Peer review of: Mutualist and pathogen traits interact to affect plant community structure in a spatially (2020)

Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
In this manuscript, the authors used simulation models to explore how changes in the traits of 
microbial pathogens and mutualists influence plant-soil feedback. Specifically, they were interested in 
determining what scenarios could resolve an apparent “paradox” in the world of plant-soil feedback – 
how to reconcile negative plant-soil feedback as a coexistence mechanism with the observation that 
common plant species often have weaker negative feedbacks. While most simulations of plant-soil 
feedback treat feedback as a fixed trait of the plant, these simulations allowed the composition of 
mutualist and pathogen communities to change based on composition of the surrounding microbial 
communities, competition among microbes, and affinity for host plants. The authors found support for 
negative plant-soil feedback generating coexistence among species and found that allowing different 
pathogen and mutualist dynamics can generate negative plant-soil feedback and the positive 
correlation between feedback and abundance. 
 
Given the interest in plant-soil feedback as a coexistence mechanism and the conundrum of negative 
feedback generating coexistence but common species having weaker negative feedback, I suspect this 
paper will be of interest to many plant community ecologists. While I am not an expert on the 
methods, they seem sound and generated interesting, plausible results. The discussion is full of 
exiting ideas that can be empirically tested. My main critique is that I believe more details on plant-
soil feedback and the model should be added to the introduction to let the reader follow along without 
having to dig into the methods. 
 
(L75) I know there are space limitations, but it would help place the work in context to provide a few 
key empirical examples of how mutualistic and pathogenic microbes differ in traits. 
 
(L83) “allow mutualist and pathogens communities to dynamically change beneath each tree following 
competition equations” – From the introduction, it is still unclear how the simulations are allowing 
microbial communities to change. Earlier (L63-66) made it seem like it was going to be a function of 
the surrounding plant community. Here, it seems like it is a function of microbial competition. After 
reading the methods, it is clear that it is a function of both factors, along with the compatibility 
between the microbes and the host. Clearly stating this in the introduction would help the reader 
understand one of the critical advances of the manuscript – dynamic feedbacks – without having to go 
to the methods. 
 
(L110-117) The result that common species can have weaker negative feedback than rare species 
because of pathogen accumulations under heterospecifics and mutualist accumulation under 
conspecifics is really cool! But, I’m worried that readers not immersed in the Is (Bever et al. 1997) 
worldview of plant-soil feedback may miss how this generates weaker negative feedback, even though 
it is verbally described in L121-125. Again, I hate to add length to the main body of the manuscript, 
but I think it might be essential to describe pairwise feedback, how it is calculated, and what it means 
(especially for coexistence) somewhere other than the methods. 
 
(L312) “tree species’ relative abundance in the seed bank” – I took this to mean the “seed back” from 
that “year” rather than an accumulation over each time step (which is what “seed back” evokes). Is 
that true or am I missing something? 
 
(Table 1) In the table, values that are most likely to drive a positive correlation between host 
abundance and feedback are reported. Is there enough data available to compare the values for some 
of these parameters to compare them to observed values? The discussion attempts to get at this and 

offer future directions for research, but it would be powerful if some of these values linked to observed 
values. 
 
Minor comments: 
(L63) Change “tree” to “plant” for a more general introduction 
(L67) “obscure” rather than “obscuring” 
(L480) Differences “in” fecundity 
 
 
 
Reviewer #2: 
Remarks to the Author: 
Feedback between plants and the soil microbiome is thought to be a phenomenon that promotes 
coexistence of a large number of plant species within a community. But the details of the mechanisms 
are not understood. To advance understanding of these mechanisms, the authors model the effects of 
plant-soil feedbacks (PSF) as factors in plant biodiversity. They show, using a stochastic one-
dimensional spatially explicit model, that both plant host abundance and the competitive abilities of 
soil pathogens and mutualists are important in creating the patterns observed. The model is able to 
explain how both the positive correlation of PSF and tree commonness and high tree diversity can 
occur together. Strict host specificity is not required, and dynamics of soil biota seems to be a key 
factor. The authors also identify, using random forest, the main parameters associated with 
maintenance of plant diversity, direction (positive or negative) of plant-soil feedback, and positive 
correlation between plant abundance and feedback. 
 
Comments 
 
The results here are new and an important contribution to understanding how interactions plant 
species and their soil microbiomes can explain plant diversity and other observed aspects of plant 
community and the soil biota communities. The authors make a number of assumptions; including a 
fixed number of individual plants, dispersal limitation assumptions, a mortality regime in which trees 
are removed and replaced at random, interactions between plants that are limited to plant-soil 
feedbacks, plant fitness differences only at the seedling level, and plants being aligned one-
dimensionally. Although these assumptions are simplifying in some respects, they are not 
oversimplifying, and the model seems to be a reasonable start towards the questions being addressed. 
Clearly a great deal of thinking has gone into the design of the model. 
 
I have a few minor questions. 
 
Line 51. The authors note that common species generally exhibit weaker negative PSF than rare 
species, and their model is able to demonstrate that such a pattern could occur while at the same time 
high plant diversity is maintained. However, in the section in Lines 427-453 it is noted that the 
‘probability of randomly achieving a simulation parameterization with strong correlation between 
feedback strength and abundance was low.” If, as stated, the phenomenon is observed in nature, is 
there a reason why it is hard to find parameter values showing that in the model? 
 
Lines 262-270. I was not quite sure of the cause of the potential slow recovery of species experiencing 
weak negative PSF. Is that it connected to relativel high abundance of pathogens beneath 
heterospecifics, which can result in low seedling survival of the focal species in sites formerly occupied 
by those heterospecifics? 
 
Lines 271-279. Also, the authors note that areas with selective logging over long periods develop 

stronger negative feedback, whereas those in which certain plants are selectively cultivated develop 
weaker negative feedbacks. Is this due to gradual loss or gain of host-specific mutualists, respectively, 
over time, or some other cause? 
 
The occurrence of soil pathogens and mutualists specific to a particular host that occur on the soil of 
heterospecifics is a key mechanism. Is there a way to determine what is the more important 
component of those soil biota; new input dispersing from nearby sites or the persistence of the biota 
after trees have died? 
 
Do individual simulations approach some sort of stable community; i.e., roughly constant proportions 
of species and spatial structure? If so, does it vary much among replicate simulations? 
 
The number of plant species is small (five). Can this easily be extended to more species; which might 
require extending the number of individuals beyond 499. 
 
Are any higher order effects noticeable; e.g., the presence of one plant species having 
disproportionate effects on another given species? 
 
 
Minor: 
 
Line 123. Change ‘mutualist’ to ‘mutualists’ 
 
Line 172. When mentioning h, relative effect of mutualists on seedling survival, it might be useful to 
refer to Equation (4), where h occurs. 
 
Line 182. When mentioning q_f as the parameter determining how long pathogens persist at a site, 
and thus governs pathogen density in heterospecifics, it may be useful to mention that it occurs in 
equation (5). 
 
Line 212. Change ‘mutualists’ to ‘mutualist’ or ‘mutualists’ ‘ 
 
Line 342. How many time steps are needed for a tree to become an adult? 
 
Line 480. Change ‘differences’ to ‘differences in’ 
 
 
Overall, this is important paper in advancing the understanding of how the detailed patterns observed 
in plants and their soil microbiome communities can be created by plant-soil feedback, using a small 
number of reasonable assumptions on plant and soil biota traits. This comprehensive modeling study 
will certainly be of great interest to a broad audience of community and ecosystem ecologists.