DOI: 10.5061/dryad.0cfxpnw20
title: The temporal dimension of plant-soil microbe interactions: mechanisms promoting feedback between generations

description: Soil microbes can influence plant competitive outcomes by stabilizing
 plant community dynamics or mediating plant competitive hierarchies. Which
 effect dominates depends on whether microbial effects can extend beyond
 the focal conditioning individual. While it is well-known that microbial
 effects can extend to other individuals through space, we lack an explicit
 theoretical understanding of the factors that regulate their spread to
 other individuals in subsequent generations. Here, we examine how the
 commonly-assumed stabilizing effects of host-specific pathogens in fact
 depend on two factors that allow microbial effects to be
 cross-generational -- which plant demographic vital rate is influenced by
 microbes and the conditioning and decay rates of soil communities. With a
 novel patch occupancy model that incorporates the transition of soil
 states following plant colonization and mortality, we show that
 host-specific pathogens enable plant coexistence when they suppress
 conspecific plant colonization of empty patches, but contribute to
 competitive hierarchies when they only modify the mortality and fecundity
 of the conditioning plant individual. In a series of model extensions, we
 further demonstrate that these latter microbial effects can still promote
 coexistence, but only when microbial communities decay slowly following
 plant death, thereby allowing microbial effects to be cross-generational.
 Our work calls for further empirical work quantifying the demographic
 rates most affected by soil conditioning as well as the time scales of
 conditioning and decay.
description: <strong>/SimulationCode</strong><br>
 /PatchOccupancyS0model_Col<br> MS_PatchOccupancyS0model_CC_Amore.c
 -&gt; C-script to simulate Fig.3a (colonization model) with plant A
 having higher initial abundance<br>
 MS_PatchOccupancyS0model_CC_Bmore.c -&gt; C-script to simulate Fig.3a
 (colonization model) with plant B having higher initial
 abundance<br> MS_PatchOccupancyS0model_DCC_Amore.c -&gt;
 C-script to simulate Fig.5a (colonization model) with plant A having
 higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Bmore.c
 -&gt; C-script to simulate Fig.5a (colonization model) with plant B
 having higher initial abundance<br>
 MS_PatchOccupancyS0model_LCC_Amore.c -&gt; C-script to simulate
 Fig.S7a (colonization model) with plant A having higher initial
 abundance<br> MS_PatchOccupancyS0model_LCC_Bmore.c -&gt;
 C-script to simulate Fig.S7a (colonization model) with plant B having
 higher initial abundance
 <strong>/PatchOccupancyS0model_Mor</strong><br>
 MS_PatchOccupancyS0model_CC_Amore.c -&gt; C-script to simulate Fig.3b
 (mortality model) with plant A having higher initial abundance<br>
 MS_PatchOccupancyS0model_CC_Bmore.c -&gt; C-script to simulate Fig.3b
 (mortality model) with plant B having higher initial abundance<br>
 MS_PatchOccupancyS0model_DCC_Amore.c -&gt; C-script to simulate Fig.5b
 (mortality model) with plant A having higher initial abundance<br>
 MS_PatchOccupancyS0model_DCC_Bmore.c -&gt; C-script to simulate Fig.5b
 (mortality model) with plant B having higher initial abundance<br>
 MS_PatchOccupancyS0model_LCC_Amore.c -&gt; C-script to simulate
 Fig.S7b (mortality model) with plant A having higher initial
 abundance<br> MS_PatchOccupancyS0model_LCC_Bmore.c -&gt;
 C-script to simulate Fig.S7b (mortality model) with plant B having higher
 initial abundance
 <strong>/PatchOccupancyS0model_Growth</strong><br> MS_PatchOccupancyS0model_CC_Amore.c -&gt; C-script to simulate Fig.3c (growth model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_CC_Bmore.c -&gt; C-script to simulate Fig.3c (growth model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Amore.c -&gt; C-script to simulate Fig.5c (growth model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Bmore.c -&gt; C-script to simulate Fig.5c (growth model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Amore.c -&gt; C-script to simulate Fig.S7c (growth model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Bmore.c -&gt; C-script to simulate Fig.S7c (growth model) with plant B having higher initial abundance <strong>/PatchOccupancyS0model_Total</strong><br> MS_PatchOccupancyS0model_CC_Amore.c -&gt; C-script to simulate Fig.2a (full model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_CC_Bmore.c -&gt; C-script to simulate Fig.2a (full model) with plant B having higher initial abundance <strong>/SimpleModel</strong><br> MS_SimpleModel_Amore.c -&gt; C-script to simulate