confirmed the effect role of host genotype affecting pathogen communities.
Objective 3. Using the temporal samples collected from the field trial in Objective 1, and virus specific primers, we analysed how the arrival sequence of viruses impacts the late season virus community structure. We found that some viruses had both positive and negative impacts on later arriving species, and that the effect is mediated by host plant genotype. The manuscript analysing priority effects mediated by host genotype is being finalized for submission to ISME J. A manuscript demonstrating the importance of induced host immune responses in shaping pathogen communities both under natural epidemics and in a controlled field trials was published in Nature Ecology & Evolution. PhD student Jokinen developed a qPCR protocol to quantify virus titer and the multifactorial greenhouse experiment addressing question 1 was completed in the summer 2022. PhD student Jokinen has funding for her PhD studies to finalize analysis and writing of this study.
Objective 4. The common garden experiment of Objective 2 was set up at Lammi Biological Station in summer 2018, and was monitored and sampled for two years. We discovered that the composition of the pathogen community has a significant effect on the fitness consequences of infection suffered by the host. The manuscript is currently revised for Evolution.
Objective 5. This year we completed the study analysing consequences of past infection for host population ecology and evolution and it has been published in Nature Communications. We demonstrated that the selection intensity which natural pathogen populations impose on their host population depends on the degree of host population isolation and that eco-evolutionary feedback loops shape the outcome of host-pathogen coevolution.
While individual hosts are known to support diverse pathogen communities, virtually nothing is known about how resistance evolves and functions given this diversity. The results of this study demonstrate both mechanistically and across scales that range from individual hosts to populations and landscapes how biotic and abiotic variation shapes pathogen diversity. I would consider the key finding to stem from the project to be the exceptionally strong support for the importance of biotic interactions to shape pathogen diversity. This was revealed in both field surveys of natural infections as well as under controlled experimental conditions. We have demonstrated – for the first time - the key role that host genotypes play in how pathogen communities are formed. Our results also shed light on how complex the interactions between pathogens may be. We find strong evidence for both direct pathogen-pathogen interactions as well as those that arise in the presence of a third species or an environmental covariate. These results will help us understand and predict how host resistance shapes pathogen communities, which will have broad basic and applied scientific impact. We have also validated the utility of cutting-edge analytical tools for the study of complex, hierarchically structured pathogen communities.
Jointly the results of this proposal provide a unique synthesis of resistance evolution under realistic pathogen loads, leading to a conceptual shift in how resistance evolution should be studied, managed, and incorporated into the next generation of theory on the dynamics of pathogen resistance in nature. A major research opportunity that this study opens up is to compare the relative importance of intra- and inter-pathogen species diversity on how infection dynamics and host resistance function.
Jointly the results of this proposal provide a unique synthesis of resistance evolution under realistic pathogen loads, leading to a conceptual shift in how resistance evolution should be studied, managed, and incorporated into the next generation of theory on the dynamics of pathogen resistance in nature. A major research opportunity that this study opens up is to compare the relative importance of intra- and inter-pathogen species diversity on how infection dynamics and host resistance function.