Increasing prevalence of plant-fungal symbiosis across two centuries of environmental change

Species' distributions and abundances are shifting in response to ongoing global climate change.  Mutualistic microbial symbionts can provide their hosts with protection from environmental stress that may contribute towards resilient responses to environmental change, however these changes may also disrupt species interactions and lead to declines in hosts and/or symbionts. Symbionts preserved within natural history specimens offer a unique opportunity to quantify changes in microbial symbiosis across broad temporal and spatial scales.  We asked how the prevalence of seed-transmitted fungal symbionts of grasses (Epichloë endophytes) have changed over time in response to climate change, and how these changes vary across host species' ranges. Specifically, we analyzed 2,346 herbarium specimens of three grass host species (Agrostis hyemalis, Agrostis perennans, Elymus virginicus) collected over the past two centuries (1824-2019) for the presence or absence of Epichloë symbiosis.  We found that endophytes increased in prevalence over the last two centuries from ca. 25% prevalence to ca. 75% prevalence, on average, across three host species. Changes in seasonal climate drivers were associated with increasing endophyte prevalence.  Notably, increasing precipitation during the peak growing season for Agrostis species and decreasing precipitation for E. virginicus were associated with increasing endophyte prevalence. Changes in the variability of precipitation and temperature during off-peak seasons were also important predictors of increasing endophyte prevalence. Our analysis performed favorably in an out-of-sample predictive test with contemporary survey data, a rare extra step in collections-based research. However, we identified greater local-scale variability in endophyte prevalence in contemporary data compared to model predictions based on historic data, suggesting new directions that could improve predictive accuracy. Our results provide novel evidence for a cryptic biological response to climate change that may contribute to the resilience of host-microbe symbiosis through context-dependent benefits that confer a fitness advantage to symbiotic hosts under environmental change.

Methods
Data includes presence/absence data of Epichloë fungal endophytes within grass host specimens collected from herbarium specimens. Specimens come from 9 herbaria, visited between 2019 and 2022, and were scored for endophyte presence by examing 5-10 seeds per specimen using 200-400X magnification and analine blue lactic acid stain. Collection locations were georeferenced using the ggmap package in R for the state/county/municpality centroid depending on the availability of that informatio to obtain Lat/Lon coordinates. Data presents the number of seeds scored as positive and negative for each specimen, as well as liberal and conservative scores denoting endophyte-free (0) and endophyte-positive (1) that consider a plant positive if at least one seed is endophyte-positive. Liberal and conservative scores may differ depending on the certainty of identifying endophytes within a sample (low uptake of stain, unusual morphology, etc.)

Additional data on endophyte prevalence from contemporary population surveys come from collection trips between 2013 and 2020. Data from Elymus virginicus were compiled from Sneck et al. 2013, and data for Agrostis hyemalis come from surveys between 2015 and 2020. At each population, seeds from up to 30 plants were collected and scored using microscopy as above. Data presents the proportion of endophyte-positive plants for each sampled population.