Extended Plant Metarhizobiome: Understanding Volatile Organic Compound Signaling in Plant-Microbe Metapopulation Networks

ABSTRACT Plant rhizobiomes consist of microbes that are influenced by the physical, chemical, and biological properties of the plant root system. While plant-microbe interactions are generally thought to be local, accumulating evidence suggests that topologically disconnected bulk soil microbiomes could be linked with plants and their associated rhizospheric microbes through volatile organic compounds (VOCs). While several studies have focused on the effect of soil physicochemical properties for VOC movement, it is less clear how VOC signaling is affected by microbial communities themselves when VOCs travel across soils. To gain a better understanding of this, we propose that soil microbe-plant communities could be viewed as “metarhizobiomes,” where VOC-mediated interactions extend the plant rhizobiome further out through interconnected microbial metapopulation networks. In this minireview, we mainly focus on soil microbial communities and first discuss how microbial interactions within a local population affect VOC signaling, leading to changes in the amount, type, and ecological roles of produced VOCs. We then consider how VOCs could connect spatially separated microbial populations into a larger metapopulation network and synthesize how (i) VOC effects cascade in soil matrix when moving away from the source of origin and (ii) how microbial metapopulation composition and diversity shape VOC-signaling between plants and microbes at the landscape level. Finally, we propose new avenues for experimentally testing VOC movement in plant-microbe metapopulation networks and suggest how VOCs could potentially be used for managing plant health in natural and agricultural soils.

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Thank you for submitting your paper to mSystems. The paper is much improved with this draft. The expansion of references to support the presented ideas was just what was needed. There are a number of minor grammatical errors that should be cleaned up, such as agreement of number between subject and verb, and choice of prepositions to clarify the relationship between clauses. Details are provided in the attachment.
Reviewer #2 (Comments for the Author): The authors have addressed most of the comments raised by the referees. The authors have softened several of the hypotheses proposed in the previous version of the manuscript and have included a number of new references that provide experimental support to the hypotheses presented in this mini-review. The manuscript reads well and I only have minor comments on this manuscript.
-Line 52: pathogenic microorganisms have not been listed within the rhizosphere microbial community. -Line 92: Change "VOCS" to "VOCs" -Line 298-299: As indicated in previous evaluation reports, VOCs emission by plants and/or rhizospheric (micro)organisms will not cause an increase in the total volume of the rhizosphere, but affect the metabolism/physiology of (micro)organisms beyond the rhizosphere environment.

Third review of Raza et al.
L52. Do references 2-4 cover suppressive soils? I don't have these references handy, but don't see anything that obviously supports microbial disease suppression. There are hundreds of references to choose from.
L196. Nothing can be 'more unique' or less unique. If it is unique, it is the only thing like it.
L212-213. 'In this case, also the rare microbiome (taxa present in low relative abundances) could be important as already small concentrations…' Should be simplified to 'In this case, taxa present in low relative abundances could be important contributors as low concentrations…' L299-301. I suggest changing 'For example, identifying potential keystone microbial species that have relatively strong VOC-mediated interactions at the community level could be potentially used as microbial inoculants, while VOC-mediated interactions could be especially important in intercropping.' to 'For example, identifying potential keystone microbial species with relatively strong VOC-mediated interactions at the community level that could be used as microbial inoculants could be especially useful during intercropping periods.' L306. It is highly unlikely that any naturally-produced VOC could be used as a biofumigant, in part because of some of the points you have made in the manuscript, but mostly because anything toxic enough to fumigate a soil environment is likely to be nondiscriminating in its killing, and if not so toxic, then unlikely to eliminate pathogens. In our experience VOCs are static agents rather than cidal, so once the agent is removed one would expect rapid recovery of the target populations. However, the idea has merit not as a fumigant but perhaps as a way to give seedlings a chance to establish in the presence of seedling disease fungi. Perhaps changing 'biofumigant' to 'a transient and ecologically compatible biological control agent' or 'an ecologically compatible stimulant of the plant's immune system' would suffice.
L310-311. Why not just say something like, '…a combination of existing and emerging omics and computational technologies' rather than giving a list that is likely to be soon outdated or that leaves out an important 'omics', like 'volatilomics'?
L337. The sentence doesn't make sense. I think the wrong word was deleted. Your manuscript has been accepted, and I am forwarding it to the ASM Journals Department for publication. For your reference, ASM Journals' address is given below. Before it can be scheduled for publication, your manuscript will be checked by the mSystems senior production editor, Ellie Ghatineh, to make sure that all elements meet the technical requirements for publication. She will contact you if anything needs to be revised before copyediting and production can begin. Otherwise, you will be notified when your proofs are ready to be viewed.
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