DOI: 10.5061/dryad.zcrjdfnbw
title: Data from: Shade tree traits and microclimate modifications: Implications for pathogen management in biodiverse coffee agroforests

description: Diversified coffee agroforests modify microclimate conditions in
 comparison to monocultures, impacting the success of significant plant
 pathogens, such as Hemileia vastatrix, which causes coffee leaf rust
 (CLR). However, research is often limited to the dichotomous analysis of
 shaded agroforestry systems or unshaded monocultures, often overlooking
 the nuanced effect of shade tree trait diversity. Our study aims to
 determine the cumulative effects of shade tree canopy architectural
 characteristics and leaf functional traits in biodiverse agroforests on
 microclimate modifications and CLR incidence. We measured plot-level
 microclimate conditions (air temperature, relative humidity, leaf wetness
 duration, throughfall kinetic energy) in three single-stratum and two
 double-strata shade tree canopy treatments, including Erythrina
 poeppigiana, Terminalia amazonia, and Chloroleucon eurycyclum. Commonly
 reported canopy characteristics and leaf traits were compared to average
 microclimate conditions and CLR incidence levels. We found that shade tree
 trait expression significantly explained most microclimate conditions, and
 that two key shade tree traits (canopy openness, leaf area) significantly
 explain CLR incidence levels (R2  = 0.211, p =
 0.036). Our results highlight the differences in microclimate
 conditions and CLR incidence among biodiverse agroforests, as well as the
 important explanatory power of shade tree traits. Specific effects of
 shade tree traits on pathogen dynamics can cirectly inform agroforestry
 system design (i.e. shade tree species selection) and sustainable coffee
 farm management practices (i.e. pruning practices).
description: Thirty circular plots were selected at
 the international coffee agroforestry research
 trial by the Centro Agronómico Tropical de Investigación y Enseñanza
 (CATIE), in Turrialba, Costa Rica located at 09°53´44” N and 83°40´7” W,
 at 685 m a.s.l. Measurements took place from May to July 2017. Within the
 site, <i>Coffea arabica</i> cv. Caturra (herein referred to as
 coffee) is planted in agroforestry systems under various management
 schemes. We included five distinct types of shade tree treatments in our
 study, including three single-stratum and two double-strata canopies:
 <i>Erythrina poeppigiana </i>(E), <i>Terminalia amazonia
 </i>(T), <i>Chloroleucon eurycyclum </i>(C)<i>, E.
 poeppigiana </i>+ <i>T. amazonia</i> (ET) and
 <i>E. poeppigiana </i>+ <i>C. eurycyclum
 </i>(EC). All shade tree treatments were repeated in two amendment
 regimes: moderate conventional
 (MC) and intensive organic
 (IO). All shade tree and amendment treatment
 combinations were repeated in three distinct blocks within the CATIE
 farm. Plots were confined to the area directly beneath a single
 representative shade tree in the single-stratum canopy treatments (E, T,
 and C), or beneath the overlapping of both shade tree canopies in the
 double-strata canopy treatments (ET,
 EC). 
 <strong>Microclimate measurements</strong>
 Microclimate conditions were measured in five plots (each of the
 shade tree treatments) in the same block simultaneously for seven
 consecutive days, rotating between each of the amendment regimes and
 blocks, for a total of nine weeks between early May and late July 2017 (n
 = 63 days per treatment). Microclimate measurements were recorded every
 five minutes. We used HOBO® datalogger (Onset Computer Corporation,
 Bourne, MA) and HOBO® microclimate sensors (air temperature and relative
 humidity sensor (S-THB-M008) and leaf wetness sensor (S-LWA-M003)), which
 were installed next to the selected central shade tree between the main
 stem and canopy’s outer edge between the coffee plant rows. All air
 temperature and relative humidity sensors were installed on a stable
 vertical post and positioned above the average coffee plant height at
 about 2 m. Daily air temperature and relative humidity values were
 calculated based on data collected from midnight CST (or time of
 microclimate station installation) until 11:55 pm CST (or time of
 microclimate station removal). Start and stop times were kept consistent
 across all sampling plots. Leaf wetness sensors were positioned on the
 same vertical post at mid-coffee plant height (about 1 m), between the
 coffee plant row directed either north or south, laying horizontally and
 tilted at a 45<sup>o</sup> angle facing east. Leaf wetness
 duration was calculated as the amount of time (hours) that the leaf
 wetness sensor was wet between 6:00 am CST and 7:00 pm CST, as all wetting
 and drying processes were captured within this timeframe. 
 Total throughfall kinetic engery (TKE) of rain events was
 measured using Tübingen splash cups (Scholten, Geißler, Goc, Kühn,
 & Wiegand, 2011) with sand calibrated to 150-250 µm (Avelino et
 al., 2020), where total sand lost after each individual rain event was
 converted to the total TKE (J/m<sup>2</sup>) of the rain event
 using the equation developed by Scholten et al. (2011). Three splash cups
 were installed within each study plot: close to the central tree stem,
 mid-way between the central tree stem and canopy edge, and near the
 central tree’s canopy edge. Each cup was positioned on a stable vertical
 post at height of about 2 m (above the average coffee plant height).