Fig.4d (fast conditioning and decay) with plant A having higher initial abundance<br> MS_SimpleModel_Bmore.c -&gt; C-script to simulate Fig.4d (fast conditioning and decay) with plant B having higher initial abundance<br> MS_SimpleModelCondition_Amore.c -&gt; C-script to simulate Fig.4e (fast decay) with plant A having higher initial abundance<br> MS_SimpleModelCondition_Bmore.c -&gt; C-script to simulate Fig.4e (fast decay) with plant B having higher initial abundance<br> MS_SimpleModelDecay_Amore.c -&gt; C-script to simulate Fig.4f (fast conditioning) with plant A having higher initial abundance<br> MS_SimpleModelDecay_Bmore.c -&gt; C-script to simulate Fig.4f (fast conditioning) with plant B having higher initial abundance <strong>/SimulationData</strong><br> /PatchOccupancyS0model_Col<br> MS_PatchOccupancyS0model_CC_Amore.txt -&gt; Data used to create Fig.3a (colonization model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_CC_Bmore.txt -&gt; Data used to create Fig.3a (colonization model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Amore.txt -&gt; Data used to create Fig.5a (colonization model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Bmore.txt -&gt; Data used to create Fig.5a (colonization model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Amore.txt -&gt; Data used to create Fig.S7a (colonization model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Bmore.txt -&gt; Data used to create Fig.S7a (colonization model) with plant B having higher initial abundance <strong>/PatchOccupancyS0model_Mor</strong><br> MS_PatchOccupancyS0model_CC_Amore.txt -&gt; Data used to create Fig.3b (mortality model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_CC_Bmore.txt -&gt; Data used to create Fig.3b (mortality model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Amore.txt -&gt; Data used to create Fig.5b (mortality model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Bmore.txt -&gt; Data used to create Fig.5b (mortality model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Amore.txt -&gt; Data used to create Fig.S7b (mortality model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Bmore.txt -&gt; Data used to create Fig.S7b (mortality model) with plant B having higher initial abundance <strong>/PatchOccupancyS0model_Growth</strong><br> MS_PatchOccupancyS0model_CC_Amore.txt -&gt; Data used to create Fig.3c (growth model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_CC_Bmore.txt -&gt; Data used to create Fig.3c (growth model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Amore.txt -&gt; Data used to create Fig.5c (growth model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_DCC_Bmore.txt -&gt; Data used to create Fig.5c (growth model) with plant B having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Amore.txt -&gt; Data used to create Fig.S7c (growth model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_LCC_Bmore.txt -&gt; Data used to create Fig.S7c (growth model) with plant B having higher initial abundance <strong>/PatchOccupancyS0model_Total</strong><br> MS_PatchOccupancyS0model_CC_Amore.txt -&gt; Data used to create Fig.2a (full model) with plant A having higher initial abundance<br> MS_PatchOccupancyS0model_CC_Bmore.txt -&gt; Data used to create Fig.2a (full model) with plant B having higher initial abundance <strong>/SimpleModel</strong><br> MS_SimpleModel_Amore.txt -&gt; Data used to create Fig.4d (fast conditioning and decay) with plant A having higher initial abundance<br> MS_SimpleModel_Bmore.txt -&gt; Data used to create Fig.4d (fast conditioning and decay) with plant B having higher initial abundance<br> MS_SimpleModelCondition_Amore.txt -&gt; Data used to create Fig.4e (fast decay) with plant A having higher initial abundance<br> MS_SimpleModelCondition_Bmore.txt -&gt; Data used to create Fig.4e (fast decay) with plant B having higher initial abundance<br> MS_SimpleModelDecay_Amore.txt -&gt; Data used to create Fig.4f (fast conditioning) with plant A having higher initial abundance<br> MS_SimpleModelDecay_Bmore.txt -&gt; Data used to create Fig.4f (fast conditioning) with plant B having higher initial abundance <strong>/PlotRscript</strong><br> MS_Figure_FullModel.R -&gt; R-script used to summarize data and create Fig.2a<br> MS_Figure_FullModelTimeseries.R -&gt; R-script used to run simulations and create Fig.2b-d<br> MS_Figure_CC.R -&gt; R-script used to summarize data and create Fig.3<br> MS_Figure_SimpleModel -&gt; R-script used to summarize data and create Fig.4d-f<br> MS_Figure_DCC.R -&gt; R-script used to summarize data and create Fig.5<br> MS_Figure_LCC.R -&gt; R-script used to summarize data and create Fig.S7