DOI: 10.5061/dryad.wpzgmsbrn
title: Data from: Effects of microclimate on disease prevalence across an urbanization gradient

description: Increased temperatures associated with urbanization (the “urban heat
 island” effect) have been shown to impact a wide range of traits across
 diverse taxa. At the same time, climatic conditions vary at fine spatial
 scales within habitats due to factors including shade from shrubs, trees,
 and built structures. Patches of shade may function as microclimate
 refugia that allow species to occur in habitats where high temperatures
 and/or exposure to ultraviolet radiation would otherwise be prohibitive.
 However, the importance of shaded microhabitats for interactions between
 species across urbanized landscapes remains poorly understood. Weedy
 plants and their foliar pathogens are a tractable system for studying how
 multiple scales of climatic variation influence infection prevalence.
 Powdery mildew pathogens are particularly well suited to this work, as
 these fungi can be visibly diagnosed on leaf surfaces. We studied the
 effects of shaded microclimates on rates of powdery mildew infection
 on Plantago host species in (1) “pandemic pivot” surveys in which
 undergraduate students recorded shade and infection status of thousands of
 plants along road verges in urban and suburban residential neighborhoods,
 (2) monthly surveys of plant populations in 22 parks along an urbanization
 gradient, and (3) a manipulative field experiment directly testing effects
 of shade on growth and transmission of powdery mildew. Together, our field
 survey results show strong positive effects of shade on mildew infection
 in wild Plantago populations across urban, suburban, and rural habitats.
 Our experiment suggests that this relationship is causal, where
 microclimate conditions associated with shade promote pathogen growth.
 Overall, infection prevalence increased with urbanization despite a
 negative association between urbanization and tree cover at the landscape
 scale. These findings highlight the importance of taking microclimate
 heterogeneity into account when establishing links between macroclimate or
 land use context and the prevalence of disease.
description: <strong>Surveys (park/field and road verge):
 </strong>In each survey, we first identified a patch of
 <em>Plantago lanceolata</em> or <em>P.
 rugelii</em>. Within this patch, we arbitrarily chose the first
 focal plant of either species and marked the survey starting location
 using a smartphone. For each focal plant, we recorded binary
 (presence/absence) data on powdery mildew infection, herbivore chewing
 damage, leaf mines, and lawnmower damage (leaves cut cleanly across by
 mower blade). In addition, we recorded whether the plant was in the sun or
 shade at the time of the survey. We also estimated the total number of
 conspecifics and number of infected conspecifics within a 1.5 m radius of
 the focal plant (ordered categorical variable in bins of 0, 1-10, 11-50,
 or 51-100 plants). We then walked a few paces in a predetermined direction
 (e.g., continuing unidirectionally along a roadside or within a park lawn
 for the entire survey) and arbitrarily selected the next focal plant.
 Focal plants were always at least 1 m from the previously selected
 conspecific in the survey. We continued until 50 plants of each species
 had been surveyed, and then recorded the end location and time. In some
 locations where <em>Plantago</em> was relatively rare, fewer
 than 50 plants were surveyed. Occasionally, surveys were cut short due to
 inclement weather or physical barriers (e.g., construction). Overall, we
 performed 68 surveys of <em>Plantago rugelii</em> and 60
 surveys of <em>P. lanceolata</em>.
 <strong>Shade experiment:</strong> We performed a
 manipulative experiment to measure the effects of shade on powdery mildew
 growth and transmission in July 2021. Seven maternal lines of <em>P.
 lanceolata</em> and six maternal lines of <em>P.
 major</em> seeds were used. Plants in the inoculated treatment were
 placed in shallow trays at four sites directly under (shade) and four
 sites midway between (sun) solar panels in an otherwise open, mowed field
 at Tyson Research Center. The four large solar panels were each separated
 by five meters. At each of the four shade and four sun locations, we
 placed four trays in a “T-intersection” formation with three trays. The
 central tray at each location contained four or five <em>P. major
 </em>individuals and four <em>P. lanceolata
 </em>individuals. For both species, replicates of the maternal lines
 were distributed among trays as evenly as possible. Due to the low
 germination rates of <em>P. major </em>and the resulting small
 sample size for this species, all <em>P. major</em>
 individuals in the experiment were placed in the central trays.
