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.