 Measurements were collected in five shade tree plots (each of the shade
 tree treatments) in the same block simultaneously, rotating between each
 of the amendment regimes and blocks, for a total of two or four events,
 for a total of 18 days of TKE measurements per treatment. All measurements
 were collected simultaneously across the shade tree treatments on each
 sampling day. <strong>Shade tree
 traits</strong> For each shade tree, we measured total
 canopy height (m), canopy base height (CBH; m), canopy diameter (m) and
 canopy openness (%). In plots with one shade tree, the central shade tree
 was used for all measurements. In double-strata canopy plots, total canopy
 height was recorded as the tallest crown height, CBH was recorded as the
 shortest tree’s CBH, and canopy diameter was recorded as the largest crown
 diameter. Canopy openness was captured using hemispherical photography and
 analyzed using Gap Light Analyzer (Simon Fraser University, 1999).
 Hemispherical photographs were collected at a height above the average
 coffee plant height (about 2 m) at three positions under the central shade
 tree: close to the tree stem, in the middle of the canopy, at the edge of
 the canopy. The average canopy openness value of the three photographs,
 determined from the zenith angles 0<sup>o</sup> to
 45<sup>o </sup>(Park & Cameron, 2008), were used in
 subsequent analyses. We used a subset of six representative
 trees per species to measure leaf functional traits. Following protocols
 outlined by Pérez-Harguindeguy et al. (2013) and Pisek, Ryu, &
 Alikas (2011), five replicate leaf samples were collected from the lower
 canopy of each tree (n = 30 leaves per shade tree species), which were
 used to determine leaf area (cm<sup>2</sup>), specific leaf
 area (SLA; mg/mm<sup>2</sup>), leaf dry matter content (LDMC;
 mg/g) and leaf angle. The large leaflets of <i>T. amazonia
 </i>and <i>E. poeppigiana </i>were analyzed as separate
 leaves. In plots with double-strata canopies, final leaf trait values were
 calculated using the relative abundance-weighted mean of the shade tree
 species present in the plot, similar to Geißler et al. (2013), calculated
 based on the percent canopy area occupied by each shade tree canopy within
 the given plot. <strong>Coffee leaf rust
 incidence</strong> Within the boundaries each plot, six
 coffee plants of similar age were selected. CLR incidence was measured in
 July 2017, where coffee plants were assessed on the same day in each of
 the treatments. CLR incidence was estimated as the average percentage of
 leaves with CLR chlorotic spots, both with and without emerging mature
 uredospores, from three branches of varying height (Avelino,
 Romero-Gurdián, Cruz-Cuellar, & Declerck, 2012). 
description: Plot traits
 <strong>Amendment: </strong>One of two amendment
 regimes used in this study, where MC is moderate conventional and IO is
 intensive organic.
 <strong>ShadeTree:</strong> One of five shade tree
 treatments, including <i>Erythrina
 poeppigiana </i>(E), <i>Terminalia amazonia </i>(T),
 <i>Chloroleucon eurycyclum </i>(C)<i>, E. poeppigiana
 </i>+ <i>T. amazonia</i> (ET) and <i>E.
 poeppigiana </i>+ <i>C. eurycyclum
 </i>(EC).
 <b>Block: </b>Each shade tree treatment and amendment
 regime was repeated in three distinct blocks at the CATIE farm. 
 <b>TreeHeight: </b>Total canopy height, measured in
 meters. <b>CBH: </b>Canopy base height,
 measured in meters. <b>Diameter: </b>Canopy
 diameter, measured in meters.
 <b>Openness: </b>Canopy openness, measured as a
 percentage. <b>LeafAngle: </b>Mean shade
 tree leaf angle, measured in degrees.
 <b>LA: </b>Mean shade tree leaf area, measured in
 cm2. <b>SLA: </b>Mean specific leaf area,
 measured in mg/mm2.
 <strong>LDMC: </strong>Mean leaf dry matter content,
 measured in mg/g.
 <strong>CLR_incidence: </strong>Plot-average CLR
 incidence at the plant-level, based on 6 coffee plants, measured as a
 percentage.  <strong>T_max, T_min,
 T_range: </strong>Mean daily maximum, minimum, and range of air
 temperature per plot, measured as degrees Celsius.
 <strong>RH_max, RH_min, RH_range: </strong>Mean daily
 maximum, minimum, and range of relative humidity per plot, measured as a
 percentage. <strong>LW: </strong>Mean leaf
 wetness duration per plot, measured in hours.
 <strong>TKE_max, TKE_min, TKE_range: </strong>Mean
 daily maximum, minimum, and range of throughfall kinetic energy per plot,
 measured as joules per square meter.
 <strong>Intensity: </strong>Mean daily rainfall
 intensity, calculated as the amount of rainfall (mm) divided by the
 duration of the rainfall event (hours).  Leaf
 traits <b>LeafRep: </b>Five
 replicate leaf samples were collected for each shade tree
 species. <b>LeafAngle: </b>Shade tree leaf
 angle, measured in degrees.
 <b>LA: </b>Shade tree leaf area, measured in
 cm2. <b>SLA: </b>Specific leaf area,
 measured in mg/mm2.
 <strong>LDMC: </strong>Leaf dry matter content,
 measured in mg/g. CLR
 <strong>CoffeeRep: </strong>Six coffee plant
 replicates were selected for each plot.
 <strong>CLR_incidence: </strong>CLR incidence at the
 plant-level, measured as a percentage.