 We used sterilized paint brushes to inoculate plants in these
 first trays by gently brushing one leaf per plant with powdery mildew
 spores from lab-inoculated source plants. Plants were inoculated with
 species-specific strains of the powdery mildew pathogen
 <em>Golovinomyces sordidus</em> that had been previously
 collected from wild plants in the St. Louis region, isolated to single
 strains, and propagated on leaf tissue in the lab following standard
 methods. The remaining <em>P. lanceolata</em> plants remained
 covered with pollination bags in the hoop house. The next day, we evenly
 divided these remaining uninoculated <em>P. lanceolata</em>
 among three additional trays in each shade and sun location (8-9 plants
 per tray). We assessed whether these uninoculated plants became infected
 over the following weeks of the experiment. The trays of inoculated plants
 were watered regularly by filling the trays with an inch of water every
 other day. Two of the trays of uninoculated plants were similarly watered.
 The third tray of uninoculated plants had holes in the bottom to allow
 water to drain; this treatment allowed us to test for plant responses to
 both the thermal environment and the amount of precipitation experienced
 in the shade and sun locations. We collected data on the infection status
 of each plant (number of infected leaves per plant) on 15 July, 23 July,
 and 6 August 2021. <strong>Shade experiment
 temperature data:</strong> We monitored microclimates by placing
 temperature loggers (HOBO MX2201) just below the soil surface in at least
 one pot per sun and shade location. To ground-truth these readings, in
 three locations we measured soil temperature in additional pots using
 temperature probes attached to Raspberry Pi computers. 
description: # Effects of microclimate on disease prevalence across an urbanization
 gradient Data (Fox et al. 2024) are available in Dryad at
 [https://doi:10.5061/dryad.wpzgmsbrn](https://doi:10.5061/dryad.wpzgmsbrn)
 and code (Fox et al. 2024) is available at Zenodo at
 [https://doi.org/10.5281/zenodo.7458687](https://doi.org/10.5281/zenodo.7458687). ## General Information: Included here are data and code from Fox et al. (2024). This study investigated how within-population microclimate variation due to shade influences rates of powdery mildew infection on *Plantago rugelii* and *P. lanceolata* host species. This study had three major components: 1) *Road verge surveys:* observational surveys along road verges in St. Louis, Missouri in 2020 focusing on the powdery mildew infection status of *Plantago* plants and shade availability, 2) *Urbanization surveys:* observational surveys from 22 urban, suburban, and rural parks in the St. Louis, Missouri metro area in 2020, also focused on mildew infection prevalence and shade availability, 3) *Shade experiment:* a manipulative field experiment in 2021 focusing on the effect of shade on powdery mildew infection and transmission success. ## Data: ### Road Verge Surveys: #### **Fox-et-al\_RoadVerge\_SurveyData.csv** Contains individual-level microclimate, flowering, mowing, herbivory, and infection data from plant-pathogen surveys of road verges conducted during the 2020 growing season. A.      Year - Year that the survey took place. B.      Month - Month of the year that the survey took place. C.     Day - Day of the month that the survey took place. D.     Species - Focal species being surveyed (rugelii = *Plantago rugelii*, lanceolata = *Plantago lanceolata*). E.      Set - Number of surveys done on the date by the surveyor for each species (1 = first survey, 2 = second, 3 = third, or 4 = fourth). F.      YearMonthDayNameSpeciesSet - Unique survey identifier - concatenation of year, month, day of the survey, surveyor name, species identity, and set number as a unique survey. G.     Plantago_present - Whether or not the focal *Plantago* species being surveyed was present at the survey site (yes = *P. rugelii / P. lanceolata* was present, no = *P. rugelii / P. lanceolata* was not present). H.     Mildew - Whether or not powdery mildew was present on the individual being surveyed (yes = individual was infected, no = individual was not infected). I.        Near_infected - Number representing a binned category of total number of infected *Plantago* individuals (conspecifics) within a 1.5-meter radius of the focal individual being surveyed. (0 = 0 infected conspecifics, 1 = 1-10 infected conspecifics, 2 = 11-50 infected conspecifics, NA = data not collected). J.        