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.

/SimulationCode
/PatchOccupancyS0model_Col
MS_PatchOccupancyS0model_CC_Amore.c -> C-script to simulate Fig.3a (colonization model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.c -> C-script to simulate Fig.3a (colonization model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_DCC_Amore.c -> C-script to simulate Fig.5a (colonization model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_DCC_Bmore.c -> C-script to simulate Fig.5a (colonization model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_LCC_Amore.c -> C-script to simulate Fig.S7a (colonization model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_LCC_Bmore.c -> C-script to simulate Fig.S7a (colonization model) with plant B having higher initial abundance

/PatchOccupancyS0model_Mor
MS_PatchOccupancyS0model_CC_Amore.c -> C-script to simulate Fig.3b (mortality model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.c -> C-script to simulate Fig.3b (mortality model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_DCC_Amore.c -> C-script to simulate Fig.5b (mortality model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_DCC_Bmore.c -> C-script to simulate Fig.5b (mortality model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_LCC_Amore.c -> C-script to simulate Fig.S7b (mortality model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_LCC_Bmore.c -> C-script to simulate Fig.S7b (mortality model) with plant B having higher initial abundance

/PatchOccupancyS0model_Growth
MS_PatchOccupancyS0model_CC_Amore.c -> C-script to simulate Fig.3c (growth model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.c -> C-script to simulate Fig.3c (growth model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_DCC_Amore.c -> C-script to simulate Fig.5c (growth model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_DCC_Bmore.c -> C-script to simulate Fig.5c (growth model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_LCC_Amore.c -> C-script to simulate Fig.S7c (growth model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_LCC_Bmore.c -> C-script to simulate Fig.S7c (growth model) with plant B having higher initial abundance

/PatchOccupancyS0model_Total
MS_PatchOccupancyS0model_CC_Amore.c -> C-script to simulate Fig.2a (full model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.c -> C-script to simulate Fig.2a (full model) with plant B having higher initial abundance

/SimpleModel
MS_SimpleModel_Amore.c -> C-script to simulate Fig.4d (fast conditioning and decay) with plant A having higher initial abundance
MS_SimpleModel_Bmore.c -> C-script to simulate Fig.4d (fast conditioning and decay) with plant B having higher initial abundance
MS_SimpleModelCondition_Amore.c -> C-script to simulate Fig.4e (fast decay) with plant A having higher initial abundance
MS_SimpleModelCondition_Bmore.c -> C-script to simulate Fig.4e (fast decay) with plant B having higher initial abundance
MS_SimpleModelDecay_Amore.c -> C-script to simulate Fig.4f (fast conditioning) with plant A having higher initial abundance
MS_SimpleModelDecay_Bmore.c -> C-script to simulate Fig.4f (fast conditioning) with plant B having higher initial abundance

/SimulationData
/PatchOccupancyS0model_Col
MS_PatchOccupancyS0model_CC_Amore.txt -> Data used to create Fig.3a (colonization model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.txt -> Data used to create Fig.3a (colonization model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_DCC_Amore.txt -> Data used to create Fig.5a (colonization model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_DCC_Bmore.txt -> Data used to create Fig.5a (colonization model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_LCC_Amore.txt -> Data used to create Fig.S7a (colonization model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_LCC_Bmore.txt -> Data used to create Fig.S7a (colonization model) with plant B having higher initial abundance

/PatchOccupancyS0model_Mor
MS_PatchOccupancyS0model_CC_Amore.txt -> Data used to create Fig.3b (mortality model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.txt -> Data used to create Fig.3b (mortality model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_DCC_Amore.txt -> Data used to create Fig.5b (mortality model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_DCC_Bmore.txt -> Data used to create Fig.5b (mortality model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_LCC_Amore.txt -> Data used to create Fig.S7b (mortality model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_LCC_Bmore.txt -> Data used to create Fig.S7b (mortality model) with plant B having higher initial abundance

/PatchOccupancyS0model_Growth
MS_PatchOccupancyS0model_CC_Amore.txt -> Data used to create Fig.3c (growth model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.txt -> Data used to create Fig.3c (growth model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_DCC_Amore.txt -> Data used to create Fig.5c (growth model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_DCC_Bmore.txt -> Data used to create Fig.5c (growth model) with plant B having higher initial abundance
MS_PatchOccupancyS0model_LCC_Amore.txt -> Data used to create Fig.S7c (growth model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_LCC_Bmore.txt -> Data used to create Fig.S7c (growth model) with plant B having higher initial abundance

/PatchOccupancyS0model_Total
MS_PatchOccupancyS0model_CC_Amore.txt -> Data used to create Fig.2a (full model) with plant A having higher initial abundance
MS_PatchOccupancyS0model_CC_Bmore.txt -> Data used to create Fig.2a (full model) with plant B having higher initial abundance

/SimpleModel
MS_SimpleModel_Amore.txt -> Data used to create Fig.4d (fast conditioning and decay) with plant A having higher initial abundance
MS_SimpleModel_Bmore.txt -> Data used to create Fig.4d (fast conditioning and decay) with plant B having higher initial abundance
MS_SimpleModelCondition_Amore.txt -> Data used to create Fig.4e (fast decay) with plant A having higher initial abundance
MS_SimpleModelCondition_Bmore.txt -> Data used to create Fig.4e (fast decay) with plant B having higher initial abundance
MS_SimpleModelDecay_Amore.txt -> Data used to create Fig.4f (fast conditioning) with plant A having higher initial abundance
MS_SimpleModelDecay_Bmore.txt -> Data used to create Fig.4f (fast conditioning) with plant B having higher initial abundance

/PlotRscript
MS_Figure_FullModel.R -> R-script used to summarize data and create Fig.2a
MS_Figure_FullModelTimeseries.R -> R-script used to run simulations and create Fig.2b-d
MS_Figure_CC.R -> R-script used to summarize data and create Fig.3
MS_Figure_SimpleModel -> R-script used to summarize data and create Fig.4d-f
MS_Figure_DCC.R -> R-script used to summarize data and create Fig.5
MS_Figure_LCC.R -> R-script used to summarize data and create Fig.S7