Near_total - Number representing a binned category of the total number of *Plantago* individuals within a 1.5-meter radius of the focal individual being surveyed (0 = 0 total conspecifics within a 1.5-m radius, 1 = 1-10 conspecifics, 2 = 11-50 conspecifics, 3 = 51 – 100 conspecifics, 4 = 101+ conspecifics, NA = data not collected). K.      Shade - Whether or not the individual being surveyed was in a shaded or sunlit microclimate (yes = individual was in shade, no = individual was in sun, NA = data was not collected). L.      Mowed - Whether or not the individual being surveyed had sustained damage from a mower (yes = individual had mower damage, no = individual had no mower damage, NA = data was not collected). M.    Herbivory - Presence and type of herbivory damage sustained by the individual being surveyed. #### **Fox-et-al\_RoadVerge\_MetaData.csv** Contains survey-level metadata for the 2020 road verge surveys. A.      Year - Year that the survey took place. B.      Month - Month of the year that the survey took place. C.     Day - Day of the month that the survey took place. D.     YearMonthDayNameSpeciesSet - Unique survey identifier - concatenation of year, month, day of the survey, surveyor name, species identity, and set number as a unique survey. E.      Species - Identity of focal species being surveyed (rugelii = *Plantago rugelii*, lanceolata = *Plantago lanceolata*). F.      Set - Rank of surveys done on the date by the surveyor for each species (1 = first survey, 2 = second, 3 = third, or 4 = fourth). G.     Time_start - Starting time (H:M) of the survey. H.     Lat_start - Starting latitude of the survey. I.        Lon_start - Starting longitude of the survey. J.        Time_end - Ending time (H:M) of the survey. K.      Lat_end - Ending latitude of the survey. L.      Lon_end - Ending longitude of the survey. M.    Species_present - Whether or not the focal *Plantago* species being surveyed was present at the survey site (yes = *P. rugelii / P. lanceolata* was present, no = *P. rugelii / P. lanceolata* was not present). ### Urbanization Surveys: #### **Fox-et-al\_Urbanization\_Figure1Data.csv** Contains site-level environmental and census data used to create Figure 1 and classify each field site along the urbanization gradient into urban, suburban, or rural site types. A.      LonRank - Longitudinal rank of each site based on location from east to west along urbanization/longitudinal gradient. 1 = furthest east, 22 = furthest west. B.      Site - Identity of the field site where the survey took place. C.     Site_Type - Classification of the site as urban, suburban, or rural. D.     Lat - Latitude of site. E.      Lon - Longitude of site. F.      CensusTractID - Site’s census tract identification number. G.     CensusBlockGroupID - Site’s census block’s group identification number. H.     CensusBlockID - Site’s census tract block identification number. I.        Imp_P - Percent impervious for the site’s census block. J.        MFor_P - Percent tree cover for site’s census block. K.      IntDen - Intersection density of walkable roads (intersections/sq mile) for the site’s census block. L.      WorldClim_AveTemp_JuneThruOct - Average temperature of the site (°C) from June through October 1970 - 2000 for the site’s census block. M.    NightRadiance - Nighttime radiance (nWcm-2sr-1) for site’s coordinates. #### **Fox-et-al\_Urbanization\_Coordinates.csv** Contains the longitudinal and latitudinal coordinates of each field site we collected monthly survey data during the annual growing season field surveys. A.      Site - Identity of the field site where the survey took place. B.      Lat - Latitude of site. C.     Lon - Longitude of site. #### **Fox-et-al\_Urbanization\_SurveyData.csv** Contains individual plant-level microclimate, flowering, mowing, herbivory, and infection data for each field site from surveys conducted monthly during the 2020 growing season. A.      Count - Unique number for each plant surveyed across monthly surveys. N.     Day - Day of the month that the survey took place. B.      Month - Month of the year that the survey took place. C.     Year - Year that the survey took place. N.     Site - Identity of the field site where the survey took place. D.     Site_Type - Classification of the site as urban, suburban, or rural. E.      Collection_Num - Number of the monthly survey (1 = first monthly survey, 2 = second monthly survey, 3 = third monthly survey, 4 = fourth monthly survey, 5 = fifth monthly survey). F.      Species - Focal species of individual being surveyed (PR = *Plantago rugelii*, PL = *Plantago lanceolata*). G.     Infected - Binary response variable for individual’s powdery mildew infection status (0 = individual being surveyed was not infected with powdery mildew, 1 = individual being surveyed was infected with powdery mildew). H.     Herbivory_Bin - Binary response variable for individual’s exposure to herbivory damage (0 = individual being surveyed did not have herbivory damage of any kind, 1 = individual being surveyed had herbivory damage of any kind). I.        Mowed_Bin - Binary response variable for individual’s exposure to mowing damage (0 = individual being surveyed did not have mowing damage, 1 = individual being surveyed had mowing damage). J.        Infected w/in 1.5m - Number representing a binned category of the total number of infected *Plantago* individuals (conspecifics) within a 1.5-meter radius of the focal individual being surveyed. (0 = 0 infected conspecifics, 1 = 1-10 infected conspecifics, 2 = 11-50 infected conspecifics, 3 = 51 – 100 infected conspecifics, 4 = 101+ infected conspecifics, NA = data not collected). K.      Total around - Number representing a binned category of the total number of *Plantago* individuals within a 1.5-meter radius of the focal individual being surveyed (0 = 0 total conspecifics within a 1.5-m radius, 1 = 1-10 conspecifics, 2 = 11-50 conspecifics, 3 = 51-100 conspecifics, 4 = 101+ conspecifics, NA = data not collected). N.     Shade - Whether or not the individual being surveyed was in a shaded or sunlit microclimate (yes = individual was in shade, no = individual was in sun, NA = data was not collected). L.      Shade_Bin - Binary response variable for individual’s exposure to shade or sunlit microclimate conditions (0 = individual being surveyed was in shade, 1 = individual being surveyed was in sunlight). ### Shade Experiment: #### **Fox-et-al\_ShadeExperiment\_Data.csv** Contains individual-level infection data from the shade (solar panel) experiment conducted in 2021. A.      ShadeSun - The microclimate treatment the tray of plants belonged to (Shade = shaded microclimate, Sun = sunlit microclimate). B.      Tray_ID - Unique identifier for each tray. Concatenation of Tray_Location, tray number within tray location, and ShadeSun treatment of tray. C.     Inoculated - Whether or not the individual was inoculated with powdery mildew spores (y = individual was inoculated, n = individual was not inoculated). D.     Tray_Location - Letter referring to the solar panel each replicate was associated with (see Figure 2 for more information). E.      Treatment - The treatment the individual belonged to (INF = infected, watered; W = infected, watered; NW = not infected, not watered). F.      Species - Focal species of individual (PR = *Plantago rugelii*, PL = *Plantago lanceolata*). G.     MaternalLine - Identity of the maternal line the individual originated from. H.     Tag_ID - Unique identifier for each individual; ID = Species (L = *lanceolata*, R= *rugelii*) - Maternal Line (represented with color or abbreviated name) - Individual number given during the propagation process. I.        Plant_ID - Unique identifier for each individual; continuous running number. J.        Infected - Binary response variable for individual’s powdery mildew infection status (0 = individual was not infected with powdery mildew, 1 = individual was infected with powdery mildew). K.      Num_Leaves_Infected - Number of leaves on individuals that were infected with powdery mildew. L.      Date - Date data were collected. M.    Collection_Num - Number of the data collection events (1 = first data collection, 2 = second data collection, 3 = third data collection). #### **Fox-et-al\_ShadeExperiment\_TempData.csv** Contains data from individual temperature dataloggers (HOBO MX2201) used in the shade experiment to find the temperature difference between microclimate treatments. A.      Serial - Serial number of each HOBO MX2201 datalogger. B.      Location - Letter referring to the solar panel datalogger was associated with (see Figure 2 for more information). C.     Treatment - The microclimate treatment the datalogger belonged to. D.     Tray - Identity of the tray that each datalogger belonged to. E.      Pot - Identity of individual plant pot that each datalogger belonged to. F.      DateTime - Date and time of each temperature data recording. G.     Temp - Temperature reading (°C). ## Software and Packages: Analysis was conducted in R version 4.1.0 (2021-05-18). Code can be found in ‘Fox-et-al_DataAnalysis_20240321.R